scholarly journals Metabolic Potential for Reductive Acetogenesis and a Novel Energy-Converting [NiFe] Hydrogenase in Bathyarchaeia From Termite Guts – A Genome-Centric Analysis

2021 ◽  
Vol 11 ◽  
Author(s):  
Hui Qi Loh ◽  
Vincent Hervé ◽  
Andreas Brune
Keyword(s):  
Large Scale ◽  
The Other ◽  
Binding Motif ◽  
Organic Substrates ◽  
Metabolic Potential ◽  
Cofactor Binding ◽  
A Genome ◽  
Key Enzyme ◽  
Metagenomic Study ◽  
Acetate Formation

Symbiotic digestion of lignocellulose in the hindgut of higher termites is mediated by a diverse assemblage of bacteria and archaea. During a large-scale metagenomic study, we reconstructed 15 metagenome-assembled genomes of Bathyarchaeia that represent two distinct lineages in subgroup 6 (formerly MCG-6) unique to termite guts. One lineage (TB2; Candidatus Termitimicrobium) encodes all enzymes required for reductive acetogenesis from CO2 via an archaeal variant of the Wood–Ljungdahl pathway, involving tetrahydromethanopterin as C1 carrier and an (ADP-forming) acetyl-CoA synthase. This includes a novel 11-subunit hydrogenase, which possesses the genomic architecture of the respiratory Fpo-complex of other archaea but whose catalytic subunit is phylogenetically related to and shares the conserved [NiFe] cofactor-binding motif with [NiFe] hydrogenases of subgroup 4 g. We propose that this novel Fpo-like hydrogenase provides part of the reduced ferredoxin required for CO2 reduction and is driven by the electrochemical membrane potential generated from the ATP conserved by substrate-level phosphorylation; the other part may require the oxidation of organic electron donors, which would make members of TB2 mixotrophic acetogens. Members of the other lineage (TB1; Candidatus Termiticorpusculum) are definitely organotrophic because they consistently lack hydrogenases and/or methylene-tetrahydromethanopterin reductase, a key enzyme of the archaeal Wood–Ljungdahl pathway. Both lineages have the genomic capacity to reduce ferredoxin by oxidizing amino acids and might conduct methylotrophic acetogenesis using unidentified methylated compound(s). Our results indicate that Bathyarchaeia of subgroup 6 contribute to acetate formation in the guts of higher termites and substantiate the genomic evidence for reductive acetogenesis from organic substrates, possibly including methylated compounds, in other uncultured representatives of the phylum.

scholarly journals Metabolic potential for reductive acetogenesis and a novel energy-converting [NiFe] hydrogenase in Bathyarchaeia from termite guts – a genome-centric analysis

2020 ◽  
Author(s):  
Hui Qi Loh ◽  
Vincent Hervé ◽  
Andreas Brune
Keyword(s):  
Large Scale ◽  
Binding Motif ◽  
Organic Substrates ◽  
Metabolic Potential ◽  
Cofactor Binding ◽  
A Genome ◽  
Key Enzyme ◽  
Metagenomic Study ◽  
Acetate Formation ◽  
Energy Converting

AbstractSymbiotic digestion of lignocellulose in the hindgut of higher termites is mediated by a diverse assemblage of bacteria and archaea. During a large-scale metagenomic study, we reconstructed 15 metagenome-assembled genomes (MAGs) of Bathyarchaeia that represent two distinct lineages in subgroup 6 (formerly MCG-6) unique to termite guts. One lineage (TB2; Candidatus Termitimicrobium) encodes all enzymes required for reductive acetogenesis from H2 and CO2 via an archaeal variant of the Wood–Ljungdahl pathway. This includes a novel 11-subunit hydrogenase, which possesses the genomic architecture of the respiratory Fpo-complex of other archaea but whose catalytic subunit is phylogenetically related to and shares the conserved [NiFe] cofactor-binding motif with [NiFe] hydrogenases of subgroup 4g. We propose that this novel Fpo-like hydrogenase provides the reduced ferredoxin required for CO2 reduction and is driven by the electrochemical membrane potential generated from the ATP conserved by substrate-level phosphorylation. Members of the other lineage (TB1; Candidatus Termiticorpusculum) are not capable of lithotrophic acetogenesis because they consistently lack hydrogenases and/or methylene-tetrahydromethanopterin reductase, a key enzyme of the pathway. Both lineages have the genomic capacity to reduce ferredoxin by oxidizing amino acids and might conduct methylotrophic acetogenesis using unidentified methylated compound(s). Our results indicate that Bathyarchaeia of subgroup 6 contribute to acetate formation in the guts of higher termites and substantiate the genomic evidence for reductive acetogenesis from organic substrates, including methylated compounds, in other uncultured representatives of the phylum.

