Metabolic control analysis of glycerol synthesis in Saccharomyces cerevisiae

Glycerol, a major by-product of ethanol fermentation by Saccharomyces cerevisiae, is of significant importance to the wine, beer, and ethanol production industries. To gain a clearer understanding of and to quantify the extent to which parameters of the pathway affect glycerol flux in S. cerevisiae, a kinetic model of the glycerol synthesis pathway has been constructed. Kinetic parameters were collected from published values. Maximal enzyme activities and intracellular effector concentrations were determined experimentally. The model was validated by comparing experimental results on the rate of glycerol production to the rate calculated by the model. Values calculated by the model agreed well with those measured in independent experiments. The model also mimics the changes in the rate of glycerol synthesis at different phases of growth. Metabolic control analysis values calculated by the model indicate that the NAD(+)-dependent glycerol 3-phosphate dehydrogenase-catalyzed reaction has a flux control coefficient (C(J)v1) of approximately 0.85 and exercises the majority of the control of flux through the pathway. Response coefficients of parameter metabolites indicate that flux through the pathway is most responsive to dihydroxyacetone phosphate concentration (R(J)DHAP= 0.48 to 0.69), followed by ATP concentration (R(J)ATP = -0.21 to -0.50). Interestingly, the pathway responds weakly to NADH concentration (R(J)NADH = 0.03 to 0.08). The model indicates that the best strategy to increase flux through the pathway is not to increase enzyme activity, substrate concentration, or coenzyme concentration alone but to increase all of these parameters in conjunction with each other.     

The aesthetic earlobe: classification of lobule ptosis on the basis of a survey of North American Caucasians

North American Caucasian male subjects (n = 59) and female subjects (n = 72) were surveyed, to investigate earlobe height preferences that could serve as guidelines for aesthetic earlobe surgical procedures and reconstructions. Subjects were asked to rank their preferences for variously shaped earlobes in life-size-scaled sketched male and female profiles. Earlobe heights were varied on the basis of previously established anatomical landmarks, including the intertragal notch, the most caudal anterior attachment of the earlobe to the cheek skin (the otobasion inferius), and the most caudal extension of the earlobe-free margin (the subaurale). While the intertragal notch-to-otobasion inferius distance (range, 5 to 20 mm) and otobasion inferius-to-subaurale distance (range, 0 to 20 mm) varied, all other facial and ear anthropometric measurements were held constant. Each of the rank orders for the female and male facial profiles completed by the female and male subjects demonstrated statistical significance, as determined by one-way analysis of variance analysis of ranks (p < 0.001 for all four groups). No difference was noted between the two sexes' rank orders for either sex (p > 0.05). Therefore, analysis of the combined male and female preferences for each sex was completed with one-way analysis of variance analysis of ranks (p < 0.001 and p < 0.001) and a post hoc Dunn's test, to delineate significant preference differences between subgroups with respect to the intertragal notch-to-otobasion inferius and otobasion inferius-to-subaurale distances. Both female and male earlobe intertragal notch-to-otobasion inferius distances were preferred at either 5, 10, or 15 mm, more so than at 20 mm (p < 0.05 for all female and male comparisons). Furthermore, both female and male earlobe otobasion inferius-to-subaurale distances were preferred, in descending order, at 5 mm > 10 mm > 0 mm > 15 mm > 20 mm (p < 0.05 for all female and male comparisons). On the basis of the findings of this survey, the first classification of earlobe ptosis (based on otobasion inferius-to-subaurale distances), as well as a criterion for earlobe pseudoptosis (intertragal notch-to-otobasion inferius distance of greater than 15 mm), is presented. These findings suggest a role for independent assessment of the lobule length with respect to its anteriorly attached cephalad component (intertragal notch-to-otobasion inferius distance) and its free-margin caudal component (otobasion inferius-to-subaurale distance).     

Roles for asparagine endopeptidase in class II MHC-restricted antigen processing

The adaptive immune response depends on the creation of suitable peptides from foreign antigens for display on MHC molecules to T lymphocytes. Similarly, MHC-restricted display of peptides derived from self proteins results in the elimination of many potentially autoreactive T cells. Different proteolytic systems are used to generate the peptides that are displayed as T cell epitopes on class I compared with class II MHC molecules. In the case of class II MHC molecules, the proteases that reside within the endosome/lysosome system of antigen-presenting cells are responsible; surprisingly, however, there are relatively few data on which enzymes are involved. Recently we have asked whether proteolysis is required simply in a generic sense, or whether the action of particular enzymes is needed to generate specific class II MHC-associated T cell epitopes. Using the recently identified mammalian asparagine endopeptidase as an example, we review recent evidence that individual enzymes can make clear and non-redundant contributions to MHC-restricted peptide display.     

