scholarly journals Growth Characteristics ofMethanomassiliicoccus luminyensisand Expression of Methyltransferase Encoding Genes

Archaea ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Lena Kröninger ◽  
Jacqueline Gottschling ◽  
Uwe Deppenmeier
Keyword(s):  
Growth Yield ◽  
Dry Weight ◽  
Transcript Level ◽  
Resting Cells ◽  
Growth Substrate ◽  
Human Gut ◽  
Genes Encoding ◽  
Seventh Order ◽  
Encoding Genes ◽  
Doubling Times

DNA sequence analysis of the human gut revealed the presence a seventh order of methanogens referred to as Methanomassiliicoccales.Methanomassiliicoccus luminyensisis the only member of this order that grows in pure culture. Here, we show that the organism has a doubling time of 1.8 d with methanol + H2and a growth yield of 2.4 g dry weight/mol CH4.M. luminyensisalso uses methylamines + H2(monomethylamine, dimethylamine, and trimethylamine) with doubling times of 2.1–2.3 d. Similar cell yields were obtained with equimolar concentrations of methanol and methylamines with respect to their methyl group contents. The transcript levels of genes encoding proteins involved in substrate utilization indicated increased amounts of mRNA from themtaBC2gene cluster in methanol-grown cells. When methylamines were used as substrates, mRNA of themtb/mttoperon and of themtmBC1cluster were found in high abundance. The transcript level ofmtaC2was almost identical in methanol- and methylamine-grown cells, indicating that genes for methanol utilization were constitutively expressed in high amounts. The same observation was made with resting cells where methanol always yielded the highest CH4production rate independently from the growth substrate. Hence,M. luminyensisis adapted to habitats that provide methanol + H2as substrates.

scholarly journals Gene Expression Patterns for Proteins With Lectin Domains in Flax Stem Tissues Are Related to Deposition of Distinct Cell Wall Types

2021 ◽  
Vol 12 ◽  
Author(s):  
Natalia Petrova ◽  
Alsu Nazipova ◽  
Oleg Gorshkov ◽  
Natalia Mokshina ◽  
Olga Patova ◽  
...  
Keyword(s):  
Cell Wall ◽  
Higher Plants ◽  
Expression Patterns ◽  
Transcript Level ◽  
Genome Wide ◽  
Distinct Cell ◽  
A Genome ◽  
Genes Encoding ◽  
Genome Wide Search ◽  
Encoding Genes

The genomes of higher plants encode a variety of proteins with lectin domains that are able to specifically recognize certain carbohydrates. Plants are enriched in a variety of potentially complementary glycans, many of which are located in the cell wall. We performed a genome-wide search for flax proteins with lectin domains and compared the expression of the encoding genes in different stem tissues that have distinct cell wall types with different sets of major polysaccharides. Over 400 genes encoding proteins with lectin domains that belong to different families were revealed in the flax genome; three quarters of these genes were expressed in stem tissues. Hierarchical clustering of the data for all expressed lectins grouped the analyzed samples according to their characteristic cell wall type. Most lectins differentially expressed in tissues with primary, secondary, and tertiary cell walls were predicted to localize at the plasma membrane or cell wall. These lectins were from different families and had various architectural types. Three out of four flax genes for proteins with jacalin-like domains were highly upregulated in bast fibers at the stage of tertiary cell wall deposition. The dynamic changes in transcript level of many genes for lectins from various families were detected in stem tissue over the course of gravitropic response induced by plant gravistimulation. The data obtained in this study indicate a large number of lectin-mediated events in plants and provide insight into the proteins that take part in tissue specialization and reaction to abiotic stress.

