bluuebunny/crossref_metadata_2025 huggingface dataset:
Right-sided weakness in a Rwandan patient with untreated Tetralogy of Fallot
Authors: Tshilombo Sylvain , Bilugan Romeo , Feeney Amanda , Im Jonathan , Kuntz Heather M. , Gandhi Kavita , Barcega Besh , Babane Jean Felix , Ndebwanimana Vincent , Guptill Mindi
Published: March 2023

Background

Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease encountered in pediatrics with surgical repair being the definitive treatment. Long-term survival after surgical repair has improved; however, reported mortality rates in untreated TOF are significant. Associated complications include neurological sequelae such as brain abscess and stroke. In countries without early intervention for congenital heart disease (including TOF), delayed presentations and complications require recognition by healthcare workers.

Case presentation

A 22-year-old male with a history of untreated TOF presented to Rwanda’s tertiary university hospital, University Teaching Hospital of Kigali, with acute right-sided hemiparesis. Diagnostic imaging identified a left-sided brain lesion consistent with brain abscess and cardiac mass, concerning endocardial vegetation. He was managed with intravenous antibiotics but subsequently died due to complications of septicemia.

Discussion

In countries where surgical repair of TOF is not available, early recognition and medical management are key in temporizing the development of devastating sequelae. Describing the prevalence of CHD in Rwanda is urgent, requiring further research by which effective prevention and treatment strategies can be developed.
Myocardial infarction in patients with severe beta thalassaemia: a case series
Authors: Premawardhena Anuja , De Silva Shamila , Rajapaksha Megha , Ratnamalala Vishaka , Nallarajah Jemimah , Galappatthy Gamini
Published: March 2023

Background

Cardiac disease remains a dominant if not the most important cause of morbidity and mortality in patients with thalassaemia, particularly in those with thalassaemia major. Myocardial infarction and coronary artery disease however are rarely reported.

Case presentations

Three older patients with three distinct thalassaemia syndromes presented with acute coronary syndrome. Two were heavily transfused whilst the other was a minimally transfused patient. Both heavily transfused patients had ST-elevation myocardial infarctions (STEMI) while the minimally transfused patient had unstable angina. Coronary angiogram (CA) was normal in two patients. One patient who developed a STEMI had a 50% plaque. All three were managed as standard ACS, although the aetiology appeared non-atherogenic.

Conclusions

The exact etiology of the presentation, remains a mystery and therefore the rational use of thrombolytic therapy, carrying out angiogram in the primary setting, using and continuing antiplatelet and high dose statins all remains unclear in this sub group of patients.
Pyogenic sacroiliitis caused by Salmonella schwarzengrund in a young healthy woman: a case report and literature review
Authors: Tokuyama Yuki , Yamada Hiroyuki , Shinozuka Ken , Yunoki Tomoyuki , Ohtsuru Shigeru
Published: March 2023

Background

Salmonella species are a leading cause of diarrheal diseases worldwide. Recent epidemiological studies have shown that Salmonella schwarzengrund (S. schwarzengrund) is highly prevalent in various regions. Herein, we report that S. schwarzengrund caused sacroiliac joint (SIJ) infection with septic shock in a young woman, although she was immunocompetent.

Case presentation

A 20-year-old woman presented with left hip pain, accompanied by vasopressor-requiring hypotension. Her imaging examinations showed fluid collection in her SIJ and a small abscess in the left iliac muscle. Later, the blood and aspiration fluid culture and genetic analysis revealed the presence of S. schwarzengrund. We diagnosed sacroiliac joint (SIJ) infection with septic shock caused by S. schwarzengrund. Her condition improved after performing several interventional radiology (IVR) procedures for SIJ abscesses and providing appropriate antibiotic treatment. Finally, she was discharged without any sequelae. Screening tests and genetic analysis about her immunodeficiency did not indicate a congenital disorder.

