bluuebunny/crossref_metadata_2025_split huggingface dataset:
Snapshot: a package for clustering and visualizing epigenetic history during cell differentiation
Authors: Xiang Guanjue , Giardine Belinda , An Lin , Sun Chen , Keller Cheryl A. , Heuston Elisabeth F. , Anderson Stacie M. , Kirby Martha , Bodine David , Zhang Yu , Hardison Ross C. 
Published: March 2023

AbstractBackgroundEpigenetic modification of chromatin plays a pivotal role in regulating gene expression during cell differentiation. The scale and complexity of epigenetic data pose significant challenges for biologists to identify the regulatory events controlling cell differentiation.ResultsTo reduce the complexity, we developed a package, called Snapshot, for clustering and visualizing candidate cis-regulatory elements (cCREs) based on their epigenetic signals during cell differentiation. This package first introduces a binarized indexing strategy for clustering the cCREs. It then provides a series of easily interpretable figures for visualizing the signal and epigenetic state patterns of the cCREs clusters during the cell differentiation. It can also use different hierarchies of cell types to highlight the epigenetic history specific to any particular cell lineage. We demonstrate the utility of Snapshot using data from a consortium project forValIdatedSystematicIntegratiON(VISION) of epigenomic data in hematopoiesis.ConclusionThe package Snapshot can identify all distinct clusters of genomic locations with unique epigenetic signal patterns during cell differentiation. It outperforms other methods in terms of interpreting and reproducing the identified cCREs clusters. The package of Snapshot is available at GitHub:https://github.com/guanjue/Snapshot.
ElasticBLAST: accelerating sequence search via cloud computing
Authors: Camacho Christiam , Boratyn Grzegorz M. , Joukov Victor , Vera Alvarez Roberto , Madden Thomas L. 
Published: March 2023

Abstract
Background
Biomedical researchers use alignments produced by BLAST (Basic Local Alignment Search Tool) to categorize their query sequences. Producing such alignments is an essential bioinformatics task that is well suited for the cloud. The cloud can perform many calculations quickly as well as store and access large volumes of data. Bioinformaticians can also use it to collaborate with other researchers, sharing their results, datasets and even their pipelines on a common platform.

Results
We present ElasticBLAST, a cloud native application to perform BLAST alignments in the cloud. ElasticBLAST can handle anywhere from a few to many thousands of queries and run the searches on thousands of virtual CPUs (if desired), deleting resources when it is done. It uses cloud native tools for orchestration and can request discounted instances, lowering cloud costs for users. It is supported on Amazon Web Services and Google Cloud Platform. It can search BLAST databases that are user provided or from the National Center for Biotechnology Information.

Conclusion
We show that ElasticBLAST is a useful application that can efficiently perform BLAST searches for the user in the cloud, demonstrating that with two examples. At the same time, it hides much of the complexity of working in the cloud, lowering the threshold to move work to the cloud.
De novo transcriptome assemblies of five major European oilseed rape insect pests
Authors: Sana Salma , Vollhardt Ines , Kubon Katharina , Rostás Michael , Scholten Stefan 
Published: March 2023

AbstractObjectiveInsect pests can cause severe losses in oilseed rape yields across Europe. Genomic and transcriptomic information is very limited for these insects. The aim of our study was to provide transcriptomic resources on several oilseed rape herbivores that will support research into their biology and help develop new methods of sustainable pest management.DataTranscriptomes for larval stages of five major European pest species werede novoassembled by Trinity assembler. Total number of transcripts ranged from 112,247 forCeutorhynchus pallidactylusto 225,110 forCeutorhyncus napi.Intermediate numbers of 140,588, 140,998 and 144,504, were found forPsylliodes chrysocephala,Dasineura brassicae, and Brassicogethes aeneus, respectively. Bench-marking universal single-copy orthologues analyses for each dataset indicated high degree of completeness for all five species. The transcriptomes extend the list of genomic data on insect larvae that constitute major pests of oilseed rape. The data provide information on larval physiology and form a basis to develop highly specific RNA interference-based plant protection.
Draft genome sequence of Enterobacter chengduensis ECC445, isolated from fresh water in the West Indies
Authors: Pot Matthieu , Ducat Célia , Reynaud Yann , Couvin David , Ferdinand Séverine , Breurec Sébastien , Talarmin Antoine , Guyomard-Rabenirina Stéphanie 
Published: March 2023

Abstract
Objectives
The Enterobacter cloacae complex is considered an important opportunistic pathogen. It comprises many members that remain difficult to delineate by phenotypic approaches. Despite its importance in human infection, there is a lack of information on associated members in other compartments. Here we report the first de novo assembled and annotated whole-genome sequence of a E. chengduensis strain isolated from the environment.

Data description
ECC445 specimen was isolated in 2018 from a drinking water catchment point in Guadeloupe. It was clearly related to E. chengduensis species according to hsp60 typing and genomic comparison. Its whole-genome sequence is 5,211,280-bp long divided into 68 contigs, and presents a G + C content of 55.78%. This genome and associated datasets provided here will serve as a useful resource for further analyses of this rarely reported Enterobacter species.
Mare-MAGE curated reference database of fish mitochondrial genes
Authors: Kasmi Yassine , Eschbach Erik , Hanel Reinhold 
Published: March 2023

AbstractBiodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems. Here we present a new reference database for fish meta-barcoding based on mitochondrial genes. The Mare-MAGE database contains quality-checked sequences of the mitochondrial 12S ribosomal RNA and Cytochrome c Oxidase I gene. All sequences were obtained from the National Center for Biotechnology Information- GenBank (NBCI-GenBank), the European Nucleotide Archive (ENA), AquaGene Database and BOLD database, and have undergone intensive processing. They were checked for false annotations and non-target anomalies, according to the Integrated Taxonomic Information System (ITIS) and FishBase. The dataset is compiled in ARB-Home, FASTA and Qiime2 formats, and is publicly available from the Mare-MAGE database website (http://mare-mage.weebly.com/). It includes altogether 231,333 COI and 12S rRNA gene sequences of fish, covering 19,506 species of 4,058 genera and 586 families.
Characterization of free fatty acid receptor family in rainbow trout (Oncorhynchus mykiss): towards a better understanding of their involvement in fatty acid signalisation
Authors: Roy Jérôme , Baranek Elodie , Marandel Lucie 
Published: March 2023

AbstractSince 20 years of research, free fatty acids receptors (FFARs) have received considerable attention in mammals. To date, four FFARs (FFAR1, FFAR2, FFAR3 and FFAR4) are especially studied owing to their physiological importance in various biological processes. This ubiquitist group of G protein-coupled receptors (GPCRs) are majors reports in the key physiological functions such as the regulation of energy balance, metabolism or fatty acid sensing. However, up till date, even some studies were interested in their potential involvement in fatty acid metabolism, no genome investigation of these FFARs have been carried out in teleost fish. Through genome mining and phylogenetic analysis, we identified and characterised 7 coding sequences for ffar2 in rainbow trout whereas no ffar3 nor ffar4 gene have been found. This larger repertoire of ffar2 genes in rainbow trout results from successive additional whole-genome duplications which occurred in early teleosts and salmonids, respectively. A syntenic analysis was used to assign a new nomenclature to the salmonid ffar2 and showed a clear conservation of genomic organisation, further supporting the identity of these genes as ffar2. RT-qPCR was then used to examine, firstly during ontogenesis and secondly on feeding response the expression pattern of ffar1 and ffar2 genes in proximal gut and brain of all trout ffar genes. Overall, this study presents a comprehensive overview of the ffar family in rainbow trout.
Genetic diversity and signatures of selection in BoHuai goat revealed by whole-genome sequencing
Authors: Yao Zhi , Zhang Shunjin , Wang Xianwei , Guo Yingwei , Xin Xiaoling , Zhang Zijing , Xu Zejun , Wang Eryao , Jiang Yu , Huang Yongzhen 
Published: March 2023

Abstract
Background
Cross breeding is an important way to improve livestock performance. As an important livestock and poultry resource in Henan Province of China, Bohuai goat was formed by crossing Boer goat and Huai goat. After more than 20 years of breeding, BoHuai goats showed many advantages, such as fast growth, good reproductive performance, and high meat yield. In order to better develop and protect Bohuai goats, we sequenced the whole genomes of 30 BoHuai goats and 5 Huai goats to analyze the genetic diversity, population structure and genomic regions under selection of BoHuai goat. Furthermore, we used 126 published genomes of world-wide goat to characterize the genomic variation of BoHuai goat.

