keyword
https://read.qxmd.com/read/38533084/forward-genetic-screen-using-a-gene-breaking-trap-approach-identifies-a-novel-role-of-grin2bb-associated-rna-transcript-grin2bbart-in-zebrafish-heart-function
#1
JOURNAL ARTICLE
Ramcharan Singh Angom, Adita Joshi, Ashok Patowary, Ambily Sivadas, Soundhar Ramasamy, Shamsudheen K V, Kriti Kaushik, Ankit Sabharwal, Mukesh Kumar Lalwani, Subburaj K, Naresh Singh, Vinod Scaria, Sridhar Sivasubbu
LncRNA-based control affects cardiac pathophysiologies like myocardial infarction, coronary artery disease, hypertrophy, and myotonic muscular dystrophy. This study used a gene-break transposon (GBT) to screen zebrafish ( Danio rerio ) for insertional mutagenesis. We identified three insertional mutants where the GBT captured a cardiac gene. One of the adult viable GBT mutants had bradycardia (heart arrhythmia) and enlarged cardiac chambers or hypertrophy; we named it "bigheart." Bigheart mutant insertion maps to grin2bb or N-methyl D-aspartate receptor (NMDAR2B) gene intron 2 in reverse orientation...
2024: Frontiers in Cell and Developmental Biology
https://read.qxmd.com/read/38533072/the-madagascar-palm-genome-provides-new-insights-on-the-evolution-of-apocynaceae-specialized-metabolism
#2
JOURNAL ARTICLE
Clément Cuello, Hans J Jansen, Cécile Abdallah, Duchesse-Lacours Zamar Mbadinga, Caroline Birer Williams, Mickael Durand, Audrey Oudin, Nicolas Papon, Nathalie Giglioli-Guivarc'h, Ron P Dirks, Michael Krogh Jensen, Sarah Ellen O'Connor, Sébastien Besseau, Vincent Courdavault
Specialized metabolites possess diverse interesting biological activities and some cardenolides- and monoterpene indole alkaloids- (MIAs) derived pharmaceuticals are currently used to treat human diseases such as cancers or hypertension. While these two families of biocompounds are produced by specific subfamilies of Apocynaceae , one member of this medicinal plant family, the succulent tree Pachypodium lamerei Drake (also known as Madagascar palm), does not produce such specialized metabolites. To explore the evolutionary paths that have led to the emergence and loss of cardenolide and MIA biosynthesis in Apocynaceae , we sequenced and assembled the P...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38532500/divergent-composition-and-transposon-silencing-activity-of-small-rnas-in-mammalian-oocytes
#3
JOURNAL ARTICLE
Li Hou, Wei Liu, Hongdao Zhang, Ronghong Li, Miao Liu, Huijuan Shi, Ligang Wu
BACKGROUND: Small RNAs are essential for germ cell development and fertilization. However, fundamental questions remain, such as the level of conservation in small RNA composition between species and whether small RNAs control transposable elements in mammalian oocytes. RESULTS: Here, we use high-throughput sequencing to profile small RNAs and poly(A)-bearing long RNAs in oocytes of 12 representative vertebrate species (including 11 mammals). The results show that miRNAs are generally expressed in the oocytes of each representative species (although at low levels), whereas endo-siRNAs are specific to mice...
March 26, 2024: Genome Biology
https://read.qxmd.com/read/38530861/aminoglycoside-resistance-genes-in-early-members-of-the-acinetobacter-baumannii-st78a-smal-italian-clone-reside-in-an-is26-bounded-island-in-the-chromosome
#4
JOURNAL ARTICLE
Christopher J Harmer, Sarah M Cahill, Johanna J Kenyon, Ruth M Hall
BACKGROUND: The Acinetobacter baumannii isolate called SMAL, previously used to determine the structures of capsular polysaccharide and lipooligosaccharide, was recovered in Pavia, Italy in 2002 among the collection of aminoglycoside-resistant isolates designated as SMAL type. This type was later called the Italian clone, then ST78. ST78 isolates are now widely distributed. OBJECTIVES: To establish the resistance gene complement and the location and structure of acquired resistance regions in early members of the Italian/ST78 clone...
March 26, 2024: Journal of Antimicrobial Chemotherapy
https://read.qxmd.com/read/38528147/an-expanded-transcriptome-atlas-for-bacteroides-thetaiotaomicron-reveals-a-small-rna-that-modulates-tetracycline-sensitivity
#5
JOURNAL ARTICLE
Daniel Ryan, Elise Bornet, Gianluca Prezza, Shuba Varshini Alampalli, Taís Franco de Carvalho, Hannah Felchle, Titus Ebbecke, Regan J Hayward, Adam M Deutschbauer, Lars Barquist, Alexander J Westermann
Plasticity in gene expression allows bacteria to adapt to diverse environments. This is particularly relevant in the dynamic niche of the human intestinal tract; however, transcriptional networks remain largely unknown for gut-resident bacteria. Here we apply differential RNA sequencing (RNA-seq) and conventional RNA-seq to the model gut bacterium Bacteroides thetaiotaomicron to map transcriptional units and profile their expression levels across 15 in vivo-relevant growth conditions. We infer stress- and carbon source-specific transcriptional regulons and expand the annotation of small RNAs (sRNAs)...
