bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein Interactomes Identify Distinct Pathways forStreptococcus mutansYidC1 and YidC2 Membrane Protein Insertases
Authors: Vasquez Patricia Lara , Mishra Surabhi , Kuppuswamy Senthil K. , Crowley Paula J. , Brady L. Jeannine 
Published: April 2020

AbstractVirulence properties of cariogenicStreptococcus mutansdepend on integral membrane proteins. Bacterial protein trafficking involves the co-translational signal recognition particle (SRP) pathway components Ffh and FtsY, the SecY translocon, and membrane-localized YidC chaperone/insertases. UnlikeEscherichia coli, S. mutanssurvives loss of the SRP pathway. In addition,S. mutanshas twoyidCparalogs. TheΔyidC2phenotype largely parallels that ofΔffhandΔftsYwhile theΔyidC1phenotype is less severe. This study defined YidC1 and YidC2 interactomes to identify their respective functions alone and in concert with the SRP, ribosome, and/or Sec translocon. A chemical cross-linking approach was employed, whereby whole cell lysates were treated with formaldehyde followed by Western blotting using anti-Ffh, FtsY, YidC1 or YidC2 antibodies and mass spectrometry (MS) analysis of gel-shifted bands. Cross-linked lysates from WT andΔyidC2strains were also reacted with anti-YidC2 antibodies coupled to magnetic Dynabeads™, with co-captured proteins identified by MS. Additionally, C-terminal tails of YidC1 and YidC2 were engineered as glutathione-S-transferase fusion proteins and subjected to 2D Difference Gel Electrophoresis and MS analysis after being reacted with non-cross-linked lysates. Results indicate that YidC2 works in concert with the SRP-pathway, while YidC1 works in concert with the SecY translocon independently of the SRP. In addition, YidC1 and/or YidC2 can act alone in the insertion of a limited number of small integral membrane proteins. The YidC2-SRP and YidC1/SecY pathways appear to function as part of an integrated machinery that couples translation and transport with cell division, as well as transcription and DNA replication.ImportanceStreptococcus mutansis a prevalent oral pathogen and causative agent of tooth decay. Many proteins that enable this bacterium to thrive in its environmental niche, and cause disease, are embedded in its cytoplasmic membrane. The machinery that transports proteins into bacterial membranes differs between Gram-negative and Gram-positive organisms. One important difference is the presence of multiple YidC paralogs in Gram-positive bacteria. Characterization of a protein’s interactome can help define its physiological role. Herein, we characterized the interactomes ofS. mutansYidC1 and YidC2. Results indicate that YidC1 and YidC2 have individualized functions in separate membrane insertion pathways, and suggest putative substrates of the respective pathways. Furthermore,S. mutansmembrane transport proteins appear as part of a larger network of proteins involved in replication, transcription, translation, and cell division/cell shape. This information contributes to our understanding of protein transport in Gram-positive bacteria in general, and informs our understanding ofS. mutanspathogenesis.
Stable Zn isotopes reveal the uptake and toxicity of zinc oxide engineered nanomaterials inPhragmites australis
Authors: Caldelas C , Poitrasson F , Viers J , Araus JL 
Published: April 2020