Results
The results showed that the nucleotide diversity of BoHuai goats was lower and the degree of linkage imbalance was higher than that of other breeds. The analysis of population structure showed that BoHuai goats have obvious differences from other goat breeds. In addition, the BoHuai goat is more closely related to the Boer goat than the Huai goat and is highly similar to the Boer goat. Group by selection signal in the BoHuai goat study, we found that one region on chromosome 7 shows a very strong selection signal, which suggests that it could well be the segment region under the intense artificial selection results. Through selective sweeps, we detected some genes related to important traits such as lipid metabolism (LDLR, STAR, ANGPTL8), fertility (STAR), and disease resistance (CD274, DHPS, PDCD1LG2).

Conclusion
In this paper, we elucidated the genomic variation, ancestry composition, and selective signals related to important economic traits in BoHuai goats. Our studies on the genome of BoHuai goats will not only help to understand the characteristics of the crossbred but also provide a basis for the improvement of cross-breeding programs.
An SPRI beads-based DNA purification strategy for flexibility and cost-effectiveness
Authors: Liu Danli , Li Qiujia , Luo Jing , Huang Qitong , Zhang Yubo 
Published: March 2023

AbstractBackgroundCurrent solid-phase reversible immobilization (SPRI) beads technology is widely used in molecular biology due to its convenience for DNA manipulation. However, the high performance commercial SPRI beads have no price advantage over our method. Furthermore, the use of commercially available SPRI beads standards does not provide the flexibility required for a number of specific nucleic acid handling scenarios.ResultsWe report an efficient DNA purification strategy by combining home-made beads-suspension buffer with SPRI beads. The method tests the critical concentrations of polyethylene glycol (PEG) 8000 and beads to maximise recovery. And the composition of the SPRI beads DNA purification system (SDPS) was determined at 20% PEG 8000, 2 M NaCl and 16.3 mM MgCl2, and 1.25 mg/ml beads (1/8th original concentration). Then, we tested the DNA recovery of the SDPS, and the result showed that it was comparable to the control (AMPure XP beads). In the study, we have also developed an adjustment SPRI beads DNA purification system (ASDPS), the volume of ASDPS per reaction is 0.6× reaction volume (beads/samples). The performance of ASDPS is similar to SDPS and the control. But the cost of our methods is only about 1/24th of the control. To further assess its performance, we prepare the DNA-seq libraries to evaluate the yield, library quality, capture efficiency and consistency. We have compared all these results with the performance of the control and confirmed its efficiency.ConclusionWe have proposed an alternative DNA purification approach with great flexibility, allowing researchers to manipulate DNA in different conditions. And ultimately, its application will benefit molecular biology research in the future.
High-throughput time series expression profiling of Plasmopara halstedii infecting Helianthus annuus reveals conserved sequence motifs upstream of co-expressed genes
Authors: Bharti Sakshi , Ploch Sebastian , Thines Marco 
Published: March 2023

AbstractDowny mildew disease of sunflower, caused by the obligate biotrophic oomycetePlasmopara halstedii,can have significant economic impact on sunflower cultivation. Using high-throughput whole transcriptome sequencing, four developmental phases in 16 time-points ofPl. halstediiinfectingHelianthus annuuswere investigated. With the aim of identifying potential functional and regulatory motifs upstream of co-expressed genes, time-series derived gene expression profiles were clustered based on their time-course similarity, and their upstream regulatory gene sequences were analyzed here. Several conserved motifs were found upstream of co-expressed genes, which might be involved in binding specific transcription factors. Such motifs were also found associated with virulence related genes, and could be studied on a genetically tractable model to clarify, if these are involved in regulating different stages of pathogenesis.
RNA binding proteins are potential novel biomarkers of egg quality in yellow catfish
Authors: Ren Fan , Zhou Quan , Meng Yinglu , Guo Wenjie , Tang Qin , Mei Jie 
Published: March 2023

Abstract
Background
Egg quality is a major concern in fish reproduction and development. An effective evaluation of egg quality prior to fertilization is helpful in improving the fertilization rate and survival rate of the larva. In this study, we aim to identify quality instructors from the combination study of fertilization rate, hatching rate, embryo malformation rate and gene expression profile.

