Miracle-dz/UniFAR-FTUs huggingface dataset:
Population Size Drives Industrial Saccharomyces cerevisiae Alcoholic Fermentation and Is under Genetic Control

ABSTRACT Alcoholic fermentation (AF) conducted by Saccharomyces cerevisiae has been exploited for millennia in three important human food processes: beer and wine production and bread leavening. Most of the efforts to understand and improve AF have been made separately for each process, with strains that are supposedly well adapted. In this work, we propose a first comparison of yeast AFs in three synthetic media mimicking the dough/wort/grape must found in baking, brewing, and wine making. The fermentative behaviors of nine food-processing strains were evaluated in these media, at the cellular, populational, and biotechnological levels. A large variation in the measured traits was observed, with medium effects usually being greater than the strain effects. The results suggest that human selection targeted the ability to complete fermentation for wine strains and trehalose content for beer strains. Apart from these features, the food origin of the strains did not significantly affect AF, suggesting that an improvement program for a specific food processing industry could exploit the variability of strains used in other industries. Glucose utilization was analyzed, revealing plastic but also genetic variation in fermentation products and indicating that artificial selection could be used to modify the production of glycerol, acetate, etc. The major result was that the overall maximum CO2 production rate (V max) was not related to the maximum CO2 production rate per cell. Instead, a highly significant correlation between V max and the maximum population size was observed in all three media, indicating that human selection targeted the efficiency of cellular reproduction rather than metabolic efficiency. This result opens the way to new strategies for yeast improvement.
The angiotensin II type 2 receptor and the kidney

Recent knowledge demonstrated that the renin-angiotensin system (RAS) functions as a local renal paracrine system. All components of the RAS are present within the kidney and include angiotensinogen, renin, angiotensin I, angiotensin-converting enzymes, angiotensin II, the angiotensin II type 1 (AT1) receptor and the angiotensin II type 2 (AT2) receptor. Angiotensin II is the major effector hormone of the RAS and contributes to a variety of renal and cardiovascular physiologic and pathologic mechanisms through stimulation of AT1 and AT2 receptors. Angiotensin receptor blockers were developed based on the advanced knowledge of the AT1 receptor contribution to development of a variety of kidney, vascular and cardiac diseases including but not limited to hypertension, diabetic nephropathy, heart failure, myocardial infarction and atherosclerosis. In contrast, knowledge concerning the role of the AT2 receptor in health and disease is still emerging. The AT2 receptor is believed to counterbalance the effects of the AT1 receptor through influencing cellular differentiation, vasodilation, inhibition of cellular proliferation and hypertrophy, nitric oxide production and natriuresis. Thus, the pursuit of a specific AT2 receptor agonist is a potentially fruitful area for combating renal and cardiovascular diseases. This review focuses on the role of the AT2 receptor in the kidney.
Low residual noise speech enhancement utilizing time-frequency filtering

Spectral subtraction is a well known technique for enhancing speech corrupted by additive wideband noise. In this technique, the "clean" signal is approximated by subtracting a noise estimate from the spectrum of the corrupted signal. A negative side effect is the residual "musical" noise that is produced when isolated spectral peaks exceed the noise estimate. In this paper, a low residual noise enhancement method is presented. This method is based on spectral subtraction but incorporates an algorithm developed to suppress "musical" noise without affecting speech. The algorithm is referred to as time-frequency filtering because spectral peaks due to noise are eliminated on the basis of duration, bandwidth, and proximity to other peaks. Results showing the effects of combining spectral subtraction and time-frequency filtering are given. <<ETX>>
ENDOMETRIAL CARCINOMA OF THE OVARY, ARISING IN ENDOMETRIAL TISSUE IN THAT ORGAN

Many interesting and important problems have presented themselves to clinicians and pathologists, who have appreciated the frequency of ectopic endometrium-like tissue in the pelvis and have had an opportunity to observe the various lesions in the ovaries and other pelvic structures resulting from this tissue. One of the most interesting problems is the source of these implantation-like lesions occurring on the surface of the various pelvic structures. Are they true implantations derived primarily from uterine or tubal epithelium escaping through the tubes into the peritoneal cavity, as the study of many of these lesions in human beings indicates 1 and as Jacobson, 2 in the autotransplantation of endometrial tissue in rabbits, has experimentally proved possible, or are they derived from scattered localized metaplasias of the serosal mesothelium or from developmental inclusions of portions of the Wolffian body or Mullerian duct? This problem has not yet been definitely solved to the
Relative Abundance of Bacteroides spp. in Stools and Wastewaters as Determined by Hierarchical Oligonucleotide Primer Extension

