bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity
Authors: Li Zexin , Pan Donald , Wei Guangshan , Pi Weiling , Wang Jiang-Hai , Peng Yongyi , Zhang Lu , Wang Yong , Hubert Casey R.J. , Dong Xiyang
Published: September 2020

In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, thus influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans, to assess viral diversity, virus-host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition.In silicopredictions linked 14.2% of the viruses to microbial host populations, with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.
Brain volumetric changes in the general population following the COVID-19 outbreak and lockdown
Authors: Salomon Tom , Cohen Adi , Barazany Daniel , Ben-Zvi Gal , Botvinik-Nezer Rotem , Gera Rani , Oren Shiran , Roll Dana , Rozic Gal , Saliy Anastasia , Tik Niv , Tsarfati Galia , Tavor Ido , Schonberg Tom , Assaf Yaniv
Published: September 2020

The COVID-19 outbreak introduced unprecedented health-risks, as well as pressure on the financial, social, and psychological well-being due to the response to the outbreak. Here, we examined the manifestations of the COVID-19 outbreak on the brain structure in the healthy population, following the initial phase of the pandemic in Israel. We pre-registered our hypothesis that the intense experience of the outbreak potentially induced stress-related brain modifications. Volumetric changes inn= 50 participants who were scanned before and after the COVID-19 outbreak and lockdown, were compared withn= 50 control participants who were scanned twice prior to the pandemic. The pandemic provided a rare opportunity to examine brain plasticity in a natural experiment. We found volumetric increases in bilateral amygdalae, putamen, and the anterior temporal cortices. Changes in the amygdalae diminished as time elapsed from lockdown relief, suggesting that the intense experience associated with the pandemic outbreak induced transient volumetric changes in brain regions commonly associated with stress and anxiety.
Scalable, multimodal profiling of chromatin accessibility and protein levels in single cells
Authors: Mimitou Eleni P. , Lareau Caleb A. , Chen Kelvin Y. , Zorzetto-Fernandes Andre L. , Takeshima Yusuke , Luo Wendy , Huang Tse-Shun , Yeung Bertrand , Thakore Pratiksha I. , Wing James Badger , Nazor Kristopher L. , Sakaguchi Shimon , Ludwig Leif S. , Sankaran Vijay G. , Regev Aviv , Smibert Peter
Published: September 2020

Recent technological advances have enabled massively parallel chromatin profiling withsingle-cellAssay forTransposaseAccessibleChromatin bysequencing (scATAC-seq) in thousands of individual cells. Here, we extend these approaches and presentATAC withSelectAntigenProfiling bysequencing, ASAP-seq, a tool to simultaneously profile accessible chromatin and protein levels in thousands of single cells. Our approach pairs sparse scATAC-seq data with robust detection of hundreds of cell surface and intracellular protein markers and optional capture of mitochondrial DNA (mtDNA) for clonal tracking, thus concomitantly capturing three distinct modalities in single cells. Importantly, ASAP-seq uses a novel bridging approach that repurposes antibody:oligo conjugates designed for existing technologies that pair protein measurements with single cell RNA-seq. We demonstrate the utility of ASAP-seq by revealing coordinated and distinct changes in chromatin, RNA, and surface proteins during native hematopoietic differentiation, peripheral blood mononuclear cell stimulation, and as a combinatorial decoder and reporter of multiplexed perturbations in primary T cells.
An evolutionarily acquired microRNA shapes development of mammalian cortical projections
Authors: Diaz Jessica L , Siththanandan Verl B , Lu Victoria , Gonzalez-Nava Nicole , Pasquina Lincoln , MacDonald Jessica L , Woodworth Mollie B , Ozkan Abduladir , Nair Ramesh , He Zihuai , Sahni Vibhu , Sarnow Peter , Palmer Theo D , Macklis Jeffrey D , Tharin Suzanne
Published: September 2020

The corticospinal tract is unique to mammals and the corpus callosum is unique to placental mammals (eutherians). The emergence of these structures is thought to underpin the evolutionary acquisition of complex motor and cognitive skills. Corticospinal motor neurons (CSMN) and callosal projection neurons (CPN) are the archetypal projection neurons of the corticospinal tract and corpus callosum, respectively. Although a number of conserved transcriptional regulators of CSMN and CPN development have been identified in vertebrates, none are unique to mammals and most are co-expressed across multiple projection neuron subtypes. Here, we discover seventeen CSMN-enriched microRNAs (miRNAs), fifteen of which map to a single genomic cluster that is exclusive to eutherians. One of these, miR-409-3p, promotes CSMN subtype identity in part via repression of LMO4, a key transcriptional regulator of CPN development.In vivo, miR-409-3p is sufficient to convert deep-layer CPN into CSMN. This is the first demonstration of an evolutionarily acquired miRNA in eutherians that refines cortical projection neuron subtype development. Our findings implicate miRNAs in the eutherians’ increase in neuronal subtype and projection diversity, the anatomic underpinnings of their complex behavior.

