bluuebunny/crossref_metadata_2025 huggingface dataset:
Palynofacies, environments, and climate changes in the Magdalena River Basin
Authors: Lorente M. A.
Published: March 2021

Four environments (swamp, shallow lake, alluvial flood plain, and lagoon) from the Lower Magdalena River Basin were studied for palynofacies’ quantitative characterization. Each environment has been described based on four criteria: palynomorph assemblage, organic matter concentration, organic matter palynological composition, and organic particle morphology.

Shallow lakes’palynological assemblages are dominated by composite and grass pollen. The POM (particulate organic matter) morphology is characterized by a maximum at Φ 5 class (silt), and it has a sphericity histogram with bimodal distribution (peaks at 0.1 and 0.5/0.6). From a composition point of view, POM is mainly opaque amorphous materials. POM concentration is usually lower than 0.1%.

Swampenvironments palynological assemblages are dominated by grass pollen with a slightly smaller amount of composite pollen. The POM is dominated by finely dispersed amorphous and indeterminate “other” types (organo-mineral gel ?), depending on the oxidation degree. The swamp concentration of organic matter a few centimeters below the water-sediment interface varies between 0.1% and 0.3%. Below that, organic concentration is usually lower than 0.1%.

Lagoonassemblages are rich in species and specimens, but assemblages are highly variable. Main components are either finely dispersed amorphous or plant cuticular/epidermal or amorphous homogeneous and heterogeneous or fungal remains. Peat lithology is rich in mangrove pollen, while clay assemblages are dominated by composites, grass, and water plants together withBotryococcusalgal remains. Lagoon sediments are the richest in POM concentration, with values between 0.13% and 1% (excluding peats). Regarding particle size and shape, in this environment, they show a trend to decrease in grain size from Φ 1 to Φ 2 class (sand) dominated assemblages to Φ 5 to Φ 6 class (silt) dominated assemblages from base to top. Elongated shapes are abundant, with 30% to 50% of particles in the tabloid to elongated tabloid classes.

Alluvial - fluvial flood basinsamples are often barren in palynomorphs and organic matter. Occasionally present grass pollen and fungal remains. The POM, when present, is mainly of organo-mineral gel type and has a bimodal grain size distribution, with a minor peak at Φ 7 class (v.f.silt) and a major peak at Φ 4 to Φ 2 class (c. silt to f. sand).

Significant changes in quantitative palynofacies occur within the top few meters of the cores, representing the last 1000 yr of sedimentation in the area. These changes are related to shifts in climate, from colder to warmer conditions or from dry to wet periods, most probably linked with E.N.S.O. A short dry and cold period related to the “Little Ice Age” was identified in the Ayapel and Cienaga de El Medio cores.
Analysis of antibody data using Finite Mixture Models based on Scale Mixtures of Skew-Normal distributions
Authors: Domingues Tiago Dias , Mouriño Helena , Sepúlveda Nuno
Published: March 2021

Finite mixture models have been widely used in antibody (or serological) data analysis in order to help classifying individuals into either antibody-positive or antibody-negative. The most popular models are the so-called Gaussian mixture models which assume a Normal distribution for each component of a mixture. In this work, we propose the use of finite mixture models based on a flexible class of scale mixtures of Skew-Normal distributions for serological data analysis. These distributions are sufficiently flexible to describe right and left asymmetry often observed in the distributions associated with hypothetical antibody-negative and antibody-positive individuals, respectively. We illustrate the advantage of these alternative mixture models with a data set of 406 individuals in which antibodies against six different human herpesviruses were measured in the context of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome.
Single-Arm, Open-Label Phase 2 Trial of Preemptive Methylprednisolone to Avert Progression to Respiratory Failure in High-Risk Patients with COVID-19
Authors: Cabanillas Fernando , Morales Javier , G. Conde José , Bertrán-Pasarell Jorge , Fernández Ricardo , Hernandez-Silva Yaimara , Liboy Idalia , Bryan-Díaz James , Arraut-Gonzalez Juan
Published: March 2021

Introduction

Covid-19 is a triphasic disorder first typified by a viral phase that lasts from the first onset of symptoms until seven days later. This is followed by a second and third phase, initially characterized by the appearance of lung infiltrates, followed in 20% by respiratory failure. The second phase is usually heralded by an elevation of serologic inflammatory markers including CRP, ferritin, IL-6, LDH as well as D-dimers. Approximately 20% proceed to the second phase and are usually then treated with dexamethasone, provided they are oxygen-dependent since these are the only cases that benefit from dexamethasone. If we had objective criteria to predict this 20% that develop severe illness, they could preemptively be treated with steroids. In this exploratory study we investigated the early use of preemptive steroids in the setting of early disease, in high-risk non-oxygen dependent cases.