ABSTRACT A molecular method, termed hierarchical oligonucleotide primer extension (HOPE), was used to determine the relative abundances of predominant Bacteroides spp. present in fecal microbiota and wastewaters. For this analysis, genomic DNA in feces of healthy human adults, bovines, and swine and in wastewaters was extracted and total bacterial 16S rRNA genes were PCR amplified and used as the DNA templates for HOPE. Nineteen oligonucleotide primers were designed to detect 14 Bacteroides spp. at different hierarchical levels (domain, order, cluster, and species) and were arranged into and used in six multiplex HOPE reaction mixtures. Results showed that species like B. vulgatus, B. thetaiotaomicron, B. caccae, B. uniformis, B. fragilis, B. eggerthii, and B. massiliensis could be individually detected in human feces at abundances corresponding to as little as 0.1% of PCR-amplified 16S rRNA genes. Minor species like B. pyogenes, B. salyersiae, and B. nordii were detected only collectively using a primer that targeted the B. fragilis subgroup (corresponding to ∼0.2% of PCR-amplified 16S rRNA genes). Furthermore, Bac303-related targets (i.e., most Bacteroidales) were observed to account for 28 to 44% of PCR-amplified 16S rRNA genes from human fecal microbiota, and their abundances were higher than those detected in the bovine and swine fecal microbiota and in wastewaters by factors of five and two, respectively. These results were comparable to those obtained by quantitative PCR and to those reported previously from studies using whole-cell fluorescence hybridization and 16S rRNA clone library methods, supporting the conclusion that HOPE can be a sensitive, specific, and rapid method to determine the relative abundances of Bacteroides spp. predominant in fecal samples.
Characterization of a Broad-Specificity β-Glucanase Acting on β-(1,3)-, β-(1,4)-, and β-(1,6)-Glucans That Defines a New Glycoside Hydrolase Family

ABSTRACT Here we report the cloning of the Pa_3_10940 gene from the coprophilic fungus Podospora anserina, which encodes a C-terminal family 1 carbohydrate binding module (CBM1) linked to a domain of unknown function. The function of the gene was investigated by expression of the full-length protein and a truncated derivative without the CBM1 domain in the yeast Pichia pastoris. Using a library of polysaccharides of different origins, we demonstrated that the full-length enzyme displays activity toward a broad range of β-glucan polysaccharides, including laminarin, curdlan, pachyman, lichenan, pustulan, and cellulosic derivatives. Analysis of the products released from polysaccharides revealed that this β-glucanase is an exo-acting enzyme on β-(1,3)- and β-(1,6)-linked glucan substrates and an endo-acting enzyme on β-(1,4)-linked glucan substrates. Hydrolysis of short β-(1,3), β-(1,4), and β-(1,3)/β-(1,4) gluco-oligosaccharides confirmed this striking feature and revealed that the enzyme performs in an exo-type mode on the nonreducing end of gluco-oligosaccharides. Excision of the CBM1 domain resulted in an inactive enzyme on all substrates tested. To our knowledge, this is the first report of an enzyme that displays bifunctional exo-β-(1,3)/(1,6) and endo-β-(1,4) activities toward beta-glucans and therefore cannot readily be assigned to existing Enzyme Commission groups. The amino acid sequence has high sequence identity to hypothetical proteins within the fungal taxa and thus defines a new family of glycoside hydrolases, the GH131 family.
Bounds on performance of optimum quantizers

A quantizer Q divides the range [0, 1] of a random variable x into K quantizing intervals the i th such interval having length \Delta x_i . We define the quantization error for a particular value of x (unusually) as the length of the quantizing interval in which x finds itself, and measure quantizer performance (unusually) by the r th mean value of the quantizing interval lengths M_r (Q) = \overline{\Delta x^{r^{1/r}}} , averaging with respect to the distribution function F of the random variable x . Q_1 is defined to be an optimum quantizer if M_r (Q_1) \leq M_r (Q) for all Q . The unusual definitions restrict the results to bounded random variables, but lead to general and precise results. We define a class Q^{\ast} of quasi-optimum quantizers; Q_2 is in Q^{\ast} if the different intervals \Delta x_i make equal contributions to the mean r th power of the interval size so that Pr \{ \Delta x_i \} \Delta x_{i^{r}} is constant for all i . Theorems 1, 2, 3, and 4 prove that Q_2 \in Q^{\ast} exists and is unique for given F, K , and r : that 1 \geq KM_r (Q_2) \geq KM_r (Q_1) \geq I_r , where I_r = \{\int_0^{1} f (x)^p dx\}^ {1/q}, f is the density of the absolutely continuous part of the distribution function F of x, p = 1/(1+ r) , and q = r /(1 + r) : that lim KM_r (Q_2) = I_r as K \rightarrow \infty ; and that if KM_r (Q) = I_r for finite K , then Q=Q^{\ast} .
Bacterial Catabolism of β-Hydroxypropiovanillone and β-Hydroxypropiosyringone Produced in the Reductive Cleavage of Arylglycerol-β-Aryl Ether in Lignin

