scholarly journals The Chloroflexi supergroup is metabolically diverse and representatives have novel genes for non-photosynthesis based CO2 fixation

2021 ◽  
Author(s):  
Jacob A West-Roberts ◽  
Paula B. Matheus Carnevali ◽  
Marie Charlotte Scholmerich ◽  
Basem Al-Shayeb ◽  
Alex Thomas ◽  
...  
Keyword(s):  
Co2 Fixation ◽  
Aerobic Oxidation ◽  
Small Subunit ◽  
Reductive Dehalogenation ◽  
Class Level ◽  
Group 3 ◽  
Phylogenomic Analyses ◽  
Close Relatives ◽  
High Level ◽  
Single Subunit

The Chloroflexi superphylum have been investigated primarily from the perspective of reductive dehalogenation of toxic compounds, anaerobic photosynthesis and wastewater treatment, but remain relatively little studied compared to their close relatives within the larger Terrabacteria group, including Cyanobacteria, Actinobacteria, and Firmicutes. Here, we conducted a detailed phylogenetic analysis of the phylum Chloroflexota, the phylogenetically proximal candidate phylum Dormibacteraeota, and a newly defined sibling phylum proposed in the current study, Eulabeiota. These groups routinely root together in phylogenomic analyses, and constitute the Chloroflexi supergroup. Chemoautotrophy is widespread in Chloroflexi. Two Form I Rubisco ancestral subtypes that both lack the small subunit are prevalent in ca. Eulabeiota and Chloroflexota, suggesting that the predominant modern pathway for CO2 fixation evolved in these groups. The single subunit Form I Rubiscos are inferred to have evolved prior to oxygenation of the Earth's atmosphere and now predominantly occur in anaerobes. Prevalent in both Chloroflexota and ca. Eulabeiota are capacities related to aerobic oxidation of gases, especially CO and H2. In fact, aerobic and anaerobic CO dehydrogenases are widespread throughout every class-level lineage, whereas traits such as denitrification and reductive dehalogenation are heterogeneously distributed across the supergroup. Interestingly, some Chloroflexota have a novel clade of group 3 NiFe hydrogenases that is phylogenetically distinct from previously reported groups. Overall, the analyses underline the very high level of metabolic diversity in the Chloroflexi supergroup, suggesting the ancestral metabolic platform for this group enabled highly varied adaptation to ecosystems that appeared in the aerobic world.

scholarly journals Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles

2021 ◽  
Author(s):  
Gitta Szabó ◽  
Frederik Schulz ◽  
Alejandro Manzano-Marín ◽  
Elena Rebecca Toenshoff ◽  
Matthias Horn
Keyword(s):  
Defense Mechanisms ◽  
Amino Acid Production ◽  
Evolutionary Transition ◽  
Evolutionary Time ◽  
Evolutionary Trajectories ◽  
Host Infection ◽  
Phylogenomic Analyses ◽  
Time Specific ◽  
High Level ◽  
Metagenomic Approach

AbstractAdelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/Adelgestardus species complex containing betaproteobacterial (“Candidatus Vallotia tarda”) and gammaproteobacterial (“Candidatus Profftia tarda”) symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other’s role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection, and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.

Chitinophaga oryzae sp. nov., an epiphytic bacterium isolated from rice root surfaces

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Nantawan Niemhom ◽  
Chanwit Suriyachadkun ◽  
Chokchai Kittiwongwattana
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Phylogenomic Analyses ◽  
Close Relatives

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16–37 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0) and 0–2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus Chitinophaga . Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with Chitinophaga eiseniae YC6729T, Chitinophaga qingshengii JN246T, Chitinophaga varians 10-7 W-9003T and Chitinophaga fulva G-6-1-13T. When the genomic sequences of strains 1303T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA–DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C15 : 0, C16 : 1  ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303T and 1310 represent members of a novel species of the genus Chitinophaga , for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303T (=KACC 22075T=TBRC 12926T).

scholarly journals The Threshold of Admission Glycemia as a Predictor of Adverse Events in Diabetic and Non-Diabetic Patients with Acute Coronary Syndrome

2009 ◽  
Vol 3 ◽  
pp. CMC.S2289 ◽  
Author(s):  
Taysir S. Garadah ◽  
Salah Kassab ◽  
Qasim M. Al-Shboul ◽  
Abdulhai Alawadi
Keyword(s):  
Acute Coronary Syndrome ◽  
Adverse Events ◽  
Diabetic Patients ◽  
Stress Hyperglycemia ◽  
Coronary Syndrome ◽  
History Of ◽  
Group 3 ◽  
Group 2 ◽  
High Level ◽  
Group 1

