bluuebunny/crossref_metadata_2025_split huggingface dataset:
The phylogenetic and global distribution of bacterial polyhydroxyalkanoate bioplastic degrading genes
Authors: Viljakainen V. R. , Hug L. A. 
Published: May 2020

SummaryPolyhydroxyalkanoates (PHAs) are a family of microbially-made polyesters commercialized as biodegradable plastics. PHA production rates are predicted to increase as concerns around environmental plastic contamination and limited fossil fuel resources have increased the importance of biodegradable and bio-based plastic alternatives. Microbially-produced PHA depolymerases are the key enzymes mediating PHA biodegradation, but only a few PHA depolymerases have been well-characterized and screens employing metagenomic sequence data are lacking. Here, we used 3,078 metagenomes to analyze the distribution of PHA depolymerases in microbial communities from diverse aquatic, terrestrial and waste management systems. We significantly expand the recognized diversity of this protein family by screening 1,914 Gb of sequence data and identifying 13,869 putative PHA depolymerases in 1,295 metagenomes. Our results indicate that PHA depolymerases are unevenly distributed across environments. We predicted the highest frequency of PHA depolymerases in wastewater systems and the lowest in marine and thermal springs. In tandem, we screened 5,290 metagenome-assembled genomes to describe the phylogenetic distribution of PHA depolymerases, which is substantially broader compared to current cultured representatives. The Proteobacteria and Bacteroidota are key lineages encoding PHA depolymerases, but PHA depolymerases were predicted from members of the Bdellovibrionota, Methylomirabilota, Actinobacteriota, Firmicutes, Spirochaetota, Desulfobacterota, Myxococcota and Planctomycetota.Originality/Significance StatementBiodegradable plastics like polyhydroxyalkanoates (PHAs) are a hot topic, following ubiquitous environmental plastic contamination, government bans on single-use plastics, and a growing need for sustainable alternatives to petroleum-based plastics. Understanding the microbial conversion of PHAs in the environment and finding biomolecular tools that can act on PHAs is increasingly important as PHAs grow in popularity. In this study, we screened thousands of metagenomes and metagenome-assembled genomes (MAGs) to substantially increase the recognized diversity of PHA depolymerases, the key enzymes mediating PHA biodegradation. We use datasets from seven continents to provide a global summary of the distribution of PHA depolymerase genes in natural environments and waste-management systems. In tandem, we increase the number of described phylum-level lineages with PHA biodegradation potential. This work contributes a new understanding of the phylogenetic and environmental distribution of PHA depolymerases.
The CCCTC-binding factor CTCF represses hepatitis B virus Enhancer I and regulates viral transcription
Authors: D’Arienzo V , Ferguson J , Giraud G , Chapus F , Harris JM , Wing PAC , Claydon A , Begum S , Zhuang X , Balfe P , Testoni B , McKeating JA , Parish JL 
Published: May 2020

ABSTRACTHepatitis B virus (HBV) infection is of global importance with over 2 billion people exposed to the virus during their lifetime and at risk of progressive liver disease, cirrhosis and hepatocellular carcinoma. HBV is a member of thehepadnaviridaefamily that replicates via episomal copies of a covalently closed circular DNA (cccDNA) genome. The chromatinization of this small viral genome, with overlapping open reading frames and regulatory elements, suggests an important role for epigenetic pathways to regulate viral transcription. The chromatin-organising transcriptional insulator protein CCCTC-binding factor (CTCF) has been reported to regulate transcription in a diverse range of viruses. We identified two conserved CTCF binding sites in the HBV genome within Enhancer I and chromatin immunoprecipitation (ChIP) analysis demonstrated an enrichment of CTCF binding to integrated or episomal copies of the viral genome. siRNA knockdown of CTCF results in a significant increase in pre-genomic RNA levels inde novoinfected HepG2 cells and those supporting episomal HBV DNA replication. Furthermore, mutation of these sites in HBV DNA minicircles abrogated CTCF binding and increased pre-genomic RNA levels, providing evidence of a direct role for CTCF in repressing HBV transcription.IMPORTANCEHepatitis B virus (HBV) is a global cause of liver disease. At least 300 million individuals are chronically infected with HBV, frequently leading to life-threatening liver cirrhosis and cancer. Following viral entry, HBV DNA enters the nucleus and is bound by histones that are subject to epigenetic modification. The HBV genome contains two enhancer elements that stimulate viral transcription but the interplay between the viral enhancers and promoters is not fully understood. We have identified the host cell protein CCCTC binding factor (CTCF) as a repressor of HBV gene expression. CTCF binds to the HBV genome within Enhancer I and represses transcription of pre-genomic RNA. These findings provide new insights into how HBV transcription is regulated and show a new role for CTCF as a transcriptional insulator by associating with the viral genome between Enhancer I and the downstream basal core promoter.
Integron Gene Cassettes Harboring Novel Variants of D-Alanine-D-Alanine Ligase Confer High-level Resistance to D-Cycloserine
Authors: Rahman Md. Ajijur , Kaiser Frank , Jamshidi Shirin , Rahman Khondaker Miraz , Mullany Peter , Roberts Adam P. 
Published: May 2020