scholarly journals Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Erika Gaspari ◽  
Antoni Malachowski ◽  
Luis Garcia-Morales ◽  
Raul Burgos ◽  
Luis Serrano ◽  
...  
Keyword(s):  
Mycoplasma Pneumoniae ◽  
Large Scale ◽  
Atypical Pneumonia ◽  
Metabolic Potential ◽  
Membrane Formation ◽  
Serum Free ◽  
A Genome ◽  
Essential Components ◽  
Free Media

Abstract Mycoplasma pneumoniae is a slow-growing, human pathogen that causes atypical pneumonia. Because it lacks a cell wall, many antibiotics are ineffective. Due to its reduced genome and dearth of many biosynthetic pathways, this fastidious bacterium depends on rich, undefined medium for growth, which makes large-scale cultivation challenging and expensive. To understand factors limiting growth, we developed a genome-scale, constraint-based model of M. pneumoniae called iEG158_mpn to describe the metabolic potential of this bacterium. We have put special emphasis on cell membrane formation to identify key lipid components to maximize bacterial growth. We have used this knowledge to predict essential components validated with in vitro serum-free media able to sustain growth. Our findings also show that glycolysis and lipid metabolism are much less efficient under hypoxia; these findings suggest that factors other than metabolism and membrane formation alone affect the growth of M. pneumoniae. Altogether, our modelling approach allowed us to optimize medium composition, enabled growth in defined media and streamlined operational requirements, thereby providing the basis for stable, reproducible and less expensive production.

scholarly journals Identification of novel tetracycline resistance gene tet(X14) and its co-occurrence with tet(X2) in a tigecycline-resistant and colistin-resistant Empedobacter stercoris

2020 ◽  
Author(s):  
Yingying Cheng ◽  
Yong Chen ◽  
Yang Liu ◽  
Yuqi Guo ◽  
Yanzi Zhou ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Large Scale ◽  
Resistance Mechanism ◽  
Gc Content ◽  
Tetracycline Resistance ◽  
Fold Increase ◽  
The Other ◽  
A Genome ◽  
The Family ◽  
Severe Infections

AbstractTigecycline is one of the last-resort antibiotics to treat severe infections. Recently, tigecycline resistance has sporadically emerged with an increasing trend, and Tet(X) family represents a new resistance mechanism of tigecycline. In this study, a novel chromosome-encoded tigecycline resistance gene, tet(X14), was identified in a tigecycline-resistant and colistin-resistant Empedobacter stercoris strain ES183 recovered from a pig fecal sample in China. Tet(X14) shows 67.14-96.39% sequence identity to the other variants [Tet(X) to Tet(X13)]. Overexpression of Tet(X14) in Escherichia coli confers 16-fold increase in tigecycline MIC (from 0.125 to 2 mg/L), which is lower than that of Tet(X3), Tet(X4) and Tet(X6). Structural modelling predicted that Tet(X14) shared a high homology with the other 12 variants with RMSD value from 0.003 to 0.055, and Tet(X14) can interact with tetracyclines by a similar pattern as the other Tet(X)s. tet(X14) and two copies of tet(X2) were identified on a genome island with abnormal GC content carried by the chromosome of ES183, and no mobile genetic elements were found surrounding, suggesting that tet(X14) might be heterologously obtained by ES183 via recombination. Blasting in Genbank revealed that Tet(X14) was exclusively detected on the chromosome of Riemerella anatipestifer, mainly encoded on antimicrobial resistance islands. E. stercoris and R. anatipestifer belong to the family Flavobacteriaceae, suggesting that the members of Flavobacteriaceae maybe the major reservoir of tet(X14). Our study reports a novel chromosome-encoded tigecycline resistance gene tet(X14). The expanded members of Tet(X) family warrants the potential large-scale dissemination and the necessity of continuous surveillance for tet(X)-mediated tigecycline resistance.