Recent studies indicated a high prevalence of hyperglycemia in non-diabetic patients presenting with acute coronary syndrome (ACS). However, the threshold of admission glucose (AG) as a predictor of adverse events in ACS is unclear. Objective The aim of this study was to assess the threshold of admission glucose (AG) as a predictor of adverse events including Major Acute Cardiac Events (MACE) and mortality, during the first week of admitting patients presenting with ACS. Material and Methods The data of 551 patients with ACS were extracted and evaluated. Patients were stratified according to their blood glucose on admission into three groups: group 1: <7 mmol/L (n = 200, 36.3%) and group 2: >7 mmol/L and <15 mmol/L (n = 178, 32.3%) and group 3: ≥15 mmol/L (n = 173, 31.4%). Stress hyperglycemia was arbitrarily defined as AG levels > 7 mmol/L (group 2 and 3). Patients with ACS were sub-divided into two groups: patients with unstable angina (UA, n = 285) and those with ST segment elevation myocardial Infarction (STEMI, n = 266) and data were analyzed separately using multiple regression analysis. Results The mean age of patients was 59.7 ± 14.8 years and 63% were males. The overall mortality in the population was 8.5% (5.4% in STEMI and 3.1% in UA) patients. In STEMI patients, the odds ratio of stress hyperglycemia as predictor of mortality in group 3 compared with group 1 was 3.3 (CI 0.99-10.98, P < 0.05), while in group 2 compared with group 1 was 2.4 (CI: 0.75-8.07, P = 0.065) after adjustment for age and sex. Similarly, in UA patients, the odds ratio of stress hyperglycemia in group 3 compared with group 1 was 2.7 (CI 0.37-18.98, P < 0.05), while in group 2 compared with group 1 was 2.4 (CI: 0.4-15.2, P = 0.344) after adjustment for age and sex. The incidence of more than 2 MACE in both STEMI and UA patients was higher in group 3 compared with the other two groups. Regression analysis showed that history of DM, high level of LDL cholesterol, high level of HbA1c, and anterior infarction were significant predictors of adverse events while other risk factors such as BMI, history of hypertension and smoking were of no significance. Conclusion This study indicates that the stress hyperglycemia on admission is a powerful predictor of increased major adverse events and hospital mortality in patients with acute coronary syndrome.

scholarly journals ASSESSMENT OF AIR POLLUTION LEVEL OF NITROGEN DIOXIDE AND TRENDS OF IT CHANGES IN THE CITIES OF UKRAINE

2018 ◽  
pp. 87-95 ◽  
Author(s):  
Y. Yatsenko ◽  
O. Shevchenko ◽  
S. Snizhko
Keyword(s):  
Air Pollution ◽  
Nitrogen Dioxide ◽  
Pollution Level ◽  
Method Of Least Squares ◽  
Statistical Parameters ◽  
Group 3 ◽  
Environmental Measures ◽  
High Level

The purpose of the work is to study the current level and the main trends of atmospheric air pollution of the cities of Ukraine with nitrogen dioxide to identify the most polluted cities, their ranking to determine the list of cities for the priority implementation of environmental measures. For the purpose of the study, the information of the Central Geophysical Observatory on the average annual concentrations of nitrogen dioxide in the air of 51 cities of Ukraine for the period 1998-2015 was used. The study used the classical methods of applied mathematical statistics (estimation of statistical parameters of distribution of concentrations, construction of time trends on the method of least squares, graphical methods of visualization of levels of air pollution), which were implemented using the available programs "MS-Excell" and "Statistica-8.0". The classification of cities according to the level of MPC exceeds average annual concentrations of nitrogen dioxide. 3 groups of cities were allocated: 1 group (21 cities) permissible level of pollution (<1 MPC); 2 group (27 cities) – increased level of pollution (1-2 MPC); group 3 (3 cities) – high level of pollution (2-3 MPC). It has been established that in the air of 21 cities (41% of all cities where nitrogen dioxide is monitored in the atmosphere) of 51 cities, there is an acceptable level of air pollution. In the remaining cities (59%) – there is a stable excess of MPC. In 23 cities, even the minimum concentrations of NO2 exceed the permissible standards. The study of long-term dynamics of nitrogen dioxide in air has shown that the increase of concentrations of this pollutant for 1998-2015 is observed in 28 cities (55%) of 51. The most significant increase in concentrations in the air occurred in Kherson, Lutsk, Donetsk and Gorishni Plavni. In 13 cities reduction of concentrations was recorded, and in 10 cities the content of this pollutant in the air practically does not change.

scholarly journals Evolutionary recent dual obligatory symbiosis among adelgids indicates a transition between fungus and insect associated lifestyles

2020 ◽  
Author(s):  
Gitta Szabó ◽  
Frederik Schulz ◽  
Alejandro Manzano-Marín ◽  
Elena Rebecca Toenshoff ◽  
Matthias Horn
Keyword(s):  
Defense Mechanisms ◽  
Amino Acid Production ◽  
Evolutionary Transition ◽  
Evolutionary Time ◽  
Evolutionary Trajectories ◽  
Host Infection ◽  
Phylogenomic Analyses ◽  
Time Specific ◽  
High Level ◽  
Metagenomic Approach

ABSTRACTAdelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/tardus species complex containing betaproteobacterial (‘ Candidatus Vallotia tarda’) and gammaproteobacterial (‘Candidatus Profftia tarda’) symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other’s role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.