AbstractDuring a PCR-based screen of antibiotic resistance genes (ARGs) associated with integrons in saliva-derived metagenomic DNA of healthy human volunteers, two novel variants of genes encoding a D-alanine-D-alanine ligase (ddl6andddl7) located within gene cassettes in the first position of a reverse integron were identified.Treponema denticolawas identified as the likely host of theddlcassettes. Bothddl6andddl7conferred high level resistance to D-cycloserine when expressed inEscherichia coliwithddl7conferring four-fold higher resistance to D-cycloserine compared toddl6. A SNP was found to be responsible for this difference in resistance phenotype between bothddlvariants. Molecular dynamics simulations were used to explain the mechanism of this phenotypic change at the atomic scale. A hypothesis for the evolutionary selection ofddlcontaining integron gene cassettes is proposed, based on molecular docking of plant metabolites within the ATP and D-cycloserine binding pockets of Ddl.Significance StatementThe drivers of antimicrobial resistance are varied and numerous. One such hypothesis is that compounds not normally considered to be antibiotics may be able to select for genes that can provide resistance to conventional antibiotics. Here we provide evidence that dietary flavonoids are likely to provide the selective pressure for two novel variants of theddlgene, encoding D-alanine-D-alanine ligases, to be maintained as the first gene cassette of a reverse integron detectable in the human oral cavities from both the UK and Bangladesh. We show that Ddl is functional, able to confer resistance to D-cycloserine and that the dietary flavonoids quercetin and apigenin are likely able to compete with both ATP and D-cycloserine within their Ddl binding sites.
Evolutionary history of inversions in the direction of architecture-driven mutational pressures in crustacean mitochondrial genomes
Authors: Zhang Dong , Zou Hong , Zhang Jin , Wang Gui-Tang , Jakovlić Ivan 
Published: May 2020

AbstractInversions of the origin of replication (ORI) of mitochondrial genomes produce asymmetrical mutational pressures that can cause artefactual clustering in phylogenetic analyses. It is therefore an absolute prerequisite for all molecular evolution studies that use mitochondrial data to account for ORI events in the evolutionary history of their dataset. The number of ORI events in crustaceans remains unknown; several studies reported ORI events in some crustacean lineages on the basis of fully inversed (e.g. negative vs. positive) GC skew patterns, but studies of isolated lineages could have easily overlooked ORI events that produced merely a reduction in the skew magnitude. In this study, we used a comprehensive taxonomic approach to systematically study the evolutionary history of ORI events in crustaceans using all available mitogenomes and combining signals from lineage-specific skew magnitude and direction (+ or -), cumulative skew diagrams, and gene rearrangements. We inferred 24 putative ORI events (14 of which have not been proposed before): 17 with relative confidence, and 7 speculative. Most of these were located at lower taxonomic levels, but there are indications of ORIs that occurred at or above the order-level: Copepoda, Isopoda, and putatively in Branchiopoda and Poecilostomatida+Cyclopoida. Several putative ORI events did not result in fully inversed skews. In many lineages skew plots were not informative for the prediction of replication origin and direction of mutational pressures, but inversions of the mitogenome fragment comprising the ancestral CR (rrnS-CR-trnI) were rather good predictors of skew inversions. We also found that skew plots can be a useful tool to indirectly infer the relative strengths of mutational/purifying pressures in some crustacean lineages: when purifying pressures outweigh mutational, GC skew plots are strongly affected by the strand distribution of genes, and when mutational > purifying, GC skew plots can be even completely (apparently) unaffected by the strand distribution of genes. This observation has very important repercussions for phylogenetic and evolutionary studies, as it implies that not only the relatively rare ORI events, but also much more common gene strand switches and same-strand rearrangements can produce mutational bursts, which in turn affect phylogenetic and evolutionary analyses. We argue that such compositional biases may produce misleading signals not only in phylogenetic but also in other types of evolutionary analyses (dN/dS ratios, codon usage bias, base composition, branch length comparison, etc.), and discuss several such examples. Therefore, all studies aiming to study the evolution of mtDNA sequences should pay close attention to architectural rearrangements.
Coordinated crosstalk between microtubules and actin by a spectraplakin regulates lumen formation and branching
Authors: Ricolo Delia , Araújo Sofia J. 
Published: May 2020