Methods

Eligible patients were those 21 years or older with a diagnosis of Covid-19 and oxygen saturation ≥91%. For patients to be classified as high-risk, they had to exhibit two or more of the following abnormalities 7-10 days after first symptom: IL-6 ≥ 10 pg/ml, ferritin > 500 ng/ml, D-dimer > 1 mg/L (1,000 ng/ml), CRP > 10 mg/dL (100 mg/L), LDH above normal range lymphopenia (absolute lymphocyte count <1,000 /µL), oxygen saturation between 91-94%, or CT chest with evidence of ground glass infiltrates. Primary endpoint was progression to respiratory failure. CALL score method was used to predict the expected number of cases of respiratory failure. High risk patients received methylprednisolone (MPS) 80 mg IV daily x 5 days starting no earlier than seven days from first onset of symptoms. The primary endpoint was progression to hypoxemic respiratory failure defined as PaO2 <60 mm Hg or oxygen saturation ≤90%. Secondary endpoints included survival at 28 days from registration, admission to intensive care and live discharge from the hospital. Change in levels of inflammatory markers and length of hospitalization were also assessed.

Results

In 76 patients, the expected number with respiratory failure was 30 (39.5%), yet only 4 (5.3%) developed that complication (p=.00001). Survival at 28 days was 98.6%.

Improvement in inflammatory markers correlated with favorable outcome.

Conclusions

Our results are encouraging and suggest that this approach is both effective and safe.
Ultra-small cells and DPANN genome unveiled inside an extinct vent chimney
Authors: Takamiya Hinako , Kouduka Mariko , Furutani Hitoshi , Mukai Hiroki , Yamamoto Takushi , Kato Shingo , Kodama Yu , Tomioka Naotaka , Ito Motoo , Suzuki Yohey
Published: March 2021

Chemosynthetic organisms flourish around deep-sea hydrothermal vents where energy-rich fluids are emitted from metal sulfide chimneys. In contrast to actively venting chimneys, the nature of microbial life in extinct chimneys without fluid venting remains largely unknown. Here, the occurrence of ultra-small cells in silica-filled grain boundaries inside an extinct chimney is demonstrated by high-resolution bio-signature mapping. The ultra-small cells are associated with extracellularly precipitated Cu2O nanocrystals. Single-gene analysis shows that the chimney interior is dominated by a member of Pacearchaeota known as a major phylum of DPANN. Genome-resolved metagenomic analysis reveals that the chimney Pacearchaeota member is equipped with a nearly full set of genes for fermentation-based energy generation from nucleic acids, in contrast to previously characterized Pacearchaeota members lacking many genes for nucleic acid fermentation. We infer that the ultra-small cells associated with silica and extracellular Cu2O nanocrystals in the grain boundaries are Pacearchaeota, on the basis of the experimentally demonstrated capability of silica to concentrate nucleic acids from seawater and the presence of Cu-exporting genes in a reconstructed Pacearchaeota genome. Given the existence of ~3-billion-year-old submarine hydrothermally deposited silica, proliferation of microbial life using silica-bound nucleic acids might be relevant to the primitive vent biosphere.
IsoSolve: an integrative framework to improve isotopic coverage and consolidate isotopic measurements by MS and/or NMR
Authors: Millard Pierre , Sokol Sergueï , Kohlstedt Michael , Wittmann Christoph , Létisse Fabien , Lippens Guy , Portais Jean-Charles
Published: March 2021

