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What is Food Microbiology?
The focus of Food Microbiology is on the detection and analysis of foodborne spoilage microorganisms. Food microbiology is the study of food micro-organisms; how we can identify and culture them, how they live, how some infect and cause disease and how we can make use of their activities. Microbes are single-cell organisms so tiny that millions can fit into the eye of a needle. They are the oldest form of life on earth. Microbe fossils date back more than 3.5 billion years to a time when the Earth was covered with oceans that regularly reached the boiling point, hundreds of millions of years before dinosaurs roamed the earth. The field of food microbiology is a very broad one, encompassing the study of microorganisms which have both beneficial and deleterious effects on the quality and safety of raw and processed foods. Food science is a discipline concerned with all aspects of food - beginning after harvesting, and ending with consumption by the consumer. It is considered one of the agricultural sciences, and it is a field which is entirely distinct from the field of nutrition. In the U.S., food science is typically studied at land-grant universities. Examples of the activities of food scientists include the development of new food products, design of processes to produce these foods, choice of packaging materials, shelf-life studies, sensory evaluation of the product with potential consumers, microbiological and chemical testing. Food scientists in universities may study more fundamental phenomena that are directly linked to the production of a particular food product. Food scientists are generally not directly involved with the creation of genetically modified (bio-engineered) foods. Some of the subdisciplines of food science: Food safety, Food engineering, Product development, Sensory analysis, Food chemistry. The primary tool of microbiologists is the ability to identify and quantitate food-borne microorganisms; however, the inherent inaccuracies in enumeration processess, and the natural variation found in all bacterial populations complicate the microbiologists job. Without microbes, we couldn’t eat or breathe. Without us, they’d probably be just fine. Understanding microbes is vital to understanding the past and the future of ourselves and our planet. Archaea look and act a lot like bacteria. So much so that until the late 1970s, scientists assumed they were a kind of “weird” bacteria. Then microbiologist Carl Woese devised an ingenious method of comparing genetic information showing that they could not rightly be called bacteria at all. Their genetic recipe is too different. So different Woese decided they deserved their own special branch on the great family tree of life, a branch he dubbed the Archaea. Archaea comes from the Greek word meaning “ancient.” An appropriate name, because many archaea thrive in conditions mimicking those found more than 3.5 billion years ago. Back then, the earth was still covered by oceans that regularly reached the boiling point — an extreme condition not unlike the hydrothermal vents and sulfuric waters where archaea are found today. Some scientists consider archaea living fossils that may provide hints about what the earliest life forms on Earth were like, and how life evolved on our planet. In addition to superheated waters, archaea have been found in acid-laden streams around old mines, in frigid Antarctic ice and in the super-salty waters of the Dead Sea. A number of other extreme-living bacterial species also enjoy these conditions, too, such as the community of cyanobacteria and bacteria shown top right. Foodborne illness or food poisoning is caused by consuming food contaminated with pathogenic bacteria, toxins, viruses, prions or parasites. Such contamination usually arises from improper handling, preparation or storage of food. Foodborne illness can also be caused by adding pesticides or medicines to food, or by accidentally consuming naturally poisonous substances like poisonous mushrooms or reef fish. Contact between food and pests, especially flies, rodents and cockroaches, is a further cause of contamination of food. Some common diseases are occasionally foodborne mainly through the water vector, even though they are usually transmitted by other routes. These include infections caused by Shigella, Hepatitis A, and the parasites Giardia lamblia and Cryptosporidium parvum. • Thermophiles like unusually hot temperatures. A few species have been found to survive even above 110 degrees Celsius (water boils at 100 degrees Celsius). • Psychrophiles like extremely cold temperatures (even down to -10 degrees Celsius). • Halophiles thrive in unusually salty habitats. Some can thrive in water that’s 9% salt; sea water contains only 0.9% salt. • Acidophiles prefer acidic conditions; Alkaliphiles prefer very alkaline environs. Accumulating sufficient data on the behaviour of microorganisms in foods requires an extensive amount of work, and is costly. In addition, while data alone can describe the response of a microorganisms in food, they provides little insight into the relationship between physiological processes and growth or survival. Scientists also use molecular tools to extract and compare bits of a particular kind of RNA from samples in order to determine if previously known or new microbes are present in a particular environment. This technique is widely used as a biomarker and for microbial ecology studies. It uses a particular kind of RNA known as 16S ribosomal RNA, or 16S rRNA. Ribosomes are the gene-translating machines in all living things. When a gene on a piece of DNA is copied into a strand of messenger RNA and ferried out of the cell nucleus into the cell fluid, ribosomes there latch onto this mRNA. The ribosomes move along the mRNA strand, reading the code contained in its sequence of nucleotide bases (the As, Gs, Cs and Us, since U replaces T in RNA) and stringing the right amino acids together based on the code to build protein chains. Pasteurization is typically associated with milk. There are two widely used methods to pasteurize milk: high temperature/short time (HTST), and ultra-high temperature (UHT). HTST is by far the most common method. Milk simply labelled "pasteurized" is usually treated with the HTST method, whereas milk labelled "ultra-pasteurized" must be treated with the UHT method. HTST involves holding the milk at a temperature of 161.5 degrees F (or 72 C) for at least 15 seconds. UHT involves holding the milk at a temperature of 280 degrees F (or 138 C) for at least two seconds. Pasteurization methods are usually standardized and controlled by national food safety agencies (such as the USDA in the United States and the Food Standards Agency in the U.K.). These agencies require milk to be HTST pasteurized in order to qualify for the "pasteurized" label. There are different standards for different dairy products, depending on the fat content and the intended usage. For example, the pasteurization standards for cream differ from the standards for fluid milk, and the standards for pasteurizing cheese are designed to preserve the phosphatase enzyme, which aids in curing the cheese. The HTST pasteurization standard was designed to achieve a 5-log (approximately one million-fold) reduction in the number of viable microorganisms in milk. This is considered adequate for destroying almost all yeasts, mold, and common spoilage bacteria and also to ensure adequate destruction of common pathogenic heat-resistant organisms (including particularly Mycobacterium tuberculosis, which causes tuberculosis and Coxiella burnetii, which causes Q fever). HTST pasteurization processes must be designed so that the milk is heated evenly, and no part of the milk is subject to a shorter time or a lower temperature. HTST pasteurized milk typically has a refrigerated shelf life of two to three weeks, whereas ultra pasteurized milk can last much longer when refrigerated, sometimes two to three months. When UHT pasteurization is combined with sterile handling and container technology, it can even be stored unrefrigerated for long periods of time. J Food Prot, 2004 Nov, 67(11), 2515 - 20Direct detection and identification of lactic acid bacteria in a food processing plant and in meat products using denaturing gradient gel electrophoresis; Takahashi H et al.; We established a novel system using denaturing gradient gel electrophoresis (DGGE) to quickly identify bacteria known to be responsible for spoilage in meat processing plants and meat products . We extracted bacterial DNA from swabbed samples at various locations in the plant and from meat products and performed PCR amplification, targeting 16S rDNA from the dominant organisms . The amplification products were subjected to DGGE, and the contaminating bacteria in the meat products and the plant were analyzed . This analysis indicated that lactic acid bacteria and spoilage-causing bacteria are widely distributed within the meat processing plant . We developed molecular size markers to identify the dominant organisms obtained from the plant and meat products . The establishment of the present method allows quick and simple identification of bacteria causing the possible deterioration of products and contamination and thus permits constant monitoring of any harmful bacteria within meat processing plants. J Food Prot, 2004 Nov, 67(11), 2456 - 64 Control of Listeria monocytogenes on frankfurters with antimicrobials in the formulation and by dipping in organic acid solutions; Barmpalia IM et al.; The antilisterial activity of sodium lactate (SL) and sodium diacetate (SD) was evaluated in a frankfurter formulation and in combination with a dipping treatment into solutions of lactic acid or acetic acid after processing and inoculation . Pork frankfurters were formulated with 1.8% SL or 0.25% SD or combinations of 1.8% SL with 0.25 or 0.125% SD . After processing, frankfurters were inoculated (2 to 3 log CFU/cm2) with a 10-strain composite of Listeria monocytogenes and left undipped or were dipped (2 min) in 2.5% solutions of lactic acid or acetic acid (23 +/- 2 degrees C) before vacuum packaging and storage at 10 degrees C for 40 days . Total microbial populations and L . monocytogenes, lactic acid bacteria, and yeasts and molds were enumerated during storage . Sensory evaluations also were carried out on frankfurters treated and/or formulated with effective antimicrobials . The combination of 1.8% SL with 0.25% SD provided complete inhibition of L . monocytogenes growth throughout storage . Dipping in lactic acid or acetic acid reduced initial populations by 0.7 to 2.1 log CFU/cm2, but during storage (12 to 20 days), populations on dipped samples without antimicrobials in the formulation reached 5.5 to 7.9 log CFU/cm2 . For samples containing single antimicrobials and dipped in lactic acid or acetic acid, L . monocytogenes growth was completely inhibited or reduced over 12 and 28 days, respectively, whereas final populations were lower (P < 0.05) than those in undipped samples of the same formulations . Bactericidal effects during storage (reductions of 0.6 to 1.0 log CFU/ cm2 over 28 to 40 days) were observed in frankfurters containing combinations of SL and SD that were dipped in organic acid solutions . Inclusion of antimicrobials in the formulation and/or dipping the product into organic acid solutions did not affect (P > 0.05) the flavor and overall acceptability of products compared with controls . The results of this study may be valuable to meat processors as they seek approaches for meeting new regulatory requirements in the United States. J Dairy Sci, 2004 Dec, 87(12), 4004 - 12 Comparison of effect of vacuum-condensed and ultrafiltered milk on cheddar cheese; Acharya MR et al.; The objective of this study was to compare the effects of vacuum-condensed (CM) and ultrafiltered (UF) milk on some compositional and functional properties of Cheddar cheese . Five treatments were designed to have 2 levels of concentration (4.5 and 6.0% protein) from vacuum-condensed milk (CM1 and CM2) and ultrafiltered milk (UF1 and UF2) along with a 3.2% protein control . The samples were analyzed for fat, protein, ash, calcium, and salt contents at 1 wk . Moisture content, soluble protein, meltability, sodium dodecyl sulfate-PAGE, and counts of lactic acid bacteria and nonstarter lactic acid bacteria were performed on samples at 1, 18, and 30 wk . At 1 wk, the moisture content ranged from 39.2 (control) to 36.5% (UF2) . Fat content ranged from 31.5 to 32.4% with no significant differences among treatments, and salt content ranged from 1.38 to 1.83% with significant differences . Calcium content was higher in UF cheeses than in CM cheeses followed by control, and it increased with protein content in cheese milk . Ultrafiltered milk produced cheese with higher protein content than CM milk . The soluble protein content of all cheeses increased during 30 wk of ripening . Condensed milk cheeses exhibited a higher level of proteolysis than UF cheeses . Sodium dodecyl sulfate-PAGE showed retarded proteolysis with increase in level of concentration . The breakdown of alphas1- casein and alphas1-I-casein fractions was highest in the control and decreased with increase in protein content of cheese milk, with UF2 being the lowest . There was no significant degradation of beta-casein . Overall increase in proteolytic products was the highest in control, and it decreased with increase in protein content of cheese milk . No significant differences in the counts of lactic starters or nonstarter lactic acid bacteria were observed . Extent as well as method of concentration influenced the melting characteristics of the cheeses . Melting was greatest in the control cheeses and least in cheese made from condensed milk and decreased with increasing level of milk protein concentration . Vacuum condensing and ultrafiltration resulted in Cheddar cheeses of distinctly different quality . Although both methods have their advantages and disadvantages, the selection of the right method would depend upon the objective of the manufacturer and intended use of the cheese. J Food Prot, 2004 Oct, 67(10), 2320 - 5 Physicochemical and microbiological profile of packed table olives; Lopez-Lopez A et al.; The water activity of different commercial products of table olives as well as their physicochemical and microbiological profiles were studied . Average values of water activity were 0.976, 0.977, and 0.990 for green, directly brined, and ripe (by alkaline oxidation) olives, respectively . Mean