bluuebunny/crossref_metadata_2025 huggingface dataset:
An adaptive randomized controlled trial of non-invasive respiratory strategies in acute respiratory failure patients with COVID-19
Authors: Perkins Gavin D , Ji Chen , Connolly Bronwen A , Couper Keith , Lall Ranjit , Baillie J Kenneth , Bradley Judy M , Dark Paul , Dave Chirag , De Soyza Anthony , Dennis Anna V , Devrell Anne , Fairbairn Sara , Ghani Hakim , Gorman Ellen A , Green Christopher A , Hart Nicholas , Hee Siew Wan , Kimbley Zoe , Madathil Shyam , McGowan Nicola , Messer Benjamin , Naisbitt Jay , Norman Chloe , Parekh Dhruv , Parkin Emma M , Patel Jaimin , Regan Scott E , Ross Clare , Rostron Anthony J , Saim Mohammad , Simonds Anita K , Skilton Emma , Stallard Nigel , Steiner Michael , Vancheeswaran Rama , Yeung Joyce , McAuley Daniel F
Published: August 2021

Background

Both continuous positive airway pressure (CPAP) and high-flow nasal oxygenation (HFNO) have been recommended for acute respiratory failure in COVID-19. However, uncertainty exists regarding effectiveness and safety.

Methods

In the Recovery-Respiratory Support multi-center, three-arm, open-label, adaptive, randomized controlled trial, adult hospitalized patients with acute respiratory failure due to COVID-19, deemed suitable for treatment escalation, were randomly assigned to receive CPAP, HFNO, or conventional oxygen therapy. Comparisons were made between each intervention and conventional oxygen therapy. The primary outcome was a composite of tracheal intubation or mortality within 30-days.

Results

Over 13-months, 1272 participants were randomized and included in the analysis (380 (29.9%) CPAP; 417 (32.8%) HFNO; 475 (37.3%) conventional oxygen therapy). The need for tracheal intubation or mortality within 30-days was lower in the CPAP group (CPAP 137 of 377 participants (36.3%) vs conventional oxygen therapy 158 of 356 participants (44.4%); unadjusted odds ratio 0.72; 95% CI 0.53 to 0.96, P=0.03). There was no difference between HFNO and conventional oxygen therapy (HFNO 184 of 414 participants (44.4%) vs conventional oxygen therapy 166 of 368 participants (45.1%); unadjusted odds ratio 0.97; 95% CI 0.73 to 1.29, P=0.85).

Conclusions

CPAP, compared with conventional oxygen therapy, reduced the composite outcome of intubation or death within 30 days of randomisation in hospitalized adults with acute respiratory failure due to COVID-19. There was no effect observed, compared with conventional oxygen therapy, with the use of HFNO.

(Funded by the UK National Institute for Health Research;ISRCTN 16912075).
Evolutionary origin of sex differentiation system in insects
Authors: Chikami Yasuhiko , Okuno Miki , Toyoda Atsushi , Itoh Takehiko , Niimi Teruyuki
Published: August 2021

The evolution of the functionality of genes and genetic systems is a major source of animal diversity. Its best example is insect sex differentiation systems: promoting male and female differentiation (dual-functionality) or only male differentiation (single-functionality). However, the evolutionary origin of such functional diversity is largely unknown. Here, we investigate the ancestral functions ofdoublesex, a key factor of insect sex differentiation system, using the apterygote insect,Thermobia domestica, and reveal that itsdoublesexis essential for only males at the phenotypic level, but contributes to promoting female-specificvitellogeninexpression in females. This functional discordance between the phenotypic and transcription-regulatory levels inT. domesticashows a new type of functionality of animal sex differentiation systems. Then, we examine how the sex differentiation system transited from the single-functionality to the dual-functionality in phenotypes and uncover that a conserved female-specific motif ofdoublesexis detected in taxa with the dual-functionaldoublesex. It is estimated that the role of the sex differentiation system for female phenotypes may have evolved through accumulating mutations in the protein motif structures that led to the enhancement of its transcription-regulatory function.
Effect of electrical hybrid-frequency waterbath stunning on the spontaneous electroencephalogram (EEG) and electrocardiogram (ECG) of broilers
Authors: La Vega L.T , Sato D , Piza L. V , Costa E. J. X
Published: August 2021

Concerns about animal welfare and meat quality have encouraged research on new methods for the stunning of broilers during animal slaughter. In this study, the electroencephalogram (EEG) and electrocardiogram (ECG) of broilers were acquired during stunning using an electrical hybrid instead of a single frequency. Considering a square-wave with a current of 220 mA and a frequency of 1100 Hz (duty-cycle 50%), the hybrid-frequency waveform is obtained generating pulses at 6600 Hertz in the pulse-width phase. Sixty broilers aged 42 days were randomly sampled; thirty were used for EEG measurement and thirty for ECG measurement. For EEG measurements, the birds’ scalps were anaesthetized, and EEG electrode needles were inserted on the subcutaneous part of the occipital scalp. For ECG, the non-invasive surface electrode was used. The electrodes were connected to a digital EEG/ECG system. The results showed that the hybrid-frequency waveform system generated epileptic forms in the birds’ EEGs. Therefore, a hybrid-frequency system may present better carcass quality results, while preserving the birds’ welfare, when compared with a single frequency system use.
Estimating the number of symptomatic SARS-CoV-2 infections among vaccinated individuals in the United States—January–April, 2021
Authors: Kugeler Kiersten J. , Williamson John , Curns Aaron T. , Healy Jessica M. , Nolen Leisha D. , Clark Thomas A. , Martin Stacey W. , Fischer Marc
Published: August 2021

