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At least 19 recordsLinked to original sources
PubMed2025

Gene behaviors-based network enrichment analysis and its application to reveal immune disease pathways enriched with COVID-19 severity-specific gene networks.

MOTIVATION: Gene network analysis is essential for understanding the complex mechanisms underlying diseases, which often involve disruptions in molecular networks rather than individual genes. Despite the availability of large-scale omics datasets and computational tools for gene network analysis, interpretation of the biological relevance of these extensive networks remains challenging. RESULTS: We propose a novel computational strategy, gene behaviors-based network enrichment analysis, which systematically identifies functional pathways enriched in phenotype-specific gene networks. Our novel method incorporates comprehensive network characteristics, i.e. gene expression levels, edge strengths, and structural patterns of edges, to rank genes based on activity and assess pathway enrichment, effectively identifying functional pathways enriched within these networks. Through simulation studies, our strategy demonstrated superior performance compared with that of existing methods in identifying enriched pathways. We applied this strategy to whole-blood RNA-seq data from 1102 COVID-19 samples provided by the Japan COVID-19 Task Force. The analysis revealed immune disease pathways enriched with COVID-19 severity-specific gene networks, including "Systemic lupus erythematosus" in asymptomatic and severe samples and "Inflammatory bowel disease," "Primary immunodeficiency," and "Rheumatoid arthritis" in mild samples. Key biomarkers of COVID-19, such as CXCL8, S100A9, and HLA class I genes, have been identified as critical hub genes and the main players within these networks. AVAILABILITY AND IMPLEMENTATION: Code is available in Figshare (https://doi.org/10.6084/m9.figshare.29093648.v3).

COVID-19↗
PubMed1978

K+--induced changes of oxygen uptake by neuronal enriched and glial enriched fractions from mouse brain cortex.

Neuronal and glial enriched fractions were incubated in a medium with 10mM pyruvate, 5mM fumarate and 0.9mM 5'-AMP and the effect of increased external K+ concentrations was studied upon oxygen uptake. A concentration of 65 mM K+ had a different effect on the oxygen consumption of glial and neuronal perikarya. The rate of oxygen uptake by glia was stimulated by 52.81% whilst an insignificant decrease of 15.79% occurred in the neurones. The highest rate of oxygen uptake by incubated cells was estimated in the presence of the substrate system containing pyruvate, fumarate and 5'-AMP. The significance of components in the substrate system for a high rate of oxygen uptake by cells was also tested with 6.2 mM K+ and 65 mM K+.

Animals↗
PubMed1979

[Steroid-transforming enzymes from microorganisms. X. Enrichment of a 4-en-3-oxosteroid-5 alpha-reductase from Mycobacterium smegmatis as well as separation and enrichment of the apoenzyme by means of affinity chromatography].

The 4-en-3-oxosteroid-5 alpha-reductase from Mycobacterium smegmatis was bound biospecifically on the affinant containing an immobilized testosterone ligand. The enzyme obtained by elution with ethylene glycol and urea in a 32 fold purity has a S. A. of 8.73 X 10(-3) microM androstenedione min-1 mg-1. The coenzyme (FAD) could be separated from the immobilized enzyme substrate complex on the affinity matrix, in the presence of (NH4)2SO4 at pH 3.0. After elution of the apoenzyme 97% of the initial enzyme activity was obtained by incubation with FAD. The reactivated enzyme results in a 40-fold enrichment.

3-Oxo-5-alpha-Steroid 4-Dehydrogenase↗
PubMed1975

Incubation at raised temperature or enrichment media, combined with secondary enrichment in Rappaport's medium, for the isolation of salmonellas from sewage.

Two FMDV strains which had been previously differentiated by complement-fixation were compared by guinea-pig protection test, kinetic neutralization and micro-neutralization tests. It was found that these tests, which have not been previously applied by the methods described, were all capable of FMDV STRAIN DIFFERENTIATION. Similar differences were found by all methods, which suggests that comparisons made by cross-CF, cross-neutr-alization or cross-protection involve measurement of the same antigen/antibody interactions.