scholarly journals Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media

2019 ◽  
Author(s):  
Erika Gaspari ◽  
Antoni Malachowski ◽  
Luis Garcia-Morales ◽  
Raul Burgos ◽  
Luis Serrano ◽  
...  
Keyword(s):  
Mycoplasma Pneumoniae ◽  
Large Scale ◽  
Atypical Pneumonia ◽  
Vaccine Production ◽  
Metabolic Potential ◽  
Membrane Formation ◽  
Serum Free ◽  
A Genome ◽  
Free Media

AbstractMycoplasma pneumoniae is a slow-growing, human pathogen that causes atypical pneumonia. Because it lacks a cell wall, many antibiotics are ineffective, and vaccination is required. Due to its reduced genome and dearth of many biosynthetic pathways, this fastidious bacterium depends on rich, undefined medium for growth, which makes large-scale cultivation for vaccine production challenging and expensive.To understand factors limiting growth, we developed a genome-scale, constraint-based model of M. pneumoniae called iEG158_mpn to describe the metabolic potential of this bacterium. We have put special emphasis on cell membrane formation to identify key lipid components to maximize bacterial growth. We have used this knowledge to predict and validate in vitro two serum-free media able to sustain growth.Our findings also show that glycolysis and lipid metabolism are much less efficient under hypoxia; these findings suggest that factors other than metabolism and membrane formation alone affect the growth of M. pneumoniae.Altogether, our modelling approach enabled us to optimize medium composition, capacitated growth in defined media and streamlined operational requirements, thereby providing the basis for stable, reproducible and less expensive vaccine production.

Birlikte Yaşama Kültürü Çerçevesinde Avrupa Birliği ve Türkiye Politikaları: Suriyelilere Yönelik Tutumun Sultanbeyli Örneği Üzerinden Değerlendirilmesi

2017 ◽  
Vol 4 (1) ◽  
pp. 41-61
Author(s):  
Pelin Sönmez ◽  
Abulfaz Süleymanov
Keyword(s):  
Civil Wars ◽  
Large Scale ◽  
Social Acceptance ◽  
Point Of View ◽  
The Other ◽  
Syrian Refugees ◽  
The European Union ◽  
International Protection ◽  
Legal Structure ◽  
Turkish People

