What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota by Blanka Sokołowska, Małgorzata Orłowska, Alicja Okrasińska, Sebastian Piłsyk, Julia Pawłowska, Anna Muszewska

“…Following the advancement in EDF genome sequencing, we carried out a systematic survey of lipid metabolism protein families across different EDF lineages. …”
Get full text

Characterization of <i>Streptococcus pyogenes</i> Strains from Tonsillopharyngitis and Scarlet Fever Resurgence, 2023—FIRST Detection of M1_UK in Bulgaria by Emma Keuleyan, Theodor Todorov, Deyan Donchev, Ani Kevorkyan, Radoslava Vazharova, Alexander Kukov, Georgi Todorov, Boriana Georgieva, Iskra Altankova, Yordanka Uzunova

“…Virulence factors were identified using multiplex PCR and whole genome sequencing (WGS). Immune responses were measured through detection of serum complement levels, lymphocyte subsets, and cytokine profiling. …”
Get full text

Genetic Background and Phenotypic Aspects of Light-Induced Carotenoid Biosynthesis in <i>Isosphaeraceae</i> Planctomycetes by Anastasia A. Ivanova, Igor Y. Oshkin, Aleksandr A. Ashikhmin, Olga V. Danilova, Svetlana N. Dedysh

“…The genes involved in the carotenoid biosynthetic pathways of strain Ch08, a non-pigmented planctomycete <i>Singulisphaera acidiphila</i> MOB10^T, and all described <i>Isosphaeraceae</i> members with determined genome sequences were analyzed. The biosynthesis of C30 carotenoids via squalene, as evidenced by the presence of <i>hpnCDE</i> and <i>crtNPQO</i> gene clusters, was encoded in genomes of all pigmented <i>Singulisphaera</i>, <i>Aquisphaera</i>, and <i>Paludisphaera</i> species. …”
Get full text

Surveillance of tick-borne encephalitis virus foci in Slovakia: A seroprevalence study in ruminants combined with virus detection in ticks by Martina Ličková, Bronislava Víchová, Markéta Derdáková, Monika Sláviková, Sabína Fumačová Havlíková, Dana Zubriková, Diana Selyemová, Michal Chvostáč, Lucia Blaňarová, Viktória Čabanová, Veronika Vaňová, Lucia Šulejová, Jana Kerlik, Tomáš Szemes, Katarína Šoltys, Boris Klempa

“…Obtained full-length genome sequences revealed high genetic diversity and phylogenetic clustering with virus strains found across Europe. …”
Get full text

Enhanced membrane protein production in HEK293T cells via ATF4 gene knockout: A CRISPR-Cas9 mediated approach by Byung-Jo Choi, Ba Reum Kim, Ho Joong Choi, Ok-Hee Kim, Say-June Kim

“…Comparative evaluations were conducted using all-in-one and two-vector systems. Genome sequencing and membrane protein productivity of ATF4-KO cells were compared to wild-type cells using next-generation sequencing (NGS) and a membrane protein isolation kit, respectively. …”
Get full text

Outbreak of carbapenem resistant Klebsiella pneumoniae in a neurorehabilitation unit: Genomic epidemiology reveals complex transmission pattern in a tertiary care hospital by Maria Grazia Silvotti, Erika Scaltriti, Luca Bolzoni, Beatrice Zerbi, Gabriella Tocci, Andrea Zappavigna, Gianfranco Lamberti, Federico Donati, Franco Federici, Stefano Pongolini, Giuliana Lo Cascio

“…We report an outbreak by KPC-Kp, in a neurorehabilitation unit in Italy, analysed through whole-genome sequencing (WGS) for transmission routes reconstruction to improve management of KPC-Kp infections in rehabilitation units. …”
Get full text

Prognostic impact of donor mitochondrial genomic variants in myelodysplastic neoplasms after stem-cell transplantation by Jing Dong, Shahram Arsang-Jang, Tao Zhang, Zhongyuan Chen, Yung-Tsi Bolon, Stephen Spellman, Raul Urrutia, Paul Auer, Wael Saber

“…Here, we performed whole-genome sequencing on 494 donors who were matched to MDS patients enrolled in the Center for International Blood and Marrow Transplant Research (CIBMTR). …”
Get full text