values of pH were 3.69, 3.92, and 6.52 while salt levels were 5.53, 4.98, and 2.55 for the same commercial products . In some of the commercial products of green and directly brined olives that were examined, a certain level of microorganisms was observed . Most of them were lactic acid bacteria and yeasts, the lactic acid bacteria being more abundant than the yeasts . Traditionally, this flora has not been considered harmful due to its resemblance to that found in natural and spontaneous fermentation . Spore-forming mesophilic aerobes, which can be considered contaminants from ingredient or product handling, were present in only some samples and were always at low levels . However, their detection does not cause any concern regarding safety because there is no reference showing that they can grow in any of the products studied given the physicochemical characteristics found. J Appl Microbiol, 2004, 97(5), 1029 - 37 Biodiversity of Listeria monocytogenes sensitivity to bacteriocin-producing Carnobacterium strains and application in sterile cold-smoked salmon; Brillet A et al.; AIMS: The aim of this study was to demonstrate the inhibitory capacity of Carnobacterium strains against a collection of Listeria monocytogenes strains in cold-smoked salmon (CSS) . METHODS AND RESULTS: Three bacteriocin-producing strains, Carnobacterium divergens V41, C . piscicola V1 and C . piscicola SF668, were screened for their antilisterial activity against a collection of 57 L . monocytogenes strains selected from the French smoked salmon industry, using an agar spot test . All the Listeria strains were inhibited but three different groups could be distinguished differing in sensitivity to the three Carnobacterium strains . However, C . divergens V41 always had the highest inhibitory effect . The antilisterial capacity was then tested in sterile CSS blocks co-inoculated with Carnobacterium spp . and mixtures of L . monocytogenes strains . C . divergens V41 was the most efficient strain, maintaining the level of L . monocytogenes at <50 CFU g(-1) during the 4 weeks of vacuum storage at 4 and 8 degrees C, whatever the sensitivity of the set of L . monocytogenes strains . CONCLUSIONS: C . divergens V41 may be a good candidate for biopreservation in CSS . SIGNIFICANCE AND IMPACT OF THE STUDY: A biopreservation strategy for CSS against the risk of L . monocytogenes was investigated using bacteriocin-producing lactic acid bacteria. Br J Nutr, 2004 Sep, 92(3), 411 - 7 Effect of a gamma-aminobutyric acid-enriched dairy product on the blood pressure of spontaneously hypertensive and normotensive Wistar-Kyoto rats; Hayakawa K et al.; We investigated the blood-pressure-lowering effects of gamma-aminobutyric acid (GABA) and a GABA-enriched fermented milk product (FMG) by low-dose oral administration to spontaneously hypertensive (SHR/Izm) and normotensive Wistar-Kyoto (WKY/Izm) rats . FMG was a non-fat fermented milk product produced by lactic acid bacteria, and the GABA contained in FMG was made from the protein of the milk during fermentation . A single oral dose of GABA or FMG (5 ml/kg; 0.5 mg GABA/kg) significantly (P<0.05) decreased the blood pressure of SHR/Izm from 4 to 8 h after administration, but did not increase that of WKY/Izm rats . The hypotensive activity of GABA was dose-dependent from 0.05 to 5.00 mg/kg in SHR/Izm . During the chronic administration of experimental diets to SHR/Izm, a significantly slower increase in blood pressure with respect to the control group was observed at 1 or 2 weeks after the start of feeding with the GABA or FMG diet respectively (P<0.05) and this difference was maintained throughout the period of feeding . The time profile of blood-pressure change due to administration of FMG was similar to that of GABA . FMG did not inhibit angiotensin 1-converting enzyme . Furthermore, an FMG peptide-containing fraction from reverse-phase chromatography lacked a hypotensive effect in SHR/Izm rats . The present results suggest that low-dose oral GABA has a hypotensive effect in SHR/Izm and that the hypotensive effect of FMG is due to GABA. Int J Food Microbiol, 2004 Nov 15, 96(3), 235 - 52 The 'buttery' attribute of wine--diacetyl--desirability, spoilage and beyond; Bartowsky EJ et al.; The diketone, diacetyl, is a major flavour metabolite produced by lactic acid bacteria (LAB) . Of the LAB associated with wine, Oenococcus oeni is encouraged during the malolactic (ML) fermentation, a biodeacidification of wine during which the metabolism of diacetyl occurs . Diacetyl, which imparts a buttery aroma and flavour to many fermented foods and beverages, is a key flavour compound of most fermented dairy products . In wine, diacetyl has important stylistic implications . The biosynthesis of diacetyl is dependent upon citric acid metabolism and diacetyl is an intermediate metabolite which can be further reduced to acetoin and the alcohol, 2,3-butanediol . This review will focus on the sensory perception, metabolism, genetics and analysis of diacetyl during wine production . The extensive knowledge of diacetyl metabolism in dairy LAB is used to enhance the understanding of diacetyl metabolism of wine LAB . Factors which can effect the formation and concentration of diacetyl in wine are discussed . These include malolactic bacterial strain, wine chemical and physical parameters (pH, temperature, citric acid, sulfur dioxide, aeration) and the presence of yeast lees . Finally, the affects of other wine components, such as phenolics, are discussed. Zhonghua Shao Shang Za Zhi, 2004 Aug, 20(4), 198 - 201 {Preliminary comparative study on the effects of early enteral supplementation of synbiotics on severely burned patients}; Lu X et al.; OBJECTIVE: To investigate the influence of early enteral nutrition with synbiotics on the plasma endotoxin level, the nutritional state, the inflammatory response and the incidence of infectious complications in severely burned patients . METHODS: Randomized double blind and control method was employed im the study . Forty severely burned patients were randomly divided into A and B groups with 20 in each group . The patients in group A received early enteral nutrition with synbiotics including four kinds of lactic acid bacteria and four kinds of fibers, while those in group B received early enteral nutrition with synbiotics including only four kinds of fibers . The patients with 80% to 280% coefficient unit burned surface(UBS) were further divided into A1 (n = 10) and B1 (n = 11) groups . The plasma endotoxin level in group A and B was determined dynamically on the 1st, 3rd, 7th, 10th, 14th, and 21st postburn days (PBD), and its abnormal rate in both groups was statistically analyzed in correlation with the normal endotoxin level . meanwhile, the mortality, the incidence of infectious complications and the blood bacterial culture results were compared between the two groups . The plasma levels of IL-1, IL-6 and prognostic inflammatory nutrition index (PINI) were also determined at the above time points . RESULTS: The plasma endotoxin level in group A (37.9 +/- 5.4) ng/L was evidently lower than that in group B (59.1 +/- 7.9) ng/L (P < 0.05) on 10 PBD . The abnormal rate of plasma endotoxin in group A (36.7%) was evidently lower than that (49.2%) in group B (P < 0.05) . Blood culture was positive in 3 patients in group A, and 5 in group B . There was no obvious difference in the incidence of infectious complication between the two groups . Two patients died in group A and 1 group B . There was no obvious difference in plasma IL-1 level between A1 and B1 groups at different time points . The plasma IL-6 level in A1 group in 10th and 14th PBD was evidently lower than that in B1 group (P < 0.05) . The PINI in A1 group on the 10 PBD was remarkably lower than that in B1 group . CONCLUSION: Early enteral nutrition with synbiotics was helpful in decreasing inflammatory stress response and lowering the plasma endotoxin level . Enteral supplementation of synbiotics might be beneficial to the controlling of burn infection. J Dairy Sci, 2004 Oct, 87(10), 3386 - 97 The passage of lactic acid bacteria from silage into rumen fluid, in vitro studies; Weinberg ZG et al.; Inoculated silages sometimes improve cattle performance, possibly because of probiotic effects of lactic acid bacteria (LAB) silage inoculants . The cause of improved animal performance following feeding with inoculated silage is unclear . One issue in studying this phenomenon is to find out whether LAB pass from silage into the rumen fluid and survive in it . The purpose of the present study was to determine whether LAB from inoculated and uninoculated silages pass into the rumen fluid in vitro . Wheat and corn silages, uninoculated or inoculated with 1 of 10 commercial silage inoculant LAB, were prepared in glass jars . After ensiling, a 2.5-g silage sample was added to 25 mL of heat-sterilized or strained rumen fluid together with 5 g/L glucose, and incubated for 48 h at 39 degrees C . Analysis of the incubated rumen fluid included pH measurement, enumeration of LAB, and determination of lactic acid and volatile fatty acids (VFA) . The pH of the rumen fluid decreased during incubation; both heat-sterilized and strained rumen fluid contained large numbers of LAB . The heat-sterilized rumen fluid contained lactic acid in addition to VFA, whereas the strained rumen fluid contained only VFA . The results indicate that LAB pass from silage samples into the rumen fluid in vitro and survive there . Their interactions with rumen microorganisms should be studied further to understand how some silage inoculant LAB exhibit probiotic effects in dairy cattle. Biochemistry, 2004 Sep 21, 43(37), 11740 - 9 NMR solution structure of ImB2, a protein conferring immunity to antimicrobial activity of the type IIa bacteriocin, carnobacteriocin B2; Sprules T et al.; Bacteriocins produced by lactic acid bacteria are potent antimicrobial compounds which are active against closely related bacteria . Producer strains are protected against the effects of their cognate bacteriocins by immunity proteins that are located on the same genetic locus and are coexpressed with the gene encoding the bacteriocin . Several structures are available for class IIa bacteriocins; however, to date, no structures are available for the corresponding immunity proteins . We report here the NMR solution structure of the 111-amino acid immunity protein for carnobacteriocin B2 (ImB2) . ImB2 folds into a globular domain in aqueous solution which contains an antiparallel four-helix bundle . Extensive packing by hydrophobic side chains in adjacent helices forms the core of the protein . The C-terminus, containing a fifth helix and an extended strand, is held against the four-helix bundle by hydrophobic interactions with helices 3 and 4 . Most of the charged and polar residues in the protein face the solvent . Helix 3 is well-defined to residue 55, and a stretch of nascent helix followed by an unstructured loop joins it to helix 4 . No interaction is observed between ImB2 and either carnobacteriocin B2 (CbnB2) or its precursor . Protection from the action of CbnB2 is only observed when ImB2 is expressed within the cell . The loop between helices 3 and 4, and a hydrophobic pocket which it partially masks, may be important for interaction with membrane receptors responsible for sensitivity to class IIa bacteriocins. Int J Food Microbiol, 2004 Oct 1, 96(1), 1 - 12 Antagonistic activity against Helicobacter pylori infection in vitro by a strain of Enterococcus faecium TM39; Tsai CC et al.; Lactic acid bacteria (LAB) strains from infant feces were screened for anti-Helicobacter pylori use . In the beginning, we selected the strains based on their capability to adhere to the human intestinal epithelial cell (Int-407), colonial enterocyte-like Caco-2 cell, human cervical epithelioid carcinoma cell (HeLa), and human gastric carcinoma cell (TSGH 9201) . Then, acid and bile salt tolerance of these LAB strains was evaluated . In addition, the ability of these LAB strains to inhibit the growth of H . pylori and to expel H . pylori cells from TSGH 9201 were studied . The spent culture supernatant (SCS) of a selected strain TM39, i.e., TM39-SCS, significantly inhibited the viability of H . pylori in vitro . It also inhibited the urease activity of H . pylori in vitro . For these antagonistic effects, in addition to pH and lactic acid, some factors in TM39-SCS might play the major role . Treatment of H . pylori with the SCS or cells of strain TM39 significant reduced its binding to TSGH 9201 cells . Although strain TM39 is identified as Enterococcus faecium, it is not vancomycin resistant and is proved to be safe through the invasion study and a 28-day feeding study with Wistar rats . J Dairy Sci, 2004 Aug, 87(8), 2660 - 8 Expression of the peptidoglycan recognition protein, PGRP, in the lactating mammary gland; Kappeler SR et al.; The peptidoglycan recognition protein, PGRP, known as an intracellular component of neutrophils, has been isolated from camel (Camelus dromedarius) milk by acid precipitation followed by heparin-sepharose affinity chromatography of the supernatant . The mean concentration in milk was about 120 mg/L . It decreased during lactation by 19% and increased in the event of severe mastitis by 45% . The protein bound to lactic acid bacteria and other gram-positive bacteria with an affinity similar to that reported for the human and murine orthologs, although the isoelectric point of the molecule was distinctly higher at pH 9.02 . The N-terminus of mature camel PGRP was determined as NH2-ArgGluAspProPro-CO2H . Calculated and measured molecular masses were both 19.1 kDa, excluding the possibility of posttranslational modifcation or binding of cation ligands . The peptide probably builds a homotrimer at high concentration . The corresponding mRNA was isolated from lactating mammary gland tissue, and 5.3 kbp of the corresponding gene was sequenced . Similarities were found to the camel lactoferrin gene with regard to sites of expression and to the region 5' upstream to the gene. Yeast, 1994 Aug, 10(8), 1111 - 5 The nucleotide sequence of TTP1, a gene encoding a predicted type II membrane protein; Romero PA et al.; The DNA sequence of a 2967 bp fragment located near the centromere of chromosome II, between the CEN2 and FUR4 genes, was determined . The segment contains a new open reading frame of 1794 bp . The product encoded by the gene, designated TTP1, is a predicted type II membrane protein of 597 amino acid residues with a short cytoplasmic NH2-terminus, a membrane-spanning region and a large COOH-terminal