SUMMARYThe establishment of branched structures by single cells involves complex cytoskeletal remodelling events. InDrosophila, epithelial tracheal system terminal cells (TCs) and dendritic arborisation neurons are models for these subcellular branching processes. During tracheal embryonic development, the generation of subcellular branches is characterized by extensive remodelling of the microtubule (MT) network and actin cytoskeleton, followed by vesicular transport and membrane dynamics. We have previously shown that centrosomes are key players in the initiation of subcellular lumen formation where they act as microtubule organizing centres (MTOCs). However, not much is known on the events that lead to the growth of these subcellular luminal branches or what makes them progress through a particular trajectory within the cytoplasm of the TC. Here, we have identified that the spectraplakinShort-stop(Shot) promotes the crosstalk between MTs and actin, which leads to the extension and guidance of the subcellular lumen within the TC cytoplasm. Shot is enriched in cells undergoing the initial steps of subcellular branching as a direct response to FGF signalling. An excess of Shot induces ectopic acentrosomal branching points in the embryonic and larval tracheal TC leading to cells with extra subcellular lumina. These data provide the first evidence for a role for spectraplakins in subcellular lumen formation and branching.
Central role and structure of the membrane pseudokinase YukC in the antibacterialBacillus subtilisType VIIb Secretion System
Authors: Tassinari Matteo , Doan Thierry , Bellinzoni Marco , Chabalier Maïalene , Ben-Assaya Mathilde , Martinez Mariano , Gaday Quentin , Alzari Pedro M. , Cascales Eric , Fronzes Rémi , Gubellini Francesca 
Published: May 2020

AbstractType VIIb Secretion System (T7SSb) has been recently identified in Firmicutes resembling the mycobacterial T7SSa. Despite limited sequence homology, T7SSa and T7SSb have substrates with striking structural similarities, the WXG100 proteins. Recent advances inStaphylococcus spp. proposed that T7SSb is involved in intra-species competition. However, the architecture and mechanism of action of this secretion complex remain largely obscure. Here, we investigate the T7SSb ofBacillus subtilisas a model system. We report the first evidence ofB. subtilisability to mediate intra- and inter-species antibacterial activity in a T7SSb-dependent manner. Then, we present the first systematic investigation of the T7SSb protein-protein network, revealing novel interactions and highlighting the central role of the pseudokinase subunit YukC in the assembly of the system. Its direct interaction with a T7SSb-secreted toxin supports its role in recruiting substrates to the secretion machinery. Finally, we solved the crystal structure of full-length transmembrane YukC defining novel structural motifs and suggesting that intrinsic flexibility modulates the orientation of the pseudokinase domains and YukC function. Overall, our results provide a better understanding on the role and molecular organisation of the T7SSb, opening new perspectives for the comprehension of this poorly characterized molecular machine.
Phototaxis of the unicellular red algaCyanidioschyzon merolaeis mediated by novel actin-driven tentacles
Authors: Maschmann Sascha , Ruban Karin , Wientapper Johanna , Walter Wilhelm J. 
Published: May 2020