Minimization of activated sludge production by chemically stimulated energy spilling

2000 ◽  
Vol 42 (12) ◽  
pp. 189-200 ◽  
Author(s):  
G.-H. Chen ◽  
H.-K. Mo ◽  
S. Saby ◽  
W.-k. Yip ◽  
Y. Liu
Keyword(s):  
Activated Sludge ◽  
Growth Yield ◽  
Dry Weight ◽  
Staining Technique ◽  
Microbial Culture ◽  
Dapi Staining ◽  
E Coli ◽  
Energy Spilling ◽  
Activated Sludge Processes ◽  
Sludge Production

Minimization of excess sludge production in activated sludge processes has been pursued around the world in order to meet stringent environmental regulations on sludge treatment and disposal. To achieve this goal, physical, chemical, and biological approaches have been proposed. In this paper, a chemical compound, 3,3′,4′,5-tetrachlorosalicylanilide (TCS) was tested for enhancing microbial energy spilling of the sludgeso as to minimize its growth. In order to examine this, an exploratory study was conducted using both batch and continuous activated sludge cultures. Batch experiments with these two cultures were carried out at different initial concentrations of TCS. It has been confirmed that an addition of TCS is effective in reducing the production of both the sludge cultures, particularly the continuous culture where the observed growth yield was reduced by around 70%, when the initial TCS concentration was 0.8 ppm. Meanwhile, the substrate removal activity of this culture was found not to be affected at this TCS concentration. To further evaluate the TCS effect, a pure microbial culture of E. coli was employed. Batch experiment results with this culture implied that TCS might be able to reduce the cell density of E. coli drastically when an initial TCS concentration was greater than 0.12 ppm. It was also found that TCS was not toxic to this type of bacteria. Microscopic examinations with a 4′, 6-diamidino-2-phenylindole (DAPI) staining technique revealed that TCS neither affected the cell division nor altered the cell size of E. coli. However, both the cell ATP content and the cell dry weight were reduced significantly with the addition of TCS.

scholarly journals Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar

2021 ◽  
Author(s):  
Fatma Ben Abid ◽  
Clement K. M. Tsui ◽  
Yohei Doi ◽  
Anand Deshmukh ◽  
Christi L. McElheny ◽  
...  
Keyword(s):  
Common Species ◽  
Clinical Samples ◽  
Whole Genome ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Genes Encoding ◽  
Encoding Genes ◽  
Sequence Types ◽  
Common Sequence

AbstractOne hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

scholarly journals Flavonoid-Modifying Capabilities of the Human Gut Microbiome—An In Silico Study

Nutrients ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 2688
Author(s):  
Tobias Goris ◽  
Rafael R. C. Cuadrat ◽  
Annett Braune
Keyword(s):  
Gut Microbiome ◽  
Large Scale ◽  
Health Impact ◽  
Gut Bacteria ◽  
Human Gut ◽  
Positive Health ◽  
Human Gut Microbiome ◽  
Nutritional Recommendations ◽  
Genes Encoding ◽  
A Minor

Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of metagenome data of the human gut microbiome and the assembly of hundreds of thousands of bacterial metagenome-assembled genomes (MAGs), large-scale screening for potential flavonoid-modifying enzymes of human gut bacteria is now feasible. With sequences of characterized flavonoid-transforming enzymes as queries, the Unified Human Gastrointestinal Protein catalog was analyzed and genes encoding putative flavonoid-modifying enzymes were quantified. The results revealed that flavonoid-modifying enzymes are often encoded in gut bacteria hitherto not considered to modify flavonoids. The enzymes for the physiologically important daidzein-to-equol conversion, well studied in Slackiaisoflavoniconvertens, were encoded only to a minor extent in Slackia MAGs, but were more abundant in Adlercreutzia equolifaciens and an uncharacterized Eggerthellaceae species. In addition, enzymes with a sequence identity of about 35% were encoded in highly abundant MAGs of uncultivated Collinsella species, which suggests a hitherto uncharacterized daidzein-to-equol potential in these bacteria. Of all potential flavonoid modification steps, O-deglycosylation (including derhamnosylation) was by far the most abundant in this analysis. In contrast, enzymes putatively involved in C-deglycosylation were detected less often in human gut bacteria and mainly found in Agathobacter faecis (formerly Roseburia faecis). Homologs to phloretin hydrolase, flavanonol/flavanone-cleaving reductase and flavone reductase were of intermediate abundance (several hundred MAGs) and mainly prevalent in Flavonifractor plautii. This first comprehensive insight into the black box of flavonoid modification in the human gut highlights many hitherto overlooked and uncultured bacterial genera and species as potential key organisms in flavonoid modification. This could lead to a significant contribution to future biochemical-microbiological investigations on gut bacterial flavonoid transformation. In addition, our results are important for individual nutritional recommendations and for biotechnological applications that rely on novel enzymes catalyzing potentially useful flavonoid modification reactions.

