bluuebunny/crossref_metadata_2025_split huggingface dataset:
The geographic distribution of reef and oceanic manta rays in the south-east Indian and south-west Pacific Oceans
Authors: Armstrong Amelia J. , Armstrong Asia O. , Bennett Michael B. , McGregor Frazer , Abrantes Kátya G. , Barnett Adam , Richardson Anthony J. , Townsend Kathy A. , Dudgeon Christine L 
Published: August 2019

AbstractThe reef manta ray,Mobula alfredi, occurs in tropical and warm temperate coastal waters, and around islands and reefs in the Pacific and Indian Oceans. Published records that relate to the distribution ofM. alfrediin the south-east Indian and south-west Pacific Oceans are largely restricted to locations where there is a focus on manta ray ecotourism, with little information from elsewhere. Even less is known about the circumglobally distributed oceanic manta ray,Mobula birostris, for which there are few published sighting records. We collatedn =11,703 sighting records from Australian waters and offshore territories forM. alfredisourced from scientific image databases (n= 10,715), aerial surveys (n= 375) and online reports (n= 613). From collated records, we confirm that the species shows an uninterrupted distribution within Australian coastal waters north of 26°S on the west coast to 31°S on the east coast, with a southernmost record at 34°S. Confirmed locations forM. birostrisencompass a latitudinal range of 10-40°S. Records from more southerly locations relate to warm-water events. Sightings ofM. birostriswere rare, but were confirmed at several geographically separate locations, probably reflecting its preference for offshore waters. The study clarifies the occurrence and range of each species within coastal waters of the south-east Indian and south-west Pacific Oceans, and highlights regions in northern Australia that are of specific interest for future research into possible movements of individuals between international marine jurisdictions.
Evolution of conserved noncoding sequences in Arabidopsis thaliana
Authors: Yocca Alan E. , Lu Zefu , Schmitz Robert J. , Freeling Michael , Edger Patrick P. 
Published: August 2019

AbstractRecent pangenome studies have revealed a large fraction of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studies, though these sequences directly modulate gene expression and phenotype. To uncover regulatory genetic variation, we generated chromosome-scale genome assemblies for thirty Arabidopsis thaliana accessions from multiple distinct habitats and characterized species level variation in Conserved Noncoding Sequences (CNS). Our analyses uncovered not only evidence for PAV and positional variation (PosV) but that diversity in CNS is non-random, with variants shared across different accessions. Using evolutionary analyses and chromatin accessibility data, we provide further evidence supporting roles for conserved and variable CNS in gene regulation. Characterizing species-level diversity in all functional genomic sequences may later uncover previously unknown mechanistic links between genotype and phenotype.
Genotype-by-environment interactions for seminal fluid expression and sperm competitive ability
Authors: Patlar Bahar , Ramm Steven A. 
Published: August 2019

AbstractSperm competition commonly occurs whenever females mate multiply, leading to variation in male paternity success. This can be due to variation in the various traits that might affect sperm competitive ability, which itself depends on both genetic and environmental factors, as well as on genotype-by-environment interactions (GEI). Seminal fluid is a major component of the male ejaculate that is often expected to mediate sperm competition, where different genotypes can differ in their seminal fluid expression as a response to different level of sperm competition (i.e., exhibit GEI). We therefore here focussed on testing for GEI in expression of two recently identified seminal fluid transcripts,suckless-1andsuckless-2, which potentially modulate sperm competitive ability in the simultaneously hermaphroditic flatwormMacrostomum lignanovia their effects on manipulating post-mating partner behaviour and ultimately the fate of transferred ejaculates. In addition, we sought to test for GEI in sperm competitive ability, to investigate the relationship between natural variation in the expression of these seminal fluid transcripts generated through GEI and relative paternity success. To do so, we manipulated social group size, which has been shown to successfully alter sperm competition level inM. lignano, in a set of inbred lines (genotypes) and then measured both the expression level ofsuckless-1andsuckless-2in focal worms together with their relative paternity success in a standardised sperm competition (P1&P2) assay. We found GEI for the expression level ofsuckless-1andsuckless-2, as well as for sperm competitive ability. Moreover, we found a positive relation between the expression ofsuckless-1and paternity success. This suggests that natural variation in the expression of this seminal fluid transcript indeed can influence sperm competition outcomes inM. lignano.
Temporal discrimination from the interaction between dynamic synapses and intrinsic subthreshold oscillations
Authors: Torres Joaquin J. , Baroni Fabiano , Latorre Roberto , Varona Pablo 
Published: August 2019

AbstractThe interaction between synaptic and intrinsic dynamics can efficiently shape neuronal input-output relationships in response to temporally structured spike trains. We use a neuron model with subthreshold oscillations receiving inputs through a synapse with short-term depression and facilitation to show that the combination of intrinsic subthreshold and synaptic dynamics leads to channel-specific nontrivial responses and recognition of specific temporal structures. We employ the Generalized Integrate-and-Fire (GIF) model, which can be subjected to analytical characterization. We map the temporal structure of spike input trains to the type of spike response, and show how the emergence of nontrivial input-output preferences is modulated by intrinsic and synaptic parameters in a synergistic manner. We demonstrate that these temporal input discrimination properties are robust to noise and to variations in synaptic strength, suggesting that they likely contribute to neuronal computation in biological circuits. Furthermore, we also illustrate the presence of these input-output relationships in conductance-based models.Author summaryNeuronal subthreshold oscillations underlie key aspects of information processing in single neuron and network dynamics. Dynamic synapses provide a channel-specific temporal modulation of input information. We combine a neuron model that displays subthreshold oscillations and a dynamic synapse to analytically assess their interplay in processing trains of spike-mediated synaptic currents. Our results show that the co-action of intrinsic and synaptic dynamics builds nontrivial input-output relationships, which are resistant to noise and to changes in synaptic strength. The discrimination of a precise temporal structure of the input signal is shaped as a function of the joint interaction of intrinsic oscillations and synaptic dynamics. This interaction can result in channel-specific recognition of precise temporal patterns, hence greatly expanding the flexibility and complexity in information processing achievable by individual neurons with respect to temporal discrimination mechanisms based on intrinsic neuronal dynamics alone.
Epigenetic age is accelerated in schizophrenia with age- and sex-specific effects and associated with polygenic disease risk
Authors: Ori Anil P.S. , Olde Loohuis Loes M. , Guintivano Jerry , Hannon Eilis , Dempster Emma , St. Clair David , Bass Nick J , McQuillin Andrew , Mill Jonathan , Sullivan Patrick F , Kahn Rene S. , Horvath Steve , Ophoff Roel A. 
Published: August 2019

AbstractBackgroundThe study of biological age acceleration may help identify at-risk individuals and contribute to reduce the rising global burden of age-related diseases. Using DNA methylation (DNAm) clocks, we investigated biological aging in schizophrenia (SCZ), a severe mental illness that is associated with an increased prevalence of age-related disabilities and morbidities. In a multi-cohort whole blood sample consisting of 1,090 SCZ cases and 1,206 controls, we investigated differential aging using three DNAm clocks (i.e. Hannum, Horvath, Levine). These clocks are highly predictive of chronological age and are known to capture different processes of biological aging.ResultsWe found that blood-based DNAm aging is significantly altered in SCZ with age- and sex-specific effects that differ between clocks and map to distinct chronological age windows. Most notably, differential phenotypic age (Levine clock) was most pronounced in female SCZ patients in later adulthood compared to matched controls. Female patients with high SCZ polygenic risk scores (PRS) present the highest age acceleration in this age group with +4.30 years (CI: 2.40-6.20, P=1.3E-05). Phenotypic age and SCZ PRS contribute additively to the illness and together explain up to 22.4% of the variance in disease status in this study. This suggests that combining genetic and epigenetic predictors may improve predictions of disease outcomes.ConclusionsSince increased phenotypic age is associated with increased risk of all-cause mortality, our findings indicate that specific and identifiable patient groups are at increased mortality risk as measured by the Levine clock. These results provide new biological insights into the aging landscape of SCZ with age- and sex-specific effects and warrant further investigations into the potential of DNAm clocks as clinical biomarkers that may help with disease management in schizophrenia.
Analysis of single-cell RNA sequencing data based on autoencoders
Authors: Tangherloni Andrea , Ricciuti Federico , Besozzi Daniela , Liò Pietro , Cvejic Ana 
Published: August 2019

AbstractBackgroundSingle-cell RNA sequencing (scRNA-Seq) experiments are gaining ground to study the molecular processes that drive normal development as well as the onset of different pathologies. Finding an effective and efficient low-dimensional representation of the data is one of the most important steps in the downstream analysis of scRNA-Seq data, as it could provide a better identification of known or putatively novel cell-types. Another step that still poses a challenge is the integration of different scRNA-Seq datasets. Though standard computational pipelines to gain knowledge from scRNA-Seq data exist, a further improvement could be achieved by means of machine learning approaches.ResultsAutoencoders (AEs) have been effectively used to capture the non-linearities among gene interactions of scRNA-Seq data, so that the deployment of AE-based tools might represent the way forward in this context. We introduce here scAEspy, a unifying tool that embodies: (1) four of the most advanced AEs, (2) two novel AEs that we developed on purpose, (3) different loss functions. We show that scAEspy can be coupled with various batch-effect removal tools to integrate data by different scRNA-Seq platforms, in order to better identify the cell-types. We benchmarked scAEspy against the most used batch-effect removal tools, showing that our AE-based strategies outperform the existing solutions.ConclusionsscAEspy is a user-friendly tool that enables using the most recent and promising AEs to analyse scRNA-Seq data by only setting up two user-defined parameters. Thanks to its modularity, scAEspy can be easily extended to accommodate new AEs to further improve the downstream analysis of scRNA-Seq data. Considering the relevant results we achieved, scAEspy can be considered as a starting point to build a more comprehensive toolkit designed to integrate multi single-cell omics.
Identification of essential oils with activity against stationary phase Staphylococcus aureus
Authors: Xiao Shuzhen , Cui Peng , Shi Wanliang , Zhang Ying 
Published: August 2019

AbstractStaphylococcus aureus is the most dominant human pathogen, responsible for a variety of chronic and severe infections. There is mounting evidence that persisters are associated with treatment failure and relapse of persistent infections. While some essential oils were reported to have antimicrobial activity against growing S. aureus, activity of essential oils against the non-growing stationary phase S. aureus enriched in persisters has not been investigated. In this study, we evaluated the activity of 143 essential oils against stationary phase S. aureus and identified 39 essential oils (Cinnamon bark, Oregano, Thyme white, Bandit “Thieves”, Lemongrass (Cymbopogon flexuosus), Sandalwood oil, Health shield, Allspice, Amyris, Palmarosa, Cinnamon leaf, Clove bud, Citronella, Geranium bourbon, Marjoram, Peppermint, Lemongrass (Cymbopogon citratus), Cornmint, Elemi, Ho wood, Head ease, Lemon eucalyptus, Litsea cubeba, Myrrh, Parsley seed, Coriander oil, Dillweed, Hyssop, Neroli, Rosewood oil, Tea tree, Cajeput, Glove bud, Lavender, Sleep tight, Vetiver, Palo santo, Sage oil, Yarrow) at 0.5% concentration, 10 essential oils (Cinnamon bark, Oregano, Thyme white, Bandit “Thieves”, Lemongrass (Cymbopogon flexuosus), Sandalwood oil, Health shield, Allspice, Amyris, Palmarosa) at 0.25% concentration, and 7 essential oils (Cinnamon bark, Oregano, Thyme white, Lemongrass (Cymbopogon flexuosus), Allspice, Amyris, Palmarosa) at 0.125% concentration to have high activity against stationary phase S. aureus with no visible growth on agar plates after five-day exposure. Among the 10 essential oils which showed high activity at 0.25% concentration, 9 (Cinnamon bark, Oregano, Thyme white, Bandit “Thieves”, Lemongrass (Cymbopogon flexuosus), Health shield, Allspice, Palmarosa, Amyris) showed higher activity than the known persister drug tosufloxacin, while the other one (Sandalwood oil) was found to be active at a higher concentration. In Oregano essential oil drug combination studies with clinical antibiotics, Oregano plus quinolone drugs (tosufloxacin, levofloxacin, ciprofloxacin) and rifampin completely eradicated all stationary phase S. aureus cells, but had no apparent enhancement for linezolid, vancomycin, sulfamethoxazole, trimethoprim, azithromycin and gentamicin. Our findings may facilitate development of more effective treatment for persistent S. aureus infections.
Epitranscriptomic regulation of the response to the air pollutant naphthalene in mouse lungs: from the perspectives of specialized translation and tolerance linked to the writer ALKBH8
Authors: Leonardi Andrea , Kovalchuk Nataliia , Yin Lei , Endres Lauren , Evke Sara , Nevins Steven , Martin Samuel , Dedon Peter C. , Melendez J. Andres , Winkle Laura Van , Zhang Qing-Yu , Ding Xinxin , Begley Thomas J. 
Published: August 2019

AbstractBackgroundThe epitranscriptomic writer Alkylation Repair Homolog 8 (ALKBH8) is a tRNA methyltransferase that modifies the wobble uridine of selenocysteine tRNA to promote the specialized translation, via stop codon recoding, of proteins that contain selenocysteine. Corresponding selenoproteins play critical roles in protecting against reactive oxygen species and environmental stress. Using a novel animal model deficient inAlkbh8, we have investigated the importance of epitranscriptomic systems in the response to naphthalene (NA), an abundant polycyclic aromatic hydrocarbon, glutathione depleter and lung toxicant found in tobacco smoke, gasoline and mothballs.ObjectivesOur goal was to define the molecular reprogramming of Alkbh8 deficient (Alkbh8def)mice and evaluate the roles that the epitranscriptomic writer ALKBH8 and selenoproteins play in mitigating NA-induced toxicity and lung dysfunction.MethodsWe performed basal lung analysis and NA exposure studies using WT,Alkbh8defandCyp2abfgs-nullmice, the latter of which lack the cytochrome P450 enzymes required for NA bioactivation. We characterized gene expression, molecular markers of damage, viability and tolerance to NA.ResultsUnder basal conditions, lungs fromAlkbh8defmice have increased oxidation-reduction potential (ORP) and 8-isoprostane levels, and have reprogrammed at the molecular level to display increased stress response transcripts. In addition, the ALKBH8 writer deficient lungs have a decreased GSH/GSSG ratio.Alkbh8defmice are more sensitive to NA than WT, showing higher susceptibility to lung damage both at the cellular and molecular levels. WT mice develop a tolerance to NA after 3 days, defined as resistance to a high challenging dose after repeated exposures, which is absent inAlkbh8defmice, with writer deficient not surviving NA exposure.DiscussionWe conclude that the epitranscriptomic writer ALKBH8 plays a protective role against NA-induced lung dysfunction and promotes NA tolerance. Our work provides an early example of how epitranscriptomic systems can regulate the response to environmental stressin vivo.
Spatial structure undermines parasite suppression by gene drive cargo
Authors: Bull James J , Remien Christopher H , Gomulkiewicz Richard , Krone Stephen M 
Published: August 2019

ABSTRACTGene drives may be used in two ways to curtail vectored diseases. Both involve engineering the drive to spread in the vector population. One approach uses the drive to directly depress vector numbers, possibly to extinction. The other approach leaves intact the vector population but suppresses the disease agent during its interaction with the vector. This second application may use a drive engineered to carry a genetic cargo that blocks the disease agent. An advantage of the second application is that it is far less likely to select vector resistance to block the drive, but the disease agent may instead evolve resistance to the inhibitory cargo. However, some gene drives are expected to spread so fast and attain such high coverage in the vector population that, if the disease agent can evolve resistance only gradually, disease eradication may be feasible. Here we use simple models to show that spatial structure in the vector population can greatly facilitate persistence and evolution of resistance by the disease agent. We suggest simple approaches to avoid some types of spatial structure, but others may be intrinsic to the populations being challenged and difficult to overcome.
Morphology of obligate ectosymbionts revealsParalaxusgen. nov., a new circumtropical genus of marine stilbonematine nematodes
Authors: Scharhauser Florian , Zimmermann Judith , Ott Jörg A. , Leisch Nikolaus , Gruber-Vodicka Harald 
Published: August 2019