AbstractThe uptake, transport, and toxicity mechanisms of zinc oxide (ZnO) engineered nanomaterials (ZnO-ENMs) in aquatic plants remain obscure. We investigated ZnO-ENM uptake and phytotoxicity inPhragmites australisby combining Zn stable isotopes and microanalysis. Plants were exposed to four ZnO materials: micron-size ZnO, nanoparticles (NPs) of <100 nm or <50 nm, and nanowires of 50 nm diameter at concentrations of 0-1000 mg l−1. All ZnO materials reduced growth, chlorophyll content, photosynthetic efficiency, and transpiration and led to Zn precipitation outside the plasma membranes of root cells. Nanoparticles <50 nm released more Zn2+and were more toxic, thus causing greater Zn precipitation and accumulation in the roots and reducing Zn isotopic fractionation during Zn uptake. However, fractionation by the shoots was similar for all treatments and was consistent with Zn2+being the main form transported to the shoots. Stable Zn isotopes are useful to trace ZnO-ENM uptake and toxicity in plants.Environmental Significance StatementOur understanding of zinc oxide nanomaterials interaction with wetland plants is hampered by the lack of scientific consensus about their uptake and toxicity mechanisms in these species. This is a serious concern given the alarming global increase in the discharge of these nanomaterials into the environment and the key ecological roles of wetland plants. The Zn isotopic signature of plant tissue integrates all the Zn metabolic pathway throughout the plant’s life, giving insight about the form of Zn taken up, even if this later transforms into another Zn species. Thus, our findings clarify the exposure routes and the mechanisms of action of zinc oxide engineered nanomaterials in wetland plants while advancing the toolbox for plant physiology and environmental studies.Table of contentsThe Zn stable isotope composition of plants demonstrates that ZnO engineered nanomaterials dissolve before their uptake and accumulation by the roots (brightest inclusions in root cortex above).
Reversed sex-biased mutation rates for indels and base substitutions inDrosophila melanogaster
Authors: Törmä Lauri , Burny Claire , Schlötterer Christian 
Published: April 2020

AbstractSex biases in mutation rates may affect the rate of adaptive evolution. In many species, males have higher mutation rates than females when single nucleotide variants (SNVs) are considered. In contrast, indel mutations in humans and chimpanzees are female-biased. InDrosophila melanogaster, direct estimates of mutation rates did not uncover sex differences, but a recent analysis suggested the presence of male-biased SNVs mutations. Here we study the sex-specific mutation processes using mutation accumulation data from mismatch-repair deficientD. melanogaster. We find that sex differences in flies are similar to the ones observed in humans: a higher mutation rate for SNVs in males and a higher indel rate in females. These results have major implications for the study of neutral variation and adaptation inDrosophila.
Runs of homozygosity in killer whale genomes provide a global record of demographic histories
Authors: Hooper Rebecca , Excoffier Laurent , Forney Karin A. , Gilbert M. Thomas P. , Martin Michael D. , Morin Phillip A. , Wolf Jochen B.W. , Foote Andrew D. 
Published: April 2020

SUMMARYRuns of homozygosity (ROH) occur when offspring receive the same ancestral haplotype from both parents, and, accordingly, reduce individual heterozygosity. Their distribution throughout the genome contains information on the probability of inbreeding mediated by mating system and population demography. Here, we investigate variation in killer whale demographic history as reflected in genome-wide heterozygosity, using a global dataset of 26 genomes. We find an overall pattern of lower heterozygosity in genomes sampled at high latitudes, with hundreds of short ROH (< 1Mbp) reflecting high background relatedness due to coalescence of haplotypes during bottlenecks associated with founder events during post-glacial range expansions. Across most of the species’ range, intermediate length ROH (1-10Mb) revealed long-term inbreeding in 22 of the 26 sampled killer whale genomes, consistent with the high social philopatry observed in all populations studied to date. Inbreeding coefficients (FROH) were comparable to those reported in other taxa with long-term low population size, such as bonobos and the Native American Karitiana of the Brazilian Amazon. The extreme outlier in this dataset, a Scottish killer whale, was homozygous over one-third of the autosomes (41.6%) with a distinct distribution of ROH length, indicating generations of inbreeding. This exceeds autozygosity in emblematic examples of long-term inbreeding, such as the Altai Neanderthal, and eastern lowland and mountain gorillas. The fate of this Scottish killer whale population, in which no calves have been born in over two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.
Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts
Authors: Zaghlool Ammar , Niazi Adnan , Björklund Åsa K. , Westholm Jakub Orzechowski , Ameur Adam , Feuk Lars 
Published: April 2020

AbstractTranscriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, and interpretation of gene expression signatures in cells. Here, we performed a comprehensive analysis of cytosolic and nuclear transcriptomes in human fetal and adult brain samples. We show significant differences in RNA expression for protein-coding and lncRNA genes between cytosol and nucleus. Transcripts displaying differential subcellular localization belong to particular functional categories and display tissue-specific localization patterns. We also show that transcripts encoding the nuclear-encoded mitochondrial proteins are significantly enriched in the cytosol compared to the rest of protein-coding genes. Further investigation of the use of the cytosolic or the nuclear transcriptome for differential gene expression analysis indicates important differences in results depending on the cellular compartment. These differences were manifested at the level of transcript types and the number of differentially expressed genes. Our data provide a resource of RNA subcellular localization in the human brain and highlight differences in using the cytosolic or the nuclear transcriptomes for differential expression analysis.
Intravenous sulforhodamine B reduces alveolar surface tension, improves oxygenation and reduces ventilation injury in a respiratory distress model
Authors: Wu You , Ngyuen Tam L. , Perlman Carrie E. 
Published: April 2020

AbstractIn the neonatal (NRDS) and acute (ARDS) respiratory distress syndromes, mechanical ventilation supports gas exchange but can cause ventilation-induced lung injury (VILI) that contributes to high mortality. Further, surface tension,T, should be elevated and VILI is proportional toT. Surfactant therapy is effective in NRDS but not ARDS. Sulforhodamine B (SRB) is a potential alternativeT-lowering therapeutic. In anesthetized male rats, we injure the lungs with 15 min of 42 ml/kg tidal volume,VT, and zero end-expiratory pressure ventilation. Then, over 4 hrs, we support the rats with protective ventilation –VTof 6 ml/kg with positive end-expiratory pressure. At the start of the support period, we administer intravenous non-T-altering fluorescein (targeting 27 μM in plasma) without or with therapeutic SRB (10 nM). Throughout the support period, we increase inspired oxygen fraction, as necessary, to maintain >90% arterial oxygen saturation. At the end of the support period we sacrifice the rat; sample systemic venous blood for injury marker ELISAs; excise the lungs; combine confocal microscopy and servo-nulling pressure measurement to determineT in situin the lungs; image fluorescein in alveolar liquid to assess local permeability; and determine lavage protein content and wet-to-dry ratio (W/D), both to assess global permeability. Lungs exhibit focal injury. Surface tension is elevated 72% throughout control lungs and in uninjured regions of SRB-treated lungs, but normal in injured regions of treated lungs. Sulforhodamine B administration improves oxygenation, reduces W/D and reduces plasma injury markers. Intravenous SRB holds promise as a therapy for respiratory distress.New and NoteworthySulforhodmaine B lowersT. Given the problematic intratracheal delivery of surfactant therapy for ARDS, intravenous SRB might constitute an alternative therapeutic. In a lung injury model, we find that intravenously administered SRB crosses the injured alveolar-capillary barrier, reducesTspecifically in injured lung regions, improves oxygenation and reduces the degree of further lung injury. Intravenous SRB administration might help respiratory distress patients, including those with the novel coronavirus, avoid mechanical ventilation or, once ventilated, survive.
Molecular investigations on a chimeric strain ofStaphylococcus aureussequence type 80
Authors: Gawlik Darius , Ruppelt-Lorz Antje , Müller Elke , Reißig Annett , Hotzel Helmut , Braun Sascha D. , Söderquist Bo , Ziegler-Cordts Albrecht , Ehricht Ralf , Monecke Stefan 
Published: April 2020