March 25, 2024: Nature Microbiology
https://read.qxmd.com/read/38526049/role-of-amino-acid-159-in-carbapenem-and-temocillin-hydrolysis-of-oxa-933-a-novel-oxa-48-variant
#6
JOURNAL ARTICLE
Mariam Rima, Saoussen Oueslati, Garance Cotelon, Elodie Creton, Rémy A Bonnin, Laurent Dortet, Bogdan I Iorga, Thierry Naas
OXA-48 has rapidly disseminated worldwide and become one of the most common carbapenemases in many countries with more than 45 variants reported with, in some cases, significant differences in their hydrolysis profiles. The R214 residue, located in the ß5-ß6 loop, is crucial for the carbapenemase activity, as it stabilizes carbapenems in the active site and maintains the shape of the active site through interactions with D159. In this study, we have characterized a novel variant of OXA-48, OXA-933 with a single D159N change...
March 25, 2024: Antimicrobial Agents and Chemotherapy
https://read.qxmd.com/read/38522841/phage-resistance-in-klebsiella-pneumoniae-and-bidirectional-effects-impacting-antibiotic-susceptibility
#7
JOURNAL ARTICLE
Sue C Nang, Jing Lu, Heidi H Yu, Hasini Wickremasinghe, Mohammad A K Azad, Meiling Han, Jinxin Zhao, Gauri Rao, Phillip J Bergen, Tony Velkov, Norelle Sherry, David T McCarthy, Saima Aslam, Robert T Schooley, Benjamin P Howden, Jeremy J Barr, Yan Zhu, Jian Li
OBJECTIVES: Bacteriophage (phage) therapy is a promising anti-infective option to combat antimicrobial resistance. However, the clinical utilisation of phage therapy has been severely compromised by the potential emergence of phage resistance. While certain phage resistance mechanisms can restore bacterial susceptibility to certain antibiotics, a lack of knowledge of phage resistance mechanisms hinders optimal use of phages and their combination with antibiotics. METHODS: Genome-wide transposon screening was performed with a mutant library of Klebsiella pneumoniae MKP103 to identify phage pKMKP103_1-resistant mutants...
March 22, 2024: Clinical Microbiology and Infection
https://read.qxmd.com/read/38522369/sucrose-fermenting-salmonella-typhimurium-n23-2364-a-challenge-for-the-diagnostic-laboratory
#8
Marc J A Stevens, Magdalena Nüesch-Inderbinen, Jule Anna Horlbog, Andrea Diethelm, Roger Stephan
We describe a case of Salmonella infection caused by a sucrose-fermenting Salmonella enterica Typhimurium sequence type 12 which acquired transposon CTnscr94 carrying the sucrose operon scrKYABR. Sucrose-fermenting Salmonella are particularly challenging for culture-based detection and may lead to failure to detect Salmonella in clinical samples.
March 20, 2024: Diagnostic Microbiology and Infectious Disease
https://read.qxmd.com/read/38521283/mobile-genetic-element-based-gene-editing-and-genome-engineering-recent-advances-and-applications
#9
REVIEW
Jaeseong Hwang, Dae-Yeol Ye, Gyoo Yeol Jung, Sungho Jang
Genome engineering has revolutionized several scientific fields, ranging from biochemistry and fundamental research to therapeutic uses and crop development. Diverse engineering toolkits have been developed and used to effectively modify the genome sequences of organisms. However, there is a lack of extensive reviews on genome engineering technologies based on mobile genetic elements (MGEs), which induce genetic diversity within host cells by changing their locations in the genome. This review provides a comprehensive update on the versatility of MGEs as powerful genome engineering tools that offers efficient solutions to challenges associated with genome engineering...
March 21, 2024: Biotechnology Advances
https://read.qxmd.com/read/38520410/miwi-n-terminal-arginines-orchestrate-generation-of-functional-pachytene-pirnas-and-spermiogenesis
#10
JOURNAL ARTICLE
Nicholas Vrettos, Jan Oppelt, Ansgar Zoch, Paraskevi Sgourdou, Haruka Yoshida, Brian Song, Ryan Fink, Dónal O'Carroll, Zissimos Mourelatos
N-terminal arginine (NTR) methylation is a conserved feature of PIWI proteins, which are central components of the PIWI-interacting RNA (piRNA) pathway. The significance and precise function of PIWI NTR methylation in mammals remains unknown. In mice, PIWI NTRs bind Tudor domain containing proteins (TDRDs) that have essential roles in piRNA biogenesis and the formation of the chromatoid body. Using mouse MIWI (PIWIL1) as paradigm, we demonstrate that the NTRs are essential for spermatogenesis through the regulation of transposons and gene expression...