Сandidate SNP-markers of rheumatoid arthritis that can significantly alter the affinity of the TATA-binding protein for human gene promoters by I. V. Chadaeva, D. A. Rasskazov, E. B. Sharypova, I. A. Drachkova, E. A. Oshchepkova, L. K. Savinkova, P. M. Ponomarenko, M. P. Ponomarenko, N. A. Kolchanov, V. A. Kozlov

“…That is why, RA fits the main idea of postgenomic predictive-preventive personalized medicine that is to give a chance to those who would like to reduce his/her risk of diseases by bringing his/her conditions and lifestyle in line with the data on his/her genome sequenced. This is very important, since doctors consider RA as one of the most frequent causes of disability. …”
Get full text

Assessment of Antibiotic Resistance and Efflux Pump Gene Expression in Neisseria Gonorrhoeae Isolates from South Africa by Quantitative Real-Time PCR and Regression Analysis by Nireshni Mitchev, Ravesh Singh, Veron Ramsuran, Arshad Ismail, Mushal Allam, Stanford Kwenda, Florah Mnyameni, Nigel Garrett, Khine Swe Swe-Han, Abraham J. Niehaus, Koleka P. Mlisana

“…This study investigated the expression profile of antibiotic resistance-associated genes (penA, ponA, pilQ, mtrR, mtrA, mtrF, gyrA, parC, parE, rpsJ, 16S rRNA, and 23S rRNA) and efflux pump genes (macAB, norM, and mtrCDE), by quantitative real-time PCR, in clinical isolates from KwaZulu-Natal, South Africa. Whole-genome sequencing was used to determine the presence or absence of mutations. …”
Get full text

A novel virulent core genome multilocus sequence type CT 11424 of Listeria monocytogenes isolate causing stillbirth in Bangladesh by Muntasir Alam, Md Saiful Islam, M. Ishrat Jahan, Arpita Shyama Deb, Afruna Rahman, Zahidul Islam, Atique Iqbal Chowdhury, Kazi Munisul Islam, Mohammad Zahid Hossain, Dilruba Ahmed, Shams El Arifeen, Emily S. Gurley, Mustafizur Rahman

“…Conclusions This is the first genome sequence of clinical L. monocytogenes from Bangladesh, which also caused stillbirth. …”
Get full text

Draft genome dataset of Streptomyces griseoincarnatus strain R-35 isolated from tidal pool sedimentsMendeley DataNCBI by Danielle Dana Mitchell, Jo-Marie Vreulink, Alaric Prins, Marilize Le Roes-Hill

“…The CARD RGI algorithm on Proksee predicted the presence of 6,107 antimicrobial resistance (AMR) features, 27 biosynthetic gene clusters (BGCs) were predicted using antiSMASH, while 189 carbohydrate-active enzymes (CAZymes) were predicted using dbCAN3. The raw genome sequencing data has been submitted to the National Center for Biotechnology (NCBI) under the BioProject ID PRJNA1129156 (BioSample ID Accession Number: SAMN42145163; Short Read Archive (SRA) Accession: SRR29633055; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1129156).…”
Get full text

The extremely halotolerant black yeast Hortaea werneckii - a model for intraspecific hybridization in clonal fungi by Polona Zalar, Jerneja Zupančič, Cene Gostinčar, Janja Zajc, G. Sybren de Hoog, Filomena De Leo, Armando Azua-Bustos, Nina Gunde-Cimerman

“…Analysis of whole-genome sequences of selected H. werneckii strains generally confirmed the phylogenetic distances estimated on the basis of ribosomal genes, but also showed substantial reticulation within the phylogenetic history of the strains. …”
Get full text

Emergence of a blaNDM-5-carrying extensively drug-resistant Enterobacter cloacae ST1718 in Saudi Arabia: Insights from comprehensive genome analysis by Ibrahim A. Al-Zahrani, Thamer M. Brek

“…Results: ECloa-JZ71 exhibited resistance to multiple antimicrobial agents, except for amikacin, gentamycin, and fosfomycin. Whole-genome sequencing revealed that ECloa-JZ71 had a rarely reported sequence type, ST1718. …”
Get full text

