bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climatic refugia in the coldest neotropical hotspot, the Andean páramo
Authors: Peyre Gwendolyn , Lopez Catalina , Diaz Maria Daniela , Lenoir Jonathan 
Published: November 2022

AbstractAimThe Andean páramo is the most biodiverse high-mountain region on Earth and past glaciation dynamics during the Quaternary are greatly responsible for its plant diversification. Here, we aim at identifying potential climatic refugia since the Last Glacial Maximum (LGM) in the páramo, according to plant family, biogeographic origin, and life-form.LocationThe páramo region in the Northern AndesMethodsWe built species distribution models for 664 plant species to generate range maps under current and LGM conditions, using five General Circulation Models (GCMs). For each species and GCM, we identified potential (suitable) and potential active (likely still occupied) refugia where both current and LGM range maps overlap. We stacked and averaged the resulting refugia maps across species and GCMs to generate consensus maps for all species, plant families, biogeographic origins and life-forms. All maps were corrected for potential confounding effect due to species richness.ResultsWe found refugia to be chiefly located in the southern and central páramos of Ecuador and Peru, especially towards the páramo ecotone with lower-elevation forests. However, we found additional specific patterns according to plant family, biogeographic origin and life-form. For instance, endemics showed refugia concentrated in the northern páramos.Main conclusionsOur findings suggest that large and connected páramo areas, but also the transitional Amotape-Huancabamba zone with the Central Andes, are primordial areas for plant species refugia since the LGM. This study therefore enriches our understanding on páramo evolution and calls for future research on plant responses to future climate change.
Appetitive cue exposure increases neural reward responses without modulating temporal discounting
Authors: Knauth Kilian , Mathar David , Kuzmanovic Bojana , Tittgemeyer Marc , Peters Jan 
Published: November 2022

AbstractWhen given a choice, humans and many animals prefer smaller but sooner over larger but later rewards, a tendency referred to as temporal discounting. Alterations in devaluation of future rewards have been reported in a range of maladaptive behaviors and clinical conditions. Although temporal discounting is highly stable over time and testing environments (e.g., laboratory vs. virtual reality), it is partly under contextual control. For example, highly appetitive cues such as erotic images might increase preferences for immediate rewards, although overall evidence remains mixed. Dopaminergic circuit activity and striatal dopamine concentrations are often assumed to drive increases in temporal discounting following appetitive cue-exposure, yet this was never explicitly tested. Here we examined cue-reactivity effects (erotic vs. neutral pictures) on subsequent temporal discounting in a pre-registered within-subjects study in healthy male participants (n=38). Functional magnetic resonance imaging (fMRI) assessed neural cue-reactivity, value-computations and choice-related effects. Preregistered analyses replicated previous findings of value coding in ventromedial prefrontal cortices, striatum and cingulate cortex. Likewise, as hypothesized, lateral prefrontal cortex activity increased during choices of delayed rewards, potentially reflecting cognitive control. As predicted, erotic vs. neutral cue exposure was associated with increased activity in attention and reward circuits. Contrary to our preregistered hypotheses, temporal discounting was largely unaffected by cue exposure. Likewise, cue-reactivity in key areas of the dopaminergic reward circuit (Nacc, VTA) was not significantly associated with changes in behavior. Our results indicate that behavioral effects of erotic cue exposure on temporal discounting might not be as unequivocal as previously thought and raise doubt on the hypothesis of an upregulated dopaminergic ramping mechanism, that might support myopic approach behavior towards immediate rewards.
mRNA targeting eliminates the need for the signal recognition particle during membrane protein insertion in bacteria
Authors: Sarmah Pinku , Shang Wenkang , Origi Andrea , Licheva Mariya , Kraft Claudine , Ulbrich Maximilian , Lichtenberg Elisabeth , Wilde Annegret , Koch Hans-Georg 
Published: November 2022

