bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effects of N-linked Glycosylation on SLC6 Transporters
Authors: Chan Matthew C. , Shukla Diwakar 
Published: July 2022

AbstractMembrane transporters of the solute carrier 6 (SLC6) family mediate various physiological processes by facilitating the translocation of amino acids, neurotransmitters, and other metabolites. In the human body, these transporters are tightly controlled through various post-translational modifications with implications on protein expression, stability, membrane trafficking, and dynamics. While N-linked glycosylation is a universal regulatory mechanism among eukaryotes, the exact molecular mechanism of how glycosylation affects the SLC6 transporter family. It is generally believed that glycans influence transporter stability and membrane trafficking, however, the role of glycosylation on transporter dynamics remains inconsistent, with differing conclusions among individual transporters across the SLC6 family. In this study, we collected over 1 millisecond of aggregated all-atom molecular dynamics (MD) simulation data to identify the impact of N-glycans of four human SLC6 transporters: the serotonin transporter, dopamine transporter, glycine transporter, and neutral amino acid transporter B0AT1. We designed our computational study by first simulating all possible combination of a glycan attached to each glycosylation sites followed by investigating the effect of larger, oligo-N-linked glycans to each transporter. Our simulations reveal that glycosylation does not significantly affect transporter structure, but alters the dynamics of the glycosylated extracellular loop. The structural consequences of glycosylation on the loop dynamics are further emphasized in the presence of larger glycan molecules. However, no apparent trend in ligand stability or movement of gating helices was observed. In all, the simulations suggest that glycosylation does not consistently affect transporter structure and dynamics among the collective SLC6 family and should be characterized at a per-transporter level to further elucidate the underlining mechanisms of in vivo regulation.
Density-dependent habitat selection alters drivers of population distribution in northern Yellowstone elk
Authors: Smith Brian J. , MacNulty Daniel R. , Stahler Daniel R. , Smith Douglas W. , Avgar Tal 
Published: July 2022

AbstractAlthough it is well established that density dependence drives changes in organismal abundance over time, relatively little is known about how density dependence affects variation in abundance over space. We tested the hypothesis that spatial tradeoffs between food and safety can change the drivers of population distribution, caused by opposing patterns of density-dependent habitat selection (DDHS) that are predicted by the multidimensional ideal free distribution. We addressed this using winter aerial survey data of northern Yellowstone elk (Cervus canadensis) spanning four decades. Supporting our hypothesis, we found positive DDHS for food (herbaceous biomass) and negative DDHS for safety (openness and roughness), such that the primary driver of habitat selection switched from food to safety as elk density decreased from 9.3 to 2.0 elk/km2. Our results demonstrate how population density can drive landscape-level shifts in population distribution, confounding habitat selection inference and prediction, and potentially affecting community-level interactions.
“Leap before you look”: Conditions that promote implicit visuomotor adaptation without explicit learning
Authors: Savalia Tejas , Cowell Rosemary A. , Huber David E. 
Published: July 2022

AbstractWhen learning a novel visuomotor mapping (e.g., mirror writing), accuracy can improve quickly through explicit learning (e.g., move left to go right) but after considerable practice, implicit learning takes over, producing fast, natural movements. This implicit learning occurs automatically, but it has been unknown whether explicit learning is similarly obligatory. Using a reaching task with a 90-degree rotation between screen position and movement direction, we found that explicit learning could be “turned off” by introducing the rotation gradually (increments of 10-degrees) and instructing participants to move quickly. These specific conditions were crucial, because both explicit and implicit learning occurred if the rotation occurred suddenly, if participants were told to emphasize accuracy, or if visual feedback during movement was removed. We reached these conclusions by examining the time course of learning (e.g., whether there was fast improvement followed by a long tail of additional improvement), by examining the aftereffects of learning when the rotation was abruptly removed, and by using formal model comparison between a dual-state (explicit and implicit) versus a single-state learning model as applied to the data.Author summaryIn some situations, the relationship between motion direction and what we see is different than normal. For instance, try using a computer mouse that is held sideways (a 90-degree rotation). When first encountering this situation, people move carefully, using explicit strategies (e.g., move right to go up). However, after many learning trials, motion becomes automatic (implicit) and natural. Prior results found that implicit visuomotor learning always occurs with enough experience. In our study, we found that this is not true of explicit visuomotor learning; in some situations, explicit learning can be turned off. More specifically, we found that this occurs when the novel visuomotor situation is: 1) introduced gradually (e.g., a gradual introduction of 90-degree rotation in steps of 10 degrees); 2) when there is pressure to move quickly; and 3) with real-time onscreen views of the motion path. If any of these three components are missing, then people use explicit learning. These conclusions were reached by examining the time course of learning (e.g., whether there was both fast and slow learning as assessed with mathematical models) and by examining the tendency to automatically move in the opposite direction from the rotation when the rotation is abruptly removed after learning.
Studying Pathogens Degrades BLAST-based Pathogen Identification
Authors: Beal Jacob , Clore Adam , Manthey Jeff 
Published: July 2022