Conclusion

These clinical courses indicate that S. schwarzengrund could cause the fatal SIJ infection irrespective of the host immunocompetence. Considering the recent increase in the diagnostic rate of S. schwarzengrund, this case emphasized the need to be more cautious about Salmonella species infection.
Associations between dietary intake and glucose tolerance in clinical and metabolomics-based metabotypes
Authors: Rundblad Amanda , Christensen Jacob J. , Hustad Kristin S. , Bastani Nasser E. , Ottestad Inger , Holven Kirsten B. , Ulven Stine M.
Published: March 2023

Background

Metabotyping is a novel concept to group metabolically similar individuals. Different metabotypes may respond differently to dietary interventions; hence, metabotyping may become an important future tool in precision nutrition strategies. However, it is not known if metabotyping based on comprehensive omic data provides more useful identification of metabotypes compared to metabotyping based on only a few clinically relevant metabolites.

Aim

This study aimed to investigate if associations between habitual dietary intake and glucose tolerance depend on metabotypes identified from standard clinical variables or comprehensive nuclear magnetic resonance (NMR) metabolomics.

Methods

We used cross-sectional data from participants recruited through advertisements aimed at people at risk of type 2 diabetes mellitus (n = 203). Glucose tolerance was assessed with a 2-h oral glucose tolerance test (OGTT), and habitual dietary intake was recorded with a food frequency questionnaire. Lipoprotein subclasses and various metabolites were quantified with NMR spectroscopy, and plasma carotenoids were quantified using high-performance liquid chromatography. We divided participants into favorable and unfavorable clinical metabotypes based on established cutoffs for HbA1c and fasting and 2-h OGTT glucose. Favorable and unfavorable NMR metabotypes were created using k-means clustering of NMR metabolites.

Results

While the clinical metabotypes were separated by glycemic variables, the NMR metabotypes were mainly separated by variables related to lipoproteins. A high intake of vegetables was associated with a better glucose tolerance in the unfavorable, but not the favorable clinical metabotype (interaction, p = 0.01). This interaction was confirmed using plasma concentrations of lutein and zeaxanthin, objective biomarkers of vegetable intake. Although non-significantly, the association between glucose tolerance and fiber intake depended on the clinical metabotypes, while the association between glucose tolerance and intake of saturated fatty acids and dietary fat sources depended on the NMR metabotypes.

Conclusion

Metabotyping may be a useful tool to tailor dietary interventions that will benefit specific groups of individuals. The variables that are used to create metabotypes will affect the association between dietary intake and disease risk.
General toxicity and genotoxicity studies of a new scale inhibitor for seawater desalination
Authors: Duan Lian , Li Yimin , Gu Wen , Wang Chao , Shi Ying , Yang Hongbin , Wang Mengmeng , Long Yuehan , Tang Song , Kong Jian , Zhang Shaoping , Zhang Lixia , Wei Lei , Wang Chong , Lu Kai
Published: March 2023

Maleic acid polymer scale inhibitor is a new domestic seawater desalination scale inhibitor. This study tested the acute oral toxicity, sub-chronic toxicity and genotoxicity of this new inhibitor. The LD50 obtained from the acute oral toxicity test was 6810 and 9260 mg/kg·BW for male and female rats, as well as 1/5, 1/10 and 1/20 LD50 were as the dose for sub-chronic toxicity test. It showed the weight of male rats with high dose was significantly lower than the control group during the exposure period (p < 0.05), and the food consumption in the first 4 weeks was lower than the control group (p_week1 = 0.0261, p_week4 = 0.00222). The blood biochemical results showed the UREA in the medium- and high-dose groups were significantly higher than the control group (p_ female medium = 0.0047, p_high = 0.0037; p_male medium = 0.0026, p_high < 0.001), and increased as a dose dependence. Based on UREA results, the NOAEL and LOAEL were 1/20 LD50 and 1/10 LD50, respectively (males: 340.5 and 681 mg/kg·BW, females: 436 and 926 mg/kg·BW). Comet assay in vitro and Mammalian Erythrocyte Micronucleus Test were jointly to judge genotoxicity. This inhibitor did not cause chromosome aberrations in mouse bone marrow cells. However, the tail moment of CHO cell in all groups (p < 0.01) and the DNA% in tail in the 1/4 IC50 and IC50 groups were higher than the negative control (p < 0.001) in comet assay, suggesting the potential DNA damage in CHO cell. The oral LD50 and the NOAEL and LOAEL obtained in this study provides a theoretical basis for further toxicity research and risk assessment.