SummarySignal-sequence dependent protein targeting is essential for the spatiotemporal organization of eukaryotic and prokaryotic cells and facilitated by dedicated protein targeting factors, such as the signal recognition particle (SRP). However, targeting signals are not exclusively contained within proteins, but can also be present within mRNAs. Byin vivoandin vitroassays, we show that mRNA targeting is controlled by the nucleotide content and by secondary structures within mRNAs. mRNA binding to bacterial membranes occurs independently of soluble targeting factors, but is dependent on the SecYEG-translocon and YidC. Importantly, membrane insertion of proteins translated from membrane-bound mRNAs occurs independently of the SRP pathway, while the latter is strictly required for proteins translated from cytosolic mRNAs. In summary, our data indicate that mRNA targeting acts in parallel to the canonical SRP-dependent protein targeting and serves as an alternative strategy for safeguarding membrane protein insertion when the SRP pathway is compromised.
On the role and regulation of glycogen catabolic isoenzymes inSynechocystissp. PCC6803
Authors: Neumann Niels , Lee Kenric , Forchhammer Karl 
Published: November 2022

AbstractGlycogen is the main carbon storage polymer in many organisms and widespread throughout all domains of life. In cyanobacteria glycogen degradation plays an essential role when metabolism changes to a heterotrophic mode during dark phases or the resuscitation from nitrogen starvation. Like many other cyanobacteria the genome ofSynechocystissp. PCC 6803 encodes for several homologues of glycogen catabolic enzymes. The role and regulation of this isoenzymes has so far been only partly understood. Here we show via biochemical analysis that the glycogen phosphorylase GlgP1 is regulated by a C-terminal redox switch unique to certain cyanobacteria. This is the first time a redox regulation of a glycogen degrading enzyme has been shown in prokaryotes. Remarkably, GlgP1 is inactivated in its reduced state and gets activated via oxidation by ROS. We conclude that GlgP1 is especially important for rapid glycogen degradation in certain stress conditions during photoautotrophic growth. We suggest that thereby carbon is channeled through the OPP pathway, to stabilize photosynthesis during situations of high ribulose-1,5-BP demands. Furthermore, we suggest that the concomitant formation of NADPH within this pathway is essential to regenerate ROS scavenging compounds like GSH to reduce potential oxidative damage and to improve survivability under prolonged phases of oxidative stress. In addition, we show for the first time the role of the two glycogen debranching isoenzymes where GlgX1 turned out to be the essential glycogen debranching enzyme during resuscitation from chlorosis, while the role of GlgX2 remains elusive.
Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England
Authors: Yu QinQin , Ascensao Joao , Okada Takashi ,   The COVID-19 Genomics UK (COG-UK) consortium, Boyd Olivia , Volz Erik , Hallatschek Oskar 
Published: November 2022

AbstractGenetic drift in infectious disease transmission results from randomness of transmission and host recovery or death. The strength of genetic drift for SARS-CoV-2 transmission is expected to be high due to high levels of superspreading, and this is expected to substantially impact disease epidemiology and evolution. However, we don’t yet have an understanding of how genetic drift changes over time or across locations. Furthermore, noise that results from data collection can potentially confound estimates of genetic drift. To address this challenge, we develop and validate a method to jointly infer genetic drift and measurement noise from time-series lineage frequency data. Our method is highly scalable to increasingly large genomic datasets, which overcomes a limitation in commonly used phylogenetic methods. We apply this method to over 490,000 SARS-CoV-2 genomic sequences from England collected between March 2020 and December 2021 by the COVID-19 Genomics UK (COG-UK) consortium and separately infer the strength of genetic drift for pre-B.1.177, B.1.177, Alpha, and Delta. We find that even after correcting for measurement noise, the strength of genetic drift is consistently, throughout time, higher than that expected from the observed number of COVID-19 positive individuals in England by 1 to 3 orders of magnitude, which cannot be explained by literature values of superspreading. Our estimates of genetic drift will be informative for parameterizing evolutionary models and studying potential mechanisms for increased drift.Author SummaryThe transmission of pathogens like SARS-CoV-2 is strongly affected by chance effects in the contact process between infected and susceptible individuals, collectively referred to as random genetic drift. We have an incomplete understanding of how genetic drift changes across time and locations. To address this gap, we developed a computational method that infers the strength of genetic drift from time series genomic data that corrects for non-biological noise and is computationally scalable to the large numbers of sequences available for SARS-CoV-2, overcoming a major challenge of existing methods. Using this method, we quantified the strength of genetic drift for SARS-CoV-2 transmission in England throughout time and across locations. These estimates constrain potential mechanisms and help parameterize models of SARS-CoV-2 evolution. More generally, the computational scalability of our method will become more important as increasingly large genomic datasets become more common.
Divergent microbial structure still results in convergent microbial function during arrested anaerobic digestion of food waste at different hydraulic retention times
Authors: Jiang Minxi , Khunjar Wendell , Li Anjie , Chandran Kartik 
Published: November 2022