Antibodies, Viral↗
PubMed1975

[Comparative studies of methods of salmonella enrichment (author's transl)].

Eight different methods of salmonella enrichment were compared in two series of experiments involving 100 samples of whole-egg powder and 80 samples of frozen whole liquid egg, respectively. 66 out of a total of 100 samples of whole-egg powder had been artificially infected with varying numbers of S. typhi-murium; 60 out of 80 samples of frozen whole liquid egg were found to be naturally infected with various salmonella species. 3 of the 8 methods (Table 1) were compared within an international collaborative study with 14 laboratories in 11 countries participating. A reduction of the pre-enrichment period from 18 to 6 hours and of volumes used in pre-enrichment and selective enrichment from 10 and 100 ml, respectively to 1 and 10 ml, respectively were found to have adverse influence upon the result of isolations, in particular in the case of weakly infected samples. In contrast, extended incubation over 48 hours as well as preparation of two sub-cultures on solid selective media following incubation of enrichment cultures over 18-24 hours and 42-48 hours, respectively always resulted in a certain increase of salmonella yield which, however, exhibited gradual differences for the individual methods examined. Preparation of a 2nd sub-culture meant, in particular, a decisive improvement of the result of isolations from artificially infected samples if selenite-cystine enrichment volumes were 10 and 100 ml, respectively. The best results could be obtained by means of the following methods of enrichment: Pre-enrichment of material in buffered peptone water at 37 degrees C over 18 hours; pipetting of 10 ml inoculated and incubated pre-enriched material into 100 ml selenite-cystine or tetrathionate enrichment medium according to MULLER-KAUFFMANN; onward incubation of the enrichment culture at 43 degrees C over 48 hours; and preparation of sub-cultures on solid selective media after 24 and 48 hours. The method using tetrathionate enrichment medium was found to be most expensive, results, however, were the most consistent ones.

Bacteriological Techniques↗
PubMed1978

Isolation and partial characterization of rat CNS axolemma enriched fractions.

Axolemma-enriched fractions were prepared from rat brain by osmotic shock of a purified preparation of myelinated axons and subsequent separation of myelin, two axolemma-enriched fractions and myelin-free axons by density gradient centrifugation. Compared with the starting whole homogenate, the fractions were enriched in specific activity of Na+K+ ATPase, acetylcholinesterase, 5'nucleotidase as well as 2',3'-cyclic nucleotide 3'phosphohydrolase. Compared with myelin, the axolemmal fractions are greatly enriched in high molecular weight proteins. The 1.0/1.2 fraction has a predominant peak of fucose-labeled glycoprotein with a molecular weight between that of the myelin associated glycoprotein and the Wolfgram protein which is absent from the myelin glycoprotein profile. Polyacrylamide gel electrophoresis showed that the protein profile of myelin isolated by this procedure was similar to that of myelin isolated by other procedures and that the myelin specific basic and proteolipid proteins were virtually absent in the axolemma-enriched fractions. Both axolemma fractions were enriched in higher MW proteins, some of which resembled proteins in the myelin protein profile. Both axolemma-enriched fractions specifically bind between 2 and 3 pmoles of [3H]tetrodotoxin per mg protein. The axolemma-enriched fractions incorporated [3H]leucine and [14C]fucose exclusively into high molecular weight proteins and glycoproteins. In contrast myelin concomitantly isolated with the axolemma-enriched fractions had a significant amount of [3H]leucine labeled protein in myelin proteolipid and basic proteins. In addition to the myelin associated g-ycoprotein the [14C]fucose labeled a glycoprotein of slightly larger apparent molecular weight than proteolipid protein was found in the myelin fraction while the comparable labeled glycoprotein was absent in the axolemma-enriched fractions. The possible extent of contamination of these fractions by myelin or myelin subfractions and relationship of these axolemma-enriched fractions to other axolemma preparations are discussed.

