Miracle-dz/UniFAR-FTUs huggingface dataset:
EMBL2checklists: A Python package to facilitate the user-friendly submission of plant DNA barcoding sequences to ENA

Background The submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant DNA barcoding. Methods A Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called “checklists”) for a subsequent upload to the public sequence database of the European Nucleotide Archive (ENA). The software tool, titled “EMBL2checklists”, automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates output that can be uploaded via the interactive Webin submission system of ENA. Results EMBL2checklists provides a simple, platform-independent tool that automates the conversion of common plant DNA barcoding sequences into easily editable spreadsheets that require no further processing but their upload to ENA via the interactive Webin submission system. The software is equipped with an intuitive graphical as well as an efficient command-line interface for its operation. The utility of the software is illustrated by its application in the submission of DNA sequences of two recent plant phylogenetic investigations and one fungal metagenomic study. Discussion EMBL2checklists bridges the gap between common software suites for DNA sequence assembly and annotation and the interactive data submission process of ENA. It represents an easy-to-use solution for plant biologists without bioinformatics expertise to generate submission-ready checklists from common plant DNA sequence data. It allows the post-processing of checklists as well as work-sharing during the submission process and solves a critical bottleneck in the effort to increase participation in public data sharing.
Improved varieties perform well in realized genetic gain trials with Norway spruce seed sources in southern Sweden

ABSTRACT Genetically improved Norway spruce (Picea abies L. Karst) has been extensively used in operational plantations in Sweden. However, there have been few studies that aimed at verifying the realized genetic gain over a longer time span in plots established with one genetical entry. Two experimental series at six sites in southern Sweden, established purely for this purpose, were assessed. Early height growth of 10 Norway spruce seedlots of different genetic levels was compared. There were significant differences in height at the age of 5 and 8 years between improved and unimproved seed sources and the differences between most advanced material from the breeding front, represented by full-sib crossings of selected plus-trees, and unimproved Swedish spruce were 36% and 30% at the age of 5 and 8 years, respectively. At the same ages, the trees originating from the second round of seed-orchards were 25% and 21% higher than unimproved material. There were also about 20% differences between the best and worst tested full-sib families, indicating large possible gain in the new generation. The study confirmed earlier estimates of genetic gain levels of different seed sources in the breeding program for Norway spruce.
Biological control of late leaf rust disease [Pucciniastrum americanum (Farl.) Arthur] in raspberry (Rubus idaeus L.) using two biological products: Bacillus subtilis (Fungizard®) and Larrea tridentata botanic extract (CleanCrop®) under screenhouse conditions

espanolRESUMEN El objetivo del presente estudio fue evaluar la idoneidad de cepas nativas de Trichoderma para el control biologico de la roya tardia de la hoja (RTH), en una plantacion organica de Rubus idaeus, bajo condiciones de malla sombra. Se evaluaron cuatro tratamientos: T1) Trichoderma sp. cepa Clombta; T2) Trichoderma sp. cepa Chlorolota; T3) Co-aplicacion de ambas cepas de Trichoderma (Clombta + Chlorolota) y T4) Control, el cual consistio en la aplicacion de dos productos biologicos: Bacillus subtilis (Fungizard®) y extracto botanico de Larrea tridentata (CleanCrop®)]. Se evaluo la severidad de la enfermedad, el indice de severidad de la enfermedad (IS) y el area bajo la curva de progreso de la enfermedad (ABCPE). La co-aplicacion de Trichoderma sp. cepas Chlorolota y Clombta (de 43,44 a 35,73%) redujo la severidad de RTH al mismo nivel que el Control (de 44,61 a 34,33%). Para el IS, Trichoderma sp. cepa Chlorolota (64,13) y la Co-aplicacion (61,11) mostraron valores similares al Control (59,84). La co-aplicacion de ambas cepas de Trichoderma obtuvo el menor ABCPE (71,2), al mismo nivel que el Control (68,7). Sin embargo, Trichoderma sp. Chlorolota (72,1) logro el mismo ABCPE que la Co-aplicacion. El uso de Trichoderma sp. Chlorolota o su Co-aplicacion con la cepa Clombta fueron capaces de reducir la RTH en R. idaeus. EnglishABSTRACT This study aimed to evaluate the suitability of native Trichoderma strains for the biological control of Late Leaf Rust Disease (LLRD) in an organic Rubus idaeus plantation under screenhouse conditions. Four treatments were evaluated: T1) Trichoderma sp. strain Clombta; T2) Trichoderma sp. strain Chlorolota; T3) Co-application of both Trichoderma strains (Clombta + Chlorolota) and T4) Control, which consisted in the application of two biological products: Bacillus subtilis (Fungizard®) and Larrea tridentata botanic extract (CleanCrop®)]. Disease severity, disease severity index (DSI) and Area Under the Disease Progress Curve (AUDPC) were evaluated. The Co-application of Trichoderma sp. strain Chlorolota and Trichoderma sp. Clombta (from 43,44 to 35,73%) reduce the LLRD severity at the same level than the Control (from 44,61 to 34,33%). For DSI, Trichoderma sp. train Chlorolota (64,13) and the Co-application (61,11) showed similar values than those from the Control (59,84). Co-application of both Trichoderma strains showed the lowest AUDPC (71,2), at the same level that the Control (68,7). However, Trichoderma sp. Chlorolota (72,1) achieved the same AUDPC that the Co-application. The use of Trichoderma sp. Chlorolota or its Co-application with Trichoderma sp. strain Clombta was able to reduce the LLRD in R. idaeus.
Morphological and Molecular Diversity Among Heliotropium greuteri Samples