region containing three potential N-glycosylation sites . Gene disruption indicated that TTP1 is not essential for cell growth. Protein Sci, 1994 Aug, 3(8), 1206 - 12 Properties of a recombinant human hemoglobin double mutant: sickle hemoglobin with Leu-88(beta) at the primary aggregation site substituted by Ala; Martin de Llano JJ et al.; A recombinant double mutant of hemoglobin (Hb), E6V/L88A(beta), was constructed to study the strength of the primary hydrophobic interaction in the gelation of sickle Hb, i.e., that between the mutant Val-6(beta) of one tetramer and the hydrophobic region between Phe-85(beta) and Leu-88(beta) on an adjacent tetramer . Thus, a construct encoding the donor Val-6(beta) of the expressed recombinant HbS and a second mutation encoding an Ala in place of Leu-88(beta) was assembled . The doubly mutated beta-globin gene was expressed in yeast together with the normal human alpha-chain, which is on the same plasmid, to produce a soluble Hb tetramer . Characterizations of the Hb double mutant by mass spectrometry, by HPLC, and by peptide mapping of tryptic digests of the mutant beta-chain were consistent with the desired mutations . The absorption spectra in the visible and the ultraviolet regions were practically superimposable for the recombinant Hb and the natural Hb purified from human red cells . Circular dichroism studies on the overall structure of the recombinant Hb double mutant and the recombinant single mutant, HbS, showed that both were correctly folded . Functional studies on the recombinant double mutant indicated that it was fully cooperative . However, its gelation concentration was significantly higher than that of either recombinant or natural sickle Hb, indicating that the strength of the interaction in this important donor-acceptor region in sickle Hb was considerably reduced even with such a conservative hydrophobic mutation. Curr Opin Cell Biol, 1994 Aug, 6(4), 555 - 60 Mechanisms of vesicle docking and fusion: insights from the nervous system; Pevsner J et al.; Upon stimulation of nerve cells, synaptic vesicles fuse with the presynaptic plasma membrane to release neurotransmitter . The biochemical pathway responsible for synaptic-vesicle docking and fusion is now being elucidated . Many of the proteins implicated in this process have homologs elsewhere in the cell . The docking and fusion mechanism discussed in this review may account for the specificity of vesicular trafficking throughout both regulated and constitutive secretory pathways. Genes Dev, 1994 Aug 1, 8(15), 1759 - 71 Collaboration of G1 cyclins in the functional inactivation of the retinoblastoma protein; Hatakeyama M et al.; The retinoblastoma gene product (pRB) constrains cell proliferation by preventing cell-cycle progression from the G1 to S phase . Its growth-inhibitory effects appear to be reversed by hyperphosphorylation occurring during G1 . This process is thought to involve G1 cyclins and cyclin-dependent kinases (cdks) . Here we report that the cell cycle-dependent phosphorylation of mammalian pRB is faithfully reproduced when it is expressed in Saccharomyces cerevisiae . As is the case in mammalian cells, this phosphorylation requires an intact oncoprotein-binding domain and is inhibited by a negative growth factor, in this case a mating pheromone . Expression of pRB in cln (-) mutants indicates that specific combinations of endogenous G1 cyclins, Cln3 and either Cln1 or Cln2 are required for pRB hyperphosphorylation in yeast . Moreover, expression of mammalian G1 cyclins in cln (-) yeast cells indicates that the functions of Cln2 and Cln3 in pRB hyperphosphorylation can be complemented by human cyclin E and cyclin D1, respectively . These observations suggest a functional heterogeneity among G1 cyclin-cdk complexes and indicate a need for the involvement of multiple G1 cyclins in promoting pRB hyperphosphorylation and resulting cell-cycle progression. Biophys J, 1994 Aug, 67(2), 737 - 45 Membrane location of apocytochrome c and cytochrome c determined from lipid-protein spin exchange interactions by continuous wave saturation electron spin resonance; Snel MM et al.; Apocytochrome c derived from horse heart cytochrome c was spin-labeled on the cysteine residue at position 14 or 17 in the N-terminal region of the primary sequence, and cytochrome c from yeast was spin-labeled on the single cysteine residue at sequence position 102 in the C-terminal region . The spin-labeled apocytochrome c and cytochrome c were bound to fluid bilayers composed of different negatively charged phospholipids that also contained phospholipid probes that were spin-labeled either in the headgroup or at different positions in the sn-2 acyl chain . The location of the spin-labeled cysteine residues on the lipid-bound proteins was determined relative to the spin-label positions in the different spin-labeled phospholipids by the influence of spin-spin interactions on the microwave saturation properties of the spin-label electron spin resonance spectra . The enhanced spin relaxation observed in the doubly labeled systems arises from Heisenberg spin exchange, which is determined by the accessibility of the spin-label group on the protein to that on the lipid . It is found that the labeled cysteine groups in horse heart apocytochrome c are located closest to the 14-C atom of the lipid acyl chain when the protein is bound to dimyristoyl- or dioleoyl-phosphatidylglycerol, and to that of the 5-C atom when the protein is bound to a dimyristoylphosphatidylglycerol/dimyristoylphosphatidylcholine (15:85 mol/mol mixture . On binding to dioleoylphosphatidylglycerol, the labeled cysteine residue in yeast cytochrome c is located closest to the phospholipid headgroups but possibly between the polar group region and the 5-C atom of the acyl chains . These data determine the extent to which the different regions of the proteins are able to penetrate negatively charged phospholipid bilayers. Trends Biochem Sci, 1994 Aug, 19(8), 336 - 40 Mechanisms of mRNA degradation in eukaryotes; Decker CJ et al.; Recent experiments have identified distinct mechanisms of eukaryotic RNA turnover . In one mechanism, deadenylation triggers decapping, exposing the messenger RNA to 5' to 3' degradation . This pathway may act at different rates on the majority of messenger RNAs . There are also degradation mechanisms, such as endonucleolytic cleavage, limited to messenger RNAs containing specific sequence elements. Electrophoresis, 1994 Aug-Sep, 15(8-9), 1078 - 83 Separation of large DNA molecules with high voltage pulsed field gel electrophoresis; Wagner L et al.; We have developed two high voltage (3 kV and 10 kV) high speed pulsed field gel electrophoresis systems for the separation of DNA as large as 460 kbp . These systems enable us to combine the rapid speed of high voltages and the separation power of pulsed field electrophoresis to achieve high resolution and short run durations . We found that large DNA fragments can be separated at voltage gradients much higher than commonly used . Yeast chromosomes as large as 460 kbp can be separated in 4 h at 20 V/cm and 1-50 kbp DNA can be rapidly separated in 30 min at 55 V/cm . This is 25 times faster in mobility for the separation of relatively small DNA fragments (< 50 kbp) . We have also found an inverse relationship between the voltage applied and the size separation limit at that particular voltage gradient (55 V/cm limits the separation to 50 kbp while 20 V/cm can separate up to 460 kbp) . Depending on the size range, DNA can be separated 8- to 25-fold faster and with better resolution than existing electrophoretic systems. J Biochem (Tokyo), 1994 Aug, 116(2), 243 - 7 Mutational analysis of the Sar1 protein, a small GTPase which is essential for vesicular transport from the endoplasmic reticulum; Nakano A et al.; SAR1 encodes a 21-kDa GTPase, which is required for vesicle formation from the endoplasmic reticulum in yeast . Although it belongs to the expanding small GTPase superfamily, there are interesting structural features that are unique to the Sar1 protein . We performed a site-directed mutational study to identify the amino acid residues that are essential for the Sar1p function . Among seven mutants we constructed, four are functionless by themselves, while two confer temperature sensitivity to cells . When the mutant proteins are overproduced in wild-type cells, all of these six show a dominant negative effect on cell growth . The replacement by serine of the only cysteine residue present in Sar1p caused no significant change in the growth phenotype . These findings are not only important for analyzing the mechanism of the Sar1p action in yeast, but will also be very useful for studying the function of Sar1p counterparts in higher eukaryotes. Nat Struct Biol, 1994 Aug, 1(8), 524 - 31 2.2 A structure of oxy-peroxidase as a model for the transient enzyme: peroxide complex; Miller MA et al.; The Fe+3-OOH complex of peroxidases has a very short half life, and its structure cannot be determined by conventional methods . The Fe+2-O2 complex provides a useful structural model for this intermediate, as it differs by only one electron and one proton from the transient Fe+3-OOH complex . We therefore determined the crystal structure of the Fe+2-O2 complex formed by a yeast cytochrome c peroxidase mutant with Trp 191 replaced by Phe . The refined structure shows that dioxygen can form a hydrogen bond with the conserved distal His residue, but not with the conserved distal Arg residue . When the transient Fe+3-OOH complex is modelled in a similar orientation, the active site of peroxidase appears to be optimized for catalysing proton transfer between the vicinal oxygen atoms of the peroxy-anion. J Biochem (Tokyo), 1994 Aug, 116(2), 386 - 92 Regulation of Src family kinases in the developing rat brain: correlation with their regulator kinase, Csk; Inomata M et al.; We have so far suggested that the functions of Src family protein-tyrosine kinases are under the control of their regulator kinase, Csk . To evaluate the role of Csk-mediated regulation in neural tissues, we examined the correlation between the activities of Src family kinases and the expression level of Csk during development of the rat brain . Csk was expressed at high levels in the developing embryonic brain and then rapidly decreased as the brain matured . Consistent with the decrease in the Csk level, the kinase activity of a member of the Src family, Fyn, was greatly enhanced, but that of Src was not correlated inversely with the level of Csk expression . Src exhibited elevated activity in the developing brain, in which a neuronal form of Src (N-Src) is expressed as the dominant form of Src . Although N-Src was readily down-regulated by Csk when coexpressed in yeast, it showed much higher specific activity than c-Src, even in the repressed form . These findings suggest that neural tissues acquire high activities of Src family kinases, which might be important for differentiation and development of the nervous system, through induction of the active form of Src (N-Src) and down-regulation of their suppresser, Csk. FEBS Lett, 1994 Aug 1, 349(2), 173 - 80 Production and characterization of monoclonal antibodies specific to multi-ubiquitin chains of polyubiquitinated proteins; Fujimuro M et al.; Polyubiquitinated proteins tagged with multi-ubiquitin chains are substrates preferred by the 26 S proteasome (a ubiquitin/ATP-dependent proteolytic complex) . Here, we developed a simple method for the efficient preparation of polyubiquitinated proteins which are degraded by the 26 S proteasome in an ATP-dependent manner . Our efficient method enabled us to produce ten monoclonal antibodies that recognized the multi-ubiquitin chains of the polyubiquitinated proteins, but not free ubiquitin or the protein moieties . Eight of the antibodies recognized only the multi-ubiquitin chains of the polyubiquitinated proteins, while the other two antibodies cross-reacted with mono-ubiquitin and methyl-ubiquitin, both of which are linked to proteins via an isopeptide bond, as well as with the multi-ubiquitin chains . Thus these antibodies are novel and useful tools for the identification and quantification of polyubiquitinated proteins in various cells and tissues under physiological and pathological conditions. Cell, 1994 Jul 29, 78(2), 275 - 89 Nup145p is required for nuclear export of mRNA and binds homopolymeric RNA in vitro via a novel conserved motif; Fabre E et al.; An essential yeast protein, Nup145p, is identified via its genetic interaction with the nucleoporin Nsp1p . Nup145p contains GLFG repeats and localizes to nuclear pores . Depletion of Nup145p in vivo leads rapidly to nuclear retention of polyadenylated RNAs and more slowly to cytoplasmic accumulation of a nuclear reporter protein . A stretch of 140 amino acids within Nup145p is conserved in two other yeast nucleoporins, Nup116p and Nup100p, and in an uncharacterized C . elegans protein . Genetic experiments in yeast reveal that the three copies of the motif carry out an essential, redundant function . Fragments of Nup145p and Nup116p including this motif bind specifically to homopolymeric RNAs in vitro . Nup145p, Nup116p, and Nup100p thus represent a novel class of nucleoporins involved in nucleocytoplasmic transport. J Biol Chem, 1994 Jul 29, 269(30), 19639 - 45 Characterization of two structurally related Xenopus laevis protein tyrosine phosphatases with homology to lipid-binding proteins; Del Vecchio RL et al.; We have chosen Xenopus laevis as a model system to study how protein tyrosine phosphatases (PTPases) function in growth and development . As an initial step, we have previously isolated in a polymerase chain reaction (PCR)-based protocol cDNA fragments which correspond to sequences within the catalytic domains of PTPases (Yang, Q., and Tonks, N . K . (1993) Adv . Protein Phosphatases 7, 359-372) . Two of these PCR products, designated X1 and X10, have now been used to screen a X . laevis ovary cDNA library to obtain complete coding sequences for two distinct PTPases . The X1 cDNA encodes a protein (PTPX1) of 693 amino acids (approximately 79 kDa); the X10 cDNA encodes a protein of 597 amino acids (approximately 69 kDa) . Both PTPX1 and PTPX10 lack potential membrane spanning sequences and therefore can be classified as non-transmembrane/cytoplasmic PTPases . While the overall structure of these PTPases are similar, sharing segments of 95% amino acid identity, they differ in that PTPX1 contains a unique 97-amino acid insert between the N-terminal segment and C-terminal catalytic domain . The