2',3'-Cyclic-Nucleotide Phosphodiesterases↗
PubMed1977

Effects of enrichment media and incubation conditions on isolating salmonellae from ground-meat filtrate.

Forty-eight combinations of enrichment media, secondary enrichment, incubation times and temperatures, and atmospheres were examined for their efficacy in recovering different serovars of Salmonella that had been inoculated into ground-meat extract. Variations included three selective-enrichment media, two (37 and 43 degrees C) incubation temperatures, two (24 and 48 h) incubation times, two (aerobic and anaerobic) incubation atmospheres, and secondary enrichment to two of the selective-enrichment media. The ratio of Salmonella to other microorganisms was 10: greater than 1,000,000. One-hundred and twenty-four tests were conducted for each enrichment under each condition of incubation. None of the methods recovered Salmonella in more than 60% of the trials. Salmonella typhimurium was recovered most frequently of the serovars tested; S. abortusovis was recovered least frequently. There was considerable variation in the results obtained by the different methods, but there was a statistically significant advantage in the 43 degrees C incubation temperature. Secondary enrichment in tetrathionate broth showed a statistically significant advantage over secondary enrichment in selenite broth. Secondary enrichment into a different medium from the primary enrichment also was advantageous.

Culture Media↗
PubMed1976

Fragility of plasma membranes in Saccharomyces cerevisiae enriched with different sterols.

Saccharomyces cerevisiae NCYC 366, grown under strictly anaerobic conditions to induce requirements for an unsaturated fatty acid (supplied by Tween 80) and a sterol, contained free sterol fractions enriched to the extent of 67 to 93% with the exogenously supplied sterol (campesterol, cholesterol, 7-dehydrocholesterol, 22, 23-dihydrobrassicasterol, beta-sitosterol, or stigmasterol). Cells enriched in any one of the sterols did not differ in volume, growth rate, contents of free sterol, esters and phospholipids, or phospholipid composition. Cholesterol-enriched cells contained about 2% more lipid than cells enriched in any of the other sterols, which was largely accounted for by increased contents of triacylglycerols and, to a lesser extent, esterified sterols. Phospholipids were enriched to the extent of about 52 to 63% with C18:1 residues. Cells enriched in ergosterol or stigmasterol were slightly less susceptible to the action of a wall-digesting basidiomycete glucanase than cells enriched with any one of the other sterols. The capacity of the plasma membrane to resist stretching, as indicated by the stability and volume of spheroplasts suspended in hypotonic solutions of buffered sorbitol (particularly in the range 0.9 to 0.7 M), was greater with spheroplasts enriched in sterols with an unsaturated side chain at C17 (ergosterol or stigmasterol) than with any of the other sterols. Plasma membranes were obtained from spheroplasts enriched in cholesterol or stigmasterol and had free sterol fractions containing 70 and 71%, respectively, of the sterol supplied exogenously to the cells. The sterol-phospholipid molar ratios in these membranes were, respectively, 1:7 and 1:8.

Anaerobiosis↗
PubMed2024

In-situ enrichment of ARGs and their carriers in soil by hydroxamate siderophore: A promising biocontrol approach for source reduction.

Pathogenic microorganisms with antibiotic resistance genes (ARGs) pose a serious threat to public health and soil ecology. Although new drugs and available antibacterial materials can kill ARG carriers but accidentally kill beneficial microorganisms. Therefore, the rapid enrichment and separation of ARGs and their carriers from soil is becoming an important strategy for controlling the diffusion of ARGs. Hydroxamate siderophore (HDS) has gained widespread attentions for its involvement in trace element transfer among microorganisms in the soil environment, we thus explored an in-situ trapping-enrichment method for ARGs and their carriers via a small molecular HDS secreted by Pseudomonas fluorescens HMP01. In this study, we demonstrate that HDS significantly in-situ traps and enriches certain ARGs, including chloramphenicol, MLS, rifamycin, and tetracycline resistance genes in the soil environment. The enrichment efficiencies were 1473-fold, 38-fold, 17-fold, and 5-fold, respectively, higher than those in the control group. Specifically, the primary enriched ARGs were rpoB, mphL, catB2, and tetA(60), and Bacillus, Rhizobium, Rossellomorea, and Agrobacterium were hosts for these ARGs. This enrichment was caused by the upregulation of chemotaxis genes (e.g., cheW, cheC, and cheD) and rapid biofilm formation within the enriched bacterial population. Notably, representative ARGs such as cat, macB, and rpoB were significantly reduced by 36%, 85.7%, and 72%, respectively, in the paddy soil after HDS enrichment. Our research sheds light on the potential application of siderophore as a rapping agent for the eco-friendly reduction of ARGs and their carriers in soil environments.