Bu calismada Heliotropium greuteri H. RIEDL bitkisinde secilen bazi morfolojik karakterler bakimindan karakterizasyonunu yapmak, ISSR markirlari vasitasiyla akrabalik ve cesitliliklerini belirlemek amaclanmistir. Bu calismada kirk yedi H. greuteri genotipi ile kontrol olarak bir H. lasiocarpum genotipi kullanilmistir. Bitki materyalleri Erciyes Universitesi ve Kayseri-Develi cevresinden toplanmistir. Bitki yapisi, cicek yapisi, tohum ozellikleri ile molekuler markir cesitlilikleri karakterize edilmistir. Bitki yuksekligi 13-100 cm (ort:28 cm), cicek capi 1,35-18,5 mm (ort: 9,78 mm) olarak belirlenmistir. Tum ozellikler bakimindan varyasyon tespit edilmesi bu bitkinin sus bitkisi olarak gelistirilebilir bir potansiyele sahip oldugunu gostermektedir. ISSR analizlerinde, secilen 13 primer ile 90 polimorfik bant elde edilmistir. Dice genetik benzerlik degerleri 0,81-0,99 arasinda bulunmustur. Muhtemelen bu tur bir darlasma ile karsi karsiya kalmistir ya da daralan cesitlilikle sonuclanan bir turlesme ortaya cikmistir. Genel olarak H. greuteri bitkileri kuraklik toleranslarinin yuksek olmasi, kokulari, ciceklenme surelerinin uzunlugu ve bal arilarini cezbetme gibi ozellikleriyle sus bitkisi olarak kullanilmalari icin onemli bir potansiyele sahiptir.
Characterization of protein interactions by mass spectrometry and bioinformatics

The molecular understanding of cellular processes requires the identification and characterization of the involved protein complexes. Affinity-purification and mass spectrometric analysis (AP–MS) are performed on a routine basis to detect proteins assembled in complexes. In particular, protein abundances obtained by quantitative mass spectrometry and direct protein contacts detected by crosslinking and mass spectrometry (XL–MS) provide complementary datasets for revealing the composition, topology and interactions of modules in a protein network. Here, we aim to combine quantitative and connectivity information by a webserver tool in order to infer protein complexes. In a first step, modeling protein abundances and functional annotations from Gene Ontology (GO) results in a network which, in a second step, is integrated with connectivity data from XL–MS analysis in order to complement and validate the protein complexes in the network. The output of our integrative approach is a quantitative protein interaction map which is supplemented with topological information of the detected protein complexes. compleXView is built up by two independent modules which are dedicated to the analysis of label-free AP–MS data and to the visualization of the detected complexes in a network together with crosslink-derived distance restraints. compleXView is available to all users without login requirements at http://xvis.genzentrum. lmu.de/compleXView.
On the Programming Impact of Multi-Core, Multi-Processor Nodes in MPI Clusters