absence of complete identity between PTPX1 and PTPX10 suggests that these two sequences are the products of separate genes and not the result of alternative splicing . This conclusion is confirmed by PCR analysis of Xenopus genomic DNA . Both PTPases share sequence identities in their N-terminal segments with two lipid-binding proteins, cellular retinaldehyde-binding protein and SEC14p, a phospholipid transferase . In addition, the unique insert sequence of PTPX1 shares identity with PSSA, a protein involved in phosphatidylserine biosynthesis . Sequence comparison suggests that PTPX10 is the Xenopus homolog of the human PTPase Meg-02, while PTPX1 is a structurally related yet distinct PTPase . Intrinsic PTPase activity of PTPX1 and PTPX10 was demonstrated in lysates of Sf9 cells infected with recombinant baculoviruses encoding either enzyme . PTPX1 can be recovered in both soluble and membrane fractions from Xenopus oocytes with the membrane form exhibiting approximately 4-fold higher activity than the soluble form. Biochem Biophys Res Commun, 1994 Jul 29, 202(2), 954 - 9 Replacement of all alpha-domain lysines with glutamates reduces metallothionein detoxification function; Cody CW et al.; Mammalian metallothioneins (MTs) possess eight highly conserved lysine residues, including three in each of two metal binding domains . We used site-directed mutagenesis to replace these intradomain lysines in Chinese hamster ovary MT2 with glutamic acid and/or glutamine . These mutant MTs were expressed in a metal sensitive yeast host . One mutant which had all three lysines in the alpha-domain replaced by glutamates (K43,51,56E) exhibited a reduced ability, relative to native MT, to protect yeast transformants against otherwise toxic levels of cadmium . This triply substituted mutant also exhibited anomalous migration on a non-denaturing gel relative to wild type MT and other MT lysine mutants, suggesting that the intradomain lysines are important in maintaining the conformational integrity of MT. Science, 1994 Jul 29, 265(5172), 674 - 6 Specific interaction of type I receptors of the TGF-beta family with the immunophilin FKBP-12; Wang T et al.; Transforming growth factor-beta (TGF-beta) family members bind to receptors that consist of heteromeric serine-threonine kinase subunits (type I and type II) . In a yeast genetic screen, the immunophilin FKBP-12, a target of the macrolides FK506 and rapamycin, interacted with the type I receptor for TGF-beta and with other type I receptors . Deletion, point mutation, and co-immunoprecipitation studies further demonstrated the specificity of the interaction . Excess FK506 competed with type I receptors for binding to FKBP-12, which suggests that these receptors share or overlap the macrolide binding site on FKBP-12, and therefore they may represent its natural ligand . The specific interaction between the type I receptors and FKBP-12 suggests that FKBP-12 may play a role in type I receptor-mediated signaling. J Biol Chem, 1994 Jul 22, 269(29), 19157 - 62 Catalytically important domains of rat carnitine palmitoyltransferase II as determined by site-directed mutagenesis and chemical modification . Evidence for a critical histidine residue; Brown NF et al.; Rat carnitine palmitoyltransferase (CPT) II was expressed in Saccharomyces cerevisiae . Mitochondrial fractions prepared from the cells displayed high CPT activity and reacted with an antibody to the rat protein on immunoblots, whereas no activity or immunoreactive protein was observed in control cells . The recombinant enzyme was largely membrane associated . Treatment of the expressed protein with diethyl pyrocarbonate, a reagent that modifies histidine residues, abolished CPT activity, but this was completely restored by reversal of the modification with hydroxylamine . It is inferred that a histidine residue plays a critical role in CPT function . Expression and analysis of site-directed mutants of CPT II showed that histidine 372, as well as aspartates 376 and 464 (all conserved throughout the carnitine/choline acyltransferase family), are essential for catalytic activity . The data suggest that the mechanism by which CPT II effects transesterification between palmitoyl-CoA and carnitine possibly involves histidine 372 and one of these aspartate residues, interacting with the carnitine hydroxyl group, in a reaction analogous to that carried out by a histidine/aspartate/serine catalytic triad in certain other enzyme systems . Mutagenic analysis of a region of CPT II that is highly conserved among the carnitine and choline acyltransferases, and which is homologous to the "adenine binding loop" of citrate synthase, implies that it has no similar function in CPT II. J Biol Chem, 1994 Jul 22, 269(29), 18727 - 30 Activation of phosphoinositide 3-kinase activity by Cdc42Hs binding to p85; Zheng Y et al.; The Ras-like GTPase Cdc42 is essential for cell polarity and bud site assembly in Saccharomyces cerevisiae by regulating cell cycle-dependent reorganization of cortical cytoskeletal elements . However, its role in mammalian cells is unknown . To identify potential effectors of Cdc42Hs, we incubated lysates from NIH 3T3 fibroblasts or PC12 cells with immobilized glutathione S-transferase (GST)-Cdc42Hs fusion proteins bound to different guanine nucleotides and observed a specific association between the 85-kDa subunit (p85) of phosphatidylinositol 3-kinase (PI 3-kinase) and GTP gamma S (guanosine 5'-3-O-(thio)triphosphate)-bound GST-Cdc42Hs . Recombinant p85 formed a complex with GTP gamma S-bound GST-Cdc42Hs and with a GTPase-defective GTP-bound GST-Cdc42Hs-Q61L mutant, but not with a GTP gamma S-bound, effector domain GST-Cdc42HsT35A mutant . Both the Rho-GAP homology domain of p85 and the Cdc42Hs-GAP competitively inhibited the binding of recombinant p85 to Cdc42Hs . In addition, PI 3-kinase activity immunoprecipitated from cell lysates with anti-p85 antibody was stimulated 2-4-fold by GST-Cdc42-GTP gamma S . Similar interactions were observed between p85 and GST-Rac1-GTP gamma S but not between p85 and GST-RhoA-GTP gamma S . These findings suggest that PI 3-kinase, through the Rho-GAP homology domain of p85, can couple to the effector domain of Cdc42Hs and that p85 may be a target for the GTP-bound forms of Cdc42Hs and Rac1. Biochim Biophys Acta, 1994 Jul 20, 1207(1), 114 - 9 Functional size of C-terminal protein carboxyl methyltransferase from kidney basolateral plasma membranes; Boivin D et al.; The functional sizes of the C-terminal isoprenylcysteine protein carboxyl methyltransferase (PCMT) from kidney cortex basolateral plasma membranes and yeast membranes have been estimated by the radiation inactivation and fragmentation method . Attempts to solubilize the methyltransferase with detergents were unsuccessful as they resulted in the irreversible denaturation of its enzymatic activity . The radiation inactivation sizes of the methyltransferases were 98 and 24 kDa for kidney and yeast, respectively . Kinetic experiments showed that irradiation affects the Vmax of the reaction but not the apparent Km for either S-adenosyl-L-methionine and N-acetyl farnesylcysteine . The functional size reported here for the kidney membrane is about 4-times larger than the size predicted for the Saccharomyces cerevisiae C-terminal PCMT deduced from the nucleotide sequence of its gene (28 kDa) . These results suggest that mammalian methyltransferase has a functional size different from that of the yeast; tetramerization of monomers is one possible hypothesis for this difference. Proc Natl Acad Sci U S A, 1994 Jul 19, 91(15), 6904 - 8 DNA-dependent protein kinase (Ku protein-p350 complex) assembles on double-stranded DNA; Suwa A et al.; The Ku protein is an autoantigen that consists of 70- and 80-kDa polypeptides . It associates with double-stranded DNA at free ends . In the present study, we examined the ability of anti-Ku antibodies to immunoprecipitate various structures from extracts of HeLa cells prepared at different salt concentrations . Under physiological conditions, these antibodies identified a complex containing the Ku protein and the 350-kDa component (p350) of DNA-dependent protein kinase (DNA-PK), which appeared to be closely associated on the DNA strand . In reconstitution experiments with cell extracts and biochemically purified components, the Ku protein-p350 complex formed only in the presence of double-stranded DNA . The reconstituted complex was catalytically active . Together with previous studies, these results indicate that the Ku protein interacts with DNA to create a binding site for p350 as the DNA-PK holoenzyme assembles. Biochemistry, 1994 Jul 19, 33(28), 8548 - 57 DNA-dependent ATPase from HeLa cells is related to human Ku autoantigen; Cao QP et al.; A 150-kDa DNA-dependent ATPase composed of 83/68-kDa subunits was previously reported to cofractionate with a 21S complex of enzymes for DNA synthesis from HeLa cells (Vishwanatha, J . K., & Baril, E . F . (1990) Biochemistry 29, 8753-8759) . The DNA-dependent ATPase was purified to electrophoretic homogeneity from a HeLa cell homogenate by a modified procedure that involves subcellular fractionation, poly(ethylene-glycol) precipitation of the combined nuclear extract/cytosol, and chromatography on Q-Sepharose and native and denatured DNA/celluloses followed by Mono-S fast protein liquid chromatography . The purified enzyme showed equimolar amounts of 83- and 68-kDa polypeptides following polyacrylamide gel electrophoresis under denaturing conditions . Sequence analysis of peptide fragments derived from the separated 83- and 68-kDa polypeptides showed 90-100% homology with the corresponding 80- and 70-kDa subunits of human Ku protein . Immunoblot analysis of the ATPase during the course of its purification and immunoprecipitation with antibodies to the 80- and 70-kDa subunits of human Ku protein confirmed the relationship of the 83- and 68-kDa polypeptides of the human DNA-dependent ATPase to the subunits of human Ku protein . Both the 83- and 68-kDa polypeptides are phosphorylated by a DNA-dependent protein kinase that cofractionates with the ATPase . The DNA-dependent ATPase activity is up regulated by phosphorylation. Biochim Biophys Acta, 1994 Jul 18, 1226(3), 307 - 14 Abnormal gene expression and regulation in the liver of jvs mice with systemic carnitine deficiency; Tomomura M et al.; Carnitine-deficient jvs mice expressed reduced levels of a group of genes which are preferentially expressed in the liver, including urea cycle enzyme genes (Biochim . Biophys . Acta 1138, 167-171, 1992) . The expression of alpha-fetoprotein and aldolase A was elevated, indicating that the liver of jvs mice is undifferentiated or dedifferentiated (FEBS Lett . 311, 63-66, 1992) . Studies of the hormone signal transduction pathway showed that serum cortisol and plasma glucagon levels of jvs mice were 2 and 3 times higher, respectively, than those of normal mice, and that the hormone binding activity of glucocorticoid receptor (GR) in the cytosol of jvs liver was 50% of normal mice, which reflected the amount of receptor protein in the cytosol . On the other hand, GR protein accumulated in the nuclear fraction in jvs mice . Exogenously administrated dexamethasone induced carbamoyl phosphate synthetase (CPS) and tyrosine aminotransferase (TAT) mRNAs in jvs mice, indicating that CPS and TAT genes in jvs mice are responsive to induction by glucocorticoid and cAMP . Analysis of transacting factors by gel retardation assay revealed that HNF-1, COUP-TF and SP-1 were detected at almost the same level in the hepatic nuclear fraction of jvs mice as in normal littermates, and C/EBP and CREB were a little higher in jvs mice, suggesting that these factors are probably not targets of jvs mutation causing abnormal gene expression in the liver . On the other hand, AP-1 binding activity was much higher in jvs mice from an early age, preceding the abnormal expression of urea cycle enzyme, and carnitine administration normalized AP-1 binding activity . We suggest that elevated AP-1 binding induced by carnitine deficiency is closely connected with the abnormal gene expression in the liver. EMBO J, 1994 Jul 15, 13(14), 3261 - 71 The ABC-transporter Ste6 accumulates in the plasma membrane in a ubiquitinated form in endocytosis mutants; Kolling R et al.; We are investigating the transport and turnover of the multispanning membrane protein Ste6 . The Ste6 protein is a member of the ABC-transporter family and is required for the secretion of the yeast mating pheromone a-factor . In contrast to the prevailing view that Ste6 is a plasma membrane protein, we found that Ste6 is mainly associated with internal membranes and not with the cell surface . Fractionation and immunofluorescence data are compatible with a Golgi localization of Ste6 . Despite its mostly intracellular localization, the Ste6 protein is in contact with the cell surface, as demonstrated by the finding that Ste6 accumulates in the plasma membrane in endocytosis mutants . The Ste6 protein which accumulates in the plasma membrane in endocytosis mutants is ubiquitinated . Ste6 is thus the second protein in yeast besides MAT alpha 2 for which ubiquitination has been demonstrated . Ste6 is a very unstable protein (half-life 13 min) which is stabilized approximately 3-fold in a ubc4 ubc5 mutant, implicating the ubiquitin system in the degradation of Ste6 . The strongest stabilizing effect on Ste6 is, however, observed in the vacuolar pep4 mutant (half-life > 2 h), suggesting that most of Ste6 is degraded in the vacuole . Secretory functions are required for efficient degradation of Ste6, indicating that Ste6 enters the secretory pathway and is transported to the vacuole by vesicular carriers. Biochem Biophys Res Commun, 1994 Jul 15, 202(1), 621 - 8 Substitution of glutamic acids for the conserved lysines in the alpha domain affects metal binding in both the alpha and beta domains of mammalian metallothionein; Pan PK et al.; Lysine residues are highly conserved in mammalian metallothioneins (MTs) . Recombinant mutant Chinese hamster MT2 in which all of the lysines (K) in the alpha-domain were substituted by glutamic acids (E) was assayed with, expressed in and purified from a cadmium sensitive strain of yeast Saccharomyces cerevisiae . Circular dichroism analyses of the mutated protein, mutein K43,51,56E, revealed that the overall structure remained unchanged . However, a 1-D 113Cd NMR study detected significant differences in the chemical shifts of the corresponding resonances between wild type protein and the recombinant mutein . Reduction of integrated intensity in the NMR spectra was also observed for resonances from the four-metal cluster (I and V-VII) in the alpha-domain of the mutein . At various temperatures, facile intermolecular exchange of metals in the beta-domain of the mutein was also observed, which was unexpected and was different from wild type . Our results thus demonstrate that replacing all three lysines by glutamic acids in the alpha-domain changed metal-thiolate interactions in both domains of the recombinant mutein . This may explain the reduced ability of the mutein to convey cadmium resistance . We propose that while the lysine residues in the alpha-domain of wild type MT are not critical for maintaining protein structure, they play a role in regulating the microenvironment and stability of both metal-binding clusters, a feature critical to metal detoxification. J Biol Chem, 1994 Jul 15, 269(28), 18576 - 82 Non-random acetylation of histone H4 by a cytoplasmic histone acetyltransferase as determined by novel methodology; Sobel RE et al.; During periods of active DNA replication and chromatin assembly, newly synthesized histone H4 is deposited in a diacetylated form . In Tetrahymena, a specific pair of residues, lysines 4 and 11, has been shown to undergo this modification in vivo (Chicoine, L . G., Schulman, I . G., Richman, R., Cook, R . G., and Allis, C . D . (1986) J . Biol . Chem . 