March 23, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38519761/oxygen-mediated-mobilization-and-co-occurrence-of-antibiotic-resistance-in-lab-scale-bioreactor-using-metagenomic-binning
#11
JOURNAL ARTICLE
Sakina Bombaywala, Abhay Bajaj, Nishant A Dafale
Sub-lethal levels of antibiotic stimulate bacteria to generate reactive oxygen species (ROS) that promotes emergence and spread of antibiotic resistance mediated by mobile genetic elements (MGEs). Nevertheless, the influence of dissolved oxygen (DO) levels on mobility of antibiotic resistance genes (ARGs) in response to ROS-induced stress remains elusive. Thus, the study employs metagenomic assembly and binning approaches to decipher mobility potential and co-occurrence frequency of ARGs and MGEs under hyperoxic (5...
March 23, 2024: World Journal of Microbiology & Biotechnology
https://read.qxmd.com/read/38517165/mutagenesis-and-functional-analysis-of-the-varicella-zoster-virus-portal-protein
#12
JOURNAL ARTICLE
Melissa A Visalli, Dakota J Nale Lovett, Ellyn M Kornfeind, Haley Herrington, Yi Tian Xiao, Daniel Lee, Patience Plair, S Garrett Wilder, Bret K Garza, Ashton Young, Robert J Visalli
Herpesviruses replicate by cleaving concatemeric dsDNA into single genomic units that are packaged through an oligomeric portal present in preformed procapsids. In contrast to what is known about phage portal proteins, details concerning herpesvirus portal structure and function are not as well understood. A panel of 65 Varicella-Zoster virus (VZV) recombinant portal proteins with five amino acid in-frame insertions were generated by random transposon mutagenesis of the VZV portal gene, ORF54. Subsequently, 65 VZVLUC recombinant viruses (TNs) were generated via recombineering...
March 22, 2024: Journal of Virology
https://read.qxmd.com/read/38514891/technical-considerations-for-cost-effective-transposon-directed-insertion-site-sequencing-tradis
#13
JOURNAL ARTICLE
Yasuhiro Kyono, Madeline Tolwinski, Stephanie A Flowers
Transposon directed insertion-site sequencing (TraDIS), a variant of transposon insertion sequencing commonly known as Tn-Seq, is a high-throughput assay that defines essential bacterial genes across diverse growth conditions. However, the variability between laboratory environments often requires laborious, time-consuming modifications to its protocol. In this technical study, we aimed to refine the protocol by identifying key parameters that can impact the complexity of mutant libraries. Firstly, we discovered that adjusting electroporation parameters including transposome concentration, transposome assembly conditions, and cell densities can significantly improve the recovery of viable mutants for different Escherichia coli strains...
March 21, 2024: Scientific Reports
https://read.qxmd.com/read/38514787/heritable-microbiome-variation-is-correlated-with-source-environment-in-locally-adapted-maize-varieties
#14
JOURNAL ARTICLE
Xiaoming He, Danning Wang, Yong Jiang, Meng Li, Manuel Delgado-Baquerizo, Chloee McLaughlin, Caroline Marcon, Li Guo, Marcel Baer, Yudelsy A T Moya, Nicolaus von Wirén, Marion Deichmann, Gabriel Schaaf, Hans-Peter Piepho, Zhikai Yang, Jinliang Yang, Bunlong Yim, Kornelia Smalla, Sofie Goormachtig, Franciska T de Vries, Hubert Hüging, Mareike Baer, Ruairidh J H Sawers, Jochen C Reif, Frank Hochholdinger, Xinping Chen, Peng Yu
Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbiota interactions in the face of environmental stresses. Here we surveyed 3,168 root and rhizosphere microbiome samples from 129 accessions of locally adapted Zea, sourced from diverse habitats and grown under control and different stress conditions. We quantified stress treatment and host genotype effects on the microbiome...
March 21, 2024: Nature Plants
https://read.qxmd.com/read/38507111/identification-and-characterization-of-acinetobacter-nosocomialis-bfmrs-two-component-regulatory-system-essential-for-biofilm-development
#15
JOURNAL ARTICLE
Chul Hee Choi, Seyoung Mun, Man Hwan Oh
BACKGROUND: Biofilm development by bacteria is considered to be an essential stage in the bacterial infection. Acinetobacter nosocomialis is an important nosocomial pathogen causing a variety of human infections. However, characteristics and specific determinants of biofilm development have been poorly characterized in A. nosocomialis. OBJECTIVE: The aim of this study was to investigate the factors involved in the biofilm development by A. nosocomialis. METHODS: Library of random transposon mutants was constructed using the Tn5 mutagenesis...