AbstractIn this study, two arrested anaerobic digestion bioreactors fed with food waste operated under different hydraulic retention times (HRTs) exhibited long-term stable volatile fatty acid (VFA) production performance including similar total yields (p= .085) with propionic acid (PA) being the most abundant VFA. Meta-omics analysis revealed distinct microbial structures (p= .02) at the two HRTs while there were no differences in potential and extant functionality as indicated by the whole-genome and whole-transcriptome sequencing, respectively. The highest potential (relative abundance of DNA sequence reads) and extant (relative abundance of mRNA sequence reads) functionality corresponded with PA production compared to other acids. The most abundant genusPrevotellaproduced PA mainly through the acryloyl-CoA pathway. Based on our results, the mechanistic basis for the similar VFA production performance observed under the HRTs tested lies in the community-level redundancy in convergent acidification functions and pathways, rather than trends in community structure.
Patterns and determinants of the global herbivorous mycobiome
Authors: Meili Casey H. , Jones Adrienne L. , Arreola Alex X. , Habel Jeffrey , Pratt Carrie J. , Hanafy Radwa A. , Wang Yan , Yassin Aymen S. , TagElDein Moustafa A. , Moon Christina D. , Janssen Peter H. , Shrestha Mitesh , Rajbhandari Prajwal , Nagler Magdalena , Vinzelj Julia M. , Podmirseg Sabine M. , Stajich Jason E. , Goetsch Arthur L. , Hayes Jerry , Young Diana , Fliegerova Katerina , Grilli Diego Javier , Vodička Roman , Moniello Giuseppe , Mattiello Silvana , Kashef Mona T. , Nagy Yosra I. , Edwards Joan A. , Dagar Sumit Singh , Foote Andrew P. , Youssef Noha H. , Elshahed Mostafa S. 
Published: November 2022

AbstractIn spite of their indispensable role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. To examine global patterns and determinants of AGF diversity, we generated and analyzed an amplicon dataset from 661 fecal samples from 34 animal species, 9 families, and 6 continents. We identified 56 novel genera, greatly expanding AGF diversity beyond current estimates. Both stochastic (homogenizing dispersal and drift) and deterministic (homogenizing selection) processes played an integral role in shaping AGF communities, with a higher level of stochasticity observed in foregut fermenters. Community structure analysis revealed a distinct pattern of phylosymbiosis, where host-associated (animal species, family, and gut type), rather than ecological (domestication status and biogeography) factors predominantly shaped the community. Hindgut fermenters exhibited stronger and more specific fungal-host associations, compared to broader mostly non-host specific associations in foregut fermenters. Transcriptomics-enabled phylogenomic and molecular clock analyses of 52 strains from 14 genera indicated that most genera with preferences for hindgut hosts evolved earlier (44-58 Mya), while those with preferences for foregut hosts evolved more recently (22-32 Mya). This pattern is in agreement with the sole dependence of herbivores on hindgut fermentation past the Cretaceous-Paleogene (K-Pg) extinction event through the Paleocene and Eocene, and the later rapid evolution of animals employing foregut fermentation strategy during the early Miocene. Only a few AGF genera deviated from this pattern of co-evolutionary phylosymbiosis, by exhibiting preferences suggestive of post-evolutionary environmental filtering. Our results greatly expand the documented scope of AGF diversity and provide an ecologically and evolutionary-grounded model to explain the observed patterns of AGF diversity in extant animal hosts.
Dependence of Nucleosome Mechanical Stability on DNA Mismatches
Authors: Ngo Thuy T. M. , Liu Bailey , Wang Feng , Basu Aakash , Wu Carl , Ha Taekjip 
Published: November 2022