Increasingly, multi-core processors, multi-processor nodes and multi-core, multi-processor nodes are finding their way into compute clusters. Clusters built using such nodes are already quite common and, inevitably, will become more so over time. As with any new technology, however, thepotentialbenefitsare seldomaseasy toattainaswe expect themto be. In thispaper, weexplore three fundamental issues related to the use of multi-core, multi-processor nodes in compute clusters using MPI: inter-communication (messaging) efficiency, cache effects (in particular processor affinity) and initial process distribution. Based on some initialexperiments usingasubset of theNASparallelbenchmarks running on a small scale cluster with dual core, dual processor nodes, we report results on the impact of these issues. From these results we attempt to extrapolate some simple, guidelines that are likely to be generally applicable for optimizingMPI code runningon clusters withmulticore, multi-processor nodes.
The Potential Role of Environment in Structuring the Microbiota of Camponotus across Parts of the Body

Several studies have attempted to understand what may influence the bacterial community of a host, but studies examining whether different bacterial species are found in different parts of the body of insects are limited. In the present study, we address the following questions: 1) How are bacterial communities distributed across different parts of the body (head, mesosoma, gaster) of Camponotus and 2) Is the diversity found explained by the environment in which these ants were collected? Our results were able to differentiate the bacterial communities present in the different parts of the body and can be explained in the following way: each part of the body has unique organs with different functions; and the complex proventriculum of Camponotus may be acting as a filter and structuring the bacterial community found in the gaster. In addition, an unexpected finding of the present study was the high diversity found associated with the head and mesosoma, and our findings were able to confirm that this diversity is associated with the environment where the ants were collected. Knowing more about the factors that can influence bacterial communities may reveal more about the importance of these associations in nature.
Single-cell analysis of the muscle stem cell hierarchy identifies heterotypic communication signals involved in skeletal muscle regeneration

Muscle stem cells (MuSCs) are an essential adult stem cell population with the capacity to self-renew and regenerate muscle tissue. Functionally heterogeneous subpopulations of MuSCs have been identified based on their expression of myogenic regulatory factors and surface markers. However, a unified organization of muscle stem and progenitor cells and their subpopulations remains unresolved. Here, we performed temporal analysis of skeletal muscle regeneration using single-cell RNA-sequencing (scRNA-seq) of myotoxin-injured adult mouse hindlimb muscles. We generated over 34,000 single-cell transcriptomes spanning four muscle regeneration time-points and identified 15 distinct cell types, including a heterogeneous population of MuSCs and progenitor cells. Our analysis provides a hierarchical map of myogenic cell populations and identifies stage-specific regulatory programs that govern their contributions to muscle regeneration. In this transcriptomic atlas, we observed cell type-specific regenerative dynamics, exemplified by waves of transient amplification and diversification of multiple immune cell types and, subsequently, myogenic cells. Unbiased trajectory inference organized the myogenic cell populations within the atlas into a continuum, consisting of a hierarchy of quiescent MuSCs, cycling progenitors, committed myoblasts, and terminally differentiated myocytes. This myogenic trajectory matched prior understanding and also revealed that MuSC stages are defined by synchronous changes in regulatory factors, cell cycle-associated, and surface receptor gene expression. Lastly, we analyzed the transcriptomic atlas to identify over 100 candidate heterotypic communication signals between myogenic and non-myogenic cell populations, including many involving the fibroblast growth factor (FGF), Notch, and Syndecan receptor families and their associated ligands. Syndecan receptors were implicated in a large fraction of these cell communication interactions and were observed to exhibit transcriptional heterogeneity within the myogenic continuum. Using multiparameter mass cytometry (CyTOF), we confirmed that cycling MuSCs exhibit diversified Syndecan-1/2 expression, which suggests that dynamic alterations in Syndecan signaling interactions may coordinate stage-specific myogenic cell fate regulation. This scRNA-seq reference atlas provides a resolved hierarchical organization of myogenic subpopulations as a resource to investigate cell-cell interactions that regulate myogenic stem and progenitor cell fates in muscle regeneration.
The multiple population genetic and demographic routes to islands of genomic divergence