scholarly journals Molecular investigation of an outbreak associated with total parenteral nutrition contaminated with NDM-producing Leclercia adecarboxylata

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Elvira Garza-González ◽  
Paola Bocanegra-Ibarias ◽  
Eduardo Rodríguez-Noriega ◽  
Esteban González-Díaz ◽  
Jesús Silva-Sanchez ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Carbapenem Resistance ◽  
Clonal Diversity ◽  
Molecular Characteristics ◽  
Molecular Evidence ◽  
Carbapenem Resistant ◽  
Parental Nutrition ◽  
Genes Encoding ◽  
Main Lineage ◽  
Encoding Genes

Abstract Background This study aimed to determine the epidemiological, microbiological, and molecular characteristics of an outbreak of carbapenem-resistant Leclercia adecarboxylata in three hospitals associated with the unintended use of contaminated total parental nutrition (TPN). Methods For 10 days, 25 patients who received intravenous TPN from the same batch of a formula developed sepsis and had blood cultures positive for L. adecarboxylata. Antimicrobial susceptibility and carbapenemase production were performed in 31 isolates, including one from an unopened bottle of TPN. Carbapenemase-encoding genes, extended-spectrum β-lactamase–encoding genes were screened by PCR, and plasmid profiles were determined. Horizontal transfer of carbapenem resistance was performed by solid mating. Clonal diversity was performed by pulsed-field gel electrophoresis. The resistome was explored by whole-genome sequencing on two selected strains, and comparative genomics was performed using Roary. Results All 31 isolates were resistant to aztreonam, cephalosporins, carbapenems, trimethoprim/sulfamethoxazole, and susceptible to gentamicin, tetracycline, and colistin. Lower susceptibility to levofloxacin (51.6%) and ciprofloxacin (22.6%) was observed. All the isolates were carbapenemase producers and positive for blaNDM-1, blaTEM-1B, and blaSHV-12 genes. One main lineage was detected (clone A, 83.9%; A1, 12.9%; A2, 3.2%). The blaNDM-1 gene is embedded in a Tn125-like element. Genome analysis showed genes encoding resistance for aminoglycosides, quinolones, trimethoprim, colistin, phenicols, and sulphonamides and the presence of IncFII (Yp), IncHI2, and IncHI2A incompatibility groups. Comparative genomics showed a major phylogenetic relationship among L. adecarboxylata I1 and USDA-ARS-USMARC-60222 genomes, followed by our two selected strains. Conclusion We present epidemiological, microbiological, and molecular evidence of an outbreak of carbapenem-resistant L. adecarboxylata in three hospitals in western Mexico associated with the use of contaminated TPN.

scholarly journals Molecular Epidemiology of NDM-1-Producing Enterobacteriaceae and Acinetobacter baumannii Isolates from Pakistan

2014 ◽  
Vol 58 (9) ◽  
pp. 5589-5593 ◽  
Author(s):  
Anna L. Sartor ◽  
Muhammad W. Raza ◽  
Shahid A. Abbasi ◽  
Kathryn M. Day ◽  
John D. Perry ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Epidemiology ◽  
Genetic Relatedness ◽  
Antibiotic Resistance Genes ◽  
Enterobacter Cloacae ◽  
Content Type ◽  
Plasmid Replicon ◽  
Genes Encoding ◽  
Clonal Spread ◽  
Encoding Genes