As of March 2021, three COVID-19 vaccines have been authorized by the U.S. Food and Drug Administration (FDA) for use in the United States. Each has substantial efficacy in preventing COVID-19. However, as efficacy from trials was <100% for all three vaccines, disease in vaccinated people is expected to occur. We created a spreadsheet-based tool to estimate the number of symptomatic vaccine breakthrough infections based on published vaccine efficacy (VE) data, percent of the population that has been fully vaccinated, and average number of COVID-19 cases reported per day. We estimate that approximately 51,000 symptomatic vaccine breakthrough infections (95% CI: ∼48,000–55,000 cases) occurred in the United States during January–April 2021 among >77 million fully vaccinated people, reflecting <0.5% of COVID-19 cases that occurred during that time. With ongoing SARS-CoV-2 transmission and increasing numbers of people vaccinated in the United States, vaccine breakthrough infections will continue to accumulate before population immunity is sufficient to interrupt transmission. Understanding expectations regarding number of vaccine breakthrough infections enables accurate public health messaging to help ensure that the occurrence of such cases does not negatively affect vaccine perceptions, confidence, and uptake.
High-risk alcohol consumption may increase the risk of SARS-CoV-2 seroconversion: a prospective seroepidemiologic cohort study among American college students
Authors: Kianersi Sina , Ludema Christina , Macy Jonathan T. , Chen Chen , Rosenberg Molly
Published: August 2021

Aims

To estimate the associations between high-risk alcohol consumption and (1) SARS-CoV-2 seroconversion, (2) self-reported new SARS-CoV-2 infection, and (3) symptomatic COVID-19.

Design

Prospective cohort

Setting

Indiana University Bloomington (IUB), a public university of 34,660 students in southern Indiana.

Participants

At the beginning of the fall 2020 semester, we randomly sampled N=1,267 IU undergraduate students, aged 18 years or older and residing in Monroe County, IN.

Measurements

Primary exposure was high-risk alcohol consumption measured with the AUDIT questionnaire. We used an AUDIT score of 8 or more as the cut-off score when detecting high-risk alcohol consumption. Primary outcome was SARS-CoV-2 seroconversion, assessed with two SARS-CoV-2 antibody tests, at baseline and endline. Secondary outcomes were a) self-reported new SARS-CoV-2 infection at the study endline, and b) self-reported symptomatic COVID-19 at baseline.

Findings

Prevalence of high-risk alcohol consumption was 34%. We found that students with high-risk alcohol consumption status had 2.34 [95% CI: (1.29, 4.24)] times the risk of SARS-CoV-2 seroconversion and 1.89 [95% CI: (1.08, 3.32)] times the risk of self-reporting a positive SARS-CoV-2 infection, compared to students with no such risk. Moreover, students with high-risk alcohol consumption were 18% more likely to develop symptomatic COVID-19, though this association was not statistically significant. Similar results were found after adjusting for sex at birth, race, and year in school. Findings from sensitivity analyses corroborated these results and suggested potential for a dose-response relationship.

Conclusions

In this sample of American college students, high-risk alcohol consumption was associated with higher risk for SARS-CoV-2 seroconversion/infection. These findings could have implications for colleges’ reopening planning in fall 2021.
The symptomatology of fever: a step towards qualitative definition of fever
Authors: Kapoor Mayank , Kumar Nitin , Panda Prasan Kumar
Published: August 2021

Background

The old definitions of fever are based on cross-sectional surveys of the population without analyzing the associated symptomatology.

Objectives

To analyze associated symptoms with fever in a longitudinal follow-up study.

Methods

In a longitudinal study over one year, 196 participants recorded three temperature readings daily, one after waking up, one between 12-3 PM, one before sleeping, and filled the symptomatology questionnaire in a thermometry diary.

Results

Per protocol analysis was done for febrile participants (n=144). Fatigue (50.3%), warmth (47.3%), headache/head heaviness (47.0%), feeling malaise/general weakness (46.7%), loss of appetite (46.5%), muscle cramps/muscle aches (45.6%), chills/shivering (44.6%), increased sweating (43.0%), nausea (42.5%), irritability (38.9%), increased breathing rate (37.1%), and restlessness/anxiety/palpitations (36.5%) were the symptoms maximally seen during the febrile phase. A higher number of associated symptoms are associated with higher temperature readings. Dehydration suggested the numerically highest temperature values (100.86 ± 1.70°F) but seen in few febrile patients.