261, 1071-1076) . Presumably, this reaction is catalyzed, at least in part, by histone acetyltransferases (HAT) of the B type, cytoplasmic enzymes displaying strong preference for free, non-chromatin-bound H4 . To investigate which lysines are preferred acetylation sites in H4 from other organisms, a cytoplasmic HAT B activity was prepared from Drosophila embryos and used to acetylate H4 from several species . When H4 or synthetic, NH2-terminal peptides from Tetrahymena were used as unblocked substrates, direct microsequence analyses showed that {3H}acetate was preferentially incorporated at lysine 11 with little, if any, incorporation at other conserved, acetylatable lysines . Drosophila H4 was chemically deblocked following its acetylation in vitro using conditions that do not deacetylate internal lysines . Direct sequence analysis verified the correct NH2-terminal sequence of Drosophila H4 and demonstrated that {3H}acetate incorporation occurred preferentially on lysine 12, the residue analogous to lysine 11 in Tetrahymena . These data show remarkable preference for lysine 11/12 by the Drosophila HAT B activity in vitro and provide support for the assertion that this activity functions to acetylate new H4, at least in part, for deposition and chromatin assembly in vivo . Since most H4s, like Drosophila, are blocked at their amino termini by an acetylthreonine or acetylserine, our results demonstrate that this deblocking and microsequencing strategy can be used to study acetylation site utilization in H4 and presumably other core histones NH2 terminally blocked with these residues. Cell, 1994 Jul 15, 78(1), 87 - 98 The karyogamy gene KAR2 and novel proteins are required for ER-membrane fusion; Latterich M et al.; We have developed assays using cells and isolated membranes to identify factors mediating fusion of the ER-nuclear membrane network in yeast . When cells containing distinctly tagged ER-nuclear envelope membranes are observed during mating, the markers of both parental membranes become colocalized in a process sharing a genetic requirement with karyogamy . Using isolated membranes, we find that fusion between ER compartments requires ATP, but not cytosol, Sec17p (alpha-SNAP), or Sec18p (NSF), the latter two being required at the fusion step in vesicular transport . Proteins tightly associated with the ER membrane are essential for fusion, as is Kar2p (BiP), an ER lumenal hsp70 homolog . BiP may activate an ER-localized fusogen, allowing nuclear fusion and karyogamy in yeast. Nucleic Acids Res, 1994 Jul 11, 22(13), 2601 - 3 Transcriptional activation of NFI/CTF1 depends on a sequence motif strongly related to the carboxyterminal domain of RNA polymerase II; Wendler W et al.; Initiation of RNA polymerase II-directed transcription is mediated by DNA sequence specific activator proteins interacting with components of the basal transcription machinery . NFI/CTF is a family of such binding proteins which have been shown to stimulate transcription via proline-rich activation domains . In order to identify residues crucial for its activator function, a pool of CTF1 mutants was cloned and fused to the bacterial repressor LexA . Transcriptional activation of these constructs was monitored in a Saccharomyces cerevisiae reporter assay . Our studies reveal the existence of a core domain in CTF1 between residues 463 and 508 essential for transcriptional activation functions . It contains the sequence motif SPTSPSYSP, which is strongly related to the heptapeptide repeat YSPTSPS present in the carboxyterminal domain (CTD) of RNA polymerase II . Removal of the entire CTD related motif, as well as substitution of key amino acids therein, abolish CTF1 mediated transcriptional activation. Gut, 2004 Nov, 53(11), 1602 - 9 Modulation of human dendritic cell phenotype and function by probiotic bacteria; Hart AL et al.; BACKGROUND: "Probiotic" bacteria are effective in treating some inflammatory bowel diseases . However which bacteria confer benefit and mechanisms of action remain poorly defined . Dendritic cells, which are pivotal in early bacterial recognition, tolerance induction, and shaping of T cell responses, may be central in mediating the effects of these bacteria . AIMS: To assess effects of different probiotic bacteria on dendritic cell function . METHODS: Human intestinal lamina propria mononuclear cells, whole blood, or an enriched blood dendritic cell population were cultured with cell wall components of the eight bacterial strains in the probiotic preparation VSL#3 (four lactobacilli, three bifidobacteria, and one streptococcal strains) . Dendritic cells were identified and changes in dendritic cell maturation/costimulatory markers and cytokine production in response to probiotic bacteria were analysed by multicolour flow cytometry, in addition to subsequent effects on T cell polarisation . RESULTS: VSL#3 was a potent inducer of IL-10 by dendritic cells from blood and intestinal tissue, and inhibited generation of Th1 cells . Individual strains within VSL#3 displayed distinct immunomodulatory effects on dendritic cells; the most marked anti-inflammatory effects were produced by bifidobacteria strains which upregulated IL-10 production by dendritic cells, decreased expression of the costimulatory molecule CD80, and decreased interferon-gamma production by T cells . VSL#3 diminished proinflammatory effects of LPS by decreasing LPS induced production of IL-12 while maintaining IL-10 production . CONCLUSIONS: Probiotic bacteria differ in their immunomodulatory activity and influence polarisation of immune responses at the earliest stage of antigen presentation by dendritic cells. Appl Environ Microbiol, 2004 Oct, 70(10), 6197 - 209 Characterization of the groEL and groES loci in Bifidobacterium breve UCC 2003: genetic, transcriptional, and phylogenetic analyses; Ventura M et al.; The bacterial heat shock response is characterized by the elevated expression of a number of chaperone complexes, including the GroEL and GroES proteins . The groES and groEL genes are highly conserved among eubacteria and are typically arranged as an operon . Genome analysis of Bifidobacterium breve UCC 2003 revealed that the groES and groEL genes are located in different chromosomal regions . The heat inducibility of the groEL and groES genes of B . breve UCC 2003 was verified by slot blot analysis . Northern blot analyses showed that the cspA gene is cotranscribed with the groEL gene, while the groES gene is transcribed as a monocistronic unit . The transcription initiation sites of these two mRNAs were determined by primer extension . Sequence and transcriptional analyses of the region flanking the groEL and groES genes of various bifidobacteria revealed similar groEL-cspA and groES gene units, suggesting a novel genetic organization of these chaperones . Phylogenetic analysis of the available bifidobacterial groES and groEL genes suggested that these genes evolved differently . Discrepancies in the phylogenetic positioning of groES-based trees make this gene an unreliable molecular marker . On the other hand, the bifidobacterial groEL gene sequences can be used as an alternative to current methods for tracing Bifidobacterium species, particularly because they allow a high level of discrimination between closely related species of this genus. Eksp Klin Gastroenterol, 2004, (2), 22 - 4, 108 {Microbiocenosis of the bowels in patients with gastroduodenal ulcers}; Clarification of interactions among microorganisms and development of co-culture system for production of useful substances; Department of Materials Science and Technology, Niigata University, Ikarashi 2-8050, Niigata 950-2181, Japan . mtanig@eng.niigata-u.ac.jp Co-culture systems containing two microorganisms for the production of useful substances are described . We developed a novel co-culture system composed of two fermentors and two microfiltration modules . The proposed co-culture system allowed regulation of the dissolved oxygen concentration at a level suitable for an individual microorganism in each fermentor, as well as the successful exchange of culture medium between two fermentors . By co-culture, using a combination of Pichia stipitis and Saccharomyces cerevisiae, ethanol was produced efficiently from a mixture of glucose and xylose . Moreover, the useful probiotic cells were simultaneously produced with a high productivity by our co-culture using a combination of Bifidobacterium and Propionibacterium . Kefiran production by Lactobacillus kefiranofaciens alone under the culture conditions, established by mimicking the presence and activities of yeast cells in kefir grains, was also investigated . The results obtained showed that under the culture conditions established by mimicking the actions of yeast cells on L . kefiranofaciens in kefir grains, the amount of kefiran produced was enhanced, even when the lactic acid bacterium alone was used. Zhonghua Shao Shang Za Zhi, 2004 Aug, 20(4), 202 - 5 {The protective effect of supplementation of probiotics combined with riboflavin on the intestinal barrier of the rats after scald injury}; Wang ZT et al.; OBJECTIVE: To investigate the effect and its possible mechanism of the supplementation of probiotics combined with riboflavin on the intestinal barriers of the rats after scald injury . METHODS: Seventy Wistar rats were used in the study and were randomly divided into scald control (SC, n = 30), scald and treatment (ST, n = 30) and normal control (NC, n = 10) groups . The rats in SC and ST groups were subjected to 30% TBSA III degree scald . 1.5 ml of isotonic saline suspension containing 5 x 10(12) CFU/L of Bifidobacteria, 5 x 10(10) CFU/L of Bacillus cereus and 5 mg/L of riboflavin was given to rats by gavage in ST group twice a day . For the rats in SC and NC group equal amount of isotonic saline was fed twice a day . The changes in the incidence of bacterial translocation, the amount of intestinal membranous flora, the synthesis and secretion of SIgA in the ileum, and the repair of injured intestinal mucosa were observed . RESULTS: The incidence of bacterial translocation in ST group was significantly lower than that in SC group (P = 0.000 - 0.025) . The plasma level of endotoxin in ST group was markedly lower than that in SC group on 3 post-scald day (PSD) (P < 0.05) . The amount of bifidobacteria in caecal membrane flora increased by about 20 to 40 fold, whereas the amounts of E . coli and fungi significantly decreased (P < 0.01) . The membranous injury scoring was 3 to 0 on 5 PSD (P < 0.05), and the SIgA content in intestinal mucus returned to normal value on the 5th PSD (P < 0.01) in the ST group . CONCLUSION: Supplementation of probiotics together with riboflavin could ameliorate translocation of bacteria and endotoxin in rats with scald injury, implying that the intestinal barrier function was effectively protected. Zhong Xi Yi Jie He Xue Bao, 2004 Sep, 2(5), 340 - 2 {Observation on intestinal flora in patients of irritable bowel syndrome after treatment of Chinese integrative medicine}; Sun X et al.; OBJECTIVE: To observe the clinical efficacy of the combination of traditional Chinese medicine and western medicine in treating irritable bowel syndrome (IBS) and the result of intestinal flora regulation . Methods: Sixty IBS patients, 36 males and 24 females, were divided into two groups, with 30 patients in each group . Herbal formula of TongxieYaofang and clostridium butyricum (Cb) were used in the first group for four weeks, while only Cb was used for four weeks in the second group . We observed the changes of coliform group, enterococcus, lactobacillus, bifidobacterium after treatment . RESULTS: The effective rate of the Tongxie Yaofang and Cb treated group was significantly higher than that of the Cb treated group (P < 0.05) . The numbers of bifidobacterium and lactobacillus increased, while the numbers of coliform group and enterococcus decreased after the treatment, and the changes of intestinal flora in the integrative medicine treated group were significantly greater than those in the Cb treated group . CONCLUSION: After treatment with the combination of traditional Chinese medicine and western medicine, the intestinal flora can be regulated to equilibrium state. Transfusion, 2004 Oct, 44(10), 1496 - 504 Photochemical treatment of platelet concentrates with amotosalen and long-wavelength ultraviolet light inactivates a broad spectrum of pathogenic bacteria; Lin L et al.; BACKGROUND: Bacterial contamination of platelet (PLT) concentrates can result in transfusion-transmitted sepsis . A photochemical treatment (PCT) process with amotosalen HCl and long-wavelength ultraviolet light (UVA), which cross-links nucleic acids, was developed to inactivate bacteria and other pathogens in PLT concentrates . STUDY DESIGN AND METHODS: High titers of pathogenic aerobic and anaerobic Gram-positive bacteria (10 species), aerobic Gram-negative bacteria (7 species), and spirochetes (2 species) were added to single-donor PLT concentrates containing 3.0 x 10(11) to 6.0 x 10(11) PLTs in approximately 300 mL of 35 percent plasma and 65 percent PLT additive solution (InterSol, Baxter Healthcare) or saline . After PCT with 150 micro mol per L amotosalen and 3 J per cm(2) UVA, residual bacterial