Soil Microbiology↗
PubMed1977

Response of the three main types of glial cells of cortex and corpus callosum in rats handled during suckling or exposed to enriched, control and impoverished environments following weaning.

The cell populations of the occipital cortex were examined in young rats subjected to different sensory experiences. In one series recently weaned animals were reared in enriched, impoverished or control environments. The enriched environment was obtained by keeping the animals among "toys" and other rats; the impoverished environment, by rearing the animals one per cage in a darkened, quiet room; and the control environment, by housing the animals three per cage under usual animal room conditions. Six recently weaned rats were kept in each environment for 30 days and ten, for 80 days. In a second series suckling rats were handled daily. Handling consisted of touching, holding and rubbing rat pups for 15 minutes per day during the first ten days after birth; twelve rats were studied, six handled and six unhandled controls. In the two series, the animals were sacrificed under anesthesia by perfusion with mixed aldehydes. Semithin epon sections of occipital cortex were stained with toluidine blue; neurons and the three main types of glia were enumerated. In addition, the thickness of the cortex was measured and the glial cells of corpus callosum counted in the animals exposed to the three environments for 80 days. Under the influence of the enriched environment, the occipital cortex enlarged, the number of oligodendrocytes increased over the controls by 27-33% in the 30- and 80-day groups and the number of astrocytes, by 13% in the 80-day group. Within the cortex, only certain layers showed the increase in glial numbers. In the corpus callosum, however, the numbers of glial cells did not differ from those in controls. In the animals exposed to the impoverished environment, neither the size of the cortex nor the number of oligodendrocytes and astrocytes differed from controls. The animals subjected to handling also showed evidence of cortical enlargement, but the only significant change in glial cells was a 12% increase in astrocytes. It is concluded that handling and enrichment produce changes in anatomical indices of neural function including depth of cortex and numbers of glial cells. The glial response was specific to the type.of manipulation since astrocytes were predominantly affected by handling and oligodendrocytes, by enrichment. The effect of handling on astrocytes may be attributed to the stimulation being applied at a time of astrocyte proliferation, whereas the effect of enriched environment on oligodendrocytes occurred at a time of active production of these cells. The differences in cell numbers were explained by changes in the rate of cell population growth; since the impoverished did not differ from the control animals, the changes probably consisted of growth acceleration in the enriched animals rather than diminution in the impoverished ones.

Animals↗
PubMed1979

Efficacy of cold enrichment techniques for recovery of Yersinia enterocolitica from human stools.

Stool specimens from children with gastroenteritis and their household contacts were cultured for Yersinia enterocolitica by direct plating onto routine laboratory media. These stools were also inoculated into phosphate-buffered saline and subcultured to the same media after 1 day or 3 weeks of incubation at 4 degrees C. Y. enterocolitica was isolated from 174 index cases and 34 household contacts. One hundred eighty-one isolates were of serotype O:3, and the remaining 21 belonged to other serotypes. Eighty-one percent (147/181) of O:3 isolates were recovered by direct plating, and 6.1% (11/181) and 13% (23/181) were recovered by 1-day and 3-week cold enrichment, respectively. For other serotypes, 26% (7/27), 0%, and 74% (20/27) were isolated by direct plating, 1-day cold enrichment, and 3-week cold enrichment, respectively. The efficacy of the cold enrichment for the patients were still symptomatic, 94 and 6% of Y. enterocolitica were identified by direct plating and cold enrichment, respectively. Isolation rates were 66% by direct plating and 34% by cold enrichment when stools were obtained from asymptomatic carriers or from those convalescing from Y. enterocolitica gastroenteritis. These results indicate that the cold enrichment methods increase the sensitivity of Y. entercolitica culture methods considerably in convalescent and asymptomatic subjects but only minimally in patients with diarrhea caused by serotype O:3.