AbstractThe organization of nucleosomes into chromatin and their accessibility are shaped by local DNA mechanics. Conversely, nucleosome positions shape genetic variations, which may originate from mismatches during replication and chemical modification of DNA. To investigate how DNA mismatches affect the mechanical stability and the exposure of nucleosomal DNA, we used an optical trap combined with single-molecule FRET and a single-molecule FRET cyclization assay. We found that a single base-pair C-C mismatch enhances DNA bendability and nucleosome mechanical stability for the 601-nucleosome positioning sequence. An increase in force required for DNA unwrapping from the histone core is observed for single base-pair C-C mismatches placed at three tested positions: at the inner turn, at the outer turn, or at the junction of the inner and outer turn of the nucleosome. The results support a model where nucleosomal DNA accessibility is reduced by mismatches, potentially explaining the preferred accumulation of single nucleotide substitutions in the nucleosome core and serving as the source of genetic variation during evolution and cancer progression. Mechanical stability of an intact nucleosome, i.e., mismatch-free, is also dependent on the species as we find that yeast nucleosomes are mechanically less stable and more symmetrical in the outer turn unwrapping compared to Xenopus nucleosomes.
The Mangrove Microbiome of the Malay Peninsula
Authors: Wainwright Benjamin J. , Millar Trevor , Bowen Lacee , Hickman Kate , Lee Jen Nie , Yeo Zee Yi , Huang Danwei , Zahn Geoffrey 
Published: November 2022

AbstractMicrobes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and without microbial cycling, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse of all the planets. They have vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and contain significant stocks of sequestered carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome are scarce, especially in the Southeast Asian biodiversity hotspot. Here we examine the microbiome ofAvicenia albaandSonneratia albaand identify a core microbiome of 81 taxa, a further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, andErythrobacter) were found to be differentially abundant suggesting key roles in this microbiome, with the identified dimethylsulfoniopropionate (DMSP) metabolisers having important functions in these habitats. The majority of those identified are involved in nutrient cycling or involved in the production of compounds that promote host survival. Increasingly, blue carbon and nature-based solutions to climate change are heralded as viable mitigation steps to limit climate change, however, this is done with little to no consideration of the microbial communities that cycle sequestered carbon in these environments. Here, we examine the microbial communities present in sediment samples taken in close proximity to each tree, sediment samples represent a major sink of atmospheric carbon and understanding how the associated communities will change as climate change advances will become an increasingly important part of carbon stock assessments. Knowing what microbes are presently there is an important first step in this process.
Classification accuracy of structural and functional connectomes across different depressive phenotypes
Authors: Yeung Hon Wah , Stolicyn Aleks , Shen Xueyi , Adams Mark J. , Romaniuk Liana , Thng Gladi , Buchanan Colin R. , Tucker-Drob Elliot M. , Bastin Mark E. , McIntosh Andrew M. , Cox Simon R. , Smith Keith M. , Whalley Heather C. 
Published: November 2022

