State of the art and new directions using DNA and other molecular markers in forensic entomology by David Haymer

“…Beginning with the use of single mitochondrial genes, the range of DNA-based markers available to forensic entomologists has grown to include a wide variety of individual mitochondrial and nuclear genes, and has further expanded to include the analysis of whole genomes and transcriptomes. The use of these new sets of markers has significantly enhanced the ability of forensic entomologists to identify insects associated with human cadavers and to provide improved estimates of the time elapsed since death, commonly referred to as the postmortem interval (PMI), along with other valuable information for crime scene investigations. …”
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Rapid expansion and specialization of the TAS2R bitter taste receptor family in amphibians. by Kathleen W Higgins, Akihiro Itoigawa, Yasuka Toda, Daniel Winston Bellott, Rachel Anderson, Roberto Márquez, Jing-Ke Weng

“…Here, we identify 9,291 TAS2Rs from 661 vertebrate genomes. Large-scale phylogenomic analyses reveal that frogs and salamanders contain unusually high TAS2R gene content, in stark contrast to other vertebrate lineages. …”
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Representative Metagenomes of Mesophilic Biogas Reactor Across South Korea by Darsha Prabhaharan, Young Wook Go, Hyunjin Kim, Seongcheol Kang, Byoung-In Sang

“…From 110 GB of raw DNA sequences, 401 metagenome-assembled genomes (MAGs) were created, which include 42,301 annotated genes. …”
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Cell-free assays reveal that the HIV-1 capsid protects reverse transcripts from cGAS immune sensing. by Tiana M Scott, Lydia M Arnold, Jordan A Powers, Delaney A McCann, Ana B Rowe, Devin E Christensen, Miguel J Pereira, Wen Zhou, Rachel M Torrez, Janet H Iwasa, Philip J Kranzusch, Wesley I Sundquist, Jarrod S Johnson

“…However, the extent to which HIV-1 shields its genome from cGAS recognition remains unclear. To study this process in mechanistic detail, we reconstituted reverse transcription, genome release, and innate immune sensing of HIV-1 in a cell-free system. …”
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Alaninaminotransferase and specific viral hepatitis markers in the blood of donors by Zh. K. Burkitbayev, G. A. Yesenbayeva, S. A. Abdrakhmanova, Zh. Zh. Bibekov, Ye. B. Zhiburt

“…No relation of ALT activity to results of parenteral virus genomes screen was revealed.…”
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How do monomorphic bacteria evolve? The Mycobacterium tuberculosis complex and the awkward population genetics of extreme clonality by Stritt, Christoph, Gagneux, Sebastien

“…Population genetic methods allowing to infer mutation, recombination, genetic drift, and natural selection make strong assumptions that are difficult to reconcile with clonal reproduction and fully linked genomes consisting mainly of coding regions. In this review, we highlight the challenges of extreme clonality by discussing population genetic inference with the Mycobacterium tuberculosis complex, a group of closely related obligate bacterial pathogens of mammals. …”
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Louis Pasteur face à la maladie du ver à soie (1865–1870) : du chimiste au biologiste by Carton, Yves

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Faster model-based estimation of ancestry proportions by Santander, Cindy G., Refoyo Martinez, Alba, Meisner, Jonas

“…We further show that fastmixture runs approximately 30$\times$ faster than ADMIXTURE on both simulated and empirical data from the 1000 Genomes Project such that our model-based approach scales to much larger sample sizes than previously possible.…”
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Molecular genetic methods for intestinal microbiome investigation by O. L. Kardymon, A. V. Kudryavtseva

“…Modern molecular genetic methods of microbial investigation combined to the established methods of classical microbiology give the chance not only to identify microorganism species and even a strain, but also to decipher their genomes, to estimate antibiotic resistance and to establish its mechanism at genetic level, to estimate specific properties of specific microbial strain that will allow to define potential and efficacy of their clinical application etc. …”
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Exploring the Mechanisms of Zhenbao Pills in the Treatment of Stroke through Network Pharmacology Combined with Mendelian Randomization by Yanhong Liu, Yunqi Hua, Xiaoe Jia

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that these targets are involved mainly in oxidative stress processes, lipid metabolism, and the PI3K–Akt signaling pathway. …”
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Tracking the genetic diversity of SARS-CoV-2 variants in Nicaragua throughout the COVID-19 pandemic by Gerald Vásquez Alemán, Cristhiam Cerpas, Jose G. Juarez, Hanny Moreira, Sonia Arguello, Josefina Coloma, Eva Harris, Aubree Gordon, Shannon N. Bennett, Ángel Balmaseda

“…This study characterizes the genomic diversity of SARS-CoV-2 in Nicaragua from March 2020 through December 2022, utilizing 1064 genomes obtained via next-generation sequencing. …”
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Genetics and biological characteristics of duck reoviruses isolated from ducks and geese in China by Xiaohong Sun, Jing Guo, Jinyan Shen, Mengdi Guan, Lili Liu, Yujiao Xie, Hongke Xu, Mengjing Wang, Anran Ren, Wenxi Li, Feng Cong, Xuyong Li

“…In this study, we identified and isolated six duck reoviruses from clinical samples of sick or deceased farmed ducks and geese and sequenced their full genomes. Phylogenetic analysis revealed the evolutionary landscape of duck reoviruses and the complex reassortment of these circulating viruses with avian orthoreovirus and Muscovy duck reovirus. …”
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Genotype B of deformed wing virus and related recombinant viruses become dominant in European honey bee colonies by Fabrice Sircoulomb, Eric Dubois, Frank Schurr, Pierrick Lucas, Marina Meixner, Alicia Bertolotti, Yannick Blanchard, Richard Thiéry

“…Chimeric sequencing reads were used to locate the recombinant junctions along the DWV genome. These were not randomly distributed, but mainly clustered in three genomic areas: the 5’UTR, leader peptide and helicase coding sequences. …”
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Simple and Fail-safe Method to Transform Miniprep Escherichia coli Strain K12 Plasmid DNA Into Viable Agrobacterium tumefaciens EHA105 Cells for Plant Genetic Transformation by Beenzu Siamalube, Emmanuel Ehinmitan, Maina Ngotho, Justus Onguso, Steven Runo

“…It enables the introduction of foreign DNA into plant genomes. