bluuebunny/crossref_metadata_2025_split huggingface dataset:
EffectorP 3.0: prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes
Authors: Sperschneider Jana , Dodds Peter N. 
Published: July 2021

AbstractMany fungi and oomycete species are devasting plant pathogens. These eukaryotic filamentous pathogens secrete effector proteins to facilitate plant infection. Fungi and oomycete pathogens have diverse infection strategies and their effectors generally do not share sequence homology. However, they occupy similar host environments, either the plant apoplast or plant cytoplasm, and may therefore share some unifying properties based on the requirements of these host compartments. Here we exploit these biological signals and present the first classifier (EffectorP 3.0) that uses two machine learning models: one trained on apoplastic effectors and one trained on cytoplasmic effectors. EffectorP 3.0 accurately predicts known apoplastic and cytoplasmic effectors in fungal and oomycete secretomes with low estimated false positive rates of 3% and 8%, respectively. Cytoplasmic effectors have a higher proportion of positively charged amino acids, whereas apoplastic effectors are enriched for cysteine residues. The combination of fungal and oomycete effectors in training leads to a higher number of predicted cytoplasmic effectors in biotrophic fungi. EffectorP 3.0 expands predicted effector repertoires beyond small, cysteine-rich secreted proteins in fungi and RxLR-motif containing secreted proteins in oomycetes. We show that signal peptide prediction is essential for accurate effector prediction, as EffectorP 3.0 recognizes a cytoplasmic signal also in intracellular, non-secreted proteins. EffectorP 3.0 is available at http://effectorp.csiro.au.
Precision Autism: Genomic Stratification of Disorders Making Up the Broad Spectrum May Demystify its “Epidemic Rates”
Authors: Torres Elizabeth B 
Published: July 2021

AbstractIn the last decade, Autism has broadened and often shifted its diagnostics criter a, allowing several neuropsychiatric and neurological disorders of known etiology. This has resulted in a highly heterogeneous spectrum with apparent exponential rates in prevalence. I ask if it is possible to leverage existing genetic information about those disorders making up Autism today and use it to stratify this spectrum. To that end, I combine genes linked to Autism in the SFARI database and genomic information from the DisGeNet portal on 25 diseases, inclusive of non-neurological ones. I use the GTEx data on genes’ expression on 54 human tissues and ask if there are overlapping genes across those associated to these diseases and those from SFARI-Autism. I find a compact set of genes across all brain-disorders which express highly in tissues fundamental for somatic-sensory-motor function, self-regulation, memory, and cognition. Then, I offer a new stratification that provides a distance-based orderly clustering into possible Autism subtypes, amenable to design personalized targeted therapies within the framework of Precision Medicine. I conclude that viewing Autism through this physiological (Precision) lens, rather than viewing it exclusively from a psychological behavioral construct, may make it a more manageable condition and dispel the Autism epidemic myth.
Catalytic cycling of human mitochondrial Lon protease
Authors: Mohammed Inayathulla , Schmitz Kai A. , Schenck Niko , Topitsch Annika , Maier Timm , Abrahams Jan Pieter 
Published: July 2021

AbstractThe mitochondrial Lon protease homolog (LonP1) hexamer controls mitochondrial health by digesting proteins from the mitochondrial matrix that are damaged or must be removed. Understanding how it is regulated requires characterizing its mechanism. Here, we show how human LonP1 functions, based on eight different conformational states that we determined by cryo-EM with a resolution locally extending to 3.6 Å for the best ordered states. LonP1 has a poorly ordered N-terminal part with apparent threefold symmetry, which apparently binds substrate protein and feeds it into its AAA+ unfoldase core. This translocates the extended substrate protein into a proteolytic cavity, in which we report an additional, previously unidentified Thr-type proteolytic center. Threefold rocking movements of the flexible N-terminal assembly likely assist thermal unfolding of the substrate protein. Our data suggest LonP1 may function as a sixfold cyclical Brownian ratchet controlled by ATP hydrolysis.
Inferring the intrinsic mutational fitness landscape of influenza-like evolving antigens from temporally ordered sequence data
Authors: Doelger Julia , Kardar Mehran , Chakraborty Arup K. 
Published: July 2021

AbstractThere still are no effective long-term protective vaccines against viruses that continuously evolve under immune pressure such as seasonal influenza, which has caused, and can cause, devastating epidemics in the human population. For finding such a broadly protective immunization strategy it is useful to know how easily the virus can escape via mutation from specific antibody responses. This information is encoded in the fitness landscape of the viral proteins (i.e., knowledge of the viral fitness as a function of sequence). Here we present a computational method to infer the intrinsic mutational fitness landscape of influenza-like evolving antigens from yearly sequence data. We test inference performance with computer-generated sequence data that are based on stochastic simulations mimicking basic features of immune-driven viral evolution. Although the numerically simulated model does create a phylogeny based on the allowed mutations, the inference scheme does not use this information. This provides a contrast to other methods that rely on reconstruction of phylogenetic trees. Our method just needs a sufficient number of samples over multiple years. With our method we are able to infer single-as well as pairwise mutational fitness effects from the simulated sequence time series for short antigenic proteins. Our fitness inference approach may have potential future use for design of immunization protocols by identifying intrinsically vulnerable immune target combinations on antigens that evolve under immune-driven selection. This approach may in the future be applied to influenza and other novel viruses such as SARS-CoV-2, which evolves and, like influenza, might continue to escape the natural and vaccine-mediated immune pressures.
Muscarinic receptors mediate motivation via preparatory neural activity in humans
Authors: Grogan John P. , Raemaekers Matthias , Van Swieten Maaike M. H. , Green Alexander L. , Gillies Martin J. , Manohar Sanjay G. 
Published: July 2021

AbstractMotivation depends on dopamine, but might be modulated by acetylcholine which influences dopamine release in the striatum, and amplifies motivation in animal studies. A corresponding effect in humans would be important clinically, since anticholinergic drugs are frequently used in Parkinson’s disease, a condition that can also disrupt motivation. Reward and dopamine make us more ready to respond, as indexed by reaction times (RT), and move faster, sometimes termed vigour. These effects may be controlled by preparatory processes that can be tracked using electroencephalography (EEG). We measured vigour in a placebo-controlled, double-blinded study of trihexyphenidyl (THP), a muscarinic antagonist, with an incentivised eye movement task and EEG. Participants responded faster and with greater vigour when incentives were high, but THP blunted these motivation effects, suggesting that muscarinic receptors facilitate invigoration by reward.Preparatory EEG build-up (contingent negative variation; CNV) was strengthened by high incentives and by muscarinic blockade, although THP reduced the incentive-effect. The amplitude of preparatory activity predicted both vigour and RT, although over distinct scalp regions; frontal activity predicted vigour, whereas a larger, earlier, central component predicted RT. The incentivisation of RT was partly mediated by the CNV, though vigour was not. Moreover, the CNV mediated the drug’s effect on dampening incentives, suggesting that muscarinic receptors underlie the motivational influence on this preparatory activity. Taken together, these findings show that a muscarinic blocker impairs motivated action in healthy people, and that medial frontal preparatory neural activity mediates this for RT.
PLB-985 neutrophil-like cells as a model to studyAspergillus fumigatuspathogenesis
Authors: Rafiq Muhammad , Rivieccio Flora , Zimmermann Ann-Kathrin , Visser Corissa , Bruch Alexander , Krüger Thomas , Rojas Katherine González , Kniemeyer Olaf , Blango Matthew G. , Brakhage Axel A. 
Published: July 2021