Significance Statement

The mammalian central nervous system contains unique projections from the cerebral cortex thought to underpin complex motor and cognitive skills, including the corticospinal tract and corpus callosum. The neurons giving rise to these projections - corticospinal and callosal projection neurons - develop from the same progenitors, but acquire strikingly different fates. The broad evolutionary conservation of known genes controlling cortical projection neuron fates raises the question of how the more narrowly conserved corticospinal and callosal projections evolved. We identify a microRNA cluster selectively expressed by corticospinal projection neurons and exclusive to placental mammals. One of these microRNAs promotes corticospinal fate via regulation of the callosal gene LMO4, suggesting a mechanism whereby microRNA regulation during development promotes evolution of neuronal diversity.
Stochastic asymmetric repartition of lytic machinery in dividing CD8+T cells generates heterogeneous killing behavior
Authors: Lafouresse Fanny , Jugele Romain , Müller Sabina , Doineau Marine , Duplan-Eche Valérie , Espinosa Eric , Puissegur Marie-Pierre , Gadat Sébastien , Valitutti Salvatore
Published: September 2020

Cytotoxic immune cells are endowed with a high degree of heterogeneity in their lytic function, but how this heterogeneity is generated is still an open question. We therefore investigated if human CD8+T cells could segregate their lytic components during telophase, using imaging flow cytometry, confocal microscopy and live cell imaging. We show that CD107a+-intracellular vesicles, perforin and granzyme B unevenly segregate in a constant fraction of telophasic cells during each division round. Mathematical modeling posits that unequal lytic molecule inheritance by daughter cells results from the random distribution of lytic granules on the two sides of the cleavage furrow. Finally, we establish that the level of lytic compartment in individual CTL dictates CTL killing capacity. Together, our results show the stochastic asymmetric distribution of effector molecules in dividing CD8+T cells. They propose uneven mitotic repartition of pre-packaged lytic components as a mechanism generating non-hereditary functional heterogeneity in CTL.
Planarian CREB-binding protein (CBP) gene family regulates stem cell maintenance and differentiation
Authors: Fraguas Susanna , Cárcel Sheila , Vivancos Coral , Molina Ma Dolores , Ginés Jordi , Mazariegos Judith , Sekaran Thileepan , Bartscherer Kerstin , Romero Rafael , Cebrià Francesc
Published: September 2020

The regulation of stem cells plasticity and differentiation is still an open question in developmental biology. CBP (CREB-binding protein)/p300 is a conserved gene family which functions as a transcriptional co-activator and shows an important role in a wide range of cellular processes, such as cell death, DNA damage response and tumorigenesis. Moreover, CBPs have an acetyl transferase activity that is relevant as histone and non-histone acetylation results in changes in chromatin architecture and protein activity that affects gene expression. Many studies have shown the conserved functions of CBP/p300 on stem cell proliferation and differentiation. The planarianSchmidtea mediterraneais an excellent model to studyin vivothe molecular mechanism underlying stem cell differentiation during regeneration. We have identified five differentSmed-cbpgenes inS. mediterraneathat show different expression patterns. Functional analyses indicate thatSmed-cbp-2seems to be essential for stem cell maintenance and cell survival. On the other hand, the silencing ofSmed-cbp-3results in the growth of apparently normal blastemas; however, these remain largely depigmented and undifferentiated.Smed-cbp-3silencing affects the differentiation of several cell lineages including neural, epidermal, digestive and excretory cell types. Finally, we have analyzed the predicted interactomes of CBP-2 and CBP-3 as an initial step to better understand their function on planarian stem cell biology.
Structure and dynamics of the quaternaryhunchbackmRNA translation repression complex
Authors: Macošek Jakub , Simon Bernd , Linse Johanna-Barbara , Winter Sophie , Foot Jaelle , Perez Kathryn , Rettel Mandy , Ivanović Miloš T. , Masiewicz Pawel , Murciano Brice , Savitski Mikhail M. , Hub Jochen S. , Gabel Frank , Hennig Janosch
Published: September 2020

A key regulatory process duringDrosophiladevelopment is the localized suppression of thehunchbackmRNA translation at the posterior, which gives rise to ahunchbackgradient governing the formation of the anterior-posterior body axis. The suppression of the RNA is achieved by a concerted action of Brain Tumour (Brat), Pumilio (Pum) and Nanos. Each protein is necessary for properDrosophiladevelopment. The RNA contacts have been elucidated for the proteins individually in several atomic-resolution structures. However, the interplay of all three proteins in the RNA suppression remains a long-standing open question. We characterize the quaternary complex of the RNA-binding domains of Brat, Pum and Nanos withhunchbackmRNA by combining NMR spectroscopy, SANS/SAXS, XL/MS with MD simulations and ITC assays. The quaternaryhunchbackmRNA suppression complex is flexible with the unoccupied nucleotides of the RNA functioning as a flexible linker between the Brat and Pum-Nanos moieties of the complex. Moreover, Brat and Pum with Nanos bind the RNA completely independently. In accordance with previous studies, showing that Brat can suppresshunchbackmRNA independently and is distributed uniformly throughout the embryo, this suggests thathunchbackmRNA suppression by Brat is functionally separate from the suppression by Pumilio and Nanos.
Analysis of SARS-CoV-2 genomes from across Africa reveals potentially clinically relevant mutations
Authors: Longjohn Modeline N. , Egbule Olivia S. , Danso Samuel O. , Akujuru Eugene E. , Ibubeleye Victor T. , Oweredaba Christabel I. , Ogharanduku Theodora , Manu Alexander , Iweriebor Benson C.
Published: September 2020