AbstractStilbonematinae are a subfamily of conspicuous marine nematodes, distinguished by a coat of sulphur-oxidizing bacterial ectosymbionts on their cuticle. As most nematodes, the worm hosts have a simple anatomy and few taxonomically informative characters, and this has resulted in numerous taxonomic reassignments and synonymizations. Recent studies using a combination of morphological and molecular traits have helped to improve the taxonomy of Stilbonematinae but also raised questions on the validity of several genera. Here we describe a new circumtropically distributed genusParalaxus(Stilbonematinae) with three species: Paralaxus cocos sp. nov.,P. bermudensissp. nov. andP. columbaesp. nov.. We used single worm metagenomes to generate host 18S rRNA and cytochrome oxidase I (COI) as well as symbiont 16S rRNA gene sequences. Intriguingly, COI alignments and primer matching analyses suggest that the COI is not suitxable for PCR-based barcoding approaches in Stilbonematinae as the genera have a highly diverse base composition and no conserved primer sites. The phylogenetic analyses of all three gene sets however confirm the morphological assignments and support the erection of the new genusParalaxusas well as corroborate the status of the other stilbonematine genera.Paralaxusmost closely resembles the stilbonematine genusLaxusin overlapping sets of diagnostic features but can be distinguished fromLaxusby the morphology of the genus-specific symbiont coat. Our re-analyses of key parameters of the symbiont coat morphology as character for all Stilbonematinae genera show that with amended descriptions, including the coat, highly reliable genus assignments can be obtained.
Comparative investigation into formycin A and pyrazofurin A biosynthesis reveals branch pathways for the construction ofC-nucleoside scaffolds
Authors: Zhang Meng , Zhang Peichao , Xu Gudan , Zhou Wenting , Gao Yaojie , Gong Rong , Cai You-Sheng , Cong Hengjiang , Deng Zixin , Price Neil P. J. , Mao Xiangzhao , Chen Wenqing 
Published: August 2019

ABSTRACTFormycin A (FOR-A) and pyrazofurin A (PRF-A) are purine-relatedC-nucleoside antibiotics, in which ribose and a pyrazole-derived base are linked by aC-glycosidic bond, however, the logic underlying the biosynthesis of these molecules has remained largely unexplored. Here, we report the discovery of the pathways for FOR-A and PRF-A biosynthesis from diverse actinobacteria, and demonstrate that their biosynthesis is initiated by a lysineN6-monooxygenase. Moreover, we show that theforTandprfE(individually related to FOR-A and PRF-A biosynthesis) mutants are correspondingly capable of accumulating the unexpected pyrazole-related intermediates, compound11and9a. We also decipher the enzymatic basis of ForT/PrfE for theC-glycosidic bond formation in FOR-A/PRF-A biosynthesis. To our knowledge, ForT/PrfE represents the first example of β-RFA-P (β-ribofuranosyl-aminobenzene 5’-phosphate) synthase-like enzymes governingC-nucleoside scaffold construction in natural product biosynthesis. These data establish a foundation for combinatorial biosynthesis of related purine nucleoside antibiotics, and also open the way for target-directed genome mining of PRF-A/FOR-A related antibiotics.IMPORTANCEFormycin A (FOR-A) and pyrazofurin A (PRF-A) are well known for their unusual chemical structures and remarkable biological activities. Actually, deciphering FOR-A/PRF-A biosynthesis will not only expand biochemical repertoire for novel enzymatic reactions, but also permit the target-oriented genome mining of FOR-A/PRF-A relatedC-nucleoside antibiotics.
ZGRF1 variants implicated in a sensory reflex epilepsy
Authors: Choudhury Shalini Roy , Satishchandra Parthasarathy , Sinha Sanjib , Anand Anuranjan 
Published: August 2019

AbstractHot water epilepsy (HWE) is a sensory reflex epilepsy in which seizures are precipitated by a stimulus such as contact with hot water. While there is a genetic basis to its etiology, identity of the genes underlying this relatively uncommon disorder has remained unknown. Here, we present the results of our studies aimed at identifying a causative gene in a south Indian four-generation family with several affected members. We conducted whole-exome sequencing and examined a known locus that maps to 4q24-q28 (HWE2, MIM: 613340) that we had previously identified. We identified a sequence variant, c.1805C>T (p.Thr602Ile) in ZGRF1, located within the HWE2 locus, co-segregating with the disorder. The transcript structure of ZGRF1 was examined in 288 HWE patients, and five additional missense variants, Arg326Gln, Glu660Gly, Arg1862*, Phe1940Leu and Asp1984Gly, present exclusively or almost exclusively in the patients were found. Functional correlates of the six variants identified were examined in cultured mammalian cells. We observed spindle pole defects during cell division and partially disrupted localization of UPF1, a protein involved in cell cycle regulation, at the spindles. Our observations provide insights into the genetic basis of HWE and suggest the involvement of hitherto unanticipated molecular process in this disorder.