Phototaxis – which is the ability to move towards or away from a light source autonomously – is a common mechanism of unicellular algae. It evolved multiple times independently in different plant lineages1. As of yet, algal phototaxis has been mainly linked to the presence of cilia, the only known locomotive organelle in unicellular algae. Consequently, phototaxis was believed to be largely absent in red algae (Rhodophyta) that lack cilia in all stages of their life cycle1. Remarkably, the unicellular red algaCyanidioschyzon merolae(C. merolae) is able to move towards the light. However, it has remained unclear howC. merolaecan achieve movement, and the presence of a completely new mechanism was suggested2.Here we show that the basis of this movement are novel retractable projections that were termed tentacles due to their distinct morphology. The tentacles could be reproducibly induced within 20 minutes by increasing the salt concentration of the culture medium. Electron microscopy revealed filamentous structures inside the tentacles that we identified to be actin filaments. This is surprising asC. merolae’s single actin gene was previously published to not be expressed3,4. Based on our findings, we propose a model forC. merolae’s actin-driven but myosin-independent motility. To our knowledge, the described tentacles represent a novel motility mechanism.
Fungi are colder than their surroundings
Authors: Cordero Radames JB , Mattoon Ellie Rose , Casadevall Arturo 
Published: May 2020

AbstractFungi play essential roles in global ecology and economy, but their thermal biology is widely unknown. Mushrooms were previously noticed to be colder than surrounding air via evaporative cooling or evapotranspiration. Here we applied infrared imaging to reveal that not just mushrooms, but also molds and yeasts maintain colder temperatures than their surroundings via evapotranspiration. On average, fungal specimens are ~2.5 °C colder than the surrounding temperature. The relatively cold temperature of mushrooms can be observed throughout the whole fruiting process and at the level of mycelium. The mushroom’s hymenium appeared the coldest and different areas of thePleurotus ostreatusmushroom appear to dissipate heat differently. Evapotranspiration in yeast and mold biofilms can be measured from the accumulation of condensed water droplets above biofilms; which is significantly higher than the surrounding agar. We also present a mushroom-based air-cooling system (MycoCooler™) capable of passively reducing the temperature of a closed compartment by approximately 10 °C in 25 minutes. These findings suggest that the fungal kingdom is characteristically cold. Since fungi make up ~2% of Earth biomass, their evapotranspiration may contribute to planetary temperatures in local environments. This study present new research avenues in fungal biology, biomedicine, microclimate, and sustainable energy.
Irisin Directly Stimulates Osteoclastogenesis and Bone ResorptionIn VitroandIn Vivo
Authors: Estell Eben G. , Le Phuong T. , Vegting Yosta , Kim Hyeonwoo , Baron Roland , Spiegelman Bruce , Rosen Clifford J. 
Published: May 2020

AbstractThe myokine irisin facilitates muscle-bone crosstalk and skeletal remodeling in part by its action on osteoblasts and osteocytes. In the current study we investigated whether irisin also directly regulates osteoclasts.In vitro, irisin (2-10 ng/mL) increased osteoclast differentiation in C57BL/6J bone marrow progenitors; this increase was blocked by a neutralizing antibody to integrin αVβ5. Irisin also increased resorption on several substratesin situ. RNAseq revealed differential gene expression induced by irisin including upregulation of markers for osteoclast differentiation and resorption, as well as osteoblast-stimulating ‘clastokines’.In vivo, forced expression of the irisin precursorFndc5in murine muscle resulted in low bone mass and increased number of osteoclasts. Taken together, our work demonstrates that irisin acts directly on cultured osteoclast progenitors to increase differentiation and promote bone resorption. These actions support the tenet that irisin not only stimulates bone remodeling but may also be an important counter-regulatory hormone during exercise.
ACE2 and TMPRSS2 are expressed on the human ocular surface, suggesting susceptibility to SARS-CoV-2 infection
Authors: Zhou Lingli , Xu Zhenhua , Castiglione Gianni M. , Soiberman Uri S. , Eberhart Charles G. , Duh Elia J. 
Published: May 2020