Graphical Abstract
Granulomatous panuveitis in disseminated sporotrichosis: case report and review of the literature
Authors: Kongwattananon Wijak , Rattanaphong Tanavadee
Published: March 2023

Purpose

To report a case of intraocular sporotrichosis presenting with bilateral granulomatous panuveitis.

Methods

Observational case report and literature review.

Case presentation

A 62-year-old woman with a history of polycythemia vera presented with a non-healing ulcer at the left index finger, generalized erythematous papules, and bilateral granulomatous panuveitis. Cultures of skin and amputated finger identified Sporothrix schenckii. The diagnosis of intraocular sporotrichosis secondary to disseminated sporotrichosis was made. Intravenous liposomal Amphotericin B and intravitreal Amphotericin B were used to control systemic and ocular disease resulting in resolution of the skin lesions and intraocular inflammation.

Conclusions

Intraocular sporotrichosis can manifest as bilateral granulomatous panuveitis in the setting of disseminated sporotrichosis. Treatment with intravenous and intravitreal antifungal therapy is useful for controlling intraocular infection.
Doxorubicin-loaded polymeric nanoparticles containing ketoester-based block and cholesterol moiety as specific vehicles to fight estrogen-dependent breast cancer
Authors: Misiak Paweł , Niemirowicz-Laskowska Katarzyna , Markiewicz Karolina H. , Wielgat Przemysław , Kurowska Izabela , Czarnomysy Robert , Misztalewska-Turkowicz Iwona , Car Halina , Bielawski Krzysztof , Wilczewska Agnieszka Z.
Published: March 2023

The presented research concerns the preparation of polymer nanoparticles (PNPs) for the delivery of doxorubicin. Several block and statistical copolymers, composed of ketoester derivative, N-isopropylacrylamide, and cholesterol, were synthesized. In the nanoprecipitation process, doxorubicin (DOX) molecules were kept in spatial polymeric systems. DOX-loaded PNPs show high efficacy against estrogen-dependent MCF-7 breast cancer cell lines despite low doses of DOX applied and good compatibility with normal cells. Research confirms the effect of PNPs on the degradation of the biological membrane, and the accumulation of reactive oxygen species (ROS), and the ability to cell cycle arrest are strictly linked to cell death.

Graphical Abstract
Genomic evaluation for two-way crossbred performance in cattle
Authors: Mei Quanshun , Liu Huiming , Zhao Shuhong , Xiang Tao , Christensen Ole F
Published: March 2023

Background

Dairy cattle production systems are mostly based on purebreds, but recently the use of crossbreeding has received increased interest. For genetic evaluations including crossbreds, several methods based on single-step genomic best linear unbiased prediction (ssGBLUP) have been proposed, including metafounder ssGBLUP (MF-ssGBLUP) and breed-specific ssGBLUP (BS-ssGBLUP). Ideally, models that account for breed effects should perform better than simple models, but knowledge on the performance of these methods is lacking for two-way crossbred cattle. In addition, the differences in the estimates of genetic parameters (such as the genetic variance component and heritability) between these methods have rarely been investigated. Therefore, the aims of this study were to (1) compare the estimates of genetic parameters for average daily gain (ADG) and feed conversion ratio (FCR) between these methods; and (2) evaluate the impact of these methods on the predictive ability for crossbred performance.

Methods

Bivariate models using standard ssGBLUP, MF-ssGBLUP and BS-ssGBLUP for the genetic evaluation of ADG and FCR were investigated. To measure the predictive ability of these three methods, we estimated four estimators, bias, dispersion, population accuracy and ratio of population accuracies, using the linear regression (LR) method.