Conclusions

Incorporation of symptom analysis in febrile patients is the need of the hour. Fatigue and warmth are found to be most prevelent symptoms during febrile phase. Associated symptoms can help in predicting the intensity of fever also.
Increasing Numbers of Non-communicable Disease Co-morbidities: Major Risk Factors for Hospitalization among a Cohort of People with HIV and COVID-19 Coinfection
Authors: Virata Michael D. , Shenoi Sheela V. , Ladines-Lim Joseph , Villanueva Merceditas S. , Barakat Lydia A.
Published: August 2021

Data regarding coronavirus disease (COVID-19) infection complications among people with HIV (PWH) are expanding but sometimes conflicting. This report presents the results of a retrospective review of 103 patients at a single urban academic health center with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The study showed that hospitalization is related to host factors such as age 65 years or older with an increasing number of specific non-communicable disease comorbidities, and not to HIV-attributable factors.
Identifying robust functional modules using three-body correlations in Escherichia coli
Authors: Chen Tianlong , Singh Pramesh , Bassler Kevin E.
Published: August 2021

Understanding the underlying structure of a gene regulatory network is crucial to understand the biological functions of genes or groups of genes. A common strategy to investigate it is to find community structure of these networks. However, methods of finding these communities are often sensitive to noise in the gene expression data and the inherent stochasticity of the community detection algorithms. Here we introduce an approach for identifying functional groups and their hierarchical organization in gene co-expression networks from expression data. A network describing the relatedness in the expression profiles of genes is first inferred using an information theoretic approach. Community structure within the inferred network is found by using modularity maximization. This community structure is further refined using three-body structural correlations to robustly identify important functional gene communities. We apply this approach to the expression data of Escherichia coli genes and identify 25 robust groups, many of which show key associations with important biological functions as demonstrated by Gene Ontology (GO) term enrichment analysis. Thus, our approach makes specific and novel predictions about the function of these genes.
Using single-cell models to predict the functionality of synthetic circuits at the population scale
Authors: Aditya Chetan , Bertaux François , Batt Gregory , Ruess Jakob
Published: August 2021

Mathematical modeling has become a major tool to guide the characterization and synthetic construction of cellular processes. However, models typically lose their capacity to explain or predict experimental outcomes as soon as any, even minor, modification of the studied system or its operating conditions is implemented. This limits our capacity to fully comprehend the functioning of natural biological processes and is a major roadblock for the de novo design of complex synthetic circuits. Here, using a specifically constructed yeast optogenetic differentiation system as an example, we show that a simple deterministic model can explain system dynamics in given conditions but loses validity when modifications to the system are made. On the other hand, deploying theory from stochastic chemical kinetics and developing models of the system’s components that simultaneously track single-cell and population processes allows us to quantitatively predict emerging dynamics of the system without any adjustment of model parameters. We conclude that carefully characterizing the dynamics of cell-to-cell variability using appropriate modeling theory may allow one to unravel the complex interplay of stochastic single-cell and population processes and to predict the functionality of composed synthetic circuits in growing populations before the circuit is constructed.
Evolutionary flexibility in routes to mat formation by Pseudomonas
Authors: Mukherjee Anuradha , Gallie Jenna
Published: August 2021

Many bacteria form mats at the air-liquid interface of static microcosms. These structures typically involve the secretion of exopolysaccharide(s), the production of which is often controlled by the secondary messenger c-di-GMP. Mechanisms of mat formation have been particularly well characterized in Pseudomonas fluorescens SBW25; mutations that lead to an increase in c-di-GMP production by diguanylate cyclases (WspR, AwsR, or MwsR) result in the secretion of cellulose, and mat formation. Here, we characterize and compare mat formation in two close relatives of SBW25: Pseudomonas simiae PICF7 and Pseudomonas fluorescens A506. We find that PICF7 – the strain more closely related to SBW25 – can form mats through mutations affecting the activity of the same three diguanylate cyclases as SBW25. However, instead of cellulose, these mutations activate the production of the Pel exopolysaccharide. We also provide evidence for at least two further – as yet uncharacterized – routes to PICF7 mat formation. P. fluorescens A506, while retaining the same mutational routes to mat formation as SBW25 and PICF7, forms mats by a semi-heritable mechanism that likely culminates in Pga and/or Psl production. Overall, our results demonstrate a high level of evolutionary flexibility in the molecular and structural routes to mat formation, even among close relatives.
Evolution of functional diversity in the holozoan tyrosine kinome
Authors: Yeung Wayland , Kwon Annie , Taujale Rahil , Bunn Claire , Venkat Aarya , Kannan Natarajan
Published: August 2021