AbstractAs synthetic biology becomes increasingly capable and accessible, it is likewise increasingly critical to be able to make accurate biosecurity determinations regarding the pathogenicity or toxicity of particular nucleic acid or amino acid sequences. At present, this is typically done using the BLAST algorithm to determine the best match with sequences in the NCBI databases. Neither BLAST nor the NCBI databases, however, are actually designed for biosafety determination. Critically, taxonomic errors or ambiguities in the NCBI databases can also cause errors in BLAST-based taxonomic categorization. With heavily studied taxa and frequently used biotechnology tools, even low frequency taxonomic categorization issues can lead to high rates of errors in biosecurity decision-making. Here we focus on the implications for false positives, finding that NCBI BLAST will now incorrectly categorize a number of commonly used biotechnology tool sequences as the pathogens or toxins with which they have been used. Paradoxically, this implies that problems are expected to be most acute for the pathogens and toxins of highest interest and the most widely used biotechnology tools. We thus conclude that biosecurity tools should shift away from BLAST against NCBI and towards new methods that are specifically tailored for biosafety purposes.
The spatial distribution and temporal trends of livestock damages caused by wolves in Europe
Authors: Singer Liam , Wietlisbach Xenia , Hickisch Raffael , Schoell Eva Maria , Leuenberger Christoph , Van den Broek Angela , Désalme Manon , Driesen Koen , Lyly Mari , Marucco Francesca , Kutal Miroslav , Pagon Nives , Papp Cristian Remus , Milioni Paraskevi , Uzdras Remigijus , Zihmanis Ilgvars , Zimmermann Fridolin , Marsden Katrina , Hackländer Klaus , López-Bao José Vicente , Klenzendorf Sybille , Wegmann Daniel 
Published: July 2022

SummaryWolf populations are recovering and expanding across Europe, causing conflicts with livestock owners. To mitigate these conflicts and reduce livestock damages, authorities spend considerable resources to compensate damages, support damage prevention measures, and manage wolf populations. However, the effectiveness of these measures remains largely unknown, especially at larger geographic scales. Here we compiled incident-based livestock damage data across 21 countries for the years 2018, 2019 and 2020, during which 39,262 wolf-caused incidents were reported from 470 administrative regions. We found substantial regional variation in all aspects of the data, including the primary target species, the density of damages, their seasonal distribution, and their temporal trend. More than half of the variation in damage densities across regions is explained by the area of extensively cultivated habitats occupied by wolves and namely natural grasslands and broad-leaved forests. Regional variation in husbandry practices and damage prevention, while difficult to quantify at a continental scale, appear important factors to further modulate these incidents. As illustrated with detailed data from Germany, for instance, the relationship between the number of wolf units and damages is diminishing over time, suggesting some adaptation of livestock owners and local authorities to their presence, for example by increasing prevention efforts. As we argue, temporal trends of damage incidents, which are robust to variation in data collection across regions, are thus informative about the local intensity of the wolf-human conflict. We estimated increasing trends for the majority of regions, reflecting the current expansion of wolves across the continent. Nonetheless, many of these increases were moderate and for more than one third of all regions, trends were negative despite growing wolf populations, thus indicating that wolf-livestock conflicts can be successfully mitigated with proper management.
Cholinergic and noradrenergic axonal activity contains a behavioral-state signal that is coordinated across the dorsal cortex
Authors: Collins Lindsay , Francis John , Emanuel Brett , McCormick David 
Published: July 2022