Results

The results show that, for both ADG and FCR, the heritabilities were low with the three methods. For FCR, the differences in the estimated genetic parameters were small between the three methods, while for ADG, those estimated with BS-ssGBLUP deviated largely from those estimated with the other two methods. Bias and dispersion were similar across the three methods. Population accuracies for both ADG and FCR were always higher with MF-ssGBLUP than with ssGBLUP, while with BS-ssGBLUP the population accuracy was highest for FCR and lowest for ADG.

Conclusions

Our results indicate that in the genetic evaluation for crossbred performance in a two-way crossbred cattle production system, the predictive ability of MF-ssGBLUP and BS-ssGBLUP is greater than that of ssGBLUP, when the estimated variance components are consistent across the three methods. Compared with BS-ssGBLUP, MF-ssGBLUP is more robust in its superiority over ssGBLUP.
New proposal of viral genome representation applied in the classification of SARS-CoV-2 with deep learning
Authors: de Souza Luísa C. , Azevedo Karolayne S. , de Souza Jackson G. , Barbosa Raquel de M. , Fernandes Marcelo A. C.
Published: March 2023

Background

In December 2019, the first case of COVID-19 was described in Wuhan, China, and by July 2022, there were already 540 million confirmed cases. Due to the rapid spread of the virus, the scientific community has made efforts to develop techniques for the viral classification of SARS-CoV-2.

Results

In this context, we developed a new proposal for gene sequence representation with Genomic Signal Processing techniques for the work presented in this paper. First, we applied the mapping approach to samples of six viral species of the Coronaviridae family, which belongs SARS-CoV-2 Virus. We then used the sequence downsized obtained by the method proposed in a deep learning architecture for viral classification, achieving an accuracy of 98.35%, 99.08%, and 99.69% for the 64, 128, and 256 sizes of the viral signatures, respectively, and obtaining 99.95% precision for the vectors with size 256.

Conclusions

The classification results obtained, in comparison to the results produced using other state-of-the-art representation techniques, demonstrate that the proposed mapping can provide a satisfactory performance result with low computational memory and processing time costs.
The personalized cancer network explorer (PeCaX) as a visual analytics tool to support molecular tumor boards
Authors: Figaschewski Mirjam , Sürün Bilge , Tiede Thorsten , Kohlbacher Oliver
Published: March 2023

Background

Personalized oncology represents a shift in cancer treatment from conventional methods to target specific therapies where the decisions are made based on the patient specific tumor profile. Selection of the optimal therapy relies on a complex interdisciplinary analysis and interpretation of these variants by experts in molecular tumor boards. With up to hundreds of somatic variants identified in a tumor, this process requires visual analytics tools to guide and accelerate the annotation process.

Results

The Personal Cancer Network Explorer (PeCaX) is a visual analytics tool supporting the efficient annotation, navigation, and interpretation of somatic genomic variants through functional annotation, drug target annotation, and visual interpretation within the context of biological networks. Starting with somatic variants in a VCF file, PeCaX enables users to explore these variants through a web-based graphical user interface. The most protruding feature of PeCaX is the combination of clinical variant annotation and gene-drug networks with an interactive visualization. This reduces the time and effort the user needs to invest to get to a treatment suggestion and helps to generate new hypotheses. PeCaX is being provided as a platform-independent containerized software package for local or institution-wide deployment. PeCaX is available for download at https://github.com/KohlbacherLab/PeCaX-docker.
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

Background

Epigenetic 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.

Results

To 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.

Conclusion

The 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

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

Objective

Insect 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.

Data

Transcriptomes 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

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

Biodiversity 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

Since 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

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

Background

Current 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.

Results

We 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.

Conclusion

We 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

Downy 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

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

Background

The 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).

Results

Over 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.

Conclusions

The 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

Introduction

During 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.

Results

Previously, 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.

Conclusion

Together, 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

Background

Bioprospecting of actinobacteria isolated from Kubuqi desert, China for antibacterial, antifungal and cytotoxic metabolites production and their structure elucidation.

Results

A 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).