ABSTRACT Sphingobium sp. strain SYK-6 converts four stereoisomers of arylglycerol-β-guaiacyl ether into achiral β-hydroxypropiovanillone (HPV) via three stereospecific reaction steps. Here, we determined the HPV catabolic pathway and characterized the HPV catabolic genes involved in the first two steps of the pathway. In SYK-6 cells, HPV was oxidized to vanilloyl acetic acid (VAA) via vanilloyl acetaldehyde (VAL). The resulting VAA was further converted into vanillate through the activation of VAA by coenzyme A. A syringyl-type HPV analog, β-hydroxypropiosyringone (HPS), was also catabolized via the same pathway. SLG_12830 (hpvZ), which belongs to the glucose-methanol-choline oxidoreductase family, was isolated as the HPV-converting enzyme gene. An hpvZ mutant completely lost the ability to convert HPV and HPS, indicating that hpvZ is essential for the conversion of both the substrates. HpvZ produced in Escherichia coli oxidized both HPV and HPS and other 3-phenyl-1-propanol derivatives. HpvZ localized to both the cytoplasm and membrane of SYK-6 and used ubiquinone derivatives as electron acceptors. Thirteen gene products of the 23 aldehyde dehydrogenase (ALDH) genes in SYK-6 were able to oxidize VAL into VAA. Mutant analyses suggested that multiple ALDH genes, including SLG_20400, contribute to the conversion of VAL. We examined whether the genes encoding feruloyl-CoA synthetase (ferA) and feruloyl-CoA hydratase/lyase (ferB and ferB2) are involved in the conversion of VAA. Only FerA exhibited activity toward VAA; however, disruption of ferA did not affect VAA conversion. These results indicate that another enzyme system is involved in VAA conversion. IMPORTANCE Cleavage of the β-aryl ether linkage is the most essential process in lignin biodegradation. Although the bacterial β-aryl ether cleavage pathway and catabolic genes have been well documented, there have been no reports regarding the catabolism of HPV or HPS, the products of cleavage of β-aryl ether compounds. HPV and HPS have also been found to be obtained from lignin by chemoselective catalytic oxidation by 2,3-dichloro-5,6-dicyano-1,4-benzoquinone/tert-butyl nitrite/O2, followed by cleavage of the β-aryl ether with zinc. Therefore, value-added chemicals are expected to be produced from these compounds. In this study, we determined the SYK-6 catabolic pathways for HPV and HPS and identified the catabolic genes involved in the first two steps of the pathways. Since SYK-6 catabolizes HPV through 2-pyrone-4,6-dicarboxylate, which is a building block for functional polymers, characterization of HPV catabolism is important not only for understanding the bacterial lignin catabolic system but also for lignin utilization.
Requirements for Construction of a Functional Hybrid Complex of Photosystem I and [NiFe]-Hydrogenase

ABSTRACT The development of cellular systems in which the enzyme hydrogenase is efficiently coupled to the oxygenic photosynthesis apparatus represents an attractive avenue to produce H2 sustainably from light and water. Here we describe the molecular design of the individual components required for the direct coupling of the O2-tolerant membrane-bound hydrogenase (MBH) from Ralstonia eutropha H16 to the acceptor site of photosystem I (PS I) from Synechocystis sp. PCC 6803. By genetic engineering, the peripheral subunit PsaE of PS I was fused to the MBH, and the resulting hybrid protein was purified from R. eutropha to apparent homogeneity via two independent affinity chromatographical steps. The catalytically active MBH-PsaE (MBHPsaE) hybrid protein could be isolated only from the cytoplasmic fraction. This was surprising, since the MBH is a substrate of the twin-arginine translocation system and was expected to reside in the periplasm. We conclude that the attachment of the additional PsaE domain to the small, electron-transferring subunit of the MBH completely abolished the export competence of the protein. Activity measurements revealed that the H2 production capacity of the purified MBHPsaE fusion protein was very similar to that of wild-type MBH. In order to analyze the specific interaction of MBHPsaE with PS I, His-tagged PS I lacking the PsaE subunit was purified via Ni-nitrilotriacetic acid affinity and subsequent hydrophobic interaction chromatography. Formation of PS I-hydrogenase supercomplexes was demonstrated by blue native gel electrophoresis. The results indicate a vital prerequisite for the quantitative analysis of the MBHPsaE-PS I complex formation and its light-driven H2 production capacity by means of spectroelectrochemistry.
Plasma Anti‐Haemophilic Factor (Factor VIII) Concentrations in Normal Families