Türkiye, Cumhuriyet tarihinin en yoğun zorunlu göç dalgasını 2011 yılından bu yana süren Suriye Savaşı ile yaşamaktadır. Suriye vatandaşlarının geçici koruma statüsü altında Türkiye toplumuna her açıdan entegrasyonları günümüzün ve geleceğin politika öncelikleri arasında düşünülmelidir. Öte yandan ülkeye kabul edilen sığınmacıların kendi kültürel kimliğini kaybetmeden içinde yaşadığı ev sahibi topluma uyumu, ortak yaşam kültürünün gelişmesi açısından önem arz etmektedir. Bu makalede, "misafir" olarak kabul edilen Suriyeli vatandaşların Türk toplumunca kabul edilmeleri ve dışlanma risklerinin azaltılmasına yönelik devlet politikaları ortaya konularak, üye ve aday ülkelere göçmenlerin dışlanmasını önlemek için Avrupa Birliği (AB) tarafından sunulan hukuki yapı ve kamu hizmeti inisiyatifleri incelenmekte, birlikte yaşam kültürü çerçevesinde Suriyeli vatandaşlara yönelik  toplumsal kabul düzeyleri ele alınmaktadır. Çalışma iki ana bölümden oluşmaktadır: göçmen ve sığınmacılara karşı toplumsal dışlanmayı engellemek için benimsenen yasa ve uygulamaların etkisi ve İstanbul-Sultanbeyli bölgesinde Suriyeli sığınmacılarla ilgili toplumsal algı çalışmasının sonuçları. Bölgede ikamet eden Suriyelilere yönelik toplumsal kabul düzeyinin yüksek olduğu görülürken, halkın Suriyelileri kendilerine  kültürel ve dini olarak yakın hissetmesi toplumsal kabul düzeyini olumlu etkilemektedir. ABSTRACT IN ENGLISHAn evaluation of the European Union and Turkish policies regarding the culture of living togetherThis article aims to determine the level of social acceptance towards Syrians within the context of cohabitation culture by evaluating EU’s legal structure and public service initiatives in order to prevent Syrian refugees from being excluded in member and candidate countries and by revealing government policies on acceptance of Syrians as “guest” by Turkish society and minimizing the exclusion risks of them. This article consists of two main parts, one of which is based on the effects of law and practices preventing refugees and asylum seekers from social exclusion, and the other is on the results of social perception on Syrians in Sultanbeyli district of Istanbul. At the end of 5-years taking in Syrian War, it is obvious that most of more than 3 million Syrian with unregistered ones in Turkey are “here to stay”. From this point of view, the primary scope of policies should be specified in order to remove side effects of refugee phenomenon seen as weighty matter by bottoming out the exclusion towards those people. To avoid possible large-scale conflicts or civil wars in the future, the struggle with exclusion phenomenon plays a crucial role regarding Turkey’s sociological situation and developing policies. In the meaning of forming a model for Turkey, a subtitle in this article is about public services for European-wide legal acquis and practices carried out since 1970s in order to prevent any exclusion from the society. On the other hand, other subtitles are about legal infrastructure and practices like Common European Asylum and Immigration Policies presented in 2005, and Law on Foreigners and International Protection introduced in 2013. In the last part of the article, the results of a field survey carried out in a district of Istanbul were used to analyze the exclusion towards refugees in Turkey. A face-to-face survey was randomly conducted with 200 settled refugees in Sultanbeyli district of Istanbul, and their perceptions towards Syrian people under temporary protection were evaluated. According to the results, the level of acceptance for Syrians living in this district seems relatively high. The fact that Turkish people living in the same district feel close to Syrian refugees culturally and religiously affect their perception in a positive way: however, it is strikingly seen and understood that local residents cop an attitude on the refugees’ becoming Turkish citizens.

HOME VISITS DURING THE FIRST MONTH OF DELIVERY FOR RECENTLY DELIVERED WOMEN IN UTTAR PRADESH, INDIA

2020 ◽  
Vol 6 (5) ◽  
pp. 1183-1189
Author(s):  
Dr. Tridibesh Tripathy ◽  
Dr. Umakant Prusty ◽  
Dr. Chintamani Nayak ◽  
Dr. Rakesh Dwivedi ◽  
Dr. Mohini Gautam
Keyword(s):  
Large Scale ◽  
National Level ◽  
Uttar Pradesh ◽  
Life Time ◽  
Structured Interview ◽  
The Other ◽  
Registration System ◽  
Action Group ◽  
Current Article ◽  
The Impact

