bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet
Authors: Chua Physilia Ying Shi , Lammers Youri , Menoni Emmanuel , Ekrem Torbjørn , Bohmann Kristine , Boessenkool Sanne , Alsos Inger Greve 
Published: March 2021

ABSTRACTConservation strategies centred around species habitat protection rely on species’ dietary information. One species at the focal point of conservation efforts is the herbivorous grouse, the western capercaillie (Tetrao urogallus). Traditional microhistological analysis of crop contents or faeces and/or direct observations are time-consuming and at low taxonomic resolution. Thus, limited knowledge on diet is hampering conservation efforts. Here we use non-invasive environmental DNA (eDNA) metabarcoding on DNA extracted from faeces to present the first large-scale molecular dietary analysis of capercaillies. Faecal samples were collected from seven populations located in Norway (Finnmark, Troms, Trøndelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n=172). We detected 122 plant taxa belonging to 46 plant families of which 37.7% of the detected taxa could be identified at species level. The average dietary richness of each sample was 7 ± 5 SD taxa. The most frequently occurring plant groups with the highest relative read abundance (RRA) were trees and dwarf shrubs, in particular,PinusandVaccinium myrtillus, respectively. There was a difference in dietary composition (RRA) between samples collected from the different locations (adonis F5,86= 11.01, p <0.05) and seasons (adonis F2,03= 0.64, p <0.05). Dietary composition also differed between sexes at each location (adonis F1,47= 2.77, p <0.05), although not significant for all data combined. In total, 35 taxa (36.84% of taxa recorded) were new capercaillie food items compared to existing knowledge. The non-invasive molecular dietary analysis applied in this study provides new ecological understanding of capercaillies’ diet which can have real conservation implications. The broad variety of diet items indicates that vegetation does not limit food intake. This plasticity in diet suggests that other factors including disturbed mating grounds and not diet could be the main threat to their survival.
Genome Size Estimation and Full-length Transcriptome ofSphingonotus tsinlingensis:Genetic Background for the Drought-Adapted Grasshopper
Authors: Zhao Lu , Wang Hang , Wu Le , Sun Kuo , Guan De-Long , Xu Sheng-Quan 
Published: March 2021

AbstractSphingonotusFieber, 1852 (Orthoptera: Acrididae) is a species-rich grasshopper genus with ~146 species. All species of this genus prefer dry environments, such as: desert, steppe, sand, and stony benchland. This genomic study aimed to understand the evolution and ecology of these grasshopper species. Here, the genome size ofSphingonotus tsinlingensiswas estimated using flow cytometry and the first high-quality full-length transcriptome of this species is presented, which may serve as a reference genetic resource for the drought-adapted grasshopper species ofSphingonotusFieber. The genome size ofSphingonotus tsinlingensiswas ~12.8 Gb. Based on the 146.98 Gb Pacbio isoform sequencing data, 221.47 Mb full-length transcripts were assembled. Among these transcripts, 88,693 non-redundant isoforms were identified with an average length of 2,497 bp and an N50 value of 2,726 bp, which was much longer than the formal grasshopper transcriptome assemblies. A total of 48,502 protein coding sequences were determined, and 37,569 were annotated in public gene function databases. A total of 36,488 simple tandem repeats, 12,765 long non-coding RNAs, and 414 transcription factors were also identified. According to gene functions, 70 heat shock proteins and 61 P450 genes that may correspond to drought adaptation ofS. tsinlingensiswere identified. The genome ofSphingonotus tsinlingensisis an ultra-large and complex genome. Full-length transcriptome sequencing is an ideal strategy for genomic research. This is the first full-length transcriptome of the genusSphingonotus.The assembly parameters were better than all known grasshopper transcriptomes. This full-length transcriptome may be used to understand its genetic background and the evolution and ecology of grasshoppers.
Glucose decoration on wall-teichoic acid is required for phage adsorption and InlB-mediated virulence inListeria ivanovii
Authors: Sumrall Eric. T. , Schneider Stephan R. , Boulos Samy , Loessner Martin J. , Shen Yang 
Published: March 2021