ABSTRACTFungal infections remain a major global concern. Emerging fungal pathogens and increasing rates of resistance mean that additional research efforts and resources must be allocated to advancing our understanding of fungal pathogenesis and developing new therapeutic interventions. Neutrophilic granulocytes are a major cell type involved in protection against the important fungal pathogenAspergillus fumigatus, where they employ numerous defense mechanisms, including production of antimicrobial extracellular vesicles. A major draw-back to work with neutrophils is the lack of a suitable cell line system for the study of fungal pathogenesis. To address this problem, we assessed the feasibility of using differentiated PLB-985 neutrophil-like cells as anin vitromodel to studyA. fumigatusinfection. We find that dimethylformamide-differentiated PLB-985 cells provide a useful recapitulation of many aspects ofA. fumigatusinteractions with primary human polymorphonuclear leukocytes. We show that differentiated PLB-985 cells phagocytose fungal conidia and acidify conidia-containing phagolysosomes similar to primary neutrophils, release neutrophil extracellular traps, and also produce antifungal extracellular vesicles in response to infection. In addition, we provide an improved method for the isolation of extracellular vesicles produced during infection by employing a size-exclusion chromatography-based approach. Advanced LC-MS/MS proteomics revealed an enrichment of extracellular vesicle marker proteins and a decrease of cytoplasmic proteins in extracellular vesicles isolated using this improved method. Ultimately, we find that differentiated PLB-985 cells can serve as a genetically tractable model to study many aspects ofA. fumigatuspathogenesis.IMPORTANCEPolymorphonuclear leukocytes are an important defense against human fungal pathogens, yet our model systems to study this group of cells remains very limited in scope. In this study, we established that differentiated PLB-985 cells can serve as a model to recapitulate several important aspects of human polymorphonuclear leukocyte interactions with the important human fungal pathogenAspergillus fumigatus. The proposed addition of a cultured neutrophil-like cell line to the experimental toolbox to study fungal pathogenesis will allow for a more mechanistic description of neutrophil antifungal biology. In addition, the easier handling of the cell line compared to primary human neutrophils allowed us to use PLB-985 cells to provide an improved method for isolation of neutrophil-derived extracellular vesicles using size-exclusion chromatography. Together, these results provide significant tools and a baseline knowledge for the future study of neutrophil-derived extracellular vesicles in the laboratory.
Environmental drivers of body size in North American bats
Authors: Alston J.M. , Keinath D.A. , Willis C.K.R. , Lausen C.L. , O’Keefe J.M. , Tyburec J.D. , Broders H.G. , Moosman P.R. , Carter T.C. , Chambers C.L. , Gillam E.H. , Geluso K. , Weller T.J , Burles D.W. , Fletcher Q.E. , Norquay K.J.O. , Goheen J.R. 
Published: July 2021

AbstractBergmann’s Rule—which posits that larger animals live in colder areas—is thought to influence variation in body size within species across space and time, but evidence for this claim is mixed. We tested four competing hypotheses for spatio-temporal variation in body size within bat species during the past two decades across North America. Bayesian hierarchical models revealed that spatial variation in body mass was most strongly (and negatively) correlated with mean annual temperature, supporting the heat conservation hypothesis (historically believed to underlie Bergmann’s Rule). Across time, variation in body mass was most strongly (and positively) correlated with net primary productivity, supporting the resource availability hypothesis. Climate change could influence body size in animals through both changes in mean annual temperature and in resource availability. Rapid reductions in body size associated with increasing temperatures have occurred in short-lived, fecund species, but such reductions likely transpire more slowly in longer-lived species.
Sensory computations in the cuneate nucleus of macaques
Authors: Suresh Aneesha K. , Greenspon Charles M. , He Qinpu , Rosenow Joshua M. , Miller Lee E. , Bensmaia Sliman J. 
Published: July 2021