Conclusions

This 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

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.
Spectrum of ctxB genotypes, antibiogram profiles and virulence genes of Vibrio cholerae serogroups isolated from environmental water sources from Odisha, India
Authors: Pal Bibhuti Bhusan , Samal Debasish , Nayak Smruti Ranjan , Pany Swatishree
Published: March 2023

Background

The present study reports on the comprehensive analysis of Vibrio cholerae O1 and non-O1/non-O139 serogroups isolated from environmental water sources during cholera outbreaks, epidemics and surveillance studies between years 2007 to 2019 from different districts of Odisha, India.

Methods

A total of 85 stocked cultures of V. cholerae O1 and non-O1/non-O139 strains were analyzed for different ctxB genotypes, toxic genes, antibiogram profiles through PCR assays and pulsotyped by pulsed-field gel electrophoresis (PFGE).

Results

From all V. cholerae strains tested, 51 isolates were O1 Ogawa and the rest 34 strains were non-O1/non-O139. All the V. cholerae O1 strains were altered El Tor variants carrying ctxB1, ctxB3 and ctxB7 genotypes. However, only ctxB1 genotypes were present in V. cholerae non-O1/non-O139. Though non-O1/non-O139 strains were negative by O1 antisera, 20% strains were positive for rfbO1 gene by PCR assay. All the V. cholerae isolates possessed a variety of virulence genes including ace, ctxAB, toxR, zot, hlyA which were in higher percentage in the case of V. cholerae O1. The Vibrio cholerae O1 and non-O1-/non-O139 strains showed multiple antibiotic resistances in 2007 and 2012. The PCR detection of four resistance associated genes (strB, dfrA1, sulll, SXT) confirmed higher prevalence in V. cholerae non-O1/non-O139 strains. The PFGE analysis revealed 3 pulsotypes having 93% similarity among V. cholerae O1 strains.

Conclusion

This study indicates the changing epidemiology, antibiogram patterns and continuous genetic variation in environmental V. cholerae strains of Odisha over the years. So continuous surveillance is necessary to understand the changing patterns of V. cholerae different serogroups isolated from stool and water samples from Odisha.
Evaluation of the mTORC activity in the presence of Toxoplasma gondii and azathioprine in human monocyte cell line
Authors: Nemati Sara , Mohammad Rahimi Hanieh , Meyfour Anna , Pazoki Hossein , Asadzadeh Aghdaei Hamid , Shahrokh Shabnam , Mirjalali Hamed
Published: March 2023

Background

Autophagy is an important part of pathogenesis of IBD. Thiopurines such as azathioprine (AZA) are approved drugs for clinical practices in IBD patients. Besides, as an escape strategy, Toxoplasma gondii can use the mTORC1 complex to inactivate autophagy.

Methods

In this study, we investigated whether T. gondii tachyzoites may modulate autophagy and interfere the effects of azathioprine in IBD treatment. PMA-activated human monocyte cell line (THP-1) was infected with fresh T. gondii RH tachyzoites. After 5 h of infection, the cells were treated with AZA for 6 h. The expression of atg5, atg7, atg12, lc3b, and β-actin (BACT) genes was evaluated using quantitative real-time PCR. To analyze the phosphorylation of ribosomal protein S6 (rpS6), western blot using specific primary antibodies was performed.

Results

The results of real-time PCR revealed that AZA, T. gondii tachyzoites, and a combination of AZA and T. gondii tachyzoites upregulated atg5 gene for 4.297-fold (P-value = 0.014), 2.49-fold (P-value = 0.006), and 4.76-fold (P-value = 0.001), respectively. The atg7 gene showed significant upregulation (2.272-fold; P-value = 0.014) and (1.51-fold; P-value = 0.020) in AZA and AZA / T. gondii, respectively. The expression of atg12 gene was significantly downregulated in AZA and T. gondii tachyzoites for (8.85-fold; P-value = 0.004) and (2.005-fold; P-value = 0.038), respectively, but upregulated in T. gondii/AZA (1.52-fold; P-value = 0.037). In addition, the lc3b gene was only significantly changed in AZA / T. gondii (3.028-fold; P-value = 0.001). Western blot analysis showed that T. gondii tachyzoites significantly phosphorylated rpS6, and tachyzoites did not interfere the effects of AZA to phosphorylate the rpS6.