AbstractListeria ivanovii(Liv) is an intracellular Gram-positive pathogen that primarily infects ruminants, but also occasionally causes enteric infections in humans. Albeit rare, this bacterium possesses the capacity to cross the intestinal epithelium of humans, similar to its more frequently pathogenic cousin,Listeria monocytogenes(Lmo). Recent studies inLmohave shown that specific glycosyl modifications on the cell wall-associated glycopolymers (termed wall-teichoic acid, or WTA) ofLmoare responsible for bacteriophage adsorption and retention of the major virulence factor, Internalin B (InlB). However, the relationship between InlB and WTA inLivremains unclear. Here, we report the identification of the unique gene,liv1070that encodes a putative glucosyltransferase in the polycistronic WTA gene cluster of theLivWSLC 3009 genome. We found that in-frame deletion ofliv1070led to loss of the glucose substitution on WTA, as revealed by UPLC-MS analysis. Interestingly, the glucose-deficient mutant became resistant to phage B025 infection due to an inability of the phage to adsorb to the bacterial surface, a binding process mediated by the receptor-binding protein B025_Gp17. As expected, deletion ofliv1070led to loss of InlB retention to the bacterial cell wall, which corresponded to a drastic decrease in cellular invasion. Genetic complementation ofliv1070restored the characteristic phenotypes, including glucose decoration, phage adsorption, and cellular invasion. Taken together, our data demonstrate that an interplay between phage, bacteria, and host cells also exists inListeria ivanovii, suggesting the trade-off between phage resistance and virulence attenuation may be a general feature in theListeriagenus.ImportanceListeria ivanoviiis a Gram-positive bacterial pathogen known to cause enteric infection in rodents and ruminants, and occasionally in immunocompromised humans. Recent investigations revealed that, in its better-known cousinListeria monocytogenes, strains develop resistance to bacteriophage attack due to loss of glycosylated surface receptors, which subsequently resulting in disconnection of one of the bacterium’s major virulence factors, InlB. However, the situation inL. ivanoviiremains unclear. Here, we show thatL. ivanoviiacquires phage resistance following deletion of a unique glycosyltransferase. This deletion also leads to dysfunction of InlB, making the resulting strain unable to invade host cells. Overall, this study suggests that the interplay between phage, bacteria and the host may be a feature common to theListeriagenus.
Transplanting increases the leaf production rate in rice, consequently modifying plant development and growth
Authors: Clerget Benoit , Pasuquin Estela , Carandang Rene , Domingo Abigail J. , Layaoen Heathel L. , Bueno Crisanta 
Published: March 2021

AbstractIn Asia, direct sowing and water savings are major trends in previously transplanted and flooded irrigated rice systems because of the higher cost of wages and increasing water shortage. Previous experiments showed that the leaf appearance rate varies between aerobic and flooded cropping systems. This study aimed to further understand how the planting method affects the development rate, flowering time, and yield of lowland irrigated rice crops. A two-year experiment was undertaken at the International Rice Research Institute, Philippines, using three contrasting rice varieties and three planting methods (transplanted, wet direct-seeded, and dry direct-seeded; at a density of 25 plants m-2) in a field submerged in 3–5 cm water from two weeks after the transplanting date. The effect of the planting method was similar in the three varieties, mostly without interaction between the two factors. In 2013, the leaf number of seedlings grown in seedling trays was two leaves behind that of direct-seeded plants at the time of transplanting. However, the young transplanted plants recovered quickly; produced new leaves at a faster rate (with a shorter phyllochron); reached panicle initiation, flag-leaf emergence and flowering time 1 week later; and developed more leaves compared to the direct-seeded plants. In 2014, growing in the nursery induced no delay in leaf appearance due to temperatures lower than those in 2013; therefore, the planting method did not affect the leaf appearance rate. Thus, plant development was primarily delayed by the density stress in the seedling trays under warm temperatures; however, the transplanted rice plants had lower plastochron duration than the direct-seeded plants, which made up for the initial delay in leaf appearance. In both years and at similar plant density, the transplanted plants produced more tillers bearing larger upper leaves that led to a higher leaf area index; however, grain yields were similar for the transplanted and direct-seeded crops.Highlights- In seedling trays, leaf appearance stopped at the appearance of the fourth leaf.- After transplanting, leaf appearance resumed at a faster rate than in direct-seeded plants.- Transplanted plants had delayed panicle initiation and flowering time, more tillers, and more and larger leaves per tiller, but similar grain yield compared to direct-seeded plants at similar planting density.
Temporally and Spatially Regulated Collagen XVIII Isoforms Impact Ureteric Patterning Through Their TSP1-like Domain
Authors: Rinta-Jaskari Mia M. , Naillat Florence , Ruotsalainen Heli J. , Akram Saad U. , Koivunen Jarkko T. , Izzi Valerio , Ronkainen Veli-Pekka , Sasaki Takako , Pietilä Ilkka , Elamaa Harri P. , Kaur Inderjeet , Manninen Aki , Vainio Seppo J. , Pihlajaniemi Taina A. 
Published: March 2021