1. The way that organisms diverge into reproductively isolated species is a major question in biology. The recent accumulation of genomic data provides promising opportunities to understand the genomic landscape of divergence, which describes the distribution of differences across genomes. Genomic areas of unusually high differentiation have been called genomic islands of divergence. Their formation has been attributed to a variety of mechanisms, but a prominent hypothesis is that they result from divergent selection over a small portion of the genome, with surrounding areas homogenised by gene flow. Such islands have often been interpreted as being associated with divergence with gene flow. However other mechanisms related to genetic architecture and population history can also contribute to the formation of genomic islands of divergence. 2. We currently lack a quantitative framework to examine the dynamics of genomic landscapes under the complex and nuanced conditions that are found in natural systems. Here, we develop an individual-based simulation to explore the dynamics of diverging genomes under various scenarios of gene flow, selection and genotype-phenotype maps. 3. Our modelling results are consistent with empirical observations demonstrating the formation of genomic islands under genetic isolation. Importantly, we have quantified the range of conditions that produce genomic islands. We demonstrate that the initial level of genetic diversity, drift, time since divergence, linkage disequilibrium, strength of selection and gene flow are all important factors that can influence the formation of genomic islands. Because the accumulation of genomic differentiation over time tends to erode the signal of genomic islands, genomic islands are more likely to be observed in recently divergent taxa, although not all recently diverged taxa will necessarily exhibit islands of genomic divergence. Gene flow primarily slows the swamping of islands of divergence with time. 4. By using this framework, further studies may explore the relative influence of particular suites of events that contribute to the emergence of genomic islands under sympatric, parapatric and allopatric conditions. This approach represents a novel tool to explore quantitative expectations of the speciation process, and should prove useful in elucidating past and projecting future genomic evolution of any taxa.
ForageGrassBase: Molecular resource for the forage grass Festuca pratensis Huds

Background Meadow fescue (Festuca pratensis Huds.) is one of the most important forage grasses in temperate regions. F. pratensis is a diploid (2n =14) outbreeding species that belongs to the genus Festuca. Together with Lolium, they are the most important genera of forage grasses in temperate regions. F. pratensis has good winter survival, with high quality dry matter yields and persistency, and is suitable both for frequent-cutting conservation regimes and for grazing. It is a significant component of species-rich permanent pastures in the temperate regions, ensuring high forage yield under harsh climatic conditions where other productive forage grass species are unable to grow. However, genomic resources for F. Pratensis is not available so far. Results The draft genome sequences of two F. pratensis genotypes “HF7/2” and “B14/16” are reported in this study. Here, using the draft genome, functional annotation datasets of two F. pratensis cultivars, we have constructed the F. pratensis genome database http://foragegrass.org/, the first open-access platform to provide comprehensive genomic resources related to this forage grass species. The current version of this database provides the most up-to-date draft genome sequence along with structural and functional annotations for genes using Genome Browser (GBrowse). In addition, we have integrated comparative genomic tracks for F. pratensis genomes by mapping F.pratensis genome to the barley, rice, Brachypodium and maize genomes. We have integrated homologus search tool BLAST also for the users to analyze their data. Combined, GBrowse, BLAST and downloadble data gives an user friendly access to F. pratensis genomic resouces. All data in the database were manually curated. Conclusion To our knowledge, ForageGrassBase is the first genome database dedicated to forage grasses. It provides valuable resources for a range of research fields related to F. pratensis and other forage crop species, as well as for plant research communities in general. The genome database can be accessed at http://foragegrass.org. In the near future, we will expand the ForageGrassBase by adding genomic tools for other forage grass species, as soon as their genomes become available.
Genome Engineering for Thermo-sensitive Genic Male Sterilty (TGMS) in rice using CRISPR/Cas9 editing system