AbstractPurposeConjunctival signs and symptoms are observed in a subset of patients with COVID-19, and SARS-CoV-2 has been detected in tears, raising concerns regarding the eye both as a portal of entry and carrier of the virus. The purpose of this study was to determine whether ocular surface cells possess the key factors required for cellular susceptibility to SARS-CoV-2 entry/infection.MethodsWe analyzed human post-mortem eyes as well as surgical specimens for the expression of ACE2 (the receptor for SARS-CoV-2) and TMPRSS2, a cell surface-associated protease that facilitates viral entry following binding of the viral spike protein to ACE2.ResultsAcross all eye specimens, immunohistochemical analysis revealed expression of ACE2 in the conjunctiva, limbus, and cornea, with especially prominent staining in the superficial conjunctival and corneal epithelial surface. Surgical conjunctival specimens also showed expression of ACE2 in the conjunctival epithelium, especially prominent in the superficial epithelium, as well as the substantia propria. All eye and conjunctival specimens also expressed TMPRSS2. Finally, western blot analysis of protein lysates from human corneal epithelium obtained during refractive surgery confirmed expression of ACE2 and TMPRSS2.ConclusionsTogether, these results indicate that ocular surface cells including conjunctiva are susceptible to infection by SARS-CoV-2, and could therefore serve as a portal of entry as well as a reservoir for person-to-person transmission of this virus. This highlights the importance of safety practices including face masks and ocular contact precautions in preventing the spread of COVID-19 disease.
Labeling subcellular structures in living specimens using live-cell incompatible dyes with excellent optical properties
Authors: Han Yubing , Zhang Zhimin , Liu Wenjie , Yao Yuanfa , Chen Yuchen , Luo Xin , Wang Wensheng , Xu Yingke , Liu Xu , Kuang Cuifang , Hao Xiang 
Published: May 2020

AbstractDespite the urgent needs of imaging living specimens for cutting-edge biological research, most of the existing fluorescent labeling methods suffer from either poor optical properties or complicated operations to realize cell-permeability and specificity. Here, we introduce a method to overcome this tradeoff by incubating living cells and tissues with fluorescent dyes, no matter if they are cell-permeable or not, at particular conditions (concentration and temperature) without physical cell-penetration or chemical modifications. Based on this method, the mitochondrial labeling capability of Atto dyes, especially Atto 647N with extraordinary optical properties, together with interesting interactions between organelles is revealed. These results indicate the great potential of using dyes, which are normally considered “live-cell incompatible”, to capture the morphology and dynamics of subcellular structures in living specimens.
Loss of clathrin heavy chain enhances actin-dependent stiffness of mouse embryonic stem cells
Authors: Mote Ridim D , Yadav Jyoti , Singh Surya Bansi , Tiwari Mahak , Patil Shivprasad , Subramanyam Deepa 
Published: May 2020

AbstractMouse embryonic stem cells (mESCs) display unique mechanical properties, including low cell stiffness, and specific responses to features of the underlying substratum. Using atomic force microscopy (AFM), we demonstrate that mESCs lacking the clathrin heavy chain (Cltc), display higher Young’s modulus, indicative of greater cellular stiffness, in comparison to WT mESCs. We have previously shown that mESCs lackingCltcdisplay a loss of pluripotency, and an initiation of differentiation. The increased stiffness observed in these cells was accompanied by the presence of actin stress fibres and accumulation of the inactive, phosphorylated, actin binding protein, Cofilin. Treatment ofCltcknockdown mESCs with actin polymerization inhibitors resulted in a decrease in the Young’s modulus, to values similar to those obtained with WT mESCs. However, the expression profile of pluripotency factors was not rescued. This indicates that a restoration of mechanical properties, through modulation of the actin cytoskeleton, may not always be accompanied by a change in the expression of critical transcription factors that regulate the state of a stem cell, and that this may be dependent on the presence of active endocytosis in a cell.
From organizing to organizations: a typological scale of human relations management outside the legal world
Authors: Neumann Martin 
Published: May 2020

PurposeThe article examines strategies of human resource management in the absence of institutional hedging by norm-enforcing institutions such as a state monopoly of violence by using case studies of criminal organizations. This condition provides a test-bed for studying the effects of human relations management strategies on organizational performance.Design/methodology/approachFor this purpose, a case study methodology is applied. Three cases are selected to build a scale from complete plasticity of an undifferentiated network via a status differentiated gang to a hierarchical organization that provides social positions. The case studies are analysed by qualitative content analysis, network analysis and agent-based simulation.FindingsAn undifferentiated network based on informal trust lacks mechanisms for conflict resolution. This is a highly vulnerable organizational structure. While a status differentiated gang is more resilient towards internal conflicts, its activities remain dependent on individually accumulated social capital. This organizational structure is not resilient over generations of actors. A hierarchical organization provides highest degree of structural resilience up to a level of a system of self-organized criticality.Originality/valueThe study of human relations management outside the legal world provides insights into the basic mechanisms and functional effects of organizational activity.