ABSTRACTCollagen XVIII (ColXVIII) is a component of the extracellular matrix implicated in embryogenesis and control of homeostasis. We provide evidence that ColXVIII has a specific role in kidney ontogenesis by regulating the interaction between mesenchymal and epithelial tissues as observed in analyses of total and isoform-specific knockout embryos, mice, andex vivoorgan primordia. ColXVIII deficiency, both temporally and spatially, impacts the 3D pattern of ureteric tree branching morphogenesisviaits specific isoforms. Proper development of ureteric tree depends on a tight control of the nephron progenitor cells (NPCs). ColXVIII-deficient NPCs are leaving the NPC pool faster than in controls. Moreover, the data suggests that ColXVIII mediates the kidney epithelial tree patterningviaits N-terminal domains, and especially the Thrombospondin-1-like domain, and that this morphogenetic effect involves ureteric epithelial integrins. Altogether, the results propose a significant role for ColXVIII in a complex signalling network regulating renal progenitors and kidney development.
Bioacoustics forin situvalidation of species distribution modelling: An example with bats in Brazil
Authors: Hintze Frederico , Machado Ricardo B. , Bernard Enrico 
Published: March 2021

AbstractSpecies distribution modelling (SDM) gained importance on biodiversity distribution and conservation studies worldwide, including prioritizing areas for public policies and international treaties. Useful for large-scale approaches and estimates, is a plus considering that a minor fraction of the planet is adequately sampled. However, SDM needs to be as reliable as possible. Minimizing errors is challenging, but essential, considering the uses and consequences of such models.In situvalidation of the SDM outputs should be a key-step – in some cases, urgent. Bioacoustics can be used to validate and refine those outputs, especially if the focal species’ vocalizations are conspicuous and species-specific. This is the case of echolocating bats. Here, we used extensive acoustic monitoring (>120 validation points, covering >758,000 km2, and >300,000 sound files) to validate MaxEnt outputs for six neotropical bat species in a poorly-sampled region of Brazil. Based onin situvalidation, we evaluated four threshold-dependent theoretical evaluation metrics’ ability in predicting models’ performance. We also assessed the performance of three widely used thresholds to convert continuous SDMs into presence/absence maps. We demonstrated that MaxEnt produces very different outputs, requiring a careful choice on thresholds and modeling parameters. Although all theoretical evaluation metrics studied were positively correlated with accuracy, we empirically demonstrated that metrics based on specificity-sensitivity and sensitivity-precision are better for testing models, considering that most SDMs are based on unbalanced data. Without independent field validation, we found that using an arbitrary threshold for modelling can be a precarious approach with many possible outcomes, even after getting good evaluation scores. Bioacoustics proved to be important for validating SDMs for the six bat species analyzed, allowing a better refinement of SDMs in large and under-sampled regions, with relatively low sampling effort. Regardless of species assessing method used, our research highlighted the vital necessity ofin situvalidation for SDMs.
Climate fluctuations drive the recruitment and growth of temperate grassland plants
Authors: Doležal Jiri , Altman Jan , Jandová Veronika , Chytrý Milan , Conti Luisa , Méndez-Castro Francisco E. , Klimešová Jitka , Zelený David , Ottaviani Gianluigi 
Published: March 2021