Horizontal transmission of epizootic ulcerative syndrome (EUS)-associated virus in the snakehead Ophicephalus striatus under simulated natural conditions

Natural transmission of the epizootic ulcerative syndrome (EUS) was conducted on na?ve snakeheads Ophicephalus striatus (also known as Channa striata) kept (A) in aquifer water, (B) in lakewater, (C) cohabiting with EUS snakeheads in lakewater, and (D) cohabiting with apparently healthy snakeheads in lakewater during the 1994 to 1995 EUS season. The results showed that EUS-like lesions developed in 6 to 14 d among na?ve snakeheads cohabiting with EUS snakeheads and with apparently healthy snakeheads in lakewater (Treatments C and D). Among na?ve fish exposed to lakewater (Treatment B), similar lesions developed in 16 to 21 d, while na?ve fish in aquifer water (Treatment A) did not develop EUS-like lesions. EUS signs began as Grade I (slight) lesions that gradually progressed to Grades III-IV (severe) 3 to 5 d from lesion onset, similar to the naturally affected EUS fish. The virus was recovered from some but not all naturally EUS-affected snakeheads, snakeheads with healing lesions and apparently healthy snakeheads, but not from na?ve snakeheads. The results provide evidence of a waterborne horizontal transmission of the EUS-associated virus. This is the first report of a successful horizontal transmission of the EUS-associated virus from apparently healthy snakeheads to na?ve fish under natural conditions and of virus recovery in tissue culture from naturally exposed experimental fish.     

Topographic prominence as a method for cluster identification in single‐molecule localisation data

Single‐molecule localisation based super‐resolution fluorescence imaging produces maps of the coordinates of fluorescent molecules in a region of interest. Cluster analysis algorithms provide information concerning the clustering characteristics of these molecules, often through the generation of cluster heat maps based on local molecular density. The goal of this study was to generate a new cluster analysis method based on a topographic approach. In particular, a topographic map of the level of clustering across a region is generated based on Getis' variant of Ripley's K‐function. By using the relative heights (topographic prominence, TP) of the peaks in the map, cluster characteristics can be identified more accurately than by using previously demonstrated height thresholds. Analogous to geological TP, the concepts of wet and dry TP and topographic isolation are introduced to generate binary maps. The algorithm is validated using simulated and experimental data and found to significantly outperform previous cluster identification methods.

Illustration of the topographic prominence based cluster analysis algorithm.     

Cellulosilyticum ruminicola,a Newly Described Rumen Bacterium That Possesses Redundant Fibrolytic-Protein-Encoding Genes and Degrades Lignocellulose with Multiple Carbohydrate- Borne Fibrolytic Enzymes