The current article of Uttar Pradesh (UP) is about the ASHAs who are the daughters-in-law of a family that resides in the same community that they serve as the grassroots health worker since 2005 when the NRHM was introduced in the Empowered Action Group (EAG) states. UP is one such Empowered Action Group (EAG) state. The current study explores the actual responses of Recently Delivered Women (RDW) on their visits during the first month of their recent delivery. From the catchment area of each of the 250 ASHAs, two RDWs were selected who had a child in the age group of 3 to 6 months during the survey. The response profiles of the RDWs on the post- delivery first month visits are dwelled upon to evolve a picture representing the entire state of UP. The relevance of the study assumes significance as detailed data on the modalities of postnatal visits are available but not exclusively for the first month period of their recent delivery. The details of the post-delivery first month period related visits are not available even in large scale surveys like National Family Health Survey 4 done in 2015-16. The current study gives an insight in to these visits with a five-point approach i.e. type of personnel doing the visit, frequency of the visits, visits done in a particular week from among those four weeks separately for the three visits separately. The current study is basically regarding the summary of this Penta approach for the post- delivery one-month period.     The first month period after each delivery deals with 70% of the time of the postnatal period & the entire neonatal period. Therefore, it does impact the Maternal Mortality Rate & Ratio (MMR) & the Neonatal Mortality Rates (NMR) in India and especially in UP through the unsafe Maternal & Neonatal practices in the first month period after delivery. The current MM Rate of UP is 20.1 & MM Ratio is 216 whereas the MM ratio is 122 in India (SRS, 2019). The Sample Registration System (SRS) report also mentions that the Life Time Risk (LTR) of a woman in pregnancy is 0.7% which is the highest in the nation (SRS, 2019). This means it is very risky to give birth in UP in comparison to other regions in the country (SRS, 2019). This risk is at the peak in the first month period after each delivery. Similarly, the current NMR in India is 23 per 1000 livebirths (UNIGME,2018). As NMR data is not available separately for states, the national level data also hold good for the states and that’s how for the state of UP as well. These mortalities are the impact indicators and such indicators can be reduced through long drawn processes that includes effective and timely visits to RDWs especially in the first month period after delivery. This would help in making their post-natal & neonatal stage safe. This is the area of post-delivery first month visit profile detailing that the current article helps in popping out in relation to the recent delivery of the respondents.   A total of four districts of Uttar Pradesh were selected purposively for the study and the data collection was conducted in the villages of the respective districts with the help of a pre-tested structured interview schedule with both close-ended and open-ended questions.  The current article deals with five close ended questions with options, two for the type of personnel & frequency while the other three are for each of the three visits in the first month after the recent delivery of respondents. In addition, in-depth interviews were also conducted amongst the RDWs and a total 500 respondents had participated in the study.   Among the districts related to this article, the results showed that ASHA was the type of personnel who did the majority of visits in all the four districts. On the other hand, 25-40% of RDWs in all the 4 districts replied that they did not receive any visit within the first month of their recent delivery. Regarding frequency, most of the RDWs in all the 4 districts received 1-2 times visits by ASHAs.   Regarding the first visit, it was found that the ASHAs of Barabanki and Gonda visited less percentage of RDWs in the first week after delivery. Similarly, the second visit revealed that about 1.2% RDWs in Banda district could not recall about the visit. Further on the second visit, the RDWs responded that most of them in 3 districts except Gonda district did receive the second postnatal visit in 7-15 days after their recent delivery. Less than half of RDWs in Barabanki district & just more than half of RDWs in Gonda district received the third visit in 15-21 days period after delivery. For the same period, the majority of RDWs in the rest two districts responded that they had been entertained through a home visit.

Should all Hypertensive Patients be Screened for Primary Aldosteronism?

2019 ◽  
Vol 15 (1) ◽  
pp. 54-56
Author(s):  
Stelina Alkagiet ◽  
Konstantinos Tziomalos
Keyword(s):  
Resistant Hypertension ◽  
Primary Aldosteronism ◽  
Large Scale ◽  
Controlled Trial ◽  
The Other ◽  
Limited Data ◽  
Hypertensive Patients ◽  
Randomized Controlled ◽  
Increased Risk ◽  
Prospective Randomized Controlled Trial

Primary aldosteronism (PA) is not only a leading cause of secondary and resistant hypertension, but is also quite frequent in unselected hypertensive patients. Moreover, PA is associated with increased cardiovascular risk, which is disproportionate to BP levels. In addition, timely diagnosis of PA and prompt initiation of treatment attenuate this increased risk. On the other hand, there are limited data regarding the usefulness of screening for PA in all asymptomatic or normokalemic hypertensive patients. More importantly, until now, no well-organized, large-scale, prospective, randomized controlled trial has proved the effectiveness of screening for PA for improving clinical outcome. Accordingly, until more relevant data are available, screening for PA should be considered in hypertensive patients with spontaneous or diuretic-induced hypokalemia as well as in those with resistant hypertension. However, screening for PA in all hypertensive patients cannot be currently recommended.