SARS-CoV-2 is a betacoronavirus, the etiologic agent of the novel Coronavirus disease 2019 (COVID-19). The World Health Organization officially declared COVID-19 as a pandemic in March 2020 after the outbreak in Wuhan, China, in late 2019. Across the continents and specifically in Africa, all index cases were travel-related. Understanding how the virus’s transportation across continents and different climatic conditions affect the genetic composition and the consequent effects on transmissibility, infectivity, and virulence of the virus is critical. Thus, it is crucial to compare COVID-19 genome sequences from the African continent with sequences from selected COVID-19 hotspots/countries in Asia, Europe, North and South America and Oceania.

To identify possible distinguishing mutations in the African SARS-CoV-2 genomes compared to those from these selected countries, we conductedin silicoanalyses and comparisons. Complete African SARS-CoV-2 genomes deposited in GISAID and NCBI databases as of June 2020 were downloaded and aligned with genomes from Wuhan, China and other SARS-CoV-2 hotspots. Using phylogenetic analysis and amino acid sequence alignments of the spike and replicase (NSP12) proteins, we searched for possible vaccine coverage targets or potential therapeutic agents. Identity plots for the alignments were created with BioEdit software and the phylogenetic analyses with the MEGA X software.

Our results showed mutations in the spike and replicate proteins of the SARS-Cov-2 virus. Phylogenetic tree analyses demonstrated variability across the various regions/countries in Africa as there were different clades in the viral proteins. However, a substantial proportion of these mutations (90%) were similar to those described in all the other settings, including the Wuhan strain. There were, however, novel mutations in the genomes of the circulating strains of the virus in African. To the best of our knowledge, this is the first study reporting these findings from Africa. However, these findings’ implications on symptomatic or asymptomatic manifestations, progression to severe disease and case fatality for those affected, and the cross efficacy of vaccines developed from other settings when applied in Africa are unknown.
Inheritance of associative memories inC. elegansnematodes
Authors: Deshe Noa , Eliezer Yifat , Hoch Lihi , Itskovits Eyal , Ben-Ezra Shachaf , Zaslaver Alon
Published: September 2020

The notion that associative memories may be transmitted across generations is intriguing, yet controversial. Here, we trainedC. elegansnematodes to associate an odorant with stressful starvation conditions, and surprisingly, this associative memory was evident two generations down of the trained animals. The inherited memory endowed the progeny with a fitness advantage, as memory reactivation induced rapid protective stress responses that allowed the animals to prepare in advance for an impending adversity. Sperm, but not oocytes, transmitted the associative memory, and the inheritance required H3K9 and H3K36 methylations, the small RNA-binding Argonaute NRDE-3, and intact neuropeptide secretion. Remarkably, activation of a single chemosensory neuron sufficed to induce a serotonin-mediated systemic stress response in both the parental trained generation and in its progeny. These findings challenge long-held concepts by establishing that associative memories may indeed be transferred across generations.
High-throughput method to test antimicrobial gels against a multispecies oral biofilm
Authors: Chathoth Kanchana , Martin Bénédicte , Bonnaure-Mallet Martine , Baysse Christine
Published: September 2020

Periodontitis, characterized by the damage of the periodontium can eventually lead to tooth loss. Moreover, severe forms of periodontitis are associated with several systemic disorders. The evolution of the disease is linked to the pathogenic switch of the oral microbiota comprising of commensal colonizers and anaerobic pathogens. Treatment with antimicrobial gels has the potential to help eradicate periodontal pathogens. Testing antibacterial gels againstin vitrobiofilm models is complicated. Recovery of detached and sessile bacteria fromin vitrobiofilms treated with gel formulations using conventional methods (microtiter plates, μ-slides, flow cells etc.,) may prove arduous. To overcome this challenge, we optimised a simple method using the principle of the Calgary Biofilm Device (CBD) for testing antimicrobial gels against multispecies oral biofilms. First, we established three-species oral biofilms consisting of two periodontal pathogens (Porphyromonas gingivalis,Treponema denticola) and a primary colonizer of the dental plaque (Streptococcus gordonii) on the surface of pegs. Next, a protocol to test gels against oral biofilms was implemented using commercially available gels with different active products. This method enables the analysis of the composition of biofilm and detached/planktonic cells to measure the effect of topical gel formulations/antibacterial gels for the treatment of periodontitis. However, the method is not restricted to oral biofilms and can be adapted for other biofilm-related studies.
Diversity and function of microbial lipases within the mammalian gut
Authors: Hitch Thomas C. A. , Masson Johannes M. , Streidl Theresa , Fischöder Thomas , Elling Lothar , Clavel Thomas
Published: September 2020

Background

Current estimates suggest the majority of microbial proteins within the mammalian gut lack meaningful annotation. One such functional group are microbial lipases (EC:3.1.1.3), which can alter host access and utilisation of dietary fat. In this paper, we describe the diversity of lipolytic bacteria, includingin vitrocharacterisation of a new lipase.

