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opencc-zeroMar 2023View details →

Behavioral responses to a series of similar but distinct novel objects in house sparrows

Generalization refers to the process by which animals assign different stimuli into cognitive categories based on their similarity/dissimilarity to previously experienced stimuli. Stimuli which strongly deviate from previous experience may be avoided due to their novelty (i.e., neophobia), while stimuli which are sufficiently similar to a known/recognized cue may elicit the same response as that cue (i.e., generalization). While generalization has been widely researched, few studies have examined among-individual variance in its expression. Our study quantified among-individual variation in neophobia and generalization in house sparrows (Passer domesticus) by placing a series of different objects next to each subject's food source on successive days and measuring the subject's latency to approach the food source in the presence vs. absence of each object. Similarly to previous work, we found that house sparrows are neophobic on average and exhibit significant among-individual variance in neophobia. More interestingly, we found that the neophobic response declined across presentations of different novel objects. This implies that the sparrows generalized some aspect(s) of the objects. We also found significant among-individual variance in the rate at which approach latency changed across this series, possibly reflecting individual differences in propensity to generalize. These results raise new questions about how neophobia, habituation, and generalization are linked and about the potential for selection to act on these traits under different ecological conditions.

opencc-by-4.0Apr 2023View details →

Novel cropping system strategies in China can increase plant protein with higher economic value but lower greenhouse gas emissions and water use

This database contains the average crop residue, manure nitrogen, manure organic carbon, net greenhouse gas emissions, and cropland area for 17 cropping systems at prefecture level during the period 2014-2018. In addition, it contained the changes of net greenhouse gas emissions caused by the optimization at prefecture level and province level.     We also shared the key code for optimizing cropping systems at prefecture level and provided the all data. Users can run it the Matlab platform.

opencc-zeroMar 2020View details →

FIG. 9. — Cryptovalsa halosarceiicola K.D in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.

FIG. 9. — Cryptovalsa halosarceiicola K.D.Hyde (BRIP 20340 – holotype): A, B, herbarium material.

opencc-zeroMar 2020View details →

FIG. 2 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.

FIG. 2. — Continuation.

opencc-zeroMar 2020View details →

FIG. 1 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.

FIG. 1. — Continuation.

opencc-by-4.0May 2022View details →

BIO4AFRICA_Report on novel bio-based value chains and markets analysis_D5.1_31/05/2022_v1.0

The BIO4Africa project will contribute to food and nutritional security and combat poverty in rural Africa through inclusive and sustainable development. This dataset includes information on the analysis of the prospective markets in which the outputs of the BIO4AFRICA project are reformed via the pilot cases of the project in Uganda, Ghana, Cote D’ Ivoire, and Senegal.

opencc-by-4.0Apr 2023View details →

Flnc: Machine Learning Improves the Identification of Novel Long Noncoding RNAs from Stand-Alone RNA-Seq Data

Flnc is software that can accurately identify full-length long noncoding RNAs (lncRNAs) from human RNA-seq data. lncRNAs are linear transcripts of more than 200 nucleotides that do not encode proteins. The most common approach for identifying lncRNAs from RNA-seq data which examines the coding abilities of assembled transcripts will result in a very high false-positive rate (30%-75%) of lncRNA identification. The falsely discovered lncRNAs lack transcriptional start sites and most of them are RNA fragments or result from transcriptional noise. Unlike the false-positive lncRNAs, true lncRNAs are full-length lncRNA transcripts that include transcriptional start sites (TSSs). To exclude these false lncRNAs, H3K4me3 chromatin immunoprecipitation sequencing (ChIP-seq) data had been used to examine transcriptional start sites of putative lncRNAs, which are transcripts without coding abilities. However, because of cost, time, and the limited availability of sample materials for generating H3K4me3 ChIP-seq data, most samples (especially clinical biospecimens) may have available RNA-seq data but lack matched H3K4me3 ChIP-seq data. This Flnc method solves the problem of lacking transcriptional initiation profiles when identifying lncRNAs. Flnc integrates seven machine-learning algorithms built with four genomic features. Flnc achieves state-of-the-art prediction power with a AUROC score over 0.92. Flnc significantly improves the prediction accuracy from less than 50% using the common approach to over 85% on five independent datasets without requiring matched H3K4me3 ChIP-seq data. In addition to the stranded polyA-selected RNA-seq data, Flnc can also be applied to identify lncRNAs from stranded RNA-seq data of ribosomal RNA depleted samples or unstranded RNA-seq data of polyA-selected samples.