AbstractFluctuations in brain and behavioral state are supported by broadly projecting neuromodulatory systems. In this study, we use mesoscale two-photon calcium imaging to examine spontaneous activity of cholinergic and noradrenergic axons in awake mice in order to determine the interaction between arousal/movement state transitions and neuromodulatory activity across the dorsal cortex at distances separated by up to 4 mm. We confirm that GCaMP6s activity within axonal projections of both basal forebrain cholinergic and locus coeruleus noradrenergic neurons track arousal, indexed as pupil diameter, and changes in behavioral engagement, as reflected by bouts of whisker movement and/or locomotion. The broad coordination in activity between even distant axonal segments indicates that both of these systems can communicate, in part, through a global signal, especially in relation to changes in behavioral state. In addition to this broadly coordinated activity, we also find evidence that a subpopulation of both cholinergic and noradrenergic axons may exhibit heterogeneity in activity that appears to be independent of our measures of behavioral state. By monitoring the activity of cholinergic interneurons in the cortex we found that a subpopulation of these cells also exhibit state-dependent (arousal/movement) activity. These results demonstrate that cholinergic and noradrenergic systems provide a prominent and broadly synchronized signal related to behavioral state, and therefore may contribute to state-dependent cortical activity and excitability.
High-throughput Identification of Novel Heat Tolerance Genes via Genome-wide Pooled Mutant Screens in the Model Green AlgaChlamydomonas reinhardtii
Authors: Mattoon Erin M. , McHargue William , Bailey Catherine E. , Zhang Ningning , Chen Chen , Eckhardt James , Daum Chris G. , Zane Matt , Pennacchio Christa , Schmutz Jeremy , O’Malley Ronan C. , Cheng Jianlin , Zhang Ru 
Published: July 2022

AbstractDifferent high temperatures adversely affect crop and algal yields with various responses in photosynthetic cells. The list of genes required for thermotolerance remains elusive. Additionally, it is unclear how carbon source availability affects heat responses in plants and algae. We utilized the insertional, indexed, genome-saturating mutant library of the unicellular, eukaryotic green algaChlamydomonas reinhardtiito perform genome-wide, quantitative, pooled screens under moderate (35°C) or acute (40°C) high temperatures with or without organic carbon sources. We identified heat-sensitive mutants based on quantitative growth rates and identified putative heat tolerance genes (HTGs). By triangulating HTGs with heat-induced transcripts or proteins in wildtype cultures and MapMan functional annotations, we present a high/medium-confidence list of 933Chlamydomonasgenes with putative roles in heat tolerance. Triangulated HTGs include those with known thermotolerance roles and novel genes with little or no functional annotation. About 50% of these high-confidence HTGs in Chlamydomonas have orthologs in green lineage organisms, including crop species.Arabidopsis thalianamutants deficient in the ortholog of a high-confidenceChlamydomonasHTG were also heat sensitive. This work expands our knowledge of heat responses in photosynthetic cells and provides engineering targets to improve thermotolerance in algae and crops.
Recent transposable element bursts triggered by insertions near genes in a fungal pathogen
Authors: Oggenfuss Ursula , Croll Daniel 
Published: July 2022