Results

Metagenomic sequence-based network analysis identified that the majority of microbial lipases in the gut of three host species (human, mouse, pig) belong to two unique clusters. These clusters were characterized by the presence of two novel motifs, AHSKGG and TTxxTPH, which may play a key functional role due to co-localisation in the active site, as identified by structural modelling. Analysis of metagenomic assembled genomes (MAGs) indicated that the majority of lipase-positive species belong to the phylum Firmicutes, although all dominant phyla within the human gut were represented by positive species. Metabolic analysis of these genomes identified a high prevalence of glycerol rather than fatty acid metabolism. The occurrence of microbial lipases determined across ~800 metagenomic gut samples depended on dietary fat consumption, with lipase expression increased in lard fed compared to palm oil fed mice. A representative lipase encoded within the genome of the speciesClostridium symbiosumwas cloned and its characterization confirmed thein silicoprediction and provided detailed annotation to 373 proteins.

Conclusions

Microbial lipases within the gut represent a conserved group characterized by unique amino acid sequence motifs. While an increase in microbial lipase occurrence was positively associated with dietary fat intake, lipase-producing species seemed unable to metabolise the released fatty acids. In this paper, we provide a global analysis of the functional importance and diversity of microbial lipases within the intestine of mammals, which will improve the resolution of future sequence-based studies and open avenues for mechanistic experiments based on isolates.
Mental Chronometry of Speaking in Dialogue: Semantic Interference Turns into Facilitation
Authors: Kuhlen Anna K. , Rahman Rasha Abdel
Published: September 2020

Numerous studies demonstrate that the production of words is delayed when speakers process in temporal proximity semantically related words. Yet the experimental settings underlying this effect are different from those under which we typically speak. This study demonstrates that semantic interference disappears, and can even turn into facilitation, when semantically related words are embedded in a meaningful communicative exchange. Experiment 1 and 3 (each N=32 university students) implemented a picture- word interference task in a game played between two participants: one named the distractor word and, after a stimulus-onset-asynchrony of -150ms or -650ms, the other named a semantically related or unrelated target picture. Semantic interference reappeared with identical experimental parameters in a single-person picture-word interference setting (Experiment 2, N=32). We conclude that the inhibitory context effects leading to semantic interference in single-subject settings are attenuated whereas facilitatory effects are enhanced in communicative settings.

Highlights

In isolated speakers processing semantically related words interferes with speaking

Yet we typically speak to communicate with others

This study transfers picture-word interference to a communicative setting

Semantically related words produced by a partner do not interfere with speaking
The Shh/Gli3 gene regulatory network precedes the origin of paired fins and reveals the deep homology between distal fins and digits
Authors: Letelier Joaquín , Naranjo Silvia , Sospedra Ismael , Lopez-Rios Javier , Martinez-Morales Juan Ramón , Shubin Neil , Gómez-Skarmeta José Luis
Published: September 2020

One of the central problems of vertebrate evolution is understanding the relationship among the distal portions of fins and limbs. Lacking comparable morphological markers of these regions in fish and tetrapods, these relationships have remained uncertain for the past century and a half. Here we show thatGli3functions in controlling the proliferative expansion of distal progenitors are shared among median and paired fins as well as tetrapod limbs. Mutant knockoutgli3fins in medaka (Oryzias latipes) form multiple radials and rays, in a pattern reminiscent of the polydactyly observed inGli3null mutant mice. In limbs,Gli3controls both anterior-posterior patterning and cell proliferation, two processes that can be genetically uncoupled.In situhybridization, quantification of proliferation markers, and analysis of regulatory regions reveal that in paired and median fins,gli3plays a main role in controlling proliferation but not in patterning. Moreover,gli3downregulation inshhmutant fins rescues fin loss in a manner similar to howGli3-deficiency restores digits in the limbs ofShhmutant mouse embryos. We hypothesize that theGli3/Shhpathway preceded the origin of paired appendages and was originally involved in modulating cell proliferation. Accordingly, the distal regions of median fins, paired fins, and limbs retain a deep regulatory and functional homology that predates the origin of paired appendages.
Decoding the Protein Composition of Whole Nucleosomes with Nuc-MS
Authors: Schachner Luis F. , Jooβ Kevin , Morgan Marc A. , Piunti Andrea , Meiners Matthew J. , Lee Alexander , Kafader Jared O. , Iwanaszko Marta , Cheek Marcus A. , Burg Jonathan M. , Howard Sarah A. , Keogh Michael-Christopher , Shilatifard Ali , Kelleher Neil L.
Published: September 2020