Conclusion

Taken together, although AZA and T. gondii similarly affects the expression levels of atg5, atg7, and atg12, but T. gondii does not seem to modulate the effects of AZA via mTORC functions.
Genome-wide identification and expression analysis of wall-associated kinase (WAK) and WAK-like kinase gene family in response to tomato yellow leaf curl virus infection in Nicotiana benthamiana
Authors: Zhong Xueting , Li Jiapeng , Yang Lianlian , Wu Xiaoyin , Xu Hong , Hu Tao , Wang Yajun , Wang Yaqin , Wang Zhanqi
Published: March 2023

Background

Tomato yellow leaf curl virus (TYLCV) is a major monopartite virus in the family Geminiviridae and has caused severe yield losses in tomato and tobacco planting areas worldwide. Wall-associated kinases (WAKs) and WAK-like kinases (WAKLs) are a subfamily of the receptor-like kinase family implicated in cell wall signaling and transmitting extracellular signals to the cytoplasm, thereby regulating plant growth and development and resistance to abiotic and biotic stresses. Recently, many studies on WAK/WAKL family genes have been performed in various plants under different stresses; however, identification and functional survey of the WAK/WAKL gene family of Nicotiana benthamiana have not yet been performed, even though its genome has been sequenced for several years. Therefore, in this study, we aimed to identify the WAK/WAKL gene family in N. benthamiana and explore their possible functions in response to TYLCV infection.

Results

Thirty-eight putative WAK/WAKL genes were identified and named according to their locations in N. benthamiana. Phylogenetic analysis showed that NbWAK/WAKLs are clustered into five groups. The protein motifs and gene structure compositions of NbWAK/WAKLs appear to be highly conserved among the phylogenetic groups. Numerous cis-acting elements involved in phytohormone and/or stress responses were detected in the promoter regions of NbWAK/WAKLs. Moreover, gene expression analysis revealed that most of the NbWAK/WAKLs are expressed in at least one of the examined tissues, suggesting their possible roles in regulating the growth and development of plants. Virus-induced gene silencing and quantitative PCR analyses demonstrated that NbWAK/WAKLs are implicated in regulating the response of N. benthamiana to TYLCV, ten of which were dramatically upregulated in locally or systemically infected leaves of N. benthamiana following TYLCV infection.

Conclusions

Our study lays an essential base for the further exploration of the potential functions of NbWAK/WAKLs in plant growth and development and response to viral infections in N. benthamiana.
Persistence of parental age effect on somatic mutation rates across generations in Arabidopsis
Authors: Bhushan Shashi , Singh Amit Kumar , Thakur Yogendra , Baskar Ramamurthy
Published: March 2023

In the model plant Arabidopsis thaliana, parental age is known to affect somatic mutation rates in their immediate progeny and here we show that this age dependent effect persists across successive generations. Using a set of detector lines carrying the mutated uidA gene, we examined if a particular parental age maintained across five consecutive generations affected the rates of base substitution (BSR), intrachromosomal recombination (ICR), frameshift mutation (FS), and transposition. The frequency of functional GUS reversions were assessed in seedlings as a function of identical/different parental ages across generations. In the context of a fixed parental age, BSR/ICR rates were unaffected in the first three generations, then dropped significantly in the 4th and increased in most instances in the 5th generation (e.g. BSR (F1 38 = 0.9, F2 38 = 1.14, F3 38 = 1.02, F4 38 = 0.5, F5 38 = 0.76)). On the other hand, with advancing parental ages, BSR/ICR rates remained high in the first two/three generations, with a striking resemblance in the pattern of mutation rates (BSR (F1 38 = 0.9, F1 43 = 0.53, F1 48 = 0.79, F1 53 = 0.83 and F2 38 = 1.14, F2 43 = 0.57, F2 48 = 0.64, F2 53 = 0.94). We adopted a novel approach of identifying and tagging flowers pollinated on a particular day, thereby avoiding biases due to potential emasculation induced stress responses. Our results suggest a time component in counting the number of generations a plant has passed through self-fertilization at a particular age in determining the somatic mutation rates.