opencc-zeroMay 2023View details →

Diet-mediated constitutive induction of novel IL4+ ILC2 cells maintains intestinal homeostasis in mice

Group 2 innate lymphoid cells (ILC2s) expressing IL-5 and IL-13 are localized at various mucosal tissues and play critical roles in the induction of type 2 inflammation, response to helminth infection, and tissue repair. Here we reveal a unique ILC2 subset in the mouse intestine that constitutively expresses IL-4 together with GATA3, ST2, KLRG1, IL-17RB, and IL-5. In this subset, IL-4 expression is regulated by mechanisms similar to but distinct from those observed in T cells and is partly affected by IL-25 signaling. Although the absence of the microbiota had marginal effects, feeding mice with a vitamin B1-deficient diet compromised the number of intestinal IL-4+ ILC2s. The decrease in the number of IL-4+ ILC2s caused by the vitamin B1 deficiency was accompanied by a reduction in IL-25-producing tuft cells. Our findings reveal that dietary vitamin B1 plays a critical role in maintaining interaction between tuft cells and IL-4+ ILC2s, a previously uncharacterized immune cell population that may contribute to maintaining intestinal homeostasis.

opencc-by-4.0Dec 2021View details →

A novel proxy to examine interspecific phosphorus facilitation between plant species

Resource complementarity can contribute to enhanced ecosystem functioning in diverse plant communities, but the role of facilitation in the enhanced complementarity is poorly understood. Here, we use leaf manganese concentration ([Mn]) as a proxy for rhizosheath carboxylate concentration to explore novel mechanisms of complementarity mediated by phosphorus (P) facilitation. In pot experiments, we showed that mixtures involving Carex korshinskyi, an efficient P-mobilizing species, exhibited greater biomass and relative complementarity effect than combinations without C. korshinskyi on P-deficient soils. Compared with monocultures, leaf [Mn] and [P] of species that are inefficient at P mobilization increased by 27 and 21% when grown with C. korshinskyi (i.e. interspecific P facilitation via carboxylates) rather than next to another inefficient P-mobilizing species. This experimental result was supported by a meta-analysis including a range of efficient P-mobilizing species. Phosphorus facilitation enhanced the relative complementarity effect in low-P environments, related to a greater change in several facilitated species of their root morphological traits relative to those in monoculture. Using leaf [Mn] as a proxy, we highlight a vital mechanism of interspecific P facilitation via belowground processes and provide evidence for the pivotal role of P facilitation mediated by the plasticity of root traits in biodiversity research.

opencc-by-4.0Mar 2023View details →

In silico prediction and biophysical validation of novel 14-3-3σ homodimer stabilizers

this dataset is related to "In silico prediction and biophysical validation of novel 14-3-3σ homodimer stabilizers" Aljabal G., Teh, A.-H., Yap B.K.

opencc-by-4.0Jun 2023View details →

ListeriaPredict Webinar - Application of novel predictive microbiology techniques to shelf-life studies on Listeria monocytogenes

An EFSA funded ListeriaPredict Webinar - Application of novel predictive microbiology techniques to shelf-life studies on Listeria monocytogenes

Data from: Crystalline silica-induced proinflammatory eicosanoid storm in novel alveolar macrophage model quelled by docosahexaenoic acid