Nuc-MS characterizes histone modifications and variants directly from intact endogenous nucleosomes. Preserving whole nucleosome particles enables precise interrogation of their protein content, as for H3.3-containing nucleosomes which had 6-fold co-enrichment of variant H2A.Z over bulk chromatin. Nuc-MS, validated by ChIP-seq, showed co-occurrence of oncogenic H3.3K27M with euchromatic marks (e.g., H4K16ac and >15-fold enrichment of H3K79me2). By capturing the entire epigenetic landscape, Nuc-MS provides a new, quantitative readout of nucleosome-level biology.
Identification of colonisation and virulence determinants ofStreptococcus pneumoniaevia experimental evolution in mouse infection models
Authors: Green Angharad E , Howarth Deborah , Chaguza Chrispin , Echlin Haley , Langendonk R Frèdi , Munro Connor , Barton Thomas E , Hinton Jay CD , Bentley Stephen D , Rosch Jason W , Neill Daniel R
Published: September 2020

Streptococcus pneumoniaeis a commensal of the human nasopharynx and a major cause of respiratory and invasive disease. Pneumococcus stimulates upper respiratory tract inflammation that promotes shedding from mucosal surfaces and transmission to new hosts. Colonisation and transmission are partially antagonistic processes. Adhesion to surfaces and evasion of host responses favours the former, whilst detachment, promoted by inflammation, is necessary for the latter. We sought to determine how adaptation and evolution of pneumococcus within its nasopharyngeal niche might progress when selective pressures associated with transmission were removed. This was achieved by serial passage of pneumococci in mouse models of nasopharyngeal carriage, manually transferring bacteria between mice. To assess the role of host environmental factors on pneumococcal evolution, we also performed analogous experimental evolution in a mouse pneumonia model, passaging pneumococci through lungs. Nasopharynx-passaged pneumococci became more effective colonisers, whilst those evolved within lungs showed reduced virulence. We observed selection of mutations in genes associated with cell wall biogenesis and metabolism in both nasopharynx and lung lineages, but identified prominent examples of parallel evolution that were niche specific. We focussed ongpsA, a gene in which the same single nucleotide polymorphism arose in two independently evolved nasopharynx-passaged lineages. We identified a single nucleotide change conferring resistance to oxidative stress and enhanced nasopharyngeal colonisation potential. We show thatgpsAis also a frequent target of mutation during human colonisation. These findings highlight the role played by the host environment in determining trajectories of bacterial evolution and the potential of experimental evolution in animal infection models for identification of novel pathogen virulence and colonisation factors.
Viral infection of algal blooms leaves a halogenated footprint on the dissolved organic matter in the ocean
Authors: Kuhlisch Constanze , Schleyer Guy , Shahaf Nir , Vincent Flora , Schatz Daniella , Vardi Assaf
Published: September 2020

Algal blooms are important hotspots of primary production in the ocean, forming the basis of the marine food web and fueling the pool of dissolved organic matter (DOM)1, which is the largest global inventory of reduced carbon and a market place for metabolic exchange in the ocean2. Marine viruses are key players in controlling algal bloom demise and act as major biogeochemical drivers of nutrient cycling and metabolic fluxes by shunting algal biomass from higher trophic levels to the DOM pool, a process termed the ‘viral shunt’3,4. Nevertheless, the metabolic composition of virus-induced DOM (vDOM) in the marine environment is unknown. To decode the metabolic footprint of the ‘viral shunt’, we induced a bloom of the ecologically important algaEmiliania huxleyiin the natural environment, and followed its succession using an untargeted exometabolomics approach. Here we show that algal bloom succession induces extensive and dynamic changes in the exometabolic landscape, especially during bloom demise. By correlating to a specific viral gene marker, we discovered a set of novel chlorine-iodine-containing metabolites that were induced by viral infection and copiously released during bloom demise. We further detected several of these chloro-iodo metabolites in virus-infected open ocean blooms ofE. huxleyi, supporting their use as sensitive biomarkers for virus-induced demise in the natural environment. Therefore, we propose halogenation to be a hallmark of theE. huxleyivDOM, providing insights into the profound metabolic consequences of viral infection for the marine DOM pool.
Effects of substrate availability on growth and metabolism in soil microbes: Insights from theoretical modeling of studies of the Warburg effect and substrate-induced respiration
Authors: Swain Anshuman , Fagan William F
Published: September 2020