ABSTRACTThe molecular epidemiology of 66 NDM-producing isolates from 2 Pakistani hospitals was investigated, with their genetic relatedness determined using repetitive sequence-based PCR (Rep-PCR). PCR-based replicon typing and screening for antibiotic resistance genes encoding carbapenemases, other β-lactamases, and 16S methylases were also performed. Rep-PCR suggested a clonal spread ofEnterobacter cloacaeandEscherichia coli. A number of plasmid replicon types were identified, with the incompatibility A/C group (IncA/C) being the most common (78%). 16S methylase-encoding genes were coharbored in 81% of NDM-producingEnterobacteriaceae.

Direct cloning of genes encoding novel xylanases from the human gut

2005 ◽  
Vol 51 (3) ◽  
pp. 251-259 ◽  
Author(s):  
Hidenori Hayashi ◽  
Takashi Abe ◽  
Mitsuo Sakamoto ◽  
Hiroki Ohara ◽  
Toshimichi Ikemura ◽  
...  
Keyword(s):  
Intestinal Bacteria ◽  
Fecal Microbiota ◽  
Coli Strain ◽  
Amino Acid Sequences ◽  
Self Organizing Map ◽  
Human Gut ◽  
Gene Encoding ◽  
Genes Encoding ◽  
Ph Range ◽  
Self Organizing

The aim of this study was to identify a novel 1,4-β-xylanase gene from the mixed genome DNA of human fecal bacteria without bacterial cultivation. Total DNA was isolated from a population of bacteria extracted from fecal microbiota. Using PCR, the gene fragments encoding 5 different family 10 xylanases (xyn10A, xyn10B, xyn10C, xyn10D, and xyn10E) were found. Amino acid sequences deduced from these genes were highly homologous with those of xylanases from anaerobic intestinal bacteria such as Bacteroides spp. and Prevotella spp. Self-organizing map (SOM) analysis revealed that xynA10 was classified into Bacteroidetes. To confirm that one of these genes encodes an active enzyme, a full-length xyn10A gene was obtained using nested primers specific to the internal fragments and random primers. The xyn10A gene encoding the xylanase Xyn10A consists of 1146 bp and encodes a protein of 382 amino acids and a molecular weight of 43 552. Xyn10A was a single module novel xylanase. Xyn10A was purified from a recombinant Escherichia coli strain and characterized. This enzyme was optimally active at 40 °C and stable up to 50 °C at pH 6.5 and over the pH range 4.0–11.0 at 25 °C. In addition, 2 ORFs (ORF1 and ORF2) were identified upstream of xyn10A. These results suggested that many unidentified xylanolytic bacteria exist in the human gut and may contribute to the breakdown of xylan which contains dietary fiber.Key words: xylanase, human gut, fecal microbiota, phylogenetic analysis, self-organizing map.

scholarly journals Sulfur application alleviates chromium stress in maize and wheat

2020 ◽  
Vol 18 (1) ◽  
pp. 1093-1104
Author(s):  
Grzegorz Kulczycki ◽  
Elżbieta Sacała
Keyword(s):  
Adverse Effects ◽  
Mineral Nutrition ◽  
Elemental Sulfur ◽  
Marked Decrease ◽  
Total Yield ◽  
Growth Yield ◽  
Dry Weight ◽  
Total Biomass ◽  
Cr Content ◽  
Chromium Stress

AbstractThis study aimed to examine the influence of increasing doses of chromium (Cr) (26, 39, and 52 mg kg−1 soil) and elemental sulfur (S) (60 mg kg−1 soil) on growth, yield, and mineral nutrition in wheat and maize. Macro- and micronutrients and Cr concentrations were determined in the aboveground parts of plants. All examined doses of Cr caused a marked decrease in the fresh and dry weight of maize. Wheat was more tolerant than maize, and lower Cr doses caused a small but statistically significant increase in the total yield. Wheat accumulated more than twofold Cr than maize, and the concentrations increased with higher Cr concentrations in the soil. The application of S significantly improved the total biomass production and lowered the Cr content in both plants. Cr changed the mineral nutrition in both cereals, but the pattern of changes observed was not the same. Applying S alleviated some adverse effects caused by the Cr. Hence, it is concluded that the application of elemental S may be an effective strategy to reduce adverse effects in plants grown on soil contaminated by heavy metals, especially Cr.