Introduction: Workplace exposure to respirable crystalline silica (cSiO2) is associated with chronic inflammatory and autoimmune diseases. At the mechanistic level, cSiO2 particles are quickly phagocytosed by resident alveolar macrophages (AMs) in the lung, causing a robust cycle of proinflammatory cytokine release, lysosomal rupture, mitochondrial toxicity, and immunogenic cell death if the particle is not efficiently cleared by the lung. We and others have demonstrated in bone marrow-derived and transformed macrophage models that supplementation with the ω-3 polyunsaturated fatty acid (PUFA) docosahexaenoic acid (DHA) contributes to increased membrane phospholipid content of DHA and subsequent suppression of cSiO2-triggered inflammatory responses. However, mechanistic exploration of ω-3 PUFA effects in AMs is challenging due to reliance on short-lived primary AMs derived from lung lavage fluid. Methods: To address these limitations, we have employed a recently developed novel self-renewing AM model from C57BL/6 mice, fetal liver-derived alveolar-like macrophages (FLAMs), that is phenotypically representative of primary lung AM populations. We found that incubation of FLAMs with 25 µM DHA as ethanolic suspensions or as complexes with bovine serum albumin were equally effective at increasing ω-3 PUFA content of phospholipids at the expense of the ω-6 PUFA arachidonic acid (ARA) and the ω-9 monounsaturated fatty acid oleic acid. Based on these findings, FLAMs were treated with 25 µM DHA in EtOH or EtOH vehicle (VEH) for 24 h, with or without LPS for 2 h, and with or without cSiO2 for 1.5 or 4 h then proinflammatory cytokine release, lysosomal membrane permeabilization, and mitochondrial depolarization assessed. In addition, oxylipin metabolites were measured using a targeted LC-MS lipidomics panel of 156 metabolites. Results: Regardless of whether FLAMs were LPS-primed, cSiO2-triggered lysosomal permeability, mitochondrial toxicity, and cell death were not impacted by DHA. LPS+cSiO2 elicited marked IL-1α, IL-1β, and TNF-α release after 1.5 and 4 h of cSiO2 exposure, which was significantly inhibited by DHA. In VEH-treated cells, cSiO2 alone and LPS+cSiO2 induced synthesis of ARA-derived proinflammatory oxylipins including prostaglandins, leukotrienes, and thromboxanes that was suppressed by DHA. In addition, DHA promoted synthesis of pro-resolving DHA-derived oxylipins at the expense of ARA-derived oxylipins. Discussion: FLAMs were amenable to lipidome modulation by DHA, which suppressed cSiO2-triggered proinflammatory cytokine responses and ARA-derived oxylipins that potentially contribute to the particle's toxicity in the lung. FLAMs are a promising in vitro alternative to primary AMs for investigating interventions against toxicant-triggered inflammation and autoimmunity in the lung.

Data for: Rapid adaptation to a novel pathogen through disease tolerance in a wild songbird

Animal hosts can adapt to emerging infectious disease through both disease resistance, which decreases pathogen numbers, and disease tolerance, which limits damage during infection without limiting pathogen replication. Both resistance and tolerance mechanisms can drive pathogen transmission dynamics. However, it is not well understood how quickly host tolerance evolves in response to novel pathogens or what physiological mechanisms underlie this defense. Using natural populations of house finches (Haemorhous mexicanus) across the temporal invasion gradient of a recently emerged bacterial pathogen (Mycoplasma gallisepticum), we find rapid evolution of tolerance (<25 years). In particular, populations with a longer history of MG endemism have less pathology but similar pathogen loads compared with populations with a shorter history of MG endemism. Further, gene expression data reveal that more targeted immune responses early in infection are associated with tolerance. These results suggest an important role for tolerance in host adaptation to emerging infectious diseases, a phenomenon with broad implications for pathogen spread and evolution.

opencc-by-4.0Jun 2023View details →

Isolation, biochemical characterization, and genome sequencing of two high-quality genomes of a novel chitinolytic Jeongeupia species

Raw data sets for the microbiologyOpen research article "Isolation, biochemical characterization, and genome sequencing of two high-quality genomes of a novel chitinolytic Jeongeupia species" including ClustalW Trees and the respective input file; canB 3.0 results; TYGS phylogenetic tree results; PGAP genome annotation files and Canu 2.0 assembly reports of the two genomes.