Cellulosilyticum ruminicola H1 is a newly described bacterium isolated from yak (Bos grunniens) rumen and is characterized by its ability to grow on a variety of hemicelluloses and degrade cellulosic materials. In this study, we performed the whole-genome sequencing of C. ruminicola H1 and observed a comprehensive set of genes encoding the enzymes essential for hydrolyzing plant cell wall. The corresponding enzymatic activities were also determined in strain H1; these included endoglucanases, cellobiohydrolases, xylanases, mannanase, pectinases, and feruloyl esterases and acetyl esterases to break the interbridge cross-link, as well as the enzymes that degrade the glycosidic bonds. This bacterium appears to produce polymer hydrolases that act on both soluble and crystal celluloses. Approximately half of the cellulytic activities, including cellobiohydrolase (50%), feruloyl esterase (45%), and one third of xylanase (31%) and endoglucanase (36%) activities were bound to cellulosic fibers. However, only a minority of mannase (6.78%) and pectinase (1.76%) activities were fiber associated. Strain H1 seems to degrade the plant-derived polysaccharides by producing individual fibrolytic enzymes, whereas the majority of polysaccharide hydrolases contain carbohydrate-binding module. Cellulosome or cellulosomelike protein complex was never isolated from this bacterium. Thus, the fibrolytic enzyme production of strain H1 may represent a different strategy in cellulase organization used by most of other ruminal microbes, but it applies the fungal mode of cellulose production.The ruminant rumens are long believed to be the anaerobic environments efficiently degrading the plant-derived polysaccharides, which is attributed to the inhabited abundant rumen microorganisms. They implement the fibrolytic degradation by the combination of the enzymes comprising of cellulases, hemicellulases, and to a lesser extent pectinases and ligninases (12). The rumen bacteria are outnumbered of the other rumen microbes; however, only a few of cellulolytic bacteria have been isolated from rumens. Ruminococcus flavefaciens, Ruminococcus albus, and Fibrobacter succinogenes are considered to be the most important cellulose-degrading bacteria in the rumen (18), and they produce a set of cellulolytic enzymes, including endoglucanases, exoglucanases (generally cellobiohydrolase), and β-glucosidases, as well as hemicellulases. In addition, the predominant ruminal hemicellulose-digesting bacteria such as Butyrivibrio fibrisolvens and Prevotella ruminicola lack the ability to digest cellulose but degrade xylan and pectin and utilize the degraded soluble sugars as substrates (10, 14). Although the robust cellulolytic species F. succinogenes degrades xylan, it cannot use the pentose product as a carbon source (24). Culture-independent approaches indicate that the three cellulolytic bacterial species represent only ∼2% of the ruminal bacterial 16S rRNA (43). Therefore, many varieties of rumen microbes remain uncultured (2). In recent years, rumen metagenomics studies have revealed the vast diversity of fibrolytic enzymes, multiple domain proteins, and the complexity of microbial composition in the ecosystem (9, 17). Hence, it is likely that the entire microbial community is necessary for the implementation of an efficient fibrolytic process in the rumen, including the uncultured species.In the rumen and other fibrolytic ecosystems, cellulolytic bacteria have to cope with the structural complexity of lignocelluloses and the interspecies competition; thus, not only a variety of plant polymer-degrading enzymes but also a noncatalytic assistant strategy, such as including adhesion of cells to substrates by a variety of anchoring domains, is required (8, 33, 38, 39). The (hemi)cellulolytic enzyme systems have been intensively studied for nonrumen anaerobic bacteria, including Clostridium thermocellum (19, 40), Clostridium cellulolyticum (6), Clostridium cellulovorans (13), and Clostridium stercorarium (47), as well as the rumen species, Rumicoccocus albus (35), Ruminococcus flavefaciens (32), and Fibrobacter succinogenes (4). The results indicate that most of them, except for Fibrobacter succinogenes, produce multiple cellulolytic enzymes integrated in a complex, cellulosome, and free individual proteins.The yak (Bos grunniens) is a large ruminant (∼1,000 kg) in the bovine family that lives mainly on the Qinghai-Tibetan Plateau in China at an altitude of 3,000 m above sea level. It is a local species that lives mainly on the world''s highest plateau. Yaks live in a full-grazing style with grasses, straws, and lichens as their exclusive feed, so the yak rumen can harbor a microbial flora distinct from those of other ruminants due to their fiber-component diet, since diet can be a powerful factor in regulating mammalian gut microbiome (27). A very different prokaryote community structure was revealed for yak rumen in our previous work based on the 16S rRNA diversity, which showed fewer phyla than for cattle but that a higher ratio of sequences was related to uncultured bacteria (2).We previously isolated a novel anaerobic fibrolytic bacterium, Cellulosilyticum ruminicola H1, from the rumen of a domesticated yak (11). Strain H1 grew robustly on natural plant fibers such as corn cob, alfalfa, and ryegrass as the sole carbon and energy sources, as well as on a variety of polysaccharides, including cellulose, xylan, mannan, and pectin, but not monosaccharides such as glucose, which is preferred by most ruminal bacteria. In the present study, using a draft of its genome and enzymatic characterization, we analyzed the enzymatic activities and the structures of the polymer hydrolases of strain H1 that were involved in the hydrolysis of complex polysaccharides.     

Metabolic syndrome and mitochondrial function: molecular replacement and antioxidant supplements to prevent membrane peroxidation and restore mitochondrial function

Metabolic syndrome consists of a cluster of metabolic conditions, such as hypertriglyceridemia, hyper-low-density lipoproteins, hypo-high-density lipoproteins, insulin resistance, abnormal glucose tolerance and hypertension, that-in combination with genetic susceptibility and abdominal obesity-are risk factors for type 2 diabetes, vascular inflammation, atherosclerosis, and renal, liver and heart disease. One of the defects in metabolic syndrome and its associated diseases is excess cellular oxidative stress (mediated by reactive oxygen and nitrogen species, ROS/RNS) and oxidative damage to mitochondrial components, resulting in reduced efficiency of the electron transport chain. Recent evidence indicates that reduced mitochondrial function caused by ROS/RNS membrane oxidation is related to fatigue, a common complaint of MS patients. Lipid replacement therapy (LRT) administered as a nutritional supplement with antioxidants can prevent excess oxidative membrane damage, restore mitochondrial and other cellular membrane functions and reduce fatigue. Recent clinical trials have shown the benefit of LRT plus antioxidants in restoring mitochondrial electron transport function and reducing moderate to severe chronic fatigue. Thus LRT plus antioxidant supplements should be considered for metabolic syndrome patients who suffer to various degrees from fatigue.