Carbon Use Efficiency (CUE) is a popular concept for measuring the efficiency of biomass production in different biological systems and, is frequently employed to understand effects of microbial processes on soil carbon dynamics. CUE in soil microbes is often measured through respiration-based studies, especially through the addition of a labile carbon substrate such as glucose. Therefore, exploring the response of microbial respiration to availability of labile substrates is crucial to understand microbial CUE in soils. In this work, we build upon a cellular model of the Warburg effect, where cells simultaneously utilize inefficient aerobic glycolysis/fermentation and efficient oxidative phosphorylation pathways for energy synthesis even at high oxygen availability, to predict microbial community response to various levels of substrate availability. We test our predictions systematically using a series of substrate-induced respiration (SIR) experiments to demonstrate prevalence of the Warburg effect in soil microbial communities. We further discuss the relevance of the underlying metabolic processes behind the Warburg effect in interpreting soil microbial CUE.
Terminal Modification, Sequence, and Length Determine Small RNA Stability in Animals
Authors: Gainetdinov Ildar , Colpan Cansu , Cecchini Katharine , Albosta Paul , Jouravleva Karina , Vega-Badillo Joel , Lee Yongjin , Özata Deniz M. , Zamore Phillip D.
Published: September 2020

In animals, piRNAs, siRNAs, and miRNAs silence transposons, fight viral infections, and regulate gene expression. piRNA biogenesis concludes with 3′ terminal trimming and 2′-O-methylation. Both trimming and methylation influence piRNA stability. Here, we report that trimming and methylation protect mouse piRNAs from different decay mechanisms. In the absence of 2′-O-methylation, mouse piRNAs with extensive complementarity to long RNAs become unstable. In flies, 2′-O-methylation similarly protects both piRNAs and siRNAs from complementarity-dependent destabilization. Animal miRNAs are unmethylated, and complementarity-dependent destabilization helps explain differences in miRNA decay rates in both mice and flies. In contrast, trimming protects mouse piRNAs from a separate degradation pathway unaffected by target complementarity but sensitive to the 3′ terminal, untrimmed sequence. Because distinct sets of mouse piRNAs are protected by each of these mechanisms, loss of both trimming and 2′-O-methylation causes the piRNA pathway to collapse, demonstrating that these two small RNA modifications collaborate to stabilize piRNAs.

Highlights

2′-O-methylation protects mouse and fly piRNAs from complementarity-dependent decay

2′-O-methylation protects fly siRNAs with extensive complementarity to long RNAs

Complementarity to long RNAs predicts the half-life of fly and mouse miRNAs

Mouse pre-piRNA decay reflects both pre-piRNA sequence and PIWI protein identity
The risk of introducing SARS-CoV-2 to the UK via international travel in August 2020
Authors: Taylor Rachel A. , McCarthy Catherine , Patel Virag , Moir Ruth , Kelly Louise A , Snary Emma L
Published: September 2020

International travel poses substantial risks for continued introduction of SARS-CoV-2. As of the 17th August 2020, travellers from 12 of the top 25 countries flying into the UK are required to self-isolate for 14 days. We estimate that 895 (CI: 834–958) infectious travellers arrive in a single week, of which 87% (779, CI: 722–837) originate from countries on the UK quarantine list. We compare alternative measures to the 14 day self-isolation (78.0% effective CI: 74.4–81.6) which could be more feasible long-term. A single RT-PCR taken upon arrival at the airport is 39.6% (CI: 35.2–43.7) effective, or equivalently, it would only detect 2 in 5 infectious passengers. Alternatively, testing four days after arrival is 64.3% (CI: 60.0–68.3) effective whereas a test at the airport plus additional test four days later is 68.9% (CI: 64.9–73.0) effective. Rapidly implementing control measures for travellers from risky countries is vital to protect public health; this methodology can be quickly updated to assess the impact of any further changes to international travel policy or disease occurrence.
Early indirect impact of COVID-19 pandemic on utilization and outcomes of reproductive, maternal, newborn, child and adolescent health services in Kenya
Authors: Shikuku Duncan , Nyaoke Irene , Gichuru Sylvia , Maina Onesmus , Eyinda Martin , Godia Pamela , Nyaga Lucy , Ameh Charles
Published: September 2020

Background

The COVID-19 global pandemic is expected to result in 8.3–38.6% additional maternal deaths in many low-income countries. The objective of this paper was to determine the initial impact of COVID-19 pandemic on reproductive, maternal, newborn, child and adolescent health (RMNCAH) services in Kenya.

Methods

Data for the first four months (March-June) of the pandemic and the equivalent period in 2019 were extracted from Kenya Health Information System. Two-sample test of proportions for hospital attendance for select RMNCAH services between the two periods were computed.

Results

There were no differences in monthly mean (±SD) attendance between March-June 2019 vs 2020 for antenatal care (400,191.2±12,700.0 vs 384,697.3±20,838.6), hospital births (98,713.0±4,117.0 vs 99,634.5±3,215.5), family planning attendance (431,930.5±19,059.9 vs 448,168.3±31,559.8), post-abortion care (3,206.5±111.7 vs 448,168.3±31,559.8) and pentavalent 1 immunisation (114,701.0±3,701.1 vs 110,915.8±7,209.4), p>0.05. However, there were increasing trends for adolescent pregnancy rate, significant increases in FP utilization among young people (25.7% to 27.0%), injectable (short-term) FP method uptake (58.2% to 62.3%), caesarean section rate (14.6% to 15.8%), adolescent maternal deaths (6.2% to 10.9%) and fresh stillbirths (0.9% to 1.0%) with a reduction in implants (long-term) uptake (16.5% to 13.0%) (p< 0.05). No significant change in maternal mortality ratio between the two periods (96.6 vs 105.8/100,000 live births, p = 0.1023) although the trend was increasing.