Results
Eggs from 25 female fish were fertilized with sperm from the same fish. The egg quality was determined by the fertilization rates, hatching rate and embryo malformation rate and divided into three categories, low-quality (< 35%), medium-quality (35 to 75%), and high-quality (> 75%). Due to the distinct difference in fertilization, hatching and embryo malformation rate between low-quality eggs and high-quality eggs, these two groups were considered for the identification of quality markers. Then RNA-seq was performed for the originally preserved eggs from the low-quality group and high-quality group. We profiled the differentially expressed genes and identified a group of RNA-binding proteins (RBPs) as potential regulators. Gene function analysis indicated that most of these genes were enriched in RNA-regulated pathways including RNA processing. The RBPs were more related to egg quality from the PLS-DA analysis. Finally, gene expression was validated by qRT-PCR.

Conclusions
We found a cluster of RBP genes including igf2bp3, zar1, elavl1, rbm25b and related regulatory factors including yy1, sirt1, anp32e, btg4 as novel biomarkers of egg quality.
Genome-wide identification of Kanamycin B binding RNA in Escherichia coli
Authors: Chang Yaowen , Sun Wenxia , Murchie Alastair I. H. , Chen Dongrong 
Published: March 2023

AbstractBackgroundThe aminoglycosides are established antibiotics that inhibit bacterial protein synthesis by binding to ribosomal RNA. Additional non-antibiotic aminoglycoside cellular functions have also been identified through aminoglycoside interactions with cellular RNAs. The full extent, however, of genome-wide aminoglycoside RNA interactions inEscherichia colihas not been determined. Here, we report genome-wide identification and verification of the aminoglycoside Kanamycin B binding toEscherichia coliRNAs. Immobilized Kanamycin B beads in pull-down assays were used for transcriptome-profiling analysis (RNA-seq).ResultsOver two hundred Kanamycin B binding RNAs were identified. Functional classification analysis of the RNA sequence related genes revealed a wide range of cellular functions. Small RNA fragments (ncRNA, tRNA and rRNA) or small mRNA was used to verify the binding with Kanamycin B in vitro. Kanamycin B and ibsC mRNA was analysed by chemical probing.ConclusionsThe results will provide biochemical evidence and understanding of potential extra-antibiotic cellular functions of aminoglycosides inEscherichia coli.
A deeper insight into the sialome of male and female Culex quinquefasciatus mosquitoes
Authors: Lu Stephen , Martin-Martin Ines , Ribeiro Jose M. , Calvo Eric 
Published: March 2023

AbstractIntroductionDuring evolution, blood-feeding arthropods developed a complex salivary mixture that can interfere with host haemostatic and immune response, favoring blood acquisition and pathogen transmission. Therefore, a survey of the salivary gland contents can lead to the identification of molecules with potent pharmacological activity in addition to increase our understanding of the molecular mechanisms underlying the hematophagic behaviour of arthropods. The southern house mosquito,Culex quinquefasciatus, is a vector of several pathogenic agents, including viruses and filarial parasites that can affect humans and wild animals.ResultsPreviously, a Sanger-based transcriptome of the salivary glands (sialome) of adult C. quinquefasciatus females was published based on the sequencing of 503 clones organized into 281 clusters. Here, we revisited the southern mosquito sialome using an Illumina-based RNA-sequencing approach of both male and female salivary glands. Our analysis resulted in the identification of 7,539 coding DNA sequences (CDS) that were functionally annotated into 25 classes, in addition to 159 long non-coding RNA (LncRNA). Additionally, comparison of male and female libraries allowed the identification of female-enriched transcripts that are potentially related to blood acquisition and/or pathogen transmission.ConclusionTogether, these findings represent an extended reference for the identification and characterization of the proteins containing relevant pharmacological activity in the salivary glands ofC. quinquefasciatusmosquitoes.
Bioprospecting of desert actinobacteria with special emphases on griseoviridin, mitomycin C and a new bacterial metabolite producing Streptomyces sp. PU-KB10–4
Authors: Saleem Maira , Hassan Ashba , Li Feina , Lu Qinpei , Ponomareva Larissa V. , Parkin Sean , Sun Chenghang , Thorson Jon S. , Shaaban Khaled A. , Sajid Imran 
Published: March 2023