levels were detected by sensitive microbiologic methods . RESULTS: The level of inactivation of viable bacteria was expressed as log reduction . Log reduction of Gram-positive bacteria for Staphylococcus epidermidis was > 6.6; for Staphylococcus aureus, 6.6; for Streptococcus pyogenes, > 6.8; for Listeria monocytogenes, > 6.3; for Corynebacterium minutissimum, > 6.3; for Bacillus cereus (vegetative), > 5.5; for Lactobacillus sp., > 6.4; for Bifidobacterium adolescentis, > 6.0; for Propionibacterium acnes, > 6.2; and for Clostridium perfringens, > 6.5 . Log reduction of Gram-negative bacteria for Escherichia coli was > 6.4; for Serratia marcescens, > 6.7; for Klebsiella pneumoniae, > 5.6; for Pseudomonas aeruginosa, 4.5; for Salmonella choleraesuis, > 6.2; for Yersinia enterocolitica, > 5.9; and for Enterobacter cloacae, 5.9 . Log reduction of spirochetes for Treponema pallidum was 6.8 to 7.0, and for Borrelia burgdorferi, > 6.9 . CONCLUSION: PCT inactivates high levels of a broad spectrum of pathogenic bacteria . The inactivation of bacteria in PLT concentrates offers the potential to prospectively prevent PLT-transfusion-associated bacteremia. J Bacteriol, 2004 Oct, 186(19), 6515 - 25 Bifidobacterium longum requires a fructokinase (Frk; ATP:D-fructose 6-phosphotransferase, EC 2.7.1.4) for fructose catabolism; Caescu CI et al.; Although the ability of Bifidobacterium spp . to grow on fructose as a unique carbon source has been demonstrated, the enzyme(s) needed to incorporate fructose into a catabolic pathway has hitherto not been defined . This work demonstrates that intracellular fructose is metabolized via the fructose-6-P phosphoketolase pathway and suggests that a fructokinase (Frk; EC 2.7.1.4) is the enzyme that is necessary and sufficient for the assimilation of fructose into this catabolic route in Bifidobacterium longum . The B . longum A10C fructokinase-encoding gene (frk) was expressed in Escherichia coli from a pET28 vector with an attached N-terminal histidine tag . The expressed enzyme was purified by affinity chromatography on a Co(2+)-based column, and the pH and temperature optima were determined . A biochemical analysis revealed that Frk displays the same affinity for fructose and ATP (Km(fructose) = 0.739 +/- 0.18 mM and Km(ATP) = 0.756 +/- 0.08 mM), is highly specific for D-fructose, and is inhibited by an excess of ATP (>12 mM) . It was also found that frk is inducible by fructose and is subject to glucose-mediated repression . Consequently, this work presents the first characterization at the molecular and biochemical level of a fructokinase from a gram-positive bacterium that is highly specific for D-fructose. FEMS Microbiol Rev, 2004 Oct, 28(4), 405 - 40 Antagonistic activities of lactobacilli and bifidobacteria against microbial pathogens; Servin AL; The gastrointestinal tract is a complex ecosystem that associates a resident microbiota and cells of various phenotypes lining the epithelial wall expressing complex metabolic activities . The resident microbiota in the digestive tract is a heterogeneous microbial ecosystem containing up to 1 x 10(14) colony-forming units (CFUs) of bacteria . The intestinal microbiota plays an important role in normal gut function and maintaining host health . The host is protected from attack by potentially harmful microbial microorganisms by the physical and chemical barriers created by the gastrointestinal epithelium . The cells lining the gastrointestinal epithelium and the resident microbiota are two partners that properly and/or synergistically function to promote an efficient host system of defence . The gastrointestinal cells that make up the epithelium, provide a physical barrier that protects the host against the unwanted intrusion of microorganisms into the gastrointestinal microbiota, and against the penetration of harmful microorganisms which usurp the cellular molecules and signalling pathways of the host to become pathogenic . One of the basic physiological functions of the resident microbiota is that it functions as a microbial barrier against microbial pathogens . The mechanisms by which the species of the microbiota exert this barrier effect remain largely to be determined . There is increasing evidence that lactobacilli and bifidobacteria, which inhabit the gastrointestinal microbiota, develop antimicrobial activities that participate in the host's gastrointestinal system of defence . The objective of this review is to analyze the in vitro and in vivo experimental and clinical studies in which the antimicrobial activities of selected lactobacilli and bifidobacteria strains have been documented. J Microbiol Methods, 2004 Nov, 59(2), 211 - 21 Comparative detection of bacterial adhesion to Caco-2 cells with ELISA, radioactivity and plate count methods; Le Blay G et al.; Different methods are used to study bacterial adhesion to intestinal epithelial cells, which is an important step in pathogenic infection as well as in probiotic colonization of the intestinal tract . The aim of this study was to compare the ELISA-based method with more conventional plate count and radiolabeling methods for bacterial adhesion detection . An ELISA-based assay was optimized for the detection of Bifidobacterium longum and Escherichia coli O157:H7, which are low and highly adherent bacteria, respectively . In agreement with previous investigations, a percentage of adhesion below 1% was obtained for B . longum with ELISA . However, high nonspecific background and low positive signals were measured due to the use of polyclonal antibodies and the low adhesion capacity with this strain . In contrast, the ELISA-based method developed for E . coli adhesion detected a high adhesion percentage (15%) . For this bacterium the three methods tested gave similar results for the highest bacterial concentrations (6.8 Log CFU added bacteria/well) . However, differences among methods increased with the addition of decreased bacterial concentration due to different detection thresholds (5.9, 5.6 and 2.9 Log CFU adherent bacteria/well for radioactivity, ELISA and plate count methods, respectively) . The ELISA-based method was shown to be a good predictor for bacterial adhesion compared to the radiolabeling method when good quality specific antibodies were used . This technique is convenient and allows handling of numerous samples. J Ind Microbiol Biotechnol, 2004 Oct, 31(9), 427 - 32 Epub 2004 Oct. A repeated batch process for cultivation of Bifidobacterium longum; Her SL et al.; A repeated batch process was performed to culture Bifidobacterium longum CCRC 14634 . An on-line device, oxidation-reduction potential (ORP), was used to monitor cell growth and uptake of nutrients in the culture . The ORP of the culture medium decreased substantially during fermentation until nutrients were depleted . Six cycles of batch fermentation using ORP as a control parameter were successfully carried out . As soon as ORP remained constant or increased, three-quarters of the broth was removed, and the same volume of fresh medium was fed to the fermenter for a new cycle of cultivation . Average cell concentrations of 1.9 x 10(9) and 3.4 x 10(9) cfu ml(-1) for repeated batch fermentation in MRS (Lactobacilli MRS broth) and WY (containing whey hydrolyzates, yeast extract, l-cysteine) medium, respectively, were achieved . Cell mass productivities for batch, fed-batch and repeated batch fermentation using MRS medium were 0.51, 0.41, and 0.64 g l(-1) h(-1), respectively, and those for batch and repeated batch using WY medium were 0.76, 0.99 g l(-1) h(-1), respectively . The results indicate a possible industrial process to culture Bifidobacteria sp. Gastroenterology, 2004 Sep, 127(3), 826 - 37 Lactobacillus paracasei normalizes muscle hypercontractility in a murine model of postinfective gut dysfunction; Verdu EF et al.; BACKGROUND & AIMS: The effects of probiotics on gut dysfunction in postinfective irritable bowel syndrome are unknown . We tested whether probiotics influence persistent muscle hypercontractility in mice after recovery from infection with Trichinella spiralis and analyzed the underlying mechanisms . METHODS: Mice were gavaged with Lactobacillus paracasei, Lactobacillus johnsonii, Bifidobacterium longum, or Bifidobacterium lactis in spent culture medium from days 10 to 21 after infection . Additional mice received heat-inactivated Lactobacillus paracasei, Lactobacillus paracasei -free spent culture medium, or heat-inactivated Lactobacillus paracasei -free spent culture medium . Lactobacilli enumeration, immunohistochemistry, and cytokine detection (enzyme-linked immunosorbent assay) were performed . Mice were also treated with Lactobacillus paracasei or Lactobacillus paracasei -free spent culture medium from days 18 to 28 after infection . Contractility was measured on days 21 and 28 after infection . RESULTS: Lactobacillus paracasei, but not Lactobacillus johnsonii, Bifidobacterium lactis, or Bifidobacterium longum, attenuated muscle hypercontractility . This was associated with a reduction in the Trichinella spiralis -associated T-helper 2 response and a reduction in transforming growth factor-beta1, cyclooxygenase-2, and prostaglandin E 2 levels in muscle . Attenuation of muscle hypercontractility by Lactobacillus paracasei -free spent culture medium was abolished after heat treatment . Improvement of muscle hypercontractility at day 28 after infection was also observed after the administration of Lactobacillus paracasei or Lactobacillus paracasei -free spent culture medium from day 18 after infection . CONCLUSIONS: Probiotics show strain-dependent attenuation of muscle hypercontractility in an animal model of postinfective irritable bowel syndrome . This likely occurs via both a modulation of the immunologic response to infection and a direct effect of Lactobacillus paracasei or a heat-labile metabolite on postinfective muscle hypercontractility . Lactobacillus paracasei may be useful in the treatment of postinfective irritable bowel syndrome. J Dairy Res, 2004 Aug, 71(3), 340 - 5 Selection of acid tolerant bifidobacteria and evidence for a low-pH-inducible acid tolerance response in Bifidobacterium longum; Takahashi N et al.; Acidity is an environmental condition commonly encountered by lactic acid bacteria and bifidobacteria in the gastrointestinal tract and fermented foods . In the present study, 22 strains of Bifidobacterium were screened for acid tolerance in artificial gastric juice (AGJ, pH 3.0) and fermented milk . AGJ tolerance was found to be strain-specific, with a pronounced variation among the strains . Several strains with a high survival rate in AGJ that belonged to Bifid . longum, Bifid . breve and Bifid . adolescentis were selected . Among them, only strain BL1 of Bifid longum was found to possess a high survival rate in fermented milk during refrigerated storage . Strain BL1 exhibited a survival rate of more than 25% in AGJ at pH 3.0 for 2 h and maintained a viable cfu level of more than 10(8) per gram of product in fermented milk (pH 4.6) under refrigerated conditions for 2 weeks . The acid tolerance of strain BL1 was found to depend on the final growth pH (<4.5) . Rapid loss of acid tolerance was observed when the cells were shifted from acid to neutral conditions by addition of NaOH . Strain BL1 cells were able to maintain much higher intracellular pH under acid conditions, in comparison with those of AGJ sensitive mutant (BL1-S) or cells that lost acid tolerance following pH shifting from acid to neutral conditions . These results suggested that a cytoplasmic pH homeostasis system may function in the acid tolerance response in this strain. Food Chem Toxicol, 2004 Oct, 42(10), 1695 - 1700 Effect of red pepper Capsicum annuum var . conoides and garlic Allium sativum on plasma lipid levels and cecal microflora in mice fed beef tallow; Kuda T et al.; Antihyperlipidemia or hypocholesterolaemic and antibacterial activities of red hot pepper and garlic are well known . To determine the effect of the dietary spices ingested to suppress blood lipids on the intestinal condition, we examined plasma lipid levels and cecal microflora in mice that were fed diets containing 19% (w/w) beef tallow and 2% red pepper Capsicum annuum var . conoides 'Takanotume' (RP) or garlic Allium sativum 'White' (GP) for 4-weeks . Plasma triacylglyceride level was suppressed by the spices . RP lowered cecal bacteroidaceae, a predominant bacterial group (from 9.4 to 9.0 log CFU/g), bifidobacteria (from 8.7 to 7.6 log CFU/g), and staphylococci . Although GP increased the cecal weight including their contents, significant differences were not shown in the cecal microflora . These results suggest that RP can affect the intestinal condition and host health through the disturbance of intestinal microflora . Int Arch Allergy Immunol, 2004 Oct, 135(2), 132 - 5 Epub 2004 Sep 02. Dietary nucleic acid and intestinal microbiota synergistically promote a shift in the Th1/Th2 balance toward Th1-skewed immunity; Sudo N et al.; BACKGROUND: Intestinal microbiota are known to play an important role in the establishment of oral tolerance, thereby protecting the organism from food allergies . Dietary intake of nucleic acid (NA) is also reported to have such an anti-allergic effect; however, one unsolved question is whether or not dietary NA would act through a process of toll-like receptor 9 signaling activated by DNA containing a CpG motif, a well-known sequence leading to immunostimulatory activity . In this study, we focused on the question of whether the addition of dietary NA lacking CpG motifs would allow continued modulation of the Th1/Th2 balance . METHODS: Germ free (GF) and Bifidobacterium-infantis-monoassociated BALB/c mice were maintained on either an NA-free casein diet or on an NA-supplemented casein diet for 4 weeks . Thereafter, both the in vivo anti-casein antibody levels and in vitro splenocyte cytokine secretion pattern were evaluated . RESULTS: Feeding with a casein diet elicited a substantial increase in the serum anti-casein-specific IgG1, IgG2a, and IgE levels of GF mice fed the NA free-diet . The in vitro cytokine production profile showed that enhanced IL-4 production in the GF mice fed the NA free-diet was markedly reduced by the supplementation with dietary NA in both the GF and B.-infantis-monoassociated mice . In addition, IFN-gamma secretion increased in the B.