AbstractAn Eritrean patient was admitted with suspected tuberculous cervical lymphadenitis. While no mycobacteria were detected in pus from this process, culture yielded PVL-positive, methicillin-susceptibleStaphylococcus aureus. Microarray hybridisation assigned the isolate to clonal complex (CC) 80 but revealed unusual features, including the presence of the ORF-CM14 enterotoxin homologue and of an ACME-III element as well as the absence ofetDandedinB.The isolate was subjected to both, Illumina and Nanopore sequencing allowing characterisation of deviating regions within the strain’s genome. Atypical features of this strain were attributable to the presence of two genomic regions that originated from otherS. aureuslineages and that comprised, respectively, 3% and 1.4% of the genome. One deviating region extended fromwalJtosirB. It comprised ORF-CM14 and the ACME-III element. A homologous, but larger fragment was also found in an atypicalS. aureusCC1/ST567 strain whose lineage might have served as donor of this genomic region. This region itself is a chimera comprising fragments from CC1 as well as fragments of unknown origin. The other region of another 3% of the genome comprised the region fromhtsBtoecfA2. It was very similar to CC1 sequences. This suggests either an incorporation of CC1 DNA into the study strain, or it might alternatively suggest a recombination event affecting “canonical” CC80. As the study strain bears witness of several recombination events, such complex and large-scale events cannot be rare and exceptional, despite a mainly clonal nature ofS. aureus. Although the exact mechanism is not yet clear, chimerism seems to be an additional pathway in the evolution ofS. aureus, possibly being responsible for the transmission also of virulence and resistance factors. An organism that can shuffle, swap or exchange major parts of its genome by a yet unknown mechanism would have an evolutionary advantage compared to a strictly clonal organism.
Organic manure managements increases soil microbial community structure and diversity in double-cropping paddy field of Southern China
Authors: Tang Haiming , Xiao Xiaoping , Li Chao , Pan Xiaochen , Cheng Kaikai , Shi Lihong , Wang Ke , Li Weiyan 
Published: April 2020

AbstractThe soil physicochemical properties were affected by different fertilizer managements, and the soil microbial communities were changed. Fertilizer regimes were closely relative to the soil texture and nutrient status in a double-cropping paddy field of southern China. However, there was limited information about the influence of different long-term fertilizer management practices on the soil microbial communities in a double-cropping rice (Oryza sativaL.) fields. Therefore, the 39-year long-term fertilizer regimes on soil bacterial and fungal diversity in a double-cropping paddy field of southern China were studied by using Illumina sequencing and quantitative PCR technology in the present paper. The filed experiment were including chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), 30% organic manure and 70% chemical fertilizer (OM), and without fertilizer input as a control (CK). The results showed that diversity indices of soil microbial communities with application of organic manure and rice straw residue treatments were higher than that without fertilizer input treatment. Application of organic manure and rice straw residue managements increase soil bacterial abundance of the phylumProteobacteria, Actinobacteria, andGammaproteobacteria, and soil fungi abundance of the phylumBasidiomycota, ZygomycotaandTremellaleswere also increased. Compared with CK treatment, the value of Richness, Shannon and McIntosh indices, and taxonomic diversity were increased with RF and OM treatments. This finding demonstrated that RF and OM treatments modify soil bacterial and fungal diversity. Therefore, the combined application of organic manure or rice straw residue with chemical fertilizer managements could significantly increase the abundance of profitable functional bacteria and fungi species in double-cropping rice fields of southern China.
Conservation genetics of regionally extinct peregrine falcons (Falco peregrinus) and unassisted recovery without genetic bottleneck in southern England
Authors: Weaving Angela , Jackson Hazel A. , Nicholls Michael K. , Franklin Jon , Vega Rodrigo 
Published: April 2020