The emergence of multicellularity is strongly correlated with the expansion of tyrosine kinases, a conserved family of signaling enzymes that regulates pathways essential for cell-to-cell communication. Although tyrosine kinases have been classified from several model organisms, a molecular-level understanding of tyrosine kinase evolution across all holozoans is currently lacking. Using a hierarchical sequence constraint-based classification of diverse holozoan tyrosine kinases, we construct a new phylogenetic tree that identifies two ancient clades of cytoplasmic and receptor tyrosine kinases separated by the presence of an extended insert segment in the kinase domain connecting the D and E helices. Present in nearly all receptor tyrosine kinases, this fast-evolving insertion imparts diverse functionalities such as post-translational modification sites and regulatory interactions. Eph and EGFR receptor tyrosine kinases are two exceptions which lack this insert, each forming an independent lineage characterized by unique functional features. We also identify common constraints shared across multiple tyrosine kinase families which warrant the designation of three new subgroups: Src Module (SrcM), Insulin Receptor Kinase-Like (IRKL), and Fibroblast, Platelet-derived, Vascular, and growth factor Receptors (FPVR). Subgroup-specific constraints reflect shared autoinhibitory interactions involved in kinase conformational regulation. Conservation analyses describe how diverse tyrosine kinase signaling functions arose through the addition of family-specific motifs upon subgroup-specific features and co-evolving protein domains. We propose the oldest tyrosine kinases, IRKL, SrcM, and Csk, originated from unicellular pre-metazoans and were co-opted for complex multicellular functions. The increased frequency of oncogenic variants in more recent tyrosine kinases suggests that lineage-specific functionalities are selectively altered in human cancers.
Increasing seed thiamin content impacts stored carbon partitioning and subsequent seedling stress tolerance
Authors: Yazdani Mohammad , Davis James A , Harper Jeffrey F , Shintani David K
Published: August 2021

Thiamin and thiamin pyrophosphate (TPP) are essential components for the function of enzymes involved in the metabolism of carbohydrates and amino acids in living organisms. In addition to its role as a cofactor, thiamin plays a key role in resistance against biotic and abiotic stresses in plants. Most of the studies used exogenous thiamin to enhance stress tolerance in plants. In this study, we achieved this objective by genetically engineering Arabidopsis thaliana and Camelina sativa for the seed-specific co-overexpression of the Arabidopsis thiamin biosynthetic genes Thi4, ThiC, and ThiE. Elevated thiamin content in the seeds of transgenic plants was accompanied by the enhanced expression levels of transcripts encoding thiamin cofactor-dependent enzymes. Furthermore, seed germination and root growth in thiamin over-producing lines were more tolerant to oxidative stress caused by salt and paraquat treatments. The transgenic seeds also accumulated more oil (up to16.4% in Arabidopsis and17.9% in C. sativa) and carbohydrate but less protein than the control seeds. The same results were also observed in TPP over-producing Arabidopsis plants generated by the seed-specific overexpression of TPK1. Together, our findings suggest that thiamin and TPP over-production in transgenic lines confer a boosted abiotic stress tolerance and alter the seed carbon partitioning as well.
Bayesian mixture model for clustering rare-variant effects in human genetic studies
Authors: Venkataraman Guhan Ram , Tanigawa Yosuke , Pirinen Matti , Rivas Manuel A.
Published: August 2021

Rare-variant aggregate analysis from exome and whole genome sequencing data typically summarizes with a single statistic the signal for a gene or the unit that is being aggregated. However, when doing so, the effect profile within the unit may not be easily characterized across one or multiple phenotypes. Here, we present an approach we call Multiple Rarevariants and Phenotypes Mixture Model (MRPMM), which clusters rare variants into groups based on their effects on the multivariate phenotype and makes statistical inferences about the properties of the underlying mixture of genetic effects. Using summary statistic data from a meta-analysis of exome sequencing data of 184,698 individuals in the UK Biobank across 6 populations, we demonstrate that our mixture model can identify clusters of variants responsible for significantly disparate effects across a multivariate phenotype; we study three lipid and three renal traits separately. The method is able to estimate (1) the proportion of non-null variants, (2) whether variants with the same predicted consequence in one gene behave similarly, (3) whether variants across genes share effect profiles across the multivariate phenotype, and (4) whether different annotations differ in the magnitude of their effects. As rare-variant data and aggregation techniques become more common, this method can be used to ascribe further meaning to association results.
Genome-wide association studies across environmental and genetic contexts reveal complex genetic architecture of symbiotic extended phenotypes
Authors: Batstone Rebecca T. , Lindgren Hanna , Allsup Cassandra M. , Goralka Laura A. , Riley Alex B. , Grillo Michael A. , Marshall-Colon Amy , Heath Katy D.
Published: August 2021

A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host’s own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here we use naturally-occurring genetic variation in 191 strains of the model microbial symbiontSinorhizobium melilotipaired with two genotypes of the hostMedicago truncatulain four genome-wide association studies to study the genomic architecture of a key symbiotic extended phenotype – partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, 1) loci whose identities depend on the environment, 2) those that depend on the host genotype with which rhizobia interact, and 3) universal loci that are likely important in all or most environments.