Stable-isotope labeling experiments are widely used to investigate the topology and functioning of metabolic networks. Label incorporation into metabolites can be quantified using a broad range of mass spectrometry (MS)and nuclear magnetic resonance (NMR)spectroscopy methods, but in general, no single approach can completely cover isotopic space, even for small metabolites. The number of quantifiable isotopic species could be increased, and the coverage of isotopic space improved, by integrating measurements obtained by different methods; however, this approach has remained largely unexplored because no framework able to deal with partial, heterogeneous isotopic measurements has yet been developed. Here, we present a generic computational framework based on symbolic calculus that can integrate any isotopic dataset by connecting measurements to the chemical structure of the molecules. As a test case, we apply this framework to isotopic analyses of amino acids, which are ubiquitous to life, central to many biological questions, and can be analyzed by a broad range of MS and NMR methods. We demonstrate how this integrative framework helps to i) clarify and improve the coverage of isotopic space, ii) evaluate the complementarity and redundancy of different techniques, iii) consolidate isotopic datasets, iv) design experiments, and v) guide future analytical developments. This framework, which can be applied to any labeled element, isotopic tracer, metabolite, and analytical platform, has been implemented in IsoSolve (available athttps://github.com/MetaSysLISBP/IsoSolveandhttps://pypi.org/project/IsoSolve), an open source software that can be readily integrated into data analysis pipelines.
In vitroandin vivointeraction of caspofungin with isavuconazole againstCandida aurisplanktonic cells and biofilms
Authors: Nagy Fruzsina , Tóth Zoltán , Nyikos Fanni , Forgács Lajos , Jakab Ágnes , Borman Andrew M. , Majoros László , Kovács Renátó
Published: March 2021

Thein vitroandin vivoefficacy of caspofungin was determined in combination with isavuconazole againstCandida auris. Drug–drug interactions were assessed utilising the fractional inhibitory concentration indices (FICIs), the Bliss independence model and an immunocompromised mouse model. Median planktonic minimum inhibitory concentrations (pMICs) of 23C. aurisisolates were between 0.5 and 2 mg/L and between 0.015 and 4 mg/L for caspofungin and isavuconazole, respectively. Median pMICs for caspofungin and isavuconazole in combination showed 2–128-fold and 2–256-fold decreases, respectively. Caspofungin and isavuconazole showed synergism in 14 out of 23 planktonic isolates (FICI range 0.03–0.5; Bliss cumulative synergy volume range 0–4.83). Median sessile MICs (sMIC) of 14 biofilm-forming isolates were between 32 and >32 mg/L and between 0.5 and >2 mg/L for caspofungin and isavuconazole, respectively. Median sMICs for caspofungin and isavuconazole in combination showed 0–128-fold and 0-512-fold decreases, respectively. Caspofungin and isavuconazole showed synergistic interaction in 12 out of 14 sessile isolates (FICI range 0.023–0.5; Bliss cumulative synergy volume range 0.13–234.32). In line with thein vitrofindings, synergistic interactions were confirmed byin vivoexperiments. The fungal kidney burden decreases were more than 3 log volumes in mice treated with combination of 1 mg/kg caspofungin and 20 mg/kg isavuconazole daily; this difference was statistically significant compared with control mice (p<0.001). Despite the favourable effect of isavuconazole in combination with caspofungin, further studies are needed to confirm the therapeutic advantage of this combination when treating an infection caused byC. auris.
Cancer drug discovery as a low rank tensor completion problem
Authors: Murali Vasanth S. , Ağaç Çobanoğlu Didem , Hsieh Michael , Zinn Meyer , Malladi Venkat S. , Gesell Jonathan , Williams Noelle S. , Welf Erik S. , Raj Ganesh V. , Çobanoğlu Murat Can
Published: March 2021

The heterogeneity of cancer necessitates developing a multitude of targeted therapies. We propose the view that cancer drug discovery is a low rank tensor completion problem. We implement this vision by using heterogeneous public data to construct a tensor of drug-target-disease associations. We show the validity of this approach computationally by simulations, and experimentally by testing drug candidates. Specifically, we show that a novel drug candidate, SU11652, controls melanoma tumor growth, including BRAFWTmelanoma. Independently, we show that another molecule, TC-E 5008, controls tumor proliferation onex vivoER+ human breast cancer. Most importantly, we identify these chemicals with only a few computationally selected experiments as opposed to brute-force screens. The efficiency of our approach enables use ofex vivohuman tumor assays as a primary screening tool. We provide a web server, the Cancer Vulnerability Explorer (accessible athttps://cavu.biohpc.swmed.edu), to facilitate the use of our methodology.
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

Conservation 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

SphingonotusFieber, 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

Listeria 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.

Importance

Listeria 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

In 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

Collagen 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

Species 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

Recent 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

Human (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

Although 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

The 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.