FOLLOWING the first quantitative assays of plasma AHF concentration by Brinkhous and his colleagues (Graham, McLendon and Brinkhous, 1953 ; Brinkhous, Langdell, Penick, Graham and Wagner, 1954) it was accepted that plasma AHF concentration is constant for the individual and genetically controlled. Indeed, most assay methods for AHF ascribe an arbitrary reference value to a standard 'normal' plasma or plasma pool and evaluate the concentration of test material as a percentage of this value. Recent evidence suggests that normal AHF values may not be as constant as was thought and may not be solely under genetic control. Cooperberg and Teitelbaum (1960) reported that plasma AHF concentration increases with age in both sexes. Pitney and Elliott (1960) described high plasma AHF values in patients with disorders associated with hyperglobulin aemia and in Australian aborigines who characteristically have higher y-globulin values than Caucasians. Previous studies in these laboratories failed to show any significant difference between the plasma AHF concentration for normal males and females (Pitney and Arnold, 1959). Cooperberg and Teitelbaum (1960), however, found that in each age group in their sample the AHF concentration was lower in females than in males, the-mean difference for the whole sample being 10.5 per cent. Graham and co-workers (1953) considered that plasma AHF concentration is under genetic control and postulated that a series of allelomorphic genes located on the X chromosome are responsible for controlling the wide range of variation in AHF concentration found in normal persons. More recently Graham (1959) has modified this concept and has suggested that at least two separate loci are concerned with AHF synthesis, the synthesis taking place in two or inore stages. Pitney and Arnold (1959) suggested that in normal individuals the inheritance of AHF concentration is under the control of autosomal genes. They postulated that the haemophilia gene located on the X chromosome either interferes with the normal expression of the autosomal genes or is itself responsible for a factor which inhibits or destroys AHF. As a result of all these observations and hypotheses it seemed desirable to investigate the plasma AHF concentration of individuals belonging to normal families. It was felt that such a study might throw additional light on the relationship between genetic constitution, sex, age and other serum protein constituents and AHF concentration.
Mitochondrial Superoxide Dismutase and Yap1p Act as a Signaling Module Contributing to Ethanol Tolerance of the Yeast Saccharomyces cerevisiae

ABSTRACT There are two superoxide dismutases in the yeast Saccharomyces cerevisiae—cytoplasmic and mitochondrial enzymes. Inactivation of the cytoplasmic enzyme, Sod1p, renders the cells sensitive to a variety of stresses, while inactivation of the mitochondrial isoform, Sod2p, typically has a weaker effect. One exception is ethanol-induced stress. Here we studied the role of Sod2p in ethanol tolerance of yeast. First, we found that repression of SOD2 prevents ethanol-induced relocalization of yeast hydrogen peroxide-sensing transcription factor Yap1p, one of the key stress resistance proteins. In agreement with this, the levels of Trx2p and Gsh1p, proteins encoded by Yap1 target genes, were decreased in the absence of Sod2p. Analysis of the ethanol sensitivities of the cells lacking Sod2p, Yap1p, or both indicated that the two proteins act in the same pathway. Moreover, preconditioning with hydrogen peroxide restored the ethanol resistance of yeast cells with repressed SOD2. Interestingly, we found that mitochondrion-to-nucleus signaling by Rtg proteins antagonizes Yap1p activation. Together, our data suggest that hydrogen peroxide produced by Sod2p activates Yap1p and thus plays a signaling role in ethanol tolerance. IMPORTANCE Baker's yeast harbors multiple systems that ensure tolerance to high concentrations of ethanol. Still, the role of mitochondria under severe ethanol stress in yeast is not completely clear. Our study revealed a signaling function of mitochondria which contributes significantly to the ethanol tolerance of yeast cells. We found that mitochondrial superoxide dismutase Sod2p and cytoplasmic hydrogen peroxide sensor Yap1p act together as a module of the mitochondrion-to-nucleus signaling pathway. We also report cross talk between this pathway and the conventional retrograde signaling cascade activated by dysfunctional mitochondria.
A Livestock-Associated, Multidrug-Resistant, Methicillin-Resistant Staphylococcus aureus Clonal Complex 97 Lineage Spreading in Dairy Cattle and Pigs in Italy