IMPORTANCE

Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.
Chronic behavioral manipulation via orally delivered chemogenetic actuator in macaques
Authors: Oyama Kei , Hori Yukiko , Nagai Yuji , Miyakawa Naohisa , Mimura Koki , Hirabayashi Toshiyuki , Inoue Ken-ichi , Takada Masahiko , Higuchi Makoto , Minamimoto Takafumi
Published: August 2021

The chemogenetic technology referred to as designer receptors exclusively activated by designer drugs (DREADDs) offers reversible means to control neuronal activity for investigating its functional correlation with behavioral action. Deschloroclozapine (DCZ), a recently-developed highly potent and selective DREADDs actuator, displays a capacity to expand the utility of DREADDs for chronic manipulation without side-effects in nonhuman primates, which has not yet been validated. Here we investigated the pharmacokinetics and behavioral effects of orally administered DCZ in macaque monkeys. Pharmacokinetic analysis and positron emission tomography (PET) occupancy examination demonstrated that oral administration of DCZ yielded slower and prolonged kinetics, and that its bioavailability was 10-20% of that in the case of systemic injection. Oral DCZ (300-1000 μg/kg) induced significant working memory impairments for at least 4 h in monkeys with hM4Di expressed in the prefrontal cortex. Repeated daily oral doses of DCZ consistently caused similar impairments over two weeks without discernible desensitization. Our results indicate that orally delivered DCZ affords a less invasive strategy for chronic but reversible chemogenetic manipulation of neuronal activity in nonhuman primates, and this has potential for clinical application.
Comprehensive analysis of pyroptosis-associated in molecular classification, immunity and prognostic of glioma
Authors: Chen Peng , Li Yanyan , Li Na , Shen Liangfang , Li Zhanzhan
Published: August 2021

Integrative analysis was performed in the Chinese Glioma Genome Atlas and The Cancer Genome Atlas to describe the pyroptosis-associated molecular classification and prognostic signature in glioma. Pyroptosis-related genes were used for consensus clustering and to develop a prognostic signature. The immune statuses, molecular alterations and clinical features of differentially expressed genes were analyzed among different subclasses and risk groups. A lncRNA-miRNA-mRNA network was built, and drug sensitivity analysis was used to identify small molecular drugs for the identified genes. Glioma can be divided into two subclasses using 30 pyroptosis-related genes. Cluster 1 displayed high immune signatures and poor prognosis as well as high immune-related function scores. A prognostic signature based on 15 pyroptosis-related genes of the CGGA cohort can predict the overall survival of glioma and was well validated in the TCGA cohort. Cluster 1 had higher risk scores. The high-risk group had high immune cell and function scores and low DNA methylation of pyroptosis-related genes. The differences in pyroptosis-related gene mutations and somatic copy numbers were significant between the high-risk and low-risk groups. The ceRNA regulatory network uncovered the regulatory patterns of different risk groups in glioma. Nine pairs of target genes and drugs were identified. In vitro, CASP8 promotes the progression of glioma cells. Pyroptosis-related genes can reflect the molecular biological and clinical features of glioma subclasses. The established prognostic signature can predict prognosis and distinguish molecular alterations in glioma patients. Our comprehensive analyses provide valuable guidelines for improving glioma patient management and individualized therapy.
Genetic evidence reveals the indispensable role of the rseC gene for autotrophy and the importance of a functional electron balance for nitrate reduction in Clostridium ljungdahlii
Authors: Klask Christian-Marco , Jäger Benedikt , Angenent Largus T. , Molitor Bastian
Published: August 2021

For Clostridium ljungdahlii, the RNF complex plays a key role for energy conversion from gaseous substrates such as hydrogen and carbon dioxide. In a previous study, a disruption of RNF-complex genes led to the loss of autotrophy, while heterotrophy was still possible via glycolysis. Furthermore, it was shown that the energy limitation during autotrophy could be lifted by nitrate supplementation, which resulted in an elevated cellular growth and ATP yield. Here, we used CRISPR-Cas12a to delete: 1) the RNF complex-encoding gene cluster rnfCDGEAB; 2) the putative RNF regulator gene rseC; and 3) a gene cluster that encodes for a putative nitrate reductase. The deletion of either rnfCDGEAB or rseC resulted in a complete loss of autotrophy, which could be restored by plasmid-based complementation of the deleted genes. We observed a transcriptional repression of the RNF-gene cluster in the rseC-deletion strain during autotrophy and investigated the distribution of the rseC gene among acetogenic bacteria. To examine nitrate reduction and its connection to the RNF complex, we compared autotrophic and heterotrophic growth of our three deletion strains with either ammonium or nitrate. The rnfCDGEAB- and rseC-deletion strains failed to reduce nitrate as a metabolic activity in non-growing cultures during autotrophy but not during heterotrophy. In contrast, the nitrate reductase deletion strain was able to grow in all tested conditions but lost the ability to reduce nitrate. Our findings highlight the important role of the rseC gene for autotrophy and contribute to understand the connection of nitrate reduction to energy metabolism.