Bacteriological Techniques↗
PubMed1979

Cognitive modifiability in retarded adolescents: effects of instrumental enrichment.

The Instrumental Enrichment program, designed to modify the cognitive structures of retarded, disadvantaged adolescents, was contrasted with a General Enrichment program both in a residential setting and a day center. This study is based on 57 matched pairs drawn from the total research sample of 218 adolescents. One group in a residential center (n = 24) and one group in a day center (n = 33) received Instrumental Enrichment; one group in a residential center (n = 24) and one group in a day center (n = 33) received General Enrichment. The Instrumental Enrichment program extended over 2 years, and the subjects were pre- and posttested on a battery of criterion measures: general and specific cognitive tests, scholastic achievement, classroom interaction, and self-concept. The results indicated significantly better performance by the groups receiving Instrumental Enrichment than by the groups receiving General Enrichment on the tests of specific cognitive functions and scholastic achievement and on some of the classroom interaction scales. Results for the residential groups compared with the day-center groups revealed significant differences on the tests of scholastic achievement, in favor of the residential groups and on the classroom interaction scales in favor of the day-center groups.

Achievement↗
PubMed1979

[Physiological effects of diet enriched in essential fatty acids in young men].

The investigations were carried out on healthy young males aged 20-21 years. Those young men, whose previously different diets were determined by the dietary habits of their families, were selected and grouped under uniform conditions (feeding, housing, physical activity). After 4 months staying under these uniform conditions their diet was changed adding E.F.A. to their previous food rations. Food rations enriched with E.F.A. were given to these young males for 3 months. Then E.F.A. additions to the diet was stopped and the observed subjects received food rations, identical as during the initial 4-month period prior to E.F.A. enrichment, these rations were given during 5 months. Immediately after grouping these men were subjected to biochemical investigation of the serum and to anthropometric and general medical examinations (examination I). The subsequent examinations (II, III, IV) were carried out while the subjects were living under uniform conditions: II) after 4 months on the diet without E.F.A. enrichment, III) after 3 months on the diet enriched with E.F.A., and IV) after 5 months of diet without E.F.A. enrichment (after withdrawal of additional E.F.A.). The investigations were begun on 97 young males (examination I). The consecutive examinations (II, III, IV) were carried out on smaller groups of subjects for reasons on with the authors had no influence. During the experiment, 2-3 times in a month, sample of daily food rations given to the studied subjects and residual food on the plates were taken for analysis. This was done for determination of actual food intake. Through the whole period of the experiment the observed subjects were inquired about additional food consumed. The biochemical investigations of the nutritional state of these young subjects included hematological indices, serum proteins, selected biochemical components in the serum, activity of certain enzymes in the serum, serum lipid components and serum level of certain vitamins. The results of these investigations show the enrichment of diets during 3 months with vegetable fats (sunflower oil, margarine containing 40% of E.F.A.) for increasing the amount of E.F.A. in the whole daily food (together with additional food calculated on the basis of inquiry information) from 14.7 g to 27.7 g (3,2% kcal and 5,8% kcal respectively) has a favorable effect on selected serum lipids. The following changes appeared: decrease of total lipid level, total cholesterol level, cholesterol content of beta and prebeta-lipoproteins levels, free fatty acid level and the favorable changes in the composition of fatty acid in total lipid and selected lipid fractions in the serum. Food enrichment with E.F.A. led to rise the level of linoleic acid and total E.F.A. level and to fall the level of saturated fatty acids. The ratio of polyunsaturated to saturated fatty acids changes favorably both in total serum lipids and in different lipid fraction...