AbstractRecent climate warming is associated with the increasing magnitude and frequency of extreme events, including heatwaves and drought periods worldwide. Such events can have major effects on the species composition of plant communities, hence on biodiversity and ecosystem functioning. Here we studied responses of Central European dry grassland plants to fluctuating temperature and precipitation over the last thirty years with monthly temporal resolution. We assessed the seasonal and annual dynamics of plant recruitment and growth based on the analysis of annual growth rings from the root collar. Although most studies so far applied such methods to trees and shrubs, we focused on typical grassland plants, two forbs and two chamaephytes. We related the recruitment and annual growth to monthly and annual precipitation, temperature and aridity between 1991 and 2019. We revealed species-specific responses, namely the (i) recruitment of deep-rooted, heavy-seeded species was positively affected by precipitation in both late winter-early spring and summer, whereas recruitment of shallow-rooted, light-seeded species was weakly influenced by climate fluctuations; (ii) growth of shallow-rooted species was more adversely affected by high summer temperature and drought than the growth of deep-rooted species. The population age structure of all the studied species was affected by the climate of the past decades. Most individuals established in the wet period of the 2000s, fewer in the precipitation-poorer 1990s, and the establishment was considerably reduced in the dry and warm period of the 2010s. Our findings indicate that the change towards warmer and drier climate has a profound effect even on drought-adapted ecosystems such as temperate dry grasslands. However, plant responses to various climatic extremes are species-specific, depending on their characteristics, such as life form or rooting depth. Consequently, the ongoing and anticipated climate warming will likely result in complex changes in species composition and other ecosystem properties of temperate grasslands
Comparative studies of the seven human coronavirus envelope proteins using topology prediction and molecular modelling to understand their pathogenicity
Authors: Schoeman Dewald , Cloete Ruben , Fielding Burtram C. 
Published: March 2021

ABSTRACTHuman (h) coronaviruses (CoVs) 229E, NL63, OC43, and HKU1 are less virulent and cause mild, self-limiting respiratory tract infections, while SARS-CoV, MERS-CoV, and SARS-CoV-2, are more virulent and have caused severe outbreaks. The CoV envelope (E) protein, an important contributor to the pathogenesis of severe hCoVs infections, may provide insight into this disparate severity of the disease. Topology prediction programs and 3D modelling software was used to predict and visualize structural aspects of the hCoV E protein related to its functions. All seven hCoV E proteins largely adopted different topologies, with some distinction between the more virulent and less virulent ones. The 3D models refined this distinction, showing the PDZ-binding motif (PBM) of SARS-CoV, MERS-CoV, and SARS-CoV-2 to be more flexible than the PBM of hCoVs 229E, NL63, OC43, and HKU1. We speculate that the increased flexibility of the PBM may provide the more virulent hCoVs with a greater degree of freedom, which can allow them to bind to different host proteins and can contribute to a more severe form of the disease. This is the first paper to predict the topologies and model 3D structures of all seven hCoVs E proteins, providing novel insights for possible drug and/or vaccine development.
Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses
Authors: Zhou Hong , Ji Jingkai , Chen Xing , Bi Yuhai , Li Juan , Hu Tao , Song Hao , Chen Yanhua , Cui Mingxue , Zhang Yanyan , Hughes Alice C. , Holmes Edward C. , Shi Weifeng 
Published: March 2021