Conclusion

COVID-19 may have contributed to increased adolescent pregnancy, adolescent maternal death and stillbirth rates in Kenya. If this trend persists, recent gains achieved in maternal and perinatal health in Kenya will be lost. With uncertainty around the duration of the pandemic, strategies to mitigate against catastrophic indirect maternal health outcomes are urgently needed.
Alleviation of neuropathic pain by over-expressing a soluble colony-stimulating factor 1 receptor
Authors: Gushchina Svetlana , Yip Ping K. , Parry Glesni A. , Sivakumar Haripriya , Li Jie , Liu Min , Bo Xuenong
Published: September 2020

In this study, we aim to alleviate neuropathic pain by suppressing microgliosis and macrophage accumulation, which is achieved by over-expressing a non-functional soluble colony-stimulating factor 1 receptor using adeno-associated virus 9 vectors (AAV9/sCSF1R). AAV9/sCSF1R and AAV9/GFP were intrathecally administered into mouse lumbar spine. Two weeks later, these mice underwent partial sciatic nerve ligation to induce neuropathic pain. GFP and sCSF1R were highly expressed in dorsal root ganglia (DRG) and spinal cords in AAV9-injected mice. Nerve ligation alone or pre-treated with AAV9/GFP led to significant microgliosis in the lumbar spinal cords and macrophage accumulation in DRG and sciatic nerves. In nerve-ligated mice pre- treated with AAV9/sCSF1R the microglia densities in the dorsal and ventral horns and macrophage densities in DRG and sciatic nerves were significantly lower compared to nerve-ligated mice pre-treated with AAV9/GFP. Behavioural tests showed that nerve-ligated mice pre- treated with AAV9/sCSF1R had a significantly higher paw withdrawal threshold, indicating the alleviation of neuropathic pain. The results implicate that viral vector-mediated expression of sCSF1R may represent a novel strategy in long-term alleviation of neuropathic pain.
Overconfidence in visual perception in Parkinson’s disease
Authors: Halperin Orly , Karni Roie , Israeli-Korn Simon , Hassin-Baer Sharon , Zaidel Adam
Published: September 2020

Background

Increased dependence on visual cues in Parkinson’s disease (PD) can unbalance the perception-action loop, impair multisensory integration, and affect everyday function of PD patients. It is currently unknown why PD patients seem to be more reliant on their visual cues.

Objectives

We hypothesized that PD patients may be overconfident in the reliability (precision) of their visual cues. In this study we tested coherent visual motion perception in PD, and probed subjective (self-reported) confidence in their visual motion perception.

Methods

20 patients with idiopathic PD, 21 healthy aged-matched controls and 20 healthy young adult participants were presented with visual stimuli of moving dots (random dot kinematograms). They were asked to report: (1) whether the aggregate motion of dots was to the left or to the right, and (2) how confident they were that their perceptual discrimination was correct.

Results

Visual motion discrimination thresholds were similar (unimpaired) in PD compared to the other groups. By contrast, PD patients were significantly overconfident in their visual perceptual decisions (p=0.002 andp<0.001 vs. the age-matched and young adult groups, respectively).

Conclusions

These results suggest intact visual motion perception, but overestimation of visual cue reliability, in PD. Overconfidence in visual (vs. other, e.g., somatosensory) cues could underlie accounts of increased visual dependence and impaired multisensory integration in PD, and could contribute to gait and balance impairments. Future work should investigate PD confidence in somatosensory function. A better understanding of altered sensory reliance in PD might open up new avenues to treat debilitating symptoms.
ErbB dysregulation impairs cognition via myelination-dependent and - independent oligodendropathy
Authors: Hu Xu , Xiao Guanxiu , He Li , Zhu Qingyu , Niu Xiaojie , Li Huashun , Xu Qi , Wei Zhengdong , Huang Hao , Luan Yifei , Qiu Mengsheng , Tanaka Kenji F. , Shen Ying , Tao Yanmei
Published: September 2020

White matter abnormalities are an emerging pathological feature of schizophrenia. However, their attributions to the disease remain largely elusive. ErbB receptors and their ligands, some of which are essential for peripheral myelination, confer susceptibility to schizophrenia. By synergistically manipulating ErbB receptor activities in a oligodendrocyte-stage-specific manner in mice after early development, we demonstrate the distinct effects of ErbB signaling on oligodendrocytes at various differentiation states. ErbB overactivation, in mature oligodendrocytes, induces necroptosis causing demyelination, whereas in oligodendrocyte precursor cells, induces apoptosis causing hypomyelination. In contrast, ErbB inhibition increases oligodendrocyte precursor cell proliferation but induces hypomyelination by suppressing the myelinating capabilities of newly-formed oligodendrocytes. Remarkably, ErbB inhibition in mature oligodendrocytes diminishes axonal conduction under energy stress and impairs working memory capacity independently of myelin pathology. This study reveals the etiological implications of oligodendrocyte vulnerability induced by ErbB dysregulation, and elucidates the pathogenetic mechanisms for variable structural and functional white matter abnormalities.
Domestic waste policy in Ireland – economization and the role of accounting
Authors: Quinn Martin , Feeney Orla
Published: September 2020

Purpose

This paper examines how accounting concepts were utilised in domestic waste collection services in Ireland over the past two decades or so. In comparison to other former “free” services in the Irish context, the prevalence of accounting concepts has been greater and delivered a more successful outcome.