Adult↗
PubMed1976

Short exposures to enriched environments can increase genetic variability of behavior in mice.

Previous work indicates that mice of different genotypes reared in enriched environments show differential increases in performance on a food-seeking task. In this study 2 experiments examined the effects in selected mice strains of short exposures to such enrichment. Experiment 1 indicated that 48 hr of exposure to enriched cages was sufficient to produce results found previously when subjects were reared from birth in enriched cages. Experiment 2 indicated that as little as 6 hr of exposure to an enriched cage was sufficient to produce almost maximal enrichment effects in C57BL/10J mice.

Age Factors↗
PubMed2025

Multiple Psychiatric Traits Enriched for Brain Tissues in the Early Postpartum Period.

BACKGROUND: The perinatal period is a high-risk time for onset of various psychiatric disorders. However, it is unclear how genetic risk factors for these disorders interact with biological changes associated with pregnancy and postpartum. This study evaluates whether psychiatric genome-wide association study (GWAS) results are enriched within various brain regions across the perinatal period. METHODS: Tissue-specific enrichment analyses were conducted to estimate the potential impact of GWAS loci on transcriptional changes in the brain across the perinatal period. GWAS summary statistics were obtained for 26 psychiatric phenotypes. RNA-sequencing data was acquired from four brain regions (hypothalamus, hippocampus, cerebellum, and neocortex) in mice at six timepoints (virgin, 14- and 16-days post-conception, and 1-, 3- and 10-days postpartum). RESULTS: Hippocampus and neocortex in the early postpartum period are significantly enriched (q-value < 0.05) for genetic variants associated with schizophrenia (SCZ), bipolar disorder (BD), depressive symptoms, and major depressive disorder with suicidal features. The most significant enrichment occurred in the neocortex for SCZ and BD, peaking at postpartum day 1 (SCZ p-value = 3.85 &#xd7; 10-8; BD p-value = 6.65 &#xd7; 10-5). In the hippocampus, BD and SCZ were enriched at postpartum day 1 (SCZ p-value = 3.27 &#xd7; 10-3; BD p-value = 4.33 &#xd7; 10-3). No enrichment was observed in cerebellum or hypothalamus for any of the psychiatric traits tested. CONCLUSIONS: The results accord with previous epidemiological studies and provide context in which to interpret GWAS results. Understanding the burden of genetic variants across the perinatal period may help prioritise pathways underlying onset of psychiatric disorders outside of pregnancy and postpartum periods.

Journal Article↗
PubMed1979

Application of oxygen-enriched aeration in the production of bacitracin by Bacillus licheniformis.

The physiological effects of controlling the dissolved oxygen tension at 0.01, 0.02, and 0.05 atm by the use of oxygen-enriched aeration were investigated during growth and bacitracin production by Bacillus licheniformis ATCC 10716. Up to a 2.35-fold increase in the final antibiotic yield and a 4-fold increase in the rate of bacitracin synthesis were observed in response to O(2)-enriched aeration. The increase in antibiotic production was accompanied by increased respiratory activity and an increase in the specific productivity of the culture from 1.3 to 3.6 g of antibiotic per g of cell mass produced. Oxygen enrichment of the aeration decreased medium carbohydrate uptake and the maximum specific growth rate of B. licheniformis from 0.6 h(-1) to as low as 0.15 h(-1), depending upon the level of enrichment and the conditions of oxygen transfer rate (impeller speed). The response of this culture to O(2) enrichment suggests that this method of controlling the dissolved oxygen tension for antibiotic-producing cultures may simulate conditions that would occur if the carbon source were fed slowly, as is often employed to optimize antibiotic production. Analysis of the biologically active bacitracins produced by B. licheniformis ATCC 10716 suggested that the ratio of biologically active peptides was not changed by O(2) enrichment, nor were any new biologically active compounds formed.

Bacillus↗