March 20, 2024: Genes & Genomics
https://read.qxmd.com/read/38502704/morc1-reestablishes-h3k9me3-heterochromatin-on-pirna-targeted-transposons-in-gonocytes
#16
JOURNAL ARTICLE
Yuta Uneme, Ryu Maeda, Gen Nakayama, Haruka Narita, Naoki Takeda, Ryuji Hiramatsu, Hidenori Nishihara, Ryuichiro Nakato, Yoshiakira Kanai, Kimi Araki, Mikiko C Siomi, Soichiro Yamanaka
To maintain fertility, male mice re-repress transposable elements (TEs) that were de-silenced in the early gonocytes before their differentiation into spermatogonia. However, the mechanism of TE silencing re-establishment remains unknown. Here, we found that the DNA-binding protein Morc1, in cooperation with the methyltransferase SetDB1, deposits the repressive histone mark H3K9me3 on a large fraction of activated TEs, leading to heterochromatin. Morc1 also triggers DNA methylation, but TEs targeted by Morc1-driven DNA methylation only slightly overlapped with those repressed by Morc1/SetDB1-dependent heterochromatin formation, suggesting that Morc1 silences TEs in two different manners...
March 26, 2024: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/38502060/conserved-non-coding-elements-evolve-around-the-same-genes-throughout-metazoan-evolution
#17
JOURNAL ARTICLE
Paul Gonzalez, Quinn C Hauck, Andreas D Baxevanis
Conserved noncoding elements (CNEs) are DNA sequences located outside of protein-coding genes that can remain under purifying selection for up to hundreds of millions of years. Studies in vertebrate genomes have revealed that most CNEs carry out regulatory functions. Notably, many of them are enhancers that control the expression of homeodomain transcription factors and other genes that play crucial roles in embryonic development. To further our knowledge of CNEs in other parts of the animal tree, we conducted a large-scale characterization of CNEs in more than 50 genomes from three of the main branches of the metazoan tree: Cnidaria, Mollusca, and Arthropoda...
March 19, 2024: Genome Biology and Evolution
https://read.qxmd.com/read/38501880/a-quorum-sensing-regulatory-cascade-for-siderophore-mediated-iron-homeostasis-in-chromobacterium-violaceum
#18
JOURNAL ARTICLE
Bianca B Batista, Vinicius M de Lima, Beatriz A Picinato, Tie Koide, José F da Silva Neto
Iron is a transition metal used as a cofactor in many biochemical reactions. In bacteria, iron homeostasis involves Fur-mediated de-repression of iron uptake systems, such as the iron-chelating compounds siderophores. In this work, we identified and characterized novel regulatory systems that control siderophores in the environmental opportunistic pathogen Chromobacterium violaceum . Screening of a 10,000-transposon mutant library for siderophore halos identified seven possible regulatory systems involved in siderophore-mediated iron homeostasis in C...
March 19, 2024: MSystems
https://read.qxmd.com/read/38501870/-ehrlichia-effector-trp120-manipulates-bacteremia-to-facilitate-tick-acquisition
#19
JOURNAL ARTICLE
Tsian Zhang, Rory C Chien, Khemraj Budachetri, Mingqun Lin, Prosper Boyaka, Weiyan Huang, Yasuko Rikihisa
UNLABELLED: Ehrlichia species are obligatory intracellular bacteria that cause a potentially fatal disease, human ehrlichiosis. The biomolecular mechanisms of tick acquisition of Ehrlichia and transmission between ticks and mammals are poorly understood. Ehrlichia japonica infection of mice recapitulates the full spectrum of human ehrlichiosis. We compared the pathogenicity and host acquisition of wild-type E. japonica with an isogenic transposon mutant of E. japonica that lacks tandem repeat protein 120 (TRP120) (ΔTRP120)...
March 19, 2024: MBio
https://read.qxmd.com/read/38501654/cell-envelope-structural-and-functional-contributions-to-antibiotic-resistance-in-burkholderia-cenocepacia
#20
JOURNAL ARTICLE
Andrew M Hogan, Anna Motnenko, A S M Zisanur Rahman, Silvia T Cardona
Antibiotic activity is limited by the physical construction of the Gram-negative cell envelope. Species of the Burkholderia cepacia complex (Bcc) are known as intrinsically multidrug-resistant opportunistic pathogens with low permeability cell envelopes. Here, we re-examined a previously performed chemical-genetic screen of barcoded transposon mutants in B. cenocepacia K56-2, focusing on cell envelope structural and functional processes. We identified structures mechanistically important for resistance to singular and multiple antibiotic classes...
March 19, 2024: Journal of Bacteriology
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