Thermosensitive genic male sterile (TGMS) rice genotypes, which are malesterile at the restrictive temperature (>26°C) but becomes male-fertile at the permissive temperature (< 22°C) are widely used in hybrid rice breeding. Mutation in tms5 gene located on chromosome 2 is responsible for the malesterility trait in rice. Through gene editing, it is possible to create a specific mutation in the tms5 locus of male fertile rice lines and convert them into male sterile lines. The CRISPR/Cas9 editing system was employed to induce specific mutation in tms5 gene of rice variety ASD16. CRISPR/Cas9 vector with guide RNA targeting the second exon of tms5 gene was constructed and used for rice transformation. Four putative transgenic ASD16 events were generated through rice immature embryo transformation and analysed for the presence of hpt and mutation in tms5 locus in T0 generation.
Anaerobic methane oxidation is an important sink for methane in the ocean's largest oxygen minimum zone

We investigated methane oxidation in the oxygen minimum zone (OMZ) of the eastern tropical North Pacific (ETNP) off central Mexico. Methane concentrations in the anoxic core of the OMZ reached ~ 20 nmol L−1 at off shelf sites and 34 nmol L−1 at a shelf site. Rates of methane oxidation were determined in ship‐board incubations with 3H‐labeled methane at O2 concentrations 0–75 nmol L−1. In vertical profiles at off‐shelf stations, highest rates were found between the secondary nitrite maximum at ~ 130 m and the methane maximum at 300–400 m in the anoxic core. Methane oxidation was inhibited by addition of 1 μmol L−1 oxygen, which, together with the depth distribution, indicated an anaerobic pathway. A coupling to nitrite reduction was further indicated by the inhibitory effect of the nitric oxide scavenger 2‐phenyl‐4,4,5,5‐tetramethylimidazoline‐1‐oxyl‐3‐oxide (PTIO). Metatranscriptomes from the anoxic OMZ core supported the likely involvement of nitrite‐reducing bacteria of the NC10 clade in anaerobic methane oxidation, but also indicated a potential role for nitrate‐reducing euryarchaeotal methane oxidizers (ANME‐2d). Gammaproteobacteria of the Methanococcales were further detected in both 16S rRNA gene amplicons and metatranscriptomes, but the role of these presumed obligately aerobic methane oxidizers in the anoxic OMZ core is unclear. Given available estimates of water residence time, the measured rates and rate constants (up to ~ 1 yr−1) imply that anaerobic methane oxidation is a substantial methane sink in the ETNP OMZ and hence attenuates the emission of methane from this and possibly other OMZs.
Biofilm formation and extended spectrum beta-lactamase production in Klebsiella pneumoniae isolates from respiratory samples in a tertiary care hospital

Nosocomial and community acquired infections are being caused by Klebsiella pneumoniae (K. pneumoniae) worldwide. K. pneumoniae among gram negative organisms is an important bacterium responsible for site specific infection when they grow as biofilm. Survival of K. pneumoniae is facilitated by biofilm formation that makes it easier to multiply and spread to various sites. Extended–spectrum beta-lactamase (ESBL) producing K. pneumoniae isolates from respiratory samples were used to know the occurrence of biofilm formation conducted in a tertiary care medical college hospital in Mangalore, Dakshina Kannada District, Karnataka, India. To know the occurrence of biofilm formation among extended–spectrum beta-lactamase (ESBL) producing K. pneumoniae isolates from respiratory samples a prospective study has been conducted in a tertiary care medical college hospital in Mangalore, Dakshina Kannada District, Karnataka, India. A total of 87 K. pneumoniae isolates from respiratory samples were characterized according to standard microbiological specific procedures. Screening was done for K. pneumonia Biofilm formation in terms of their antibiotic sensitivity pattern by using standard Kirby Bauer disc diffusion method and presumptive ESBL production by double disk synergy test (DDST). Out of 87 clinical isolates from respiratory samples, 45 (51.72%) were found to be biofilm producers. 29 (33.33%) isolates were ESBL producers and all them produced biofilm. ESBL forming K. pneumoniae isolates had a significantly greater capacity to form strong biofilm (72.4%) than non ESBL producing K. pneumoniae isolates (27.58%). Keywords: Klebsiella pneumoniae, Nosocomial infections, ESBL production, Kirby-Bauer, Biofilm formation.