Mapping Antimicrobial Resistance in <i>Staphylococcus epidermidis</i> Isolates from Subclinical Mastitis in Danish Dairy Cows by Desiree Corvera Kløve, Mikael Lenz Strube, Peter M. H. Heegaard, Lærke Boye Astrup

“…<b>Methods:</b> Phenotypic resistance was measured by antimicrobial susceptibility testing and minimum inhibitory concentration (MIC) analysis, and genotypic resistance was examined through whole-genome sequencing and identification of antimicrobial resistance genes (ARGs). …”
Get full text

Passive infusion of an S2-Stem broadly neutralizing antibody protects against SARS-CoV-2 infection and lower airway inflammation in rhesus macaques. by Christopher T Edwards, Kirti A Karunakaran, Elijah Garcia, Nathan Beutler, Matthew Gagne, Nadia Golden, Hadj Aoued, Kathryn L Pellegrini, Matthew R Burnett, Christopher Cole Honeycutt, Stacey A Lapp, Thang Ton, Mark C Lin, Amanda Metz, Andrei Bombin, Kelly Goff, Sarah E Scheuermann, Amelia Wilkes, Jennifer S Wood, Stephanie Ehnert, Stacey Weissman, Elizabeth H Curran, Melissa Roy, Evan Dessasau, Mirko Paiardini, Amit A Upadhyay, Ian N Moore, Nicholas J Maness, Daniel C Douek, Anne Piantadosi, Raiees Andrabi, Thomas R Rogers, Dennis R Burton, Steven E Bosinger

“…We observed a significant reduction in inflammatory cytokines and macrophages within the lower airway of animals infused with 10mg/kg and 1mg/kg doses of CC40.8. Viral genome sequencing demonstrated a lack of escape mutations in the CC40.8 epitope. …”
Get full text

ANALYSIS OF GENETIC CHARACTERISTICS OF INFLUENZA VIRUS A/CHICKEN/CHELYABINSK/30/2019 H9N2 ISOLATED IN CHELYABINSK OBLAST by N. G. Zinyakov, Щю S. Osipova, P. B. Akshalova, V. Yu. Sosipatorova, A. V. Andriyasov, D. B. Andreychuk, I. A. Chvala

“…The complete nucleotide genome sequence of the studied pathogen was determined. …”
Get full text

In Silico Exploration of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>) Evolution Based on Phylogenetic Relationship of <i>ccrAB/C</i> by Huawei Wang, Jinxing He

“…In addition, whole-genome sequencing-based macro-analysis was unable to provide sufficiently detailed evolutionary information on SCC<i>mec</i>. …”
Get full text

Microscale total genomic DNA was used to explore the complete mitochondrial genomes of two biting midge species of the family Ceratopogonidae (Insecta: Diptera) by Xiaohong Jiang, Yao Xie, Qiongyou Liu

“…The complete mitochondrial genome sequences of some insect species were cloned by long PCR, but degenerate or multiple pairs of primers were needed; thus, the long PCR method was optimized and improved in this study. …”
Get full text

Detection of Delafloxacin Resistance Mechanisms in Multidrug-Resistant <i>Klebsiella pneumoniae</i> by András Kubicskó, János Juhász, Katalin Kamotsay, Dora Szabo, Béla Kocsis

“…Four delafloxacin-resistant <i>K. pneumoniae</i> strains were selected for whole-genome sequencing (WGS). <b>Results:</b> The MIC50 values for the 43 <i>K. pneumoniae</i> strains were as follows: ciprofloxacin 0.5 mg/L, levofloxacin 0.25 mg/L, moxifloxacin 0.5 mg/L, and delafloxacin 0.25 mg/L. …”
Get full text

Integrating Metabolomics and Genomics to Uncover the Impact of Fermented Total Mixed Ration on Heifer Growth Performance Through Host-Dependent Metabolic Pathways by Zhenzhen Hu, Minyu Zuo, Shixuan Ding, Yifan Zhong, Mingyuan Xue, Huichao Zheng

“…A total of 157 heifers aged 7–8 months were selected, and their hair was collected for whole-genome sequencing. They were randomly assigned into four groups of 18 to 21 cattle each and fed FTMR containing varying levels of rice straw (21% in LSF, 28% in MSF, 35% in HSF) or 31% sheath and leaves of <i>Zizania latifolia</i> (ZF) for a two-month period. …”
Get full text