Data from: Novel microsatellite markers for epiphytic bromeliad Tillandsia recurvata L., in an urban landscape in South-eastern Brazil

The authors present seven novel microsatellite markers for Tillandsia recurvata L. The genome assemble sequences of T. recurvata were obtained from NCBI (7.2Gb) (Sayers et al. 2022). The BioProject Accession and accession numbers are PRJNA701548 and SRX10089449, respectively. The microsatellite identification software Krait (0.5.2) (Du et al. 2018) was used to detect suitable microsatellites, both genome-wide and in the noncoding regions of T. recurvata. The single sequence repeats (SSRs) were refined to a minimum number of seven repeats of di-, tri-, or tetra-nucleotide repeat motifs. These sequences were further limited to SSRs of more than 100bp in length and low GC content (<50%). Krait (0.5.2) (Du et al. 2018) was also used to design the primers for the selected SSR sequences, in conjunction with the integrated Primer3 software. The criteria for primer selection included: a primer length of 18-26bp, an optimal melting temperature (Tm) of 54-59°C and GC content of <50%. These designed primers were single-plexed and amplified using the following PCR cycle: initial denaturation (95°C for 3 min), 34 cycles of 95°C for 30s, annealing for 30s (JP01-JP12: 54°C, 4873TD + 35251TD: 56°C, 19286TD: 53°C, 5044TD + 186664TD + 214633TD: 58°C), 72°C for 1 min and a final extension of 72°C for 5 mins. The authors make this information available to other researchers, to continue the investigation of epiphyte genetics.

Data from: Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here, we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyze how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploidal karyotype with a complete set of syntenic chromosomes (2n=10x=80) yet with a clear indication of subgenome dominance and highly diploidized gene contents. The male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and harbored three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with the specific expression in the digestive zone, where specialized cells digest prey and absorb derived nutrients. Novel gene evolution in recessive subgenomes is likely to be prevalent there because duplicates were enriched with Nepenthes-specific genes with tissue-specific expression, including those expressed in pitcher-specific tissues. Thus, subgenome dominance likely contributed to evolutionary novelty by allowing recessive subgenomes to serve as a preferred host of novel tissue-specific duplicates. Our results provide insight into how polyploids, which may frequently be evolutionary dead-ends, have given rise to novel traits in exceptionally thriving high-ploidy lineages.

Novel environments induce variability in fitness-related traits

Environmental change from anthropogenic activities threatens individual organisms, the persistence of populations, and entire species. Rapid environmental change puts organisms in a double bind, they are forced to contend with novel environmental conditions but with little time to respond. Phenotypic plasticity can act quickly to promote establishment and persistence of individuals and populations in novel or altered environments. In typical environmental conditions, fitness-related traits can be buffered, reducing phenotypic variation in expression of traits, and allowing underlying genetic variation to accumulate without selection. In stressful conditions, buffering mechanisms can break down, exposing underlying phenotypic variation and permitting the expression of phenotypes that may allow populations to persist in the face of altered or otherwise novel environments. Using reciprocal transplant experiments of freshwater snails, we demonstrate that novel conditions induce higher variability in growth rates and, to a lesser degree, morphology (area of the shell opening) relative to natal conditions. Our findings suggest a potentially important role of phenotypic plasticity in population persistence as organisms face a rapidly changing, human-altered world.

opencc-by-4.0Dec 2022View details →

A novel preclinical secondary pharmacology resource illuminates target-adverse drug reaction associations of marketed drugs - Supplementary Material

All Supplementary materials and source data for the manuscript. The reported analyses and results can be reproduced via the described IPython notebooks which can be found under www.github.com/Novartis/SPD

opencc-by-4.0Jul 2023View details →

The isolation of novel species expands the genomic diversity of Lachnospiraceae

A comprehensive understanding of the diversity of Lachnospiraceae, one of the most promising next-generation probiotics, is currently lacking, which limits the selection of strains for subsequent applications. To address this, we performed an in-depth genomic and functional analysis of 1,868 high-quality isolated genomes by integrating data from public databases and our new isolates, representing 387 colonization selective species-level clusters, of which 9 genera represent multi-lineage clusters. Pan-genome analysis, single nucleotide polymorphism (SNP) identification, and probiotic functional predictions revealed that species taxonomy, habitats, and geography shape the functional diversity of Lachnospiraceae. Finally, analyses of associations with atherosclerotic cardiovascular disease (ACVD) indicated that many strains of the potentially novel species can reduce the abundance of opportunistic pathogens. Together, the large-scale genomics diversity analysis of Lachnospiraceae highlights the importance of potentially novel species and provides the ability for strain-level metagenomic association analysis to guide the selection of strains for the next-generation probiotics.