AbstractPhenotyping of major depressive disorder (MDD) in research can vary from study to study, which, together with heterogeneity of the disorder, may contribute to the inconsistent associations with various risk factors including neuroimaging features. These aspects also potentially underlie previous problems with machine learning methods using imaging data to inform predictive biomarkers. In this study we therefore aimed to examine the classification accuracy of structural and functional connectomes across different depressive phenotypes, including separating MDD subgroups into those with and without early childhood adversity (one of the largest risk factors for MDD associated with brain development). We applied logistic ridge regression to classify control and MDD participants defined according to six different MDD definitions in a large community-based sample (N= 14, 507). We used brain connectomic data based on six structural and two functional network weightings and conducted a comprehensive analysis to (i) explore how well different connectome modalities predict different MDD phenotypes commonly used in research, (ii) investigate whether stratification of MDD based on the presence or absence of early childhood adversity (measured with the childhood trauma questionnaire) can improve prediction accuracies, and (iii) identify important predictive features that are consistent across MDD phenotypes. We find that functional connectomes consistently outperform structural connectomes as features for MDD classification across phenotypes. Highest accuracy of 61.06% (chance level 50.0%) was achieved when predicting the Currently Depressed phenotype (i.e. the phenotype defined by the presence of more than five symptoms of depression in the past two weeks) with features based on partial correlation functional connectomes. Accuracy of classifying Currently Depressed participants with added CTQ threshold criterion rose to 65.74%. Application of the Jaccard index to assess predictive feature overlap indicated that there were neurobiological differences between MDD patients with and without childhood adversity. Further to that, analysis of predictive features for different MDD phenotypes with binomial tests revealed sensorimotor and visual functional subnetworks as consistently important for prediction. Our results provide the basis for future research, and indicate that differences in sensorimotor and visual subnetworks may serve as important biomarkers of MDD.
Vesicle-mediated transport of ALIX and ESCRT-III to the intercellular bridge during cytokinesis
Authors: Pust Sascha , Brech Andreas , Wegner Catherine Sem , Stenmark Harald , Haglund Kaisa 
Published: November 2022

AbstractCellular abscission is the final step of cytokinesis that leads to the physical separation of the two daughter cells. The scaffold protein ALIX and the ESCRT-I protein TSG101 contribute to recruiting ESCRT-III to the midbody, which orchestrates the final membrane scission of the intercellular bridge. Here, we addressed by which mechanisms ALIX and the ESCRT-III subunit CHMP4B are transported to the midbody. Structured illumination microscopy revealed gradual accumulation of ALIX at the midbody, resulting in the formation of spiral-like structures extending from the midbody to the abscission site, which strongly co-localized with CHMP4B. Live-cell microscopy uncovered that ALIX appeared together with CHMP4B in vesicular structures, whose motility was microtubule-dependent. Depletion of ALIX led to structural alterations of the midbody and delayed recruitment of CHMP4B, resulting in delayed abscission. Likewise, depletion of the kinesin-1 motor KIF5B reduced the motility of ALIX-positive vesicles and caused delayed recruitment of ALIX, TSG101 and CHMP4B to the midbody, accompanied by impeded abscission. We propose that ALIX, TSG101 and CHMP4B are associated with endosomal vesicles transported along microtubules by kinesin-1, leading to their directional transport to the cytokinetic bridge and midbody, thereby contributing to their function in abscission.
Échele Cabeza as a harm reduction project and activist movement in Colombia
Authors: Díaz Moreno Mauro , Alarcón Ayala Nathalia , Estrada Yarelix , Morris Vannesa , Quintero Julián 
Published: November 2022

Purpose
The purpose of this paper is to present the results and context of the drug checking service (DCS) performed by the harm reduction project Échele Cabeza (EC) in Colombia.

Design/methodology/approach
Data from several years are presented with a focus on data from 2021. In 2021, data were derived from 2,339 questionnaires filled out by DCS users and a total of 2,868 drug checking test results from samples collected at the fixed-site service in Bogotá and 30 music festivals in 8 cities nationwide.

Findings
The tusi phenomenon is gaining strength in Colombia revealing a problem associated with the changing makeup of tusi and, thus, polydrug use. MDMA adulteration and misrepresentations have increased in comparison to 2019. There is an increasing number of people who want to use the DCS in Colombia, which is encouraging but also exposes the limitations of the drug checking methods available to EC.

Originality/value
This paper offers the first publication of the pioneering drug checking organization EC in Latin America.