-infantis-reconstituted mice fed the diet containing NA . CONCLUSIONS: These results suggest that dietary intake of NA devoid of CpG motifs may prevent the development of allergies via acceleration of Th1-dominant immunity. Appl Environ Microbiol, 2004 Sep, 70(9), 5603 - 12 Cloning and characterization of the bile salt hydrolase genes (bsh) from Bifidobacterium bifidum strains; Kim GB et al.; Biochemical characterization of the purified bile salt hydrolase (BSH) from Bifidobacterium bifidum ATCC 11863 revealed some distinct characteristics not observed in other species of Bifidobacterium . The bsh gene was cloned from B . bifidum, and the DNA flanking the bsh gene was sequenced . Comparison of the deduced amino acid sequence of the cloned gene with previously known sequences revealed high homology with BSH enzymes from several microorganisms and penicillin V amidase (PVA) of Bacillus sphaericus . The proposed active sites of PVA were highly conserved, including that of the Cys-1 residue . The importance of the SH group in the N-terminal cysteine was confirmed by substitution of Cys with chemically and structurally similar residues, Ser or Thr, both of which resulted in an inactive enzyme . The transcriptional start point of the bsh gene has been determined by primer extension analysis . Unlike Bifidobacterium longum bsh, B . bifidum bsh was transcribed as a monocistronic unit, which was confirmed by Northern blot analysis . PCR amplification with the type-specific primer set revealed the high level of sequence homology in their bsh genes within the species of B . bifidum. Appl Environ Microbiol, 2004 Sep, 70(9), 5066 - 73 Characterization and heterologous expression of the oxalyl coenzyme A decarboxylase gene from Bifidobacterium lactis; Federici F et al.; Oxalyl coenzyme A (CoA) decarboxylase (Oxc) is a key enzyme in the catabolism of the highly toxic compound oxalate, catalyzing the decarboxylation of oxalyl-CoA to formyl-CoA . The gene encoding a novel oxalyl-CoA decarboxylase from Bifidobacterium lactis DSM 10140 (oxc) was identified and characterized . This strain, isolated from yogurt, showed the highest oxalate-degrading activity in a preliminary screening with 12 strains belonging to Bifidobacterium, an anaerobic intestinal bacterial group largely used in probiotic products . The oxc gene was isolated by probing a B . lactis genomic library with a probe obtained by amplification of the oxalyl-CoA decarboxylase gene from Oxalobacter formigenes, an anaerobic bacterium of the human intestinal microflora . The oxc DNA sequence analysis revealed an open reading frame of 1,773 bp encoding a deduced 590-amino-acid protein with a molecular mass of about 63 kDa . Analysis of amino acid sequence showed a significant homology (47%) with oxalyl-CoA decarboxylase of O . formigenes and a typical thiamine pyrophosphate-binding site that has been reported for several decarboxylase enzymes . Primer extension experiments with oxc performed by using RNA isolated from B . lactis identified the transcriptional start site 28 bp upstream of the ATG start codon, immediately adjacent to a presumed promoter region . The protein overexpressed in Escherichia coli cross-reacted with an anti-O . formigenes oxalyl-CoA decarboxylase antibody . Enzymatic activity, when evaluated by capillary electrophoresis analysis, demonstrated that the consumption substrate oxalyl-CoA was regulated by a product inhibition of the enzyme . These findings suggest a potential role for Bifidobacterium in the intestinal degradation of oxalate. Poult Sci, 2004 Aug, 83(8), 1302 - 6 Efficacy of Leuconostoc mesenteroides (ATCC 13146) isomaltooligosaccharides as a poultry prebiotic; Chung CH et al.; The complex dietary carbohydrates, called prebiotics, have been used to control Salmonella and improve intestinal bacterial balance in broilers . Leuconostoc mesenteroides (ATCC 13146) isomaltooligosaccharides (IMO) stimulate growth of Bifidobacterium and Lactobacillus and are not used by Salmonella or Escherichia coli . We tested the efficacy of these IMO as a prebiotic . IMO, compared with fructooligosaccharides (FOS) as sole carbon source, promoted growth of chicken cecal isolates and Bifidobacterium . Cecal isolates and Salmonella typhimurium grown in mixed culture on IMO reduced the Salmonella population . Cecal isolates grown on IMO showed higher viable counts and faster growth than Salmonella, indicating a potential value for these oligomers for poultry intestinal microflora modification. Acta Crystallogr D Biol Crystallogr, 2004 Sep, 60(Pt 9), 1665 - 7 Epub 2004 Aug 26. Expression, purification, crystallization and preliminary X-ray diffraction analysis of conjugated bile salt hydrolase from Bifidobacterium longum; Kumar RS et al.; Conjugated bile salt hydrolase (BSH) catalyses the hydrolysis of the amide bond that conjugates bile acids to glycine and to taurine . The BSH enzyme from Bifidobacterium longum was overexpressed in Escherichia coli BL21(DE3), purified and crystallized . Crystallization conditions were screened using the hanging-drop vapour-diffusion method . Crystal growth, with two distinct morphologies, was optimal in experiments carried out at 303 K . The crystals belong to the hexagonal system, space group P622 with unit-cell parameters a = b = 124.86, c = 219.03 A, and the trigonal space group P321, with unit-cell parameters a = b = 125.24, c = 117.03 A . The crystals diffracted X-rays to 2.5 A spacing . Structure determination using the multiple isomorphous replacement method is in progress. The genes for ribosomal RNA have changed little over millions of years as organisms evolved. The slight changes that have occurred provide clues as to how closely or distantly various organisms are related. Because the 16S rRNA gene is very short, just 1,542 nucleotide bases, it can be quickly and cheaply copied and sequenced. So when a scientist has a test tube full of pond water or dirt from an arid mountainside, she must first pull out the rRNA that’s mixed up with all the other RNA, DNA and other stuff in that tube. To do this, she cleans and purifies the sample first, getting rid of unwanted debris. She then uses one or several techniques designed to break open cells like a kid cracking open a piggybank. Now she has to find the 16S rRNA genes in and amongst all the other genes. Although 16S rRNA genes from different microbes will have a few different nucleotides scattered throughout the sequences, those nucleotides at the very beginning or end of the gene are the same from organism to organism. The scientist uses several copies of another bit of RNA called a primer. A primer is like a mirror image of a short bit of RNA or single strand of DNA; that is, its sequence of nucleotides is the direct complement to the sequence of nucleotides in a known part of the target RNA or DNA. In this instance, the primer would be the mirror image of the beginning or end of the 16S rRNA sequence. Because complementary nucleotides pair up like the two halves of Velcro, the primer enables the scientist to pick out the 16S rRNA in the sample. The scientist then uses PCR to make millions of copies of these genes. She then has enough 16S rRNA to compare the sequences of the genes from her sample to libraries of stored 16S rRNA genes from numerous known bacteria. If some of her gene sequences match up perfectly, she knows that these are microbes that have been previously identified. But if others among her sampled sequences show differences, she knows she has found previously unknown microbes. Bacteria can be found virtually everywhere. They are in the air, the soil, and water, and in and on plants and animals, including us. A single teaspoon of topsoil contains about a billion bacterial cells (and about 120,000 fungal cells and some 25,000 algal cells). The human mouth is home to more than 500 species of bacteria. Some bacteria (along with archaea) thrive in the most forbidding, uninviting places on Earth, from nearly-boiling hot springs to super-chilled Antarctic lakes buried under sheets of ice. Microbes that dwell in these extreme habitats are aptly called extremophiles. Like dinosaurs, bacteria left behind fossils. The big difference is that it takes a microscope to see them. And they are older. Bacteria and their microbial cousins the archaea were the earliest forms of life on Earth. And may have played a role in shaping our planet into one that could support the larger life forms we know today by developing photosynthesis. Cyanobacteria fossils date back more than 3 billion years. These photosynthetic bacteria paved the way for today's algae and plants. Cyanobacteria grow in the water, where they produce much of the oxygen that we breathe. Once considered a form of algae, they are also known as blue-green algae. The human body consists of millions of different cells. A bacterium consists of a single cell. A bacterium’s genetic information is contained in a single DNA molecule suspended in a jelly-like substance called cytoplasm. In most cases, this and other cell parts are surrounded by a flexible membrane that is itself surrounded by a tough, rigid cell wall. A few species, such as the mycoplasmas, don’t have cell walls. Even though bacteria have only one cell each, they come in a wide range of shapes, sizes, and colors. Does a bacterium’s cell wall, shape, way of moving, and environment really matter? Yes! The more we know about bacteria, the more we are able to figure out how to make microbes work for us or stop dangerous ones from causing serious harm. And, for those of us who like to ponder more philosophical questions like the origins of the Earth, there may be some clues there as well. Whether a bacteria has a thin or a thick cell wall determines what antibiotic will work against it. If you’ve ever been sick and waited for the results of a culture and sensitivity test, you may have heard the terms “Gram-positive” or “Gram-negative.” Bacteria with thick cell walls retain dye from a cell-staining method developed by Christian Gram; bacteria with thin walls do not. Knowing the difference can and does save lives, time and money, and ensures that you or your loved one is getting the best and most effective treatment. Some bacteria look like little balls (Micrococcus) while others appear like tangled strings or corkscrews (Leptospira) under a microscope. Others look like medicine capsules (Salmonella) or segmented ribbons (Cyanobacteria) or sticks. Still others look like fat commas (Vibrios). Some bacteria are stalked (Caulobacter) while others have buds (Rhodomicrobium). Some have sheaths (Sphaerotilus) while others don’t. Bacteria like mycoplasmas that lack a hard cell wall don’t have any particular shape at all. Just like in animals, where size ranges from the giant blue whale to the tiny gnat, bacteria vary from 1 millimeter in diameter at the largest end of the scale to 20 nanometers in length at the smallest. The largest bacteria found so far can actually be seen without the use of a microscope (Thiomargarita namibiensis and Epulopiscium fischelsoni). The smallest known bacteria are so tiny that they were once thought to be viruses (Mycoplasmas). Some bacteria have hair- or whip-like appendages called flagella used to ‘swim’ around. Others produce thick coats of slime and ‘glide’ about. Some stick out thin, rigid spikes called fimbriae to help hold them to surfaces. Some contain little particles of minerals that orient with the planet’s magnetic fields to help the bacteria figure out whether they’re swimming up or down. Fungi are eukaryotic organisms. This means that their DNA-containing chromosomes are enclosed within a nucleus inside their cells. (The chromosomes of bacteria and archaea are not walled off inside nuclei, making them prokaryotic organisms.) Many decades ago, scientists thought that fungi were primitive kinds of plants. New studies looking at the DNA of fungi have confirmed that these organisms are not plants. Unlike plants, fungi do not make their own food energy via photosynthesis, but dine on organic matter like rotting leaves, wood, and other debris, or upon the tissues of living plants and animals. Fungi, along with bacteria, are the planet’s major composters and recyclers. In addition to the standard HTST and UHT pasteurization standards, there are other lesser-known pasteurization techniques. The first technique, called "batch pasteurization", involves heating large batches of milk to a lower temperature, typically 155 degrees fahrenheit (or 68 C). The other technique is called higher-heat/shorter time (HHST), and it lies somewhere between HTST and UHT in terms of time and temperature. The batch pasteurization step, which is cheap at a large scale, is often performed prior to standard pasteurization. Batch pasteurized milk is often called "raw milk" or, confusingly, "unpasteurized milk". It cannot be called "pasteurized", even though a significant number of pathogens are destroyed during the process. In recent years, there has been some consumer interest in raw milk products, due to perceived health benefits. Advocates of raw milk maintain, correctly, that vitamins and nutrients survive much better in milk that has not been pasteurized. They also maintain that organic raw milk (most retail raw milk is also organic) is less likely to contain harmful pathogens due to better husbandry in organic dairy herds. This may be true, but it has not been proven. However, doctors (and even most raw milk advocates) acknowledge that certain people (e.g. pregnant or breast-feeding mothers, those undergoing immunosuppression treatment for cancer, organ transplant or autoimmune diseases, and those who are immunocompromised due to diseases like AIDS) should not risk consumption of raw milk. In fact, some doctors suggest that babies and breast-feeding mothers avoid all but UHT pasteurized dairy products. In Africa, it is common to boil milk whenever it is harvested. This intense heating greatly changes the flavor of milk, which the people in Africa are accustomed to. Although fungi may seem like a nuisance when they dine in your fruit bowl or refrigerator, their ability to degrade some of the toughest organic materials, including tree wood and insect exoskeletons, means that our planet is not cluttered with a mass of debris. Fungi dine at home, eating whatever they’re growing on. Fungi secrete digestive enzymes in order to break down complex food sources, such as animal corpses and tree stumps, into smaller components they can absorb. Algae are plant-like microorganisms that preceded plants in developing photosynthesis, the ability to turn sunlight into energy. Algae cells contain light-absorbing chloroplasts and produce oxygen through photosynthesis. Although plants generally get the credit for producing the oxygen we breathe, some 75% or more of the oxygen in the planet’s atmosphere is actually