Significance Statement

Acetogenic bacteria are widely known for their ability to convert gaseous substrates, such as hydrogen, carbon dioxide, and carbon monoxide, into short-chain fatty acids and alcohols, which can be utilized as sustainable platform chemicals and fuels. However, acetogenic bacteria conserve energy at the thermodynamic limit of life during autotrophy, and thus the production of more complex and energy-dense chemicals is limited due to low ATP yields. Therefore, it is key to decipher the interplay of the electron balancing reactions to understand and optimize the acetogenic metabolism. Recent findings with alternative electron acceptors that accelerated the cellular growth and ATP yield during autotrophy, such as nitrate, provide an opportunity to overcome energetic barriers in the acetogenic metabolism. The interrogation of the nitrate metabolism and the interplay between nitrate reduction and energy conservation in C. ljungdahlii, will contribute to fine-tuning of the acetogenic metabolism for biotechnological applications.
A Codon Constrained Method for Both Eliminating and Creating Intragenic Bacterial Promoters
Authors: Logel Dominic Y. , Trofimova Ellina , Jaschke Paul R.
Published: August 2021

Future applications of synthetic biology will require refactored genetic sequences devoid of internal regulatory elements within coding sequences. These regulatory elements include cryptic and intragenic promoters which may constitute up to a third of predicted Escherichia coli promoters. Promoter activity is dependent on the structural interaction of core bases with a σ factor. Rational engineering can be used to alter key promoter element nucleotides interacting with σ factors and eliminate downstream transcriptional activity. In this paper, we present COdon Restrained Promoter SilEncing (CORPSE), a system for removing intragenic promoters. CORPSE exploits the DNA-σ factor structural relationship to disrupt σ70 promoters embedded within gene coding sequences, with a minimum of synonymous codon changes. Additionally, we present an inverted CORPSE system, iCORPSE, which can create highly active promoters within a gene sequence while not perturbing the function of the modified gene.
Local regulation of extracellular vesicle traffic by the synaptic endocytic machinery
Authors: Blanchette Cassandra R. , Scalera Amy L. , Harris Kathryn P. , Zhao Zechuan , Koles Kate , Yeh Anna , Apiki Julia K. , Stewart Bryan A. , Rodal Avital A.
Published: August 2021

Neuronal extracellular vesicles (EVs) can be locally released from presynaptic terminals, carrying cargoes that are important in intercellular signaling and disease. EVs are derived from endosomes, but it remains unclear how synaptic cargoes are directed to the EV pathway, rather than undergoing conventional retrograde endosomal transport and degradation. Here, we find that the clathrin-mediated endocytic machinery plays an unexpected role in maintaining a release-competent pool of synaptic EV cargoes. Endocytic mutants, including nervous wreck (nwk), Shibire/Dynamin, and AP-2, exhibit local depletion of multiple cargoes in EV donor terminals. Accordingly, nwk mutants phenocopy synaptic plasticity defects associated with loss of the EV cargo Synaptotagmin-4, and suppress lethality upon overexpression of the EV cargo Amyloid Precursor Protein. These EV defects are genetically separable from canonical functions of endocytic proteins in synaptic vesicle recycling and synaptic growth. This endocytic pathway opposes the endosomal retromer complex to regulate EV cargo levels, and acts upstream of synaptic cargo removal by retrograde axonal transport. Our data suggest a novel molecular mechanism that protects EV cargoes from local depletion at synapses.
Rock traits drive complex microbial communities at the edge of life
Authors: Coleine Claudia , Delgado-Baquerizo Manuel , Zerboni Andrea , Turchetti Benedetta , Buzzini Pietro , Selbmann Laura
Published: August 2021

Antarctic deserts are among the driest and coldest ecosystems of the planet; there, some microbes hang on to life under these extreme conditions inside porous rocks, forming the so-called endolithic communities. Yet, the contribution of distinct rock traits to support complex microbial assemblies remains poorly determined. Here, we combined an extensive Antarctic rock survey with rock microbiome sequencing and ecological networks, and found that contrasting combinations of microclimatic and rock traits such as thermal inertia, porosity, iron concentration and quartz cement can help explain the multiple complex and independent microbial assemblies found in Antarctic rocks. Our work highlights the pivotal role of rocky substrate heterogeneity in sustaining contrasting groups of microorganisms, which is essential to understand life at the edge on Earth, and for searching life on other rocky planets such as Mars.
Exploring the impact of terminators on transgene expression in Chlamydomonas reinhardtii with a synthetic biology approach
Authors: Geisler Katrin , Scaife Mark A. , Mordaka Paweł M. , Holzer Andre , Mehrshahi Payam , Ochoa Gonzalo Mendoza , Smith Alison G.
Published: August 2021

Chlamydomonas reinhardtii has many attractive features for use as a model organism for both fundamental studies and as a biotechnological platform. Nonetheless, despite the many molecular tools and resources that have been developed, there are challenges for its successful engineering, in particular to obtain reproducible and high levels of transgene expression. Here we describe a synthetic biology approach to screen several hundred independent transformants using standardised parts to explore different parameters that might affect transgene expression. We focused on terminators and, using a standardised workflow and quantitative outputs, tested 9 different elements representing three different size classes of native terminators to determine their ability to support high level expression of a GFP reporter gene. We found that the optimal size reflected the median size of element found in the C. reinhardtii genome. The behaviour of the terminator parts was similar with different promoters, in different host strains and with different transgenes. This approach is applicable to the systematic testing of other genetic elements, facilitating comparison to determine optimal transgene design.
GRAMD1C regulates autophagy initiation and mitochondrial bioenergetics through ER-mitochondria cholesterol transport
Authors: Wui Ng Matthew Yoke , Charsou Chara , Lapao Ana , Singh Sakshi , Trachsel-Moncho Laura , Nakken Sigve , Munson Michael J. , Simonsen Anne
Published: August 2021