ABSTRACT Pandemic methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 97 (CC97) lineages originated from livestock-to-human host jumps. In recent years, CC97 has become one of the major MRSA lineages detected in Italian farmed animals. The aim of this study was to characterize and analyze differences in MRSA and methicillin-susceptible S. aureus (MSSA) mainly of swine and bovine origins. Forty-seven CC97 isolates, 35 MRSA isolates, and 6 MSSA isolates from different Italian pig and cattle holdings; 5 pig MRSA isolates from Germany; and 1 human MSSA isolate from Spain were characterized by macrorestriction pulsed-field gel electrophoresis (PFGE) analysis, multilocus sequence typing (MLST), spa typing, staphylococcal cassette chromosome mec (SCCmec) typing, and antimicrobial resistance pattern analysis. Virulence and resistance genes were investigated by PCR and microarray analysis. Most of the isolates were of SCCmec type V (SCCmec V), except for two German MRSA isolates (SCCmec III). Five main clusters were identified by PFGE, with the German isolates (clusters I and II) showing 60.5% similarity with the Italian isolates, most of which (68.1%) grouped into cluster V. All CC97 isolates were Panton-Valentine leukocidin (PVL) negative, and a few (n = 7) tested positive for sak or scn. All MRSA isolates were multidrug resistant (MDR), and the main features were erm(B)- or erm(C)-mediated (n = 18) macrolide-lincosamide-streptogramin B resistance, vga(A)-mediated (n = 37) pleuromutilin resistance, fluoroquinolone resistance (n = 33), tet(K) in 32/37 tet(M)-positive isolates, and blaZ in almost all MRSA isolates. Few host-associated differences were detected among CC97 MRSA isolates: their extensive MDR nature in both pigs and dairy cattle may be a consequence of a spillback from pigs of a MRSA lineage that originated in cattle as MSSA and needs further investigation. Measures should be implemented at the farm level to prevent spillover to humans in intensive farming areas.
Influence of Stress on Single-Cell Lag Time and Growth Probability for Listeria monocytogenes in Half Fraser Broth

ABSTRACT The impacts of 12 common food industry stresses on the single-cell growth probability and single-cell lag time distribution of Listeria monocytogenes were determined in half Fraser broth, the primary enrichment broth of the International Organization for Standardization detection method. First, it was determined that the ability of a cell to multiply in half Fraser broth is conditioned by its history (the probability for a cell to multiply can be decreased to 0.05), meaning that, depending on the stress in question, the risk of false-negative samples can be very high. Second, it was established that when cells are injured, the single-cell lag times increase in mean and in variability and that this increase represents a true risk of not reaching the detection threshold of the method in the enrichment broth. No relationship was observed between the impact on single-cell lag times and that on growth probabilities. These results emphasize the importance of taking into account the physiological state of the cells when evaluating the performance of methods to detect pathogens in food.
Role Played by Exosporium Glycoproteins in the Surface Properties of Bacillus cereus Spores and in Their Adhesion to Stainless Steel

ABSTRACT Bacillus cereus spores are surrounded by a loose-fitting layer called the exosporium, whose distal part is mainly formed from glycoproteins. The role played by the exosporium glycoproteins of B. cereus ATCC 14579 (BclA and ExsH) was investigated by considering hydrophobicity and charge, as well as the properties of spore adhesion to stainless steel. The absence of BclA increased both the isoelectric point (IEP) and hydrophobicity of whole spores while simultaneously reducing the interaction between spores and stainless steel. However, neither the hydrophobicity nor the charge associated with BclA could explain the differences in the adhesion properties. Conversely, ExsH, another exosporium glycoprotein, did not play a significant role in spore surface properties. The monosaccharide analysis of B. cereus ATCC 14579 showed different glycosylation patterns on ExsH and BclA. Moreover, two specific glycosyl residues, namely, 2-O-methyl-rhamnose (2-Me-Rha) and 2,4-O-methyl-rhamnose (2,4-Me-Rha), were attached to BclA, in addition to the glycosyl residues already reported in B. anthracis.