AbstractTactile nerve fibers fall into a few classes that can be readily distinguished based on their spatiotemporal response properties. Because nerve fibers reflect local skin deformations, they individually carry ambiguous signals about object features. In contrast, cortical neurons exhibit heterogeneous response properties that reflect computations applied to convergent input from multiple classes of afferents, which confer to them a selectivity for behaviorally relevant features of objects. The conventional view is that these complex response properties arise within the cortex itself, implying that sensory signals are not processed to any significant extent in the two intervening structures – the cuneate nucleus (CN) and the thalamus. To test this hypothesis, we recorded the responses evoked in CN to a battery of stimuli that have been extensively used to characterize tactile coding in both the periphery and cortex, including skin indentations, vibrations, random dot patterns, and scanned edges. We found that CN responses are more similar to their cortical counterparts than they are to their inputs: CN neurons receive input from multiple classes of nerve fibers, they have spatially complex receptive fields, and they exhibit selectivity for object features. Contrary to consensus, then, CN plays a key role in processing tactile information.SignificancePerception is the outcome of the sequential processing of sensory signals at multiple stages along the neuraxis. The conventional view is that tactile signals are processed predominantly in the cerebral cortex. We tested this view by investigating the response properties of neurons in the cuneate nucleus (CN), the first potential stage of processing along the primary touch neuraxis. We found that CN responses more nearly resemble those of cortical neurons than they do those of nerve fibers: CN neurons have spatially complex receptive fields reflecting convergent input from multiple classes of nerve fibers and exhibit a selectivity for object features, absent in the nerve. We conclude that CN plays a key, early role in the processing of tactile information.
Long term conservation of DNA at ambient temperature. Implications for DNA data storage
Authors: Coudy Delphine , Colotte Marthe , Luis Aurélie , Tuffet Sophie , Bonnet Jacques 
Published: July 2021

AbstractDNA conservation is central to many applications. This leads to an ever-increasing number of samples which are more and more difficult and costly to store or transport. A way to alleviate this problem is to develop procedures for storing samples at room temperature while maintaining their stability. A variety of commercial systems have been proposed but they fail to completely protect DNA from deleterious factors, mainly water. On the other side, Imagene company has developed a procedure for long-term conservation of biospecimen at room temperature based on the confinement of the samples under an anhydrous and anoxic atmosphere maintained inside hermetic capsules. The procedure has been validated by us and others for purified RNA, and DNA in buffy coat or white blood cells lysates, but a precise determination of purified DNA stability is still lacking. We used the Arrhenius law to determine the DNA degradation rate at room temperature. We found that extrapolation to 25 °C gave a degradation rate constant equivalent to about 1 cut/century/100 000 nucleotides, a stability several orders of magnitude larger than the current commercialized processes. Such a stability is fundamental for many applications such as the preservation of very large DNA molecules (particularly interesting in the context of genome sequencing) or oligonucleotides for DNA data storage. Capsules are also well suited for this latter application because of their high capacity. One can calculate that the 64 zettabytes of data produced in 2020 could be stored, standalone, for centuries, in about 20 kg of capsules.
An active RNA transport mechanism into plant vacuoles
Authors: Floyd BE , Wong MM , Liu AY , Morriss SC , Mugume Y , Kazibwe Z , Ridout V , Luo X , MacIntosh GC , Bassham DC 
Published: July 2021

AbstractRNA degradation inside the plant vacuole by the ribonuclease RNS2 is essential for maintaining nucleotide concentrations and cellular homeostasis via the nucleotide salvage pathway. However, the mechanisms by which RNA is transported into the vacuole are not well understood. While selective macroautophagy may contribute to this transport, macroautophagy-independent transport pathways also exist. Here we demonstrate a mechanism for direct RNA transport into vacuoles that is active in purified vacuoles and is ATP hydrolysis-dependent. We identify the RNA helicase SKI2 as a factor required for this transport pathway, asski2mutant vacuoles are defective in transport.ski2mutants have an increased autophagy phenotype that can be rescued by exogenous addition of inosine, consistent with a function in nucleotide salvage. This newly-described transport mechanism is therefore critical for RNA degradation, recycling and cytoplasmic nucleotide homeostasis.
Synaptotagmin 1 oligomerization via the juxtamembrane linker regulates spontaneous and evoked neurotransmitter release
Authors: Courtney Kevin C. , Li Yueqi , Vevea Jason D. , Wu Zhenyong , Zhang Zhao , Chapman Edwin R. 
Published: July 2021