AbstractBackgroundBioprospecting of actinobacteria isolated from Kubuqi desert, China for antibacterial, antifungal and cytotoxic metabolites production and their structure elucidation.ResultsA total of 100 actinobacteria strains were selectively isolated from Kubuqi desert, Inner Mongolia, China. The taxonomic characterization revealedStreptomycesas the predominant genus comprising 37 different species, along with the rare actinobacterial genusLentzea. The methanolic extracts of 60.8% of strains exhibited potent antimicrobial activities againstStaphylococcus aureus,Micrococcus luteus,Bacillus subtilis,Escherichia coli,Salmonella enterica,Saccharomyces cerevisiaeand high to mild in vitro cytotoxicity against PC3 (prostate cancer) and A549 (lung carcinoma) cell lines. The metabolomics analysis by TLC, HPLC-UV/vis, HPLC-MS and NMR showed the presence of compounds with molecular weights ranging from 100 to 1000 Da. The scale-up fermentation of the prioritized anti-Gram-negative strain PU-KB10–4 (Streptomyces griseoviridis), yielded three pure compounds including; griseoviridin (1; 42.0 mgL− 1) with 20 fold increased production as compared to previous reports and its crystal structure as monohydrate form is herein reported for the first time, mitomycin C (2; 0.3 mgL− 1) and a new bacterial metabolite 4-hydroxycinnamide (3; 0.59 mgL− 1).ConclusionsThis is the first report of the bioprospecting and exploration of actinobacteria from Kubuqi desert and the metabolite 4-hydroxycinnamide (3) is first time isolated from a bacterial source. This study demonstrated that actinobacteria from Kubuqi desert are a potential source of novel bioactive natural products. Underexplored harsh environments like the Kubuqi desert may harbor a wider diversity of actinobacteria, particularlyStreptomyces, which produce unique metabolites and are an intriguing source to develop medicinally valuable natural products.
Antimicrobial potential of myricetin-coated zinc oxide nanocomposite against drug-resistant Clostridium perfringens
Authors: Gomaa Nada H. , El-Aziz Norhan K. Abd , El-Naenaeey El-sayed Y. , Abdelaziz Walaa S. , Sewid Alaa H. 
Published: March 2023

Abstract
Background
Clostridium perfringens (C. perfringens) is an important pathogen in livestock animals and humans causing a wide array of systemic and enteric diseases. The current study was performed to investigate the inhibitory activity of myricetin (MYR), polyvinyl alcohol (PVA), and zinc oxide (ZnO) nanocomposite against growth and α-hemolysin of C. perfringens isolated from beef meat and chicken sources.

Results
The overall occurrence of C. perfringens was 29.8%. The prevalence of C. perfringens was higher in chicken (38.3%) than in beef meat products (10%). The antimicrobial susceptibility testing revealed that C. perfringens isolates exhibited high resistance levels for metronidazole (93%), bacitracin (89%), penicillin G (84%), and lincomycin (76%). Of note, 1% of C. perfringens isolates were pandrug-resistant (PDR), 4% were extensive drug-resistant (XDR), while 91% were multidrug-resistant. The results of broth microdilution technique revealed that all tested C. perfringens isolates were susceptible to MYR-loaded ZnO/PVA with minimum inhibitory concentrations (MICs) ranged from 0.125 to 2 µg/mL. Moreover, the MYR either alone or combined with the nanocomposite had no cytotoxic activities on chicken red blood cells (cRBCs). Transcriptional modifications of MYR, ZnO, ZnO/PVA, and ZnO/PVA/MYR nanocomposite were determined, and the results showed significant down-regulation of α-hemolysin fold change to 0.5, 0.7, 0.6, and 0.28, respectively compared to the untreated bacteria.

Conclusion
This is an in vitro study reporting the antimicrobial potential of MYR-coated ZnO nanocomposite as an effective therapeutic candidate against C. perfringens. An in vivo approach is the next step to provide evidence for applying these alternatives in the treatment and prevention of C. perfringens-associated diseases.