HIGHLIGHTS

Homogeneous 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

There 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.
DNA methylation inEnsiferspecies during free-living growth and during nitrogen-fixing symbiosis withMedicagospp.
Authors: diCenzo George C. , Cangioli Lisa , Nicoud Quentin , Cheng Janis H.T. , Blow Matthew J. , Shapiro Nicole , Woyke Tanja , Biondi Emanuele G , Alunni Benoît , Mengoni Alessio , Mergaert Peter
Published: March 2021

Methylation of specific DNA sequences is ubiquitous in bacteria and has known roles in immunity and regulation of cellular processes, such as the cell cycle. Using single-molecule real-time sequencing, six genome-wide methylated motifs were identified across fourEnsiferstrains, five of which were strain-specific. Only the GANTC motif, recognized by the cell cycle-regulated CcrM methyltransferase, was methylated in all strains. In actively dividing cells, methylation of GANTC motifs increased progressively from theoritoterregions in each replicon, in agreement with a cell cycle-dependent regulation of CcrM. In contrast, there was near full genome-wide GANTC methylation in the early stage of symbiotic differentiation. This was followed by a moderate decrease in the overall extent methylation and a progressive decrease in chromosomal GANTC methylation from theoritoterregions in later stages of differentiation. We interpret these observations as evidence of dysregulated and constitutive CcrM activity during terminal differentiation, and we hypothesize that it is a driving factor for endoreduplication of terminally differentiated bacteroids.
Activation of a signaling pathway by the physical translocation of a chromosome
Authors: Guzzo Mathilde , Sanderlin Allen G. , Castro Lennice K. , Laub Michael T.
Published: March 2021

In every organism, the cell cycle requires the execution of multiple cellular processes in a strictly defined order. However, the mechanisms used to ensure such order remain poorly understood, particularly in bacteria. Here, we show that the activation of the essential CtrA signaling pathway that triggers cell division inCaulobacter crescentusis intrinsically coupled to the successful initiation of DNA replication via the physical translocation of a newly-replicated chromosome, powered by the ParABS system. We demonstrate that ParA accumulation at the new cell pole during chromosome segregation recruits ChpT, an intermediate component of the CtrA signaling pathway. ChpT is normally restricted from accessing the selective PopZ polar microdomain until the new chromosome and ParA arrive. Consequently, any disruption to DNA replication initiation prevents the recruitment of ChpT and, in turn, cell division. Collectively, our findings reveal how major cell-cycle events are coordinated inCaulobacterand, importantly, how the physical translocation of a chromosome triggers an essential signaling pathway.
Integrin α5β1 nano-presentation regulates collective keratinocyte migration independent of substrate rigidity
Authors: Di Russo Jacopo , Young Jennifer L. , Wegner Julian W. R. , Steins Timmy , Kessler Horst , Spatz Joachim P.
Published: March 2021

Nanometer-scale properties of the extracellular matrix influence many biological processes, including cell motility. While much information is available for single cell migration, to date, no knowledge exists on how the nanoscale presentation of extracellular matrix receptors influences collective cell migration. In wound healing, basal keratinocytes collectively migrate on a fibronectin-rich provisional basement membrane to re-epithelialize the injured skin. Among other receptors, the fibronectin receptor integrin α5β1 plays a pivotal role in this process. Using a highly specific integrin α5β1 peptidomimetic combined with nanopatterned hydrogels, we show that keratinocyte sheets regulate their migration ability at an optimal integrin α5β1 nanospacing. This efficiency relies on the effective propagation of stresses within the cell monolayer independent of substrate stiffness. For the first time, this work highlights the importance of extracellular matrix receptor nanoscale organization required for efficient tissue regeneration.
HERMES: a molecular formula-oriented method to target the metabolome
Authors: Giné Roger , Capellades Jordi , Badia Josep M. , Vughs Dennis , Schwaiger-Haber Michaela , Vinaixa Maria , Brunner Andrea M. , Patti Gary J. , Yanes Oscar
Published: March 2021

Comprehensive metabolome analyses are hampered by low identification rates of metabolites due to suboptimal strategies in MS and MS2 acquisition, and data analysis. Here we present a molecular formula-oriented and peak detection-free method, HERMES, that improves sensitivity and selectivity for metabolite profiling in MS and structural annotation in MS2. An analysis of environmental water,E. coli, and human plasma extracts by HERMES showed increased biological specificity of MS2 scans, leading to improved mass spectral similarity scoring and identification rates when compared to iterative data-dependent acquisition (DDA). HERMES is available as an R package with a user-friendly graphical interface to allow data analysis and interactive tracking of compound annotations.
Ecosystem size and complexity dictate riverine biodiversity
Authors: Terui Akira , Kim Seoghyun , Dolph Christine L. , Kadoya Taku , Miyazaki Yusuke
Published: March 2021

Larger ecosystems support more species; this ubiquitous pattern is the foundation of current conservation schemes. However, many ecosystems possess a complex spatial structure that cannot be represented by area, and the role of such complexity in scaling biodiversity is largely unknown. Here, we use theory and extensive fish community data from two distinct geographic regions (Japan and United States) to show that ecosystem size and complexity dictate riverine biodiversity. We found that larger and more branched ‘complex’ river networks harbored greater species richness due to increased space and environmental heterogeneity. The complexity effect was comparable to the size effect, and this pattern has emerged regardless of ecological contexts. The dual control of biodiversity may be a pervasive feature that has far-reaching implications for biodiversity conservation.