ABSTRACTSynaptotagmin-1 (syt1) is a Ca2+sensor that regulates synaptic vesicle exocytosis. Cell-based experiments suggest that syt1 functions as a multimer, however biochemical and electron microscopy studies have yielded contradictory findings regarding putative self-association. Here, we performed dynamic light scattering on syt1 in solution, followed by electron microscopy, and used atomic force microscopy to study syt1 self-association on supported lipid bilayers under aqueous conditions. Ring-like multimers were clearly observed. Multimerization was enhanced by Ca2+and required anionic phospholipids. Large ring-like structures (∼180 nm) were reduced to smaller rings (∼30 nm) upon neutralization of a cluster of juxtamembrane lysine residues; further substitution of residues in the second C2-domain completely abolished self-association. When expressed in neurons, syt1 mutants with graded reductions in self-association activity exhibited concomitant reductions in: a) clamping spontaneous release, and b) triggering and synchronizing evoked release. Thus, the juxtamembrane linker of syt1 plays a crucial role in exocytosis by mediating multimerization.
The complete genome of carbapenem-resistant Escherichia coli ST410 harbored blaNDM-5 isolated from reservoir water in Singapore
Authors: Zhong Yang , Guo Siyao , Ming Glendon Ong Hong , Schlundt Joergen 
Published: July 2021

AbstractObjectiveEscherichia coli ST410 with blaNDM-5 has been increasingly detected as multidrug resistance pathogens globally, even though there are very few reports of infections caused by blaNDM-5 producing E. coli in Singapore[1]. And significantly limit sequencing information of blaNDM-5 carried E. coli strain from Singapore. In 2018, our group obtained a carbapenem resistance E. coli ST410 strain SrichA-1 isolated from reservoir water in Singapore, determined to harbor the NDM-5 gene. (BioSample Accession: SAMN18579051).MethodsThe susceptibility test to antimicrobials was performed with microdilution minimum inhibitory concentration (MIC) test and interpreted according to the Clinical And Laboratory Standards Institute (CLSI) -M100 standards. The genomic DNA of this strain was extracted and send for Whole-genome sequencing(WGS) with the Illumina platform. The WGS analysis was processed with the Center for Genomic Epidemiology (CGE, DTU) server.ResultsDuring the minimum inhibitory concentration (MIC) test, SrichA-1 has shown strong resistance to all the beta-lactams, including cephalosporin and carbapenem, which can not be inhibited by the clavulanic acid. Further whole genome sequencing analysis has shown that the strain harboring five beta-lactamase genes covers all class A to D, including the carbapenemase genes as blaNDM-5.ConclusionHere, we reported the complete chromosome sequence of this isolate as well as the sequence of a cycler plasmid. The pSGNDM-5 plasmid was furtherly identified to carry four beta-lactamase genes, including blaNDM-5, blaCTX-M-15, blaTEM-1B, blaOXA-1, while a blaCMY-2 was detected to be located on the chromosome.
The need for a comprehensive facility decision-making process
Authors: Backus Erik Carl , Bruhl Jakob C. 
Published: July 2021

Purpose
The facility decision-making process (FDMP), as described in this paper, is a framework based on decades of proven effectiveness in analogous military applications. The purpose of this paper is to evaluate key factors which justify the need for the FDMP before describing the FDMP.

Design/methodology/approach
This paper conducts a literature review as it relates to facilities specific decision-making, puts forward a new concept for those processes and provides an abridged case study of the concept in application.

Findings
Facilities management is a key function for nearly every type of business or enterprise. As part of facilities management, many decisions are made about physical assets that a business or enterprise owns or maintains. Currently, there is no uniform decision-making framework, in literature or in practice, which enables consistency, robustness and scalability for facility management decisions. Such a framework would enable facility managers to effectively justify decisions related to capital and operational expenses.

Practical implications
The FDMP provides a robust procedure for facilities managers and engineers that enables enhanced strength in the face of business enterprise scrutiny as compared with the often-intuitive decision-making processes currently used in practice.

Originality/value
This novel conceptual process articulates the opportunity to provide for a comprehensive facilities decision-making process that enables better decisions especially as it relates to what are often ill-defined problem sets in facilities management.