ABSTRACTThe activity of transposable elements (TEs) contributes significantly to genome evolution. TEs often destabilize genome integrity but may also confer adaptive variation in phenotypic traits. De-repression of epigenetically silenced TEs often initiates bursts of transposition activity that may be counteracted by purifying selection and genome defenses. However, how these forces interact to determine the expansion routes of TEs within a species remains largely unknown. Here, we analyzed a set of 19 telomere-to-telomere genomes of the fungal wheat pathogenZymoseptoria tritici. Phylogenetic reconstruction and ancestral state estimates of individual TE families revealed that TEs have undergone distinct activation and repression periods resulting in highly uneven copy numbers between genomes of the same species. Most TEs are clustered in gene poor niches, indicating strong purifying selection against insertions near coding sequences. TE families with high copy numbers have low sequence divergence and strong signatures of defense mechanisms (i.e., RIP). In contrast, small non-autonomous TEs (i.e., MITEs) are less impacted by defense mechanisms and are often located in close proximity to genes. Individual TE families have experienced multiple distinct burst events that generated many nearly identical copies. We found that aCopiaelement burst was initiated from recent copies inserted substantially closer to genes compared to older insertions. Overall, TE bursts tended to initiate from copies in GC-rich niches that escaped inactivation by genomic defenses. Our work shows how specific genomic environments features provide triggers for TE proliferation.
Selective loss of CD107a TIGIT+ memory HIV-1-specific CD8+ T cells in PLWH over a decade of ART
Authors: Blanch-Lombarte Oscar , Ouchi Dan , Jiménez-Moyano Esther , Carabelli Julieta , Marin Miguel Angel , Peña Ruth , Pelletier Adam , Talla Aarthi , Sharma Ashish , Dalmau Judith , Santos José Ramón , Sékaly Rafik-Pierre , Clotet Bonaventura , Prado Julia G. 
Published: July 2022

AbstractThe co-expression of inhibitory receptors (IRs) is a hallmark of CD8+ T-cell exhaustion (Tex) in people living with HIV-1 (PLWH). Understanding alterations of IRs expression in PLWH on long-term antiretroviral treatment (ART) remains elusive but is critical to overcoming CD8+ Tex and designing novel HIV-1 cure immunotherapies. To address this, we combine high-dimensional supervised and unsupervised analysis of IRs concomitant with functional markers across the CD8+ T-cell landscape on 24 PLWH over a decade on ART. We define irreversible alterations of IRs co-expression patterns in CD8+ T cells not mitigated by ART and identify negative associations between the frequency of TIGIT+ and TIGIT+TIM-3+ and CD4+ T-cell levels. Moreover, changes in total, SEB-activated, and HIV-1-specific CD8+ T-cells delineate a complex reshaping of memory and effector-like cellular clusters on ART. Indeed, we identify a selective reduction of HIV-1 specific-CD8+ T-cell memory-like clusters sharing TIGIT expression and low CD107a that can be recovered by mAb TIGIT blockade independently of IFNγ and IL-2. Collectively, these data characterize with unprecedented detail the patterns of IRs expression and functions across the CD8+ T-cell landscape and indicate the potential of TIGIT as a target for Tex precision immunotherapies in PLWH at all ART stages.
Sequence, Structure, and Epitope Analysis of the Polymorphic Membrane Protein Family in Chlamydia trachomatis
Authors: Cervantes Patrick W. , Segelke Brent , Lau Edmond Y. , de la Maza Luis , Coleman Matthew , D’haeseleer Patrik 
Published: July 2022

AbstractThe polymorphic membrane proteins are a family of autotransporters that play an important role in infection, adhesion and immunity in Chlamydia trachomatis. Here we show that the characteristic GGA(I,L,V) and FxxN tetrapeptide repeats fit into a larger repeat sequence, and that these repeats correspond to the coils of a large beta-helical domain in high quality structure predictions. While the tetranucleotide motifs themselves are predicted to play a structural role in folding and close stacking of the beta-helical backbone of the passenger domain, we found many of the interesting features of Pmps are localized to the side loops jutting out from the beta helix - including protease cleavage, host cell adhesion, and B-cell epitopes; while T-cell epitopes are predominantly found in the beta-helix itself.
Genome-scale analysis of cellular restriction factors that inhibit transgene expression from adeno-associated virus vectors
Authors: Ngo Ashley M , Puschnik Andreas S 
Published: July 2022