AbstractThe peregrine falcon (Falco peregrinus) has been affected by persecution, pollution, trade and habitat degradation, but it is considered a flagship conservation success story because of successful reintroductions. However, in the UK there were never formal reintroduction programmes for peregrine falcons, and it appears that UK populations – and specifically the Sussex peregrines of the English south coast – recently recovered from a population crash unassisted. To study this, we obtained samples from contemporary populations in southern England, Ireland, continental Europe, domestic-bred peregrine falcons, and from England pre-population crash. Using microsatellite and mtDNA control region data, the genetic diversity and structure, signatures of genetic bottlenecks, and potential origin of the Sussex peregrines was investigated. We found low levels of genetic diversity across all peregrine falcon populations, low but significant genetic differentiation among all populations, and a few private alleles, indicating some level of genetic structure in European peregrines. Although we could not pinpoint the origin of the Sussex peregrines, the data suggests that it is not likely to have originated from escaped domestic birds or from adjacent European populations. The results obtained here parallel other studies on peregrines elsewhere showing low genetic diversity but genetic structure. We conclude that not enough time elapsed for genetic erosion to occur due to the population bottleneck, and that at least for the Sussex peregrines there is no need for genetic conservation by wild-take and subsequent captive breeding programmes as long as current protection measures remain in place.
D4: Deep Drug-drug interaction Discovery and Demystification
Authors: Noor Adeeb , Liu-Wei Wang , Barnawi Ahmed , Nour Redhwan , Assiri Abdullah A , Chan Bukhari Syed Ahmad , Hoehndorf Robert 
Published: April 2020

AbstractMotivationDrug-drug interactions (DDIs) are complex processes which may depend on many clinical and non-clinical factors. Identifying and distinguishing ways in which drugs interact remains a challenge. To minimize DDIs and to personalize treatment based on accurate stratification of patients, it is crucial that mechanisms of interaction can be identified. Most DDIs are a consequence of metabolic mechanisms of interaction, but DDIs with different mechanisms occur less frequently and are therefore more difficult to identify.ResultsWe developed a method (D4) for computationally identifying potential DDIs and determining whether they interact based on one of eleven mechanisms of interaction. D4 predicts DDIs and their mechanisms through features that are generated through a deep learning approach from phenotypic and functional knowledge about drugs, their side-effects and targets. Our findings indicate that our method is able to identify known DDIs with high accuracy and that D4 can determine mechanisms of interaction. We also identify numerous novel and potential DDIs for each mechanism of interaction and evaluate our predictions using DDIs from adverse event reporting systems.Availabilityhttps://github.com/bio-ontology-research-group/D4Contactarnoor@kau.edu.sa and robert.hoehndorf@kaust.edu.sa
Metabolic differences between symbiont subpopulations in the deep-sea tubewormRiftia pachyptila
Authors: Hinzke Tjorven , Kleiner Manuel , Meister Mareike , Schlüter Rabea , Hentschker Christian , Pané-Farré Jan , Hildebrandt Petra , Felbeck Horst , Sievert Stefan M. , Bonn Florian , Völker Uwe , Becher Dörte , Schweder Thomas , Markert Stephanie 
Published: April 2020

AbstractThe hydrothermal vent tube wormRiftia pachyptilalives in intimate symbiosis with intracellular sulfur-oxidizing gammaproteobacteria. Although the symbiont population consists of a single 16S rRNA phylotype, bacteria in the same host animal exhibit a remarkable degree of metabolic diversity: They simultaneously utilize two carbon fixation pathways and various energy sources and electron acceptors. Whether these multiple metabolic routes are employed in the same symbiont cells, or rather in distinct symbiont subpopulations, was unclear. AsRiftiasymbionts vary considerably in cell size and shape, we enriched individual symbiont cell sizes by density gradient centrifugation in order to test whether symbiont cells of different sizes show different metabolic profiles. Metaproteomic analysis and statistical evaluation using clustering and random forests, supported by microscopy and flow cytometry, strongly suggest thatRiftiasymbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: Small symbionts actively divide and may establish cellular symbiont-host interaction, as indicated by highest abundance of the cell division key protein FtsZ and highly abundant chaperones and porins in this initial phase. Large symbionts, on the other hand, apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Highest abundance of enzymes for CO2fixation, carbon storage and biosynthesis in large symbionts indicates that in this late differentiation stage the symbiont’s metabolism is efficiently geared towards the production of organic material. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.