334 DNA SYNTHESIS DURING THE FIRST CELL CYCLE OF PORCINE OOCYTES FOLLOWING DIFFERENT ACTIVATION TREATMENTS

2007 ◽  
Vol 19 (1) ◽  
pp. 282
Author(s):  
S.-A. Ock ◽  
D. Kang ◽  
J. Han
Keyword(s):  
Cell Cycle ◽  
Dna Synthesis ◽  
Molecular Signaling ◽  
Oocyte Activation ◽  
Group 4 ◽  
Group 3 ◽  
Group 2 ◽  
Nuclear Ploidy ◽  
High Level ◽  
Group 1

Inhibitors of protein synthesis and phosphorylation have been widely used for oocyte activation and have been reported to induce abnormalities in nuclear ploidy due to aberrant DNA synthesis (DNAS). The present experiment was designed to compare the DNAS during the first cell cycle of porcine parthenotes following different activation treatments. Cumulus–oocyte complexes were cultured in TCM-199 supplemented with 0.5 �g mL-1 LH and FSH, 10 ng mL-1 EGF, and 0.1% PVA for 22 h, and additionally cultured in media without LH and FSH for 22 h. MII oocytes were then electrically pulsed twice in 0.28 M mannitol containing 0.05 mM CaCl2 and 0.1 mM MgSO4 at 1.8 kV cm-1 for 30 �s (group 1), followed by 7.5 �g mL-1 cytochalasin B (CCB, group 2), 10 �g mL-1 cycloheximide (CHX, group 3), or 1.9 mM 6-dimethylaminopurine (6-DMAP, group 4) for 3 h. Eggs were incubated with 100 �M 5-bromo-222-deoxyuridine (BrdU) for 1 h at 0, 2, 4, 6, 8, 10, and 12 h after activation to evaluate DNAS (Adenot et al. 1997 Development 124, 4615–4625) by determining the BrdU signal under a fluorescence microscope. Experiments were replicated 4 times; results were expressed as mean � SD and analyzed using one-way ANOVA by SPSS 10.0. The percentage of DNAS was calculated by dividing the number of BrdU-positive eggs by the total number of eggs used. DNAS in groups 1, 3, and 4 initiated at 2–3 h post-activation (hpa) but at 4–5 hpa in group 2. In group 1, DNAS was faint until 3 hpa, gradually increasing thereafter until 11 hpa (20.7 � 19.6, 29.4 � 17.0, 41.3 � 16.7, and 64.4 � 6.2, at 4–5, 6–7, 8–9, and 10–11 hpa, respectively). There was a significant (P &lt; 0.05) increase in DNAS at 10–11 h, but a significant (P &lt; 0.05) decrease (34.3 � 6.4) at 12–13 hpa. In groups 2 and 3, after 4–5 hpa, DNAS gradually increased until 7 h (6.2 � 1.4 and 29.8 � 16.6 at 4–5 hpa, and 21.1 � 13.7 and 40.0 � 18.7 at 6–7 hpa, respectively), but a DNAS peak was observed at 8–9 h (44.6 � 9.0) in group 2 and at 10–11 h (40.5 � 22.1) in group 3. Interestingly, group 4 parthenotes showed a different DNAS pattern compared with other groups, as it started at 2–3 hpa (24.8 � 11.7), reached a significantly (P &lt; 0.05) high level at 4–5 hpa (56.3 � 9.0), and gradually decreased at 6–7 hpa (42.7 � 10.3) until 12–13 hpa (29.5 � 14.9). In conclusion, CCB, CHX, and 6-DMAP used for oocyte activation exhibited different patterns of DNA synthesis during the first cell cycle of porcine parthenotes. Therefore, further experiments are required to evaluate the molecular signaling that regulates DNAS, embryonic developmental velocity, and ploidy of 2-cell parthenotes.