SummaryAlthough a variety of SARS-CoV-2 related coronaviruses have been identified, the evolutionary origins of this virus remain elusive. We describe a meta-transcriptomic study of 411 samples collected from 23 bat species in a small (~1100 hectare) region in Yunnan province, China, from May 2019 to November 2020. We identified coronavirus contigs in 40 of 100 sequencing libraries, including seven representing SARS-CoV-2-like contigs. From these data we obtained 24 full-length coronavirus genomes, including four novel SARS-CoV-2 related and three SARS-CoV related genomes. Of these viruses, RpYN06 exhibited 94.5% sequence identity to SARS-CoV-2 across the whole genome and was the closest relative of SARS-CoV-2 in the ORF1ab, ORF7a, ORF8, N, and ORF10 genes. The other three SARS-CoV-2 related coronaviruses were nearly identical in sequence and clustered closely with a virus previously identified in pangolins from Guangxi, China, although with a genetically distinct spike gene sequence. We also identified 17 alphacoronavirus genomes, including those closely related to swine acute diarrhea syndrome virus and porcine epidemic diarrhea virus. Ecological modeling predicted the co-existence of up to 23Rhinolophusbat species in Southeast Asia and southern China, with the largest contiguous hotspots extending from South Lao and Vietnam to southern China. Our study highlights both the remarkable diversity of bat viruses at the local scale and that relatives of SARS-CoV-2 and SARS-CoV circulate in wildlife species in a broad geographic region of Southeast Asia and southern China. These data will help guide surveillance efforts to determine the origins of SARS-CoV-2 and other pathogenic coronaviruses.
Hillslope geodiversity shapes ammonia-oxidizing communities and other microbial regulators in a semi-arid shrubland
Authors: Szitenberg Amir , Alexander-Shani Rivka , Yizhak Hezi , Stavi Ilan 
Published: March 2021

ABSTRACTThe determinants and consequences of drought-related shrub mortality were studied for over a decade, as a model for desertification processes, in a semi-arid long-term ecological research station. Recent studies have shown that geodiversity is an important spatial predictor of plant viability under extreme drought conditions. Homogeneous hillslopes, with a deep soil profile and lack of stoniness, could not support shrubs under long term drought conditions due to low water storage in their soil. Conversely, heterogeneous hillslopes, with shallow soil profiles and high stoniness, supported shrub communities under similar conditions, due to the comparatively greater soil-water content. In the current study, we investigated the effect of hillslope geodiversity on the soil microbial diversity. Using DNA metabarcoding, we found small but consistent differences in the microbial community compositions of the homogeneous and heterogeneous hillslopes; more ammonia oxidizing and reducing-sugar degrading bacteria are found in the homogeneous hillslopes, possibly dwindling the ammonia supply to shrubs. Additionally, based on functional metagenomic reconstruction, we suggest that homogeneous hillslopes have lower superoxide and antibiotics production, leading to reduced protection against pathogens. In fungi, we observed an increase in possible pathogens, at the expense of lichen forming fungi. Lichens are considered to support soil-water by slowly releasing intercepted raindrops. In conclusion, we show that not only plant-diversity but also microbial-diversity is shaped by geodiversity, and that the community shift in homogeneous hillslopes may further promote shrub mortality in this drought-prone, water limited ecosystem.HIGHLIGHTSHomogeneous hillslopes reduce soil water storage and increase aeration.Ammonia oxidizers and reducing-sugar degraders dwindle ammonia supply for plants.Homogenous hillslopes do not support moisture providing lichens.Reduced antibiotics and superoxide secretion capacitate pathogens.Geodiversity facilitates microbial regulation during drought.GRAPHICAL ABSTRACT
Leveraging omic features with F3UTER enables identification of unannotated 3’UTRs for synaptic genes
Authors: Sethi Siddharth , Zhang David , Guelfi Sebastian , Chen Zhongbo , Garcia-Ruiz Sonia , Ryten Mina , Saini Harpreet , Botia Juan A. 
Published: March 2021

AbstractThere is growing evidence for the importance of 3’ untranslated region (3’UTR) dependent regulatory processes. However, our current human 3’UTR catalogue is incomplete. Here, we developed a machine learning-based framework, leveraging both genomic and tissue-specific transcriptomic features to predict previously unannotated 3’UTRs. We identify unannotated 3’UTRs associated with 1,513 genes across 39 human tissues, with the greatest abundance found in brain. These unannotated 3’UTRs were significantly enriched for RNA binding protein (RBP) motifs and exhibited high human lineage-specificity. We found that brain-specific unannotated 3’UTRs were enriched for the binding motifs of important neuronal RBPs such asTARDBPandRBFOX1, and their associated genes were involved in synaptic function and brain- related disorders. Our data is shared through an online resource F3UTER (https://astx.shinyapps.io/F3UTER/). Overall, our data improves 3’UTR annotation and provides novel insights into the mRNA-RBP interactome in the human brain, with implications for our understanding of neurological and neurodevelopmental diseases.