During autophagy, cytosolic cargo is sequestered into double-membrane vesicles called autophagosomes. The origin and identity of the membranes that form the autophagosome remain to be fully characterized. Here, we investigated the role of cholesterol in starvation- induced autophagy and identify a role for the ER-localized cholesterol transport protein GRAMD1C in the regulation of autophagy and mitochondrial function. We demonstrate that cholesterol depletion leads to a rapid induction of autophagy, possibly caused by a corresponding increased abundance of curved autophagy membranes. We further show that GRAMD1C is a negative regulator of starvation-induced autophagy. Similar to its yeast orthologue, GRAMD1C is recruited to mitochondria through its GRAM domain. Additionally, we find that GRAMD1C depletion leads to increased mitochondrial cholesterol accumulation and mitochondrial oxidative phosphorylation. Finally, we demonstrate that expression of GRAM family genes is linked to clear cell renal carcinoma survival, highlighting the pathophysiological relevance of cholesterol transport proteins.
Learning graph networks: sleep targets highly connected global and local nodes for consolidation
Authors: Feld GB , Bernard M , Rawson AB , Spiers HJ
Published: August 2021

Much of our long-term knowledge is organised in complex networks. Sleep is thought to be critical for abstracting knowledge and enhancing important item memory for long-term retention. Thus, sleep should aid the development of memory for networks and the abstraction of their structure for efficient storage. However, this remains unknown because past sleep studies have focused on discrete items. Here we explored the impact of sleep (night-sleep/day-wake within-subject paradigm) on memory for graph-networks where some items were important due to dense local connections (degree centrality) or, independently, important due to greater global connections (closeness / betweenness centrality). A network of 27 planets (nodes) sparsely interconnected by 36 teleporters (edges) was learned via discrete associations without explicit indication of any network structure. Despite equivalent exposure to all connections in the network, we found that memory for the links between items with high local centrality or high global centrality were better retained after sleep. These results highlight that sleep has the capacity for strengthening both global and local structure from the world and abstracting over multiple experiences to efficiently form internal networks of knowledge.
Modifying root/shoot ratios improves root water influxes in wheat under drought stress
Authors: Bacher Harel , Sharaby Yoav , Walia Harkamal , Peleg Zvi
Published: August 2021

Drought intensity as experienced by plants depends upon soil moisture status and atmospheric variables such as temperature, radiation, and air vapour pressure deficit (VPD). Although the role of shoot architecture with these edaphic and atmospheric factors is well-characterized, the extent to which shoot and root dynamic interactions as a continuum are controlled by genotypic variation is less known. Here, we targeted these interactions using a wild emmer introgression line (IL20) with a distinct drought-induced shift in the shoot-to-root ratio and its drought-sensitive recurrent parent Svevo. Using a gravimetric platform, we show that IL20 maintained higher root water influx and gas exchange under drought stress, which supported a greater growth. Interestingly, the advantage of IL20 in root water influx and transpiration was expressed earlier during the daily diurnal cycle under lower VPD and therefore supported higher transpiration efficiency. Application of structural equation model indicates that under drought, VPD and radiation are antagonistic to transpiration rate, whereas the root water influx operates as feedback for the higher atmospheric responsiveness of leaves. Collectively, our results suggest that a drought-induced shift in root-to-shoot ratio can improve plant water uptake potential in a short preferable time window determined by both water and atmospheric parameters.
Dynamic configuration of large-scale cortical networks during an inhibitory task accounts for heterogeneity in attention-deficit/hyperactivity disorder traits
Authors: Kember Jonah , Hare Carolynn , Tekok-Kilic Ayda , Marshall William , Emrich Stephen , Segalowitz Sidney J. , Panda Erin J.
Published: August 2021

The heterogeneity of attention-deficit/hyperactivity disorder (ADHD) traits (inattention vs. hyperactivity/impulsivity) complicates diagnosis and intervention. Identifying how the configuration of large-scale functional brain networks during cognitive processing correlate with this heterogeneity could help us understand the neural mechanisms altered across ADHD presentations. Here, we recorded high-density EEG while 62 non-clinical participants (ages 18-24; 32 male) underwent an inhibitory control task (Go/No-Go). Functional EEG networks were created using sensors as nodes and across-trial phase-lag index values as edges. Using cross-validated LASSO regression, we examined whether graph-theory metrics applied to both static networks (averaged across time-windows: -500–0ms, 0–500ms) and dynamic networks (temporally layered with 2ms intervals), were associated with hyperactive/impulsive and inattentive traits. Network configuration during response execution/inhibition was associated with hyperactive/impulsive (mean R2across test sets = .20, SE = .02), but not inattentive traits. Post-stimulus results at higher frequencies (Beta, 14-29Hz; Gamma, 30-90Hz) showed the strongest association with hyperactive/impulsive traits, and predominantly reflected less burst-like integration between modules in oscillatory beta networks during execution, and increased integration/small-worldness in oscillatory gamma networks during inhibition. We interpret the beta network results as reflecting weaker integration between specialized pre-frontal and motor systems during motor response preparation, and the gamma results as reflecting a compensatory mechanism used to integrate processing between less functionally specialized networks. This research demonstrates that the neural network mechanisms underlying response execution/inhibition might be associated with hyperactive/impulsive traits, and that dynamic, task-related changes in EEG functional networks may be useful in disentangling ADHD heterogeneity.
The role of antifreeze glycopeptides (AFGP) and polyvinyl alcohol/polyglycerol (X/Z-1000) cocktails as ice modulators during partial freezing of rat livers
Authors: Tessier Shannon N. , Haque Omar , Pendexter Casie A. , Cronin Stephanie E.J. , Weng Lindong , Yeh Heidi , Markmann James F. , Taylor Michael J. , Fahy Gregory M. , Toner Mehmet , Uygun Korkut
Published: August 2021