The Glucose, Insulin and Glutamine Requirements of Suspension Cultures of HeLa Cells in a Difined Culture Medium

1971 ◽  
Vol 9 (2) ◽  
pp. 529-537
Author(s):  
G. J. BLAKER ◽  
J. R. BIRCH ◽  
S. J. PIRT
Keyword(s):  
Amino Acid ◽  
Hela Cells ◽  
Growth Yield ◽  
Dry Weight ◽  
Defined Medium ◽  
Cell Populations ◽  
Serum Supplement ◽  
Protamine Sulphate ◽  
Protamine Zinc Insulin ◽  
Maximum Cell

The serum supplement in a defined medium for the growth of HeLa cells could be replaced by protamine-zinc-insulin (0.2 u./ml). Insulin (0.4 u./ml) replaced the growth-stimulatory properties of protamine-zinc-insulin, whilst protamine sulphate (5 µg/ml) was found to be toxic to the cells. The addition of insulin to cultures depleted of insulin increased both cell growth rates and maximum cell populations. In the defined medium, HeLa cells could only utilize glutamate when a small amount of glutamine was included. Glucose, at a level of 2 mg/ml, was shown to limit maximum cell populations. The growth yield from glucose was 295 µg cell dry weight/mg glucose. When the medium glucose concentration was increased to 4 mg/ml, HeLa cell populations in excess of 16 x 105 cells (i.e. 640 µg dry weight)/ml were routinely achieved in the defined medium supplemented with insulin. Growth is then limited by the amino acid supply. Increasing the amino acid concentration of the medium by 50% raised the maximum cell population to 23.5x105 cells (i.e. 940 µg dry weight)/ml.

scholarly journals Effect of arsenic on Amaranthus gangeticus

2018 ◽  
Vol 53 (4) ◽  
pp. 259-264
Author(s):  
MZ Hossain ◽  
Sushmita Dey ◽  
MS Islam
Keyword(s):  
Irrigation Water ◽  
Crop Production ◽  
Growth Yield ◽  
Dry Weight ◽  
Arsenic Contamination ◽  
Pot Experiment ◽  
Production Potential ◽  
Groundwater Arsenic ◽  
Major Nutrients

Groundwater arsenic contamination has become a threat to the crop production potential in the soils of vast areas of Bangladesh. Situation is grave in some districts of the country, particularly the southern part. A pot experiment was conducted to investigate the effects of arsenic treated irrigation water (0, 1, 2, 5 and 10 mgL-1), where a total of ten (10) irrigations were provided thus the treatments received 0, 10, 20, 50, and 100 mg arsenic (As) pot-1. Effects of applied levels of arsenic on Amaranthus gangeticus (Lal shak) were evaluated in terms of the growth, yield, major nutrients’ content, and their translocation in the plant. As treatments significantly reduced (p≤0.05) the dry weight of shoot and root by 19.31% and 44.03% respectively. Both total and available concentrations of nitrogen (N), potassium (K) and sulfur (S) were significantly (p≤ 0.05) suppressed by the As treatments, while only higher three doses significantly (p≤ 0.05) affected both levels of concentrations of phosphorus (P), calcium (Ca) and magnesium (Mg). Translocation coefficients for soil to root for P, K, S, and Mg were significantly reduced (p≤ 0.05), while translocation coefficients for root to shoot were significantly increased (p≤ 0.05) for K and S by 5 and 10 mgL-1 of arsenic treatments.Bangladesh J. Sci. Ind. Res.53(4), 259-264, 2018

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