ABSTRACTAdeno-associated virus (AAV) vectors are one of the leading platforms for gene delivery for the treatment of human genetic diseases, but the antiviral cellular mechanisms that interfere with optimal transgene expression are incompletely understood. Here, we performed two genome-scale CRISPR screens to identify cellular factors that restrict transgene expression from recombinant AAV vectors. Our screens revealed several components linked to DNA damage response, chromatin remodeling and transcriptional regulation. Inactivation of the Fanconi Anemia gene FANCA, the Human Silencing Hub (HUSH) associated methyltransferase SETDB1 and the gyrase, Hsp90, histidine kinase and MutL (GHKL)-type ATPase MORC3 led to increased transgene expression. Moreover, SETDB1 and MORC3 knockout improved transgene levels of several AAV serotypes as well as other viral vectors, such as lentivirus and adenovirus. Finally, we demonstrated that inhibition of FANCA, SETDB1 or MORC3 also enhanced transgene expression in human primary cells, suggesting that these could be physiologically relevant pathways that restrict AAV transgene levels in therapeutic settings.IMPORTANCERecombinant AAV (rAAV) vectors have been successfully developed for the treatment of genetic diseases. The therapeutic strategy often involves the replacement of a defective gene by expression of a functional copy from the rAAV vector genome. However, cells possess antiviral mechanisms that recognize and silence foreign DNA elements thereby limiting transgene expression and its therapeutic effect. Here, we utilize a functional genomics approach to uncover a comprehensive set of cellular restriction factors that inhibit rAAV-based transgene expression. Genetic inactivation of selected restriction factors increased rAAV transgene expression. Hence, modulation of identified restriction factors has the potential to enhance AAV gene replacement therapies.
Structural basis of organic cation transporter-3 inhibition
Authors: Khanppnavar Basavraj , Maier Julian , Herborg Freja , Gradisch Ralph , Lazzarin Erika , Luethi Dino , Yang Jae-Won , Qi Chao , Holy Marion , Jäntsch Kathrin , Kudlacek Oliver , Schicker Klaus , Werge Thomas , Gether Ulrik , Stockner Thomas , Korkhov Volodymyr M. , Sitte Harald H. 
Published: July 2022

AbstractOrganic cation transporters (OCTs) facilitate the translocation of catecholamines and xenobiotics across the plasma membrane in various tissues throughout the human body. OCT3 plays a key role in low-affinity, high-capacity uptake of monoamines in most tissues including heart, brain and liver. Its deregulation plays a role in diseases. Despite its importance, the structural basis of OCT3 function and its inhibition has remained enigmatic. Here we describe the cryo-EM structure of human OCT3 at 3.2 Å resolution. Structures of OCT3 bound to two inhibitors, corticosterone and decynium-22, define the ligand binding pocket and reveal common features of major facilitator transporter inhibitors. In addition, we relate the functional characteristics of an extensive collection of previously uncharacterized human genetic variants to structural features, thereby providing a basis for understanding the impact of OCT3 polymorphisms.
Regulatory framework on the UAM operational concepts of the ASSURED-UAM project
Authors: Mazur Anna Maria , ten Thije Jens , Vreeken Joost , Hesselink Henk , Dziugieł Bartosz , Wyka Sylwester , Liberacki Adam , Idzikowska Teresa , Stanczyk Anna Dorota , Utracka Agata , Ginter Piotr , Czupryn Sandra , Giannuzzi Michele , Melo Sandra , Witkowska-Konieczny Adriana , Di Vito Vittorio , Menichino Aniello 
Published: July 2022

Purpose
The purpose of this paper is to study the overall framework in which the Urban Air Mobility (UAM) deployment is expected to be implemented. Another aim of the study is to give a better overview on the current regulations and standards including the impact of the regulations on the industry, operations and cities.

Design/methodology/approach
This paper performs a literature review on the regulatory framework, which provides a clear view of the current regulations and standards. The review includes the insight into the details of possible international rules for the future, considering operations in the specific and certified categories. The impact and trends of current and future regulations are also presented.

Findings
The analysis described in this paper shows a strong upward trend in UAM technical and operational developments as well as further potential for a successful incorporation in city mobility concepts. This paper indicates the importance of the representatives of guideline development organizations, industry, agencies and other important players involved in the standard development process.

Practical implications
This section describes synthesis on the required level of safety for UAM operations as well as description on the impact of the regulations from different perspectives, including industry and certification of urban aircraft, operations and air traffic management, cities and the governance of the urban airspace and well as technology.

Originality/value
Barriers such as legislation do not allow the common UAM to be deployed. This paper studies the overall framework in which the UAM deployment is expected to be implemented.