The current liver organ shortage has pushed the field of liver transplantation to develop new methods to prolong the preservation time of livers from the current clinical standard of static cold storage. Our approach, termed partial freezing, aims to induce a thermodynamically stable frozen state at deeper storage temperatures (−10°C to −15°C) than can be achieved with supercooling, while simultaneously maintaining a sufficient unfrozen fraction to limit dehydration and ice damage. This research first demonstrated that partially frozen glycerol treated rat livers were functionally similar after thawing from either −10 or −15°C with respect to subnormothermic machine perfusion metrics and histology. Next, we assessed the effect of adding either of two ice modulators, antifreeze glycoprotein (AFGP) and a polyvinyl alcohol/polyglycerol combination (X/Z-1000), on the viability and structural integrity of partially frozen rat livers compared to glycerol-only control livers. Results showed that AFGP livers had high levels of ATP and the least edema but suffered from significant endothelial cell damage. X/Z-1000 livers had the highest levels of ATP and energy charge (EC) but also demonstrated endothelial damage and post-thaw edema. Glycerol-only control livers exhibited the least DNA damage on Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining but also had the lowest levels of ATP and EC. Further research is necessary to optimize the ideal ice modulator cocktail for our partial-freezing protocol. Modifications to cryoprotective agent (CPA) combinations, as well as improvements to machine perfusion CPA loading and unloading, can help improve the viability of these partially frozen organs.
Intercontinental comparison of ferns community assemblages in Malaysian and Nigerian tropical forests
Authors: Akomolafe Gbenga F. , Rosazlina Rusly Binti , Rahmad Zakaria , Oloyede Fatai A.
Published: August 2021

Research on ferns ecology has gained attention in the last decade, yet there is paucity of information on the intercontinental comparison of ferns community across two continents. This study focused on comparing the ferns community assemblages in tropical forests of Malaysia and Nigeria, thereby assessing the patterns of the species richness and diversity across the two continents. The diversity and taxonomic compositions of ferns were assessed using 180 plots of size 10 m x 10 m in each country. The species richness and other diversity indices were determined using the combined forests data for each country and for the individual forests. The observed and rarefied–extrapolated fern species richness are significantly higher in Malaysian forests than Nigerian forests. Also, the other diversity indices (Simpson index, Margalef index, and Fisher’s alpha) are significantly higher in Malaysian forests except Shannon index which showed no significant difference between the two biogeographic regions. There is a very low similarity in the taxonomic composition of ferns between the two biogeographic areas, although the similarity in composition increased with increasing taxonomic levels (genus and family levels). Terrestrial and epiphytic ferns are more dominant than the other life forms in the two countries. Since the two countries receive varying degrees of environmental factors, we then hypothesize that these observed differences are due to climatic differences as well as historical and evolutionary processes.
Height-diameter allometry for tropical forest in northern Amazonia
Authors: de Lima Robson Borges , Görgens Eric Bastos , Elias Fernando , de Abreu Jadson Coelho , Baia Aldine Luiza , de Oliveira Cinthia Pereira , da Silva Diego Armando Silva , Batista Anderson Pedro Bernardina , Lima Robson Carmo , Sotta Eleneide Doff
Published: August 2021

Height measurements are essential to manage and monitor forest biomass and carbon stocks. However, accurate estimation of this variable in tropical ecosystems is still difficult due to species heterogeneity and environmental variability. In this article, we compare and discuss six nonlinear allometric models parameterized at different scales (local, regional and pantropical). We also evaluate the height measurements obtained in the field by the hypsometer when compared with the true tree height. We used a dataset composed of 180 harvested trees in two distinct areas located in the Amapá State. The functional form of the Weibull model was the best local model, showing similar performance to the pantropical model. The inaccuracy detected in the hypsometer estimates reinforces the importance of incorporating new technologies in measuring individual tree heights. Establishing accurate allometric models requires knowledge of ecophysiological and environmental processes that govern vegetation dynamics and tree height growth. It is essential to investigate the influence of different species and ecological gradients on the diameter/height ratio.