One sentence summary

This study provides the first evidence that ecosystem size and complexity play comparable roles in regulating biodiversity.
Oncogenic ZMYND11-MBTD1 fusion protein anchors the NuA4/TIP60 histone acetyltransferase complex to the coding region of active gene
Authors: Devoucoux Maëva , Fort Victoire , Khelifi Gabriel , Xu Joshua , Alerasool Nader , Galloy Maxime , Wong Nicholas , Bourriquen Gaëlle , Fradet-Turcotte Amélie , Taipale Mikko , Hope Kristin , Hussein Samer M. I. , Côté Jacques
Published: March 2021

A chromosomal translocation found in cannibalistic acute myeloid leukemia (AML) leads to an in-frame fusion of the transcription elongation repressor ZMYND11 to MBTD1, a subunit of the NuA4/TIP60 histone acetyltransferase (HAT) complex. In contrast to the NuA4/TIP60 complex, ZMYND11 is linked to repression of actively transcribed genes through recognition of H3.3K36me3. To understand the abnormal molecular events that expression of this ZMYND11-MBTD1 fusion protein can create, we performed its biochemical and functional characterization in comparison to each individual fusion partner. ZMYND11-MBTD1 is stably incorporated into the endogenous NuA4/TIP60 complex but does not bring any additional interactors as the fusion lacks the MYND domain of ZMYND11. Nevertheless, this truncated ZMYND11 moiety in the fusion leads to mislocalization of the NuA4/TIP60 complex on the body of genes normally bound by ZMYND11 in the genome, in a PWWP-H3.3K36me3 interaction-dependent manner. This can be correlated to increased chromatin acetylation and altered gene transcription, most notably on theMYConcogene, and alternative splicing. Importantly, expression of ZMYND11-MBTD1, but not the individual fusion partners, during embryonic stem cell differentiation, leads to decreased expression of specific differentiation markers, while favoring Myc-driven pluripotency. It also favors self-renewal of hematopoietic stem/progenitor cells. Altogether, these results indicate that the ZMYND11-MBTD1 fusion protein functions primarily by mistargeting the NuA4/TIP60 complex to the body of genes, altering normal transcription of specific genes, likely driving oncogenesis in part through the Myc regulatory network.

Highlights

-A recurrent chromosomal translocation detected in cannibalistic acute myeloid leukemia leads to the production of a ZMYND11-MBTD1 fusion protein.

-The ZMYND11-MBTD1 fusion protein is stably incorporated into the endogenous NuA4/TIP60 complex.

-ZMYND11-MBTD1 leads to mistargeting of NuA4/TIP60 activity to the coding region of ZMYND11-target genes, altering gene expression and splicing.

-ZMYND11-MBTD1 binds theMYCgene leading to its upregulation, favoring growth and pluripotency while inhibiting differentiation markers.
A viral genome packaging ring-ATPase is a flexibly coordinated pentamer
Authors: Dai Li , Singh Digvijay , Lu Suoang , Kottadiel Vishal , Vafabakhsh Reza , Mahalingam Marthandan , Chemla Yann R. , Ha Taekjip , Rao Venigalla B.
Published: March 2021

Multi-subunit ring-ATPases carry out a myriad of biological functions, including genome packaging in viruses. Though the basic structures and functions of these motors have been well-established, the mechanisms of ATPase firing and motor coordination are poorly understood. Here, by direct counting using single-molecule fluorescence, we have determined that the active bacteriophage T4 DNA packaging motor consists of five subunits of gp17. By systematically doping motors with an ATPase-defective subunit and selecting single motors containing a precise count of active/inactive subunit(s), we found, unexpectedly, that the packaging motor can tolerate an inactive sub-unit. However, motors containing an inactive subunit(s) exhibit fewer DNA engagements, a higher failure rate in encapsidation, reduced packaging velocity, and increased pausing. These findings suggest a new packaging model in which the motor, by re-adjusting its grip on DNA, can skip an inactive subunit and resume DNA translocation, contrary to the prevailing notion of strict coordination amongst motor subunits of other packaging motors.