Individual and class room predictors of same-cultural friendship preferences in multicultural schools

2014 ◽  
Vol 39 (3) ◽  
pp. 255-265 ◽  
Author(s):  
Elisabeth Stefanek ◽  
Dagmar Strohmeier ◽  
Rens van de Schoot
Keyword(s):  
Multicultural Education ◽  
Cultural Diversity ◽  
First Generation ◽  
Individual Level ◽  
Generation Immigrant ◽  
Class Level ◽  
Class Room ◽  
The Individual ◽  
High Level ◽  
First And Second Generation

This study was an investigation of individual and contextual predictors for same-cultural friendship preferences among non-immigrant ( N = 125), Turkish ( N = 196) and former Yugoslavian ( N = 256) immigrant youths ( M age = 14.39 years) in 36 multicultural classes. At the individual level age, gender, cultural group, number of friends, and acculturation variables, such as immigrant status, cultural pride and racist victimization were investigated. At the class level, predictors drawn from contact theory such as cultural diversity and multicultural education were analyzed. Multilevel analyses have revealed that being a former Yugoslavian first and second generation immigrant, being a Turkish first generation immigrant, having fewer friends, a high level of cultural pride and a high level of cultural diversity in classes are related to more same-cultural friendship preferences. The present findings highlight the importance of acculturation-related and contextual factors for same-cultural friendship preferences.

scholarly journals Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

2016 ◽  
Author(s):  
Mei Fang Lin ◽  
Wen Hwa Chou ◽  
Marcelo V Kitahara ◽  
Chao Lun Allen Chen ◽  
David John Miller ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Single Copy ◽  
Scleractinian Corals ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Nuclear Markers ◽  
Protein Coding ◽  
Mitochondrial Sequences ◽  
Phylogenomic Analyses ◽  
Close Relatives

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

scholarly journals Protection of Renal Function ByHyperbaric OxygenDuring Plasmodium berghei ANKA Infection

2020 ◽  
Vol 13 (1) ◽  
pp. 69-74
Author(s):  
Prawesty Diah Utami ◽  
Herin Setianingsih
Keyword(s):  
Renal Function ◽  
Control Group ◽  
Group 4 ◽  
Wistar Strain ◽  
Significant Difference ◽  
Post Test ◽  
Group 3 ◽  
Group 5 ◽  
Major Factors ◽  
High Level

Background:Malaria cases have consistently increased and the number of deaths remains largely unchanged.Malaria associated renal injury has a high level of morbidity and mortality. High level of blood urea nitrogen / BUN and plasma creatinine is one of the major factors associated with mortality in humans infected with malaria, indicating that impairment of renal function. HBO is widely used as an adjunctive therapy for many diseases, it is known that HBO hasan action as antiplasmodium, antiinflammation and antioxidant effects. Objective: The aim of this study was to determine the effect of HBO on BUN and creatinine levels in rats infected with P. berghei ANKA. Methods:This research was conducted experimentally post-test only control group on six groups of rats. The samples used were 24 male Rattus norvegicus wistar strain that have been infected by Plasmodium bergheiANKA and divided into 6 groups. Group 1 was given combination artesunate and 1, 5 ATA HBO, grup 2 was given combination artesunate and 3, 0 ATA HBO, group 3 was given 1, 5 ATA HBO, group 4 was given 3, 0 ATA HBO, group 5 was given artesunate and group 6 was given aquadest. HBO therapy is carried out for 10 days and the observation of the levels of BUN and creatinine in mice after treatment on tenth day. Results:Descriptive analysis and statistical analysis (Kruskal wallis snd Mann whitney U posthoc) showed a significant difference (p < α = 0.05) on mean levels of BUN and creatinine group receiving combination of artesunate and HBO 3,0 ATA compared to other groups.Hyperbaric oxygen has the effect of reducing the levels of BUN and creatinine in rats infected by P.berghei ANKA.

scholarly journals Optimized photochemistry and enzymology enable efficient analysis of RNA structures and interactions in cells and virus infections

2020 ◽  
Author(s):  
Minjie Zhang ◽  
Kongpan Li ◽  
Willem A. Velema ◽  
Jianhui Bai ◽  
Chengqing Yu ◽  
...  
Keyword(s):  
Binding Sites ◽  
Genome Structure ◽  
Direct Determination ◽  
Small Subunit ◽  
Virus Infections ◽  
Rna Structures ◽  
Entry Site ◽  
Viral Pathogen ◽  
High Level ◽  
In Cells

SUMMARYDirect determination of RNA structures and interactions in living cells is critical for understanding their functions. Current crosslinking and proximity-ligation approaches are fundamentally limited due to inefficient RNA crosslinking, purification and high-level photochemical damages. Here we present PARIS2 (psoralen analysis of RNA interactions and structures, second generation), a re-invented method for capturing RNA duplexes in cells with three orders of magnitude improved efficiency. PARIS2 captures ribosome small subunit (SSU) binding sites on mRNAs, reporting translation status on a transcriptome wide scale, and captures spliceosomal snRNP binding sites on various RNA targets. We determine the RNA genome structure of enterovirus D68, a re-emerging viral pathogen associated with severe neurological symptoms, and discover alternative conformations in the internal ribosome entry site (IRES) that controls translation initiation. Together, these results reveal new aspects of RNA photochemistry and enzymology, and enable highly efficient interrogation of the RNA structurome and interactome in cells.

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