Design/methodology/approach

Drawing on the concepts of calculation, the “economic” and economization, events around domestic waste policy in Ireland are examined, and the increasing prevalence of concepts such as price, cost and profitability in these processes are a focal point. Publicly available documents such as government policy documents, parliamentary records and media reports are utilised to draw out these concepts. The period of analysis is 1996–2018.

Findings

The findings reveal the role of accounting concepts in the economization of domestic waste policy in Ireland. The result of the economization process was a fully privatised, profit-oriented, price-monitored system.

Research limitations/implications

This research provides a broad view of accounting concepts in the management of domestic waste. It highlights how waste policy in Ireland travelled through instances of being political and economic over time. The research is limited by its use of secondary data.

Originality/value

This study highlights how accounting concepts were used in varying ways to bring about a satisfactory solution to domestic waste disposal in Ireland, namely the privatisation of waste services.
Contribution of prejudiced clustering education system in developing horizontal and vertical mismatch in job market: quality of employees in banking sector
Authors: Alam Gazi Mahabubul , Roslan Samsilah
Published: September 2020

Purpose

Education system supplies the required manpower in order to ensure the national prosperity. A salient link between education and business sector is a prerequisite to cater economically productive manpower. Economic and social development supplements each other that can only be ensured via a functional education system. A dysfunction education system created by a biased clustering policy develops a greater horizontal and vertical mismatch with the job market in many developing nations. This mismatch dents the quality of business management that halts the national prosperity. Therefore, the role of education has become questionable. This research aims to bridge between education and business sectors.

Design/methodology/approach

Given the differentiated nature of research questions, multiple techniques are used to collect the data. However, this research bears the norms of qualitative method. Both secondary and primary data are used. While, secondary data are collected by the banks, Bangladesh Bureau of Educational Information and Statistics (BANBEIS) and by the University Grants Commission (UGC), primary data are collected through interviews. Document review and data collected through personal communication with members of staff of sampled banks and institutes of HE also supplements. Data were collected from six commercial banks and from the Central Bank.

Findings

Findings suggest that clustering system favours science graduates by depriving business counterpart, which creates an atmosphere of educational disparity. This disparity affects the symbiotic and reciprocal relationship that exists amongst different provisions (i.e. secondaryand tertiary) of education. Favoured clustering system further contributes for a larger “horizontal educational mismatch” with job market. Therefore, science graduates occupy the places in the banks where business graduates should ideally be employed. Being a dysfunction system, education fails to support substantially for social and economic developments.

Originality/value

A few studies are conducted in the area of HE in Bangladesh but none covers the issue of impact of clustering system of education in secondary provision on HE and job market. Graduates' performance in carrying out the jobs is seen as the most important element for the business management. This study has suggested a unique way forward which would be able to reduce the mismatch between education system and job market, enabling a substantial business management process. Considering this, the paper is first on its kind.
Global to small island; a cross-scale foresight scenario exercise
Authors: Drakes Crystal , Cashman Adrian , Kemp-Benedict Eric , Laing Timothy
Published: September 2020

Purpose

The use of socio-economic scenarios in small island developing states (SIDS) when assessing, and planning for, the impacts of global changes on national socioeconomic and environmental systems is still in its infancy. The research conducts a cross-scale foresight scenario exercise to produce regional scenarios and national storylines for Caribbean islands that are of “partial” consistency to the shared socioeconomic pathways (SSPs) and representative concentration pathways (RCPs) and shows how future socioeconomic and climatic changes can be applied to inform natural resource management decisions.

Design/methodology/approach

To develop the scenarios, the study uses a three-staged linking process using mixed methods to “triangulate” each technique to compensate for weaknesses of one method by introducing a complementary method at each stage. A participatory-expert stepwise approach with feedback loops is used and complemented with a climate sensitive tourism water demand model.

Findings

Four regional exploratory socio-economic scenarios were constructed that are partially consistent with global scenarios. In addition, national storylines for four island states were developed based on the regional scenarios. Using RCP 4.5 hotel water demand in Barbados is estimated under three of the regional scenarios based on compatibility. The results indicate there is a 17% difference between the highest and lowest estimated water demand, indicating the effect of varying socio-economic conditions on water demand.

Originality/value

The paper contributes to the literature by presenting regional socio-economic scenarios, specifically for SIDS, that are partially consistent with both global climatic RCPs and SSPs using a cross-scale approach. The scenarios are then used to demonstrate how future socio-economic pathways impact on freshwater demand.