Talking about MOTION in Middle English

2017 ◽  
Author(s):  
Judith Huber
Keyword(s):  
Middle English ◽  
Old English ◽  
Language Contact ◽  
Large Scale ◽  
The Other ◽  
Motion Verbs ◽  
Text Type ◽  
Anglo Norman ◽  
Contact Situation ◽  
Analysis Of Motion

Chapter 6 begins with an overview of the language contact situation with (Anglo-) French and Latin, resulting in large-scale borrowing in the Middle English period. The analysis of 465 Middle English verbs used to express intransitive motion shows that there are far more French/Latin loans in the path verbs than in the other motion verbs. The range of (new) manner of motion verbs testifies to the manner salience of Middle English: caused motion verbs are also found in intransitive motion meanings, as are French loans which do not have motion uses in continental French. Their motion uses in Anglo-Norman are discussed in terms of contact influence of Middle English. The analysis of motion expression in different texts yields a picture similar to the situation in Old English, with path typically expressed in satellites, and neutral as well as manner of motion verbs being most frequent, depending on text type.

scholarly journals Massive and Microscopic Sensemaking During COVID-19 Times

2020 ◽  
pp. 107780042096247 ◽  
Author(s):  
Annette N. Markham ◽  
Anne Harris ◽  
Mary Elizabeth Luka
Keyword(s):  
Critical Pedagogy ◽  
Lived Experience ◽  
Large Scale ◽  
Ethic Of Care ◽  
Feminist Perspective ◽  
The Other ◽  
Self And Other ◽  
Planetary Scale ◽  
Making Sense ◽  
Ongoing Experiment

How does this pandemic moment help us to think about the relationships between self and other, or between humans and the planet? How are people making sense of COVID-19 in their everyday lives, both as a local and intimate occurrence with microscopic properties, and a planetary-scale event with potentially massive outcomes? In this paper we describe our approach to a large-scale, still-ongoing experiment involving more than 150 people from 26 countries. Grounded in autoethnography practice and critical pedagogy, we offered 21 days of self guided prompts to for us and the other participants to explore their own lived experience. Our project illustrates the power of applying a feminist perspective and an ethic of care to engage in open ended collaboration during times of globally-felt trauma.

scholarly journals Arabidopsis Genes Essential for Seedling Viability: Isolation of Insertional Mutants and Molecular Cloning

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1765-1778
Author(s):  
Gregory J Budziszewski ◽  
Sharon Potter Lewis ◽  
Lyn Wegrich Glover ◽  
Jennifer Reineke ◽  
Gary Jones ◽  
...  
Keyword(s):  
Large Scale ◽  
Protein Translocation ◽  
Gene Families ◽  
Mutant Phenotype ◽  
Lethal Mutant ◽  
A Genome ◽  
Genes Encoding ◽  
High Level ◽  
Mutant Lines ◽  
Genome Scale

Abstract We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening ~38,000 insertional mutant lines, we identified >500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for >200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. Although a high level of functional redundancy in Arabidopsis might be expected because 65% of genes are members of gene families, we found that 41% of the essential genes found in this study are members of Arabidopsis gene families. In addition, we isolated several interesting classes of mutants and genes. We found three mutants in the recently discovered nonmevalonate isoprenoid biosynthetic pathway and mutants disrupting genes similar to Tic40 and tatC, which are likely to be involved in chloroplast protein translocation. Finally, we directly compared T-DNA and Ac/Ds transposon mutagenesis methods in Arabidopsis on a genome scale. In each population, we found only about one-third of the insertion mutations cosegregated with a mutant phenotype.

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