produced by photosynthetic algae and cyanobacteria. Algae also play an important role as the foundation for the aquatic food chain. All higher aquatic life forms depend either directly or indirectly on microscopic gardens of algae. Most unicellular algae live in water, some dwell in moist soil, and others join with fungi to form lichens. Green algae The most clearly plant-like algae, this species gets its namesake hue from high levels of chlorophyll. Their cell walls are made up of cellulose, the same material that makes up the cell walls in larger, multicellular plants. Like plants, they store the food they make through photosynthesis as starches. Growing in large masses, these algae can form visible layers of slick, green scum on the surfaces and sides of ponds, puddles or damp soil. Fossil records suggest that the first green algae originated 500 to 600 million years ago. Early algae probably gave rise to multicellular plants. Dinoflagellates have long whip-like structures called flagella that let them turn, maneuver and spin about through the water. About 90% of these algae dwell in the ocean. Some species glow in the dark in a process called bioluminescence. These species contain a compound called luciferin (the same compound found in fireflies). The glow increases markedly if the algae cells are agitated, as when a ship churns through the water. About half the species of dinoflagellates are photosynthetic; the other half are predators that attack bacteria, algae, and even fish. Dinoflagellate neurotoxins can concentrate in the bodies of shellfish and fish that eat the algal cells, in turn causing people who eat these seafoods to come down with illnesses such as paralytic shellfish poisoning and ciguatera (a combination of gastrointestinal, neurological, and cardiovascular disorders.) So-called “red tides” occur when enormous blooms of trillions of dinoflagellates are triggered by an upwelling of nutrients from the water’s depths during warmer seasons. The population of dinoflagellates can jump to more than 20 million cells per liter of sea water along some coasts during these blooms, turning the water a reddish hue. The name protozoa means “first animals.” As the principal hunters and grazers of the microbial world, protozoa play a key role in maintaining the balance of bacterial, algal, and other microbial life. They also are themselves an important food source for larger creatures and the basis of many food chains. Protozoa have been found in almost every kind of soil environment from peat bogs to arid desert sands. They teem in the deep sea as well as near the surface of waters, and can be found even in frigid Arctic and Antarctic waters. Some species of protozoa are part of the normal microbial flora of animals, and live in the guts of insects and mammals, helping to break down complex food particles into simpler molecules. A very small number of species cause disease in people, including Plasmodium vivax, which causes malaria. Bacterial infection is the most common cause of food poisoning. In the United Kingdom during 2000 the individual bacteria involved were as follows: Campylobacter jejuni 77.3%, Salmonella 20.9%, Escherichia coli O157:H7 1.4%, and all others less than 0.1% [4] (http://www.food.gov.uk/science/sciencetopics/microbiology/58736). Symptoms for bacterial infections are delayed because the bacteria need time to multiply. They are usually not seen until 12-36 hours after eating contaminated food. Common bacterial foodborne pathogens are: Aeromonas hydrophila, Aeromonas caviae, Aeromonas sobria Bacillus cereus Brucella spp. Campylobacter jejuni which causes Guillain-Barré syndrome Corynebacterium ulcerans Coxiella burnetii or Q fever Crohn's disease Escherichia coli O157:H7 enterohemorrhagic (EHEC) which causes hemolytic-uremic syndrome Escherichia coli - enteroinvasive (EIEC) Escherichia coli - enteropathogenic (EPEC) Escherichia coli - enterotoxigenic (ETEC) Listeria monocytogenes Plesiomonas shigelloides Salmonella spp. Shigella spp. Streptococcus Vibrio cholerae, including O1 and non-O1 Vibrio parahaemolyticus Vibrio vulnificus Yersinia enterocolitica and Yersinia pseudotuberculosis The four main subgroups of protozoa are the ciliates, the flagellates, the sarcodina, and the apicomplexans. A few ciliates can grow up to 2 millimeters in length, big enough to be seen without a microscope. Flagellates Similarly complex single-celled organisms, flagellates have whip-like appendages called flagella sticking out of their cells. The flagella are used for locomotion and to direct food particles or cells into the organism’s mouth-like opening. Flagellates dine on bacteria, algae, and other protozoa. Several well-known flagellates cause parasitic diseases, such as trypanosomes that cause sleeping sickness, and Giardia lamblia, a parasite found in mountain streams and rivers that causes severe gastrointestinal distress. Heliozoa, radiozoa, and forams tend to be passive grazers and predators, relying on suitable food swimming or drifting past to come into contact with their pseudopods. Several species in the sarcodina group, including some species of amoebas, cover themselves with protective shell-like coverings called tests. These tests are stippled with many small and large openings through which water can flow in and out and through which the pseudopods protrude. The tests of radiozoa are made up of silica (the same substance in diatom cell walls) and can form very intricate, lacy designs that may be studded with long spines that increase buoyancy and ward off predators. The tests of forams are made up of sand grains or organic compounds. These can become quite large, the biggest reaching a little over 2 inches in diameter, making them some of the largest single-celled organisms known. When forams die, their tests sink and accumulate in large batches; the Great Pyramids of Egypt are built from sandstone composed largely of fossilized giant Nummulites, an ancient kind of foram. The famous White Cliffs of Dover are limestone cliffs formed from the skeletal remains of forams. Apicomplexans These protozoa are obligatory intracellular parasites: they must spend at least part if not all of their life cycle in a host animal. Apicomplexans are characterized by the presence of special organelles (tiny organ-like structures) located at the tips (apices) of the cells. These organelles contain enzymes that punch through, slice open and otherwise penetrate host tissues. The best known apicomplexan is Plasmodium, the agent that causes malaria. Plasmodium spends part of its life cycle in mosquitoes and the other part in human hosts where it ultimately infects and ruptures blood cells in large numbers. Another familiar apicomplexan is Cryptosporidium parvum. This water-borne parasite forms extremely durable cyst-like structures that enable it to survive UV radiation and sometimes chlorine in swimming pools and treated water. An outbreak of Cryptosporidium in Milwaukee’s drinking water supply in 1993 killed 50 people and sickened more than 400,000. Probably the best known and most deadly case of contamination in the U.S. in recent years happened in Milwaukee in 1993, when the municipal water supply was contaminated by Cryptosporidium, an intestinal protozoan. At least 50 people died, and some 400,000 people became ill, 4,000 badly enough to be hospitalized. In 1973, a Dallas resident went out to the backyard only to stumble upon a reddish, jelly-like mass pulsating in the grass. News reports on the discovery claimed that a “new life form” had been found, and many people couldn’t help recalling the cult classic sci-fi thriller The Blob. Scientists called to the scene, however, put any fears of menacing goo or alien creatures to rest by identifying the mass as an unusually large (46 centimeters or more than 14 inches in diameter) plasmodial slime mold. Slime molds were once considered fungi, but unlike fungi, they can move, and their cell membranes are made of different stuff. Slime molds are made up of individual cells that form an aggregate mass. In their visible, aggregate states, they look like blobs, gooey or foamy masses, spilled jelly, or even dog vomit. They may be bright orange, red, yellow, brown, black, blue, or white. These large masses act like giant amoebas, creeping slowly along and engulfing food particles along the way. If a slime mold aggregate is diced up, the pieces will pull themselves back together. The blobs can navigate and avoid obstacles and if a food source is placed nearby, they seem to sense it and head unerringly for it. j, a. There are two kinds of slime molds. Plasmodial slime molds (the most common kind) share one big cell wall that surrounds thousands or millions of nuclei. Proteins called microfilaments act like tiny muscles that enable the mass to crawl at rates of about 1/25th of an inch per hour. As long as there is enough food and moisture, the mass thrives. But when food and water are scarce, the mass separates into smaller blobs. The Plasmodium forms stalks topped by sphere-like fruiting bodies that contain spores that are carried by the rain or wind to new locations. Cellular slime molds also produce spores, but these germinate into amoeba-like cells. The cells happily go their individual ways, as long as food and water are available. When nutrients and moisture are scarce, individual cells send out a chemical beacon to attract other cells of the same species. The cells join up to form a mass that looks and acts like a slug to take them to a more favorable location. Cells in cellular slime molds retain their individual cell walls when they form a mass, so the visible slug is actually a collection of hundreds of thousands of individual cells joined together. Slime molds eat decaying vegetation, bacteria, fungi, and even other slime molds. They are most commonly found in forests. Milk pasteurization standards have been subject to increasing scrutiny in recent years, due to the discovery of pathogens that are both widespread and heat resistant (able to survive pasteurization in significant numbers). Researchers have developed more sensitive diagnostics, such as real-time PCR and improved culture methods, that have enabled them to identify pathogens in pasteurized milk. Note: The following paragraphs in this section discuss controversial, ongoing research. One bacterium in particular, the organism Mycobacterium avium subspecies paratuberculosis (MAP), which causes Johne's disease in cattle and is suspected of causing at least some Crohn's disease in humans, has been found to survive pasteurization in retail milk in the U.S., the U.K., Greece, and the Czech Republic. The food safety authorities in the U.K. have decide to re-evaluate pasteurization standards in light of the MAP results and other evidence of harmful, pasteurization-resistant pathogens. The USDA (which is responsible for setting pasteurization stardards in the U.S.) has not re-evaluated their position on pasteurization adequacy. They do not dispute the studies, which are at this point accepted by the scientific community, but maintain that the presence of MAP in retail pasteurized milk must be due to post-pasteurization contamination. However, some researchers within the FDA, which is responsible for food safety in the U.S., have begun pushing for a re-evaluation of these results. There is a small but growing body of criticism directed at these agencies by Crohn's disease sufferers, scientists, and doctors. Some have suggested that the U.S. dairy industry has been successful in suppressing the agencies' response to a potential health crisis, for fear of consumer panic which would lead to a decrease in milk consumption. It is worth noting that while MAP has not been definitely proven to be harmful in humans, all other mycobacteria are pathogenic, and it has been definitively shown to cause disease in cattle and other ruminants. The term cold pasteurization is used sometimes for the use of radioactivity or other means (e.g. chemical) to kill bacteria in food. Water molds are always found in wet environments, especially in fresh water sources and near the upper layers of moist soil. Officially named Oomycota, they are also known as downy mildews and white rusts. Water molds were long considered fungi because they produce fungi-like filamentous hyphae and feed on decaying tissue like rotting logs and mulch. The Oomycota species Phytophthora infestans caused the Great Potato Famine that killed nearly a million people in Ireland in 1846–1847. The water mold virtually wiped out the country’s potato crops, which were an essential staple in the Irish diet (sometimes the only food on the table.) Microbes break down food molecules our body’s enzymes and acids can’t dissolve, helping us squeeze all the nutrients out of our food. Some make valuable vitamins that our body needs. Many microbial species have proved to be consummate evolutionary wheelers and dealers, arranging collaborations, mergers, and acquisitions that usually serve both partners well. If you could peer deep into one of the many cells in your body, you’d see little blobs, squiggles, and coils. e, k. These are the cell’s organelles, structures that perform specialized functions in cells the same way that the lungs, heart, and other organs do in a body. Mitochondria are the energy factories found in each cell of fungi, protozoa, insects, and animals. Once nutrients are absorbed or digested, they move in the form of minuscule molecules into the mitochondria, which convert the molecules into chemical energy to power the cell. Chloroplasts undertake a similar function in the cells of plants, algae, and some protozoa. They capture sunlight and, through a series of chemical reactions called photosynthesis, use the light to make energy. These organelles are absolutely essential to the existence of all higher life forms on Earth. If all of the mitochondria in our bodies were to suddenly shut down, we would die. The same is true for plants were they to lose their chloroplasts. So where did they come from? As microscopes improved over the years, scientists began noticing striking similarities in the appearances of mitochondria, chloroplasts, and bacterial cells. They discovered that these two organelles contain their own DNA, or gene set, organized very much like the DNA in bacterial cells. Mitochondria and chloroplasts also reproduce independently from the cells in which they reside, in a manner very like bacterial fission. Many microbiologists think it is likely that mitochondria and chloroplasts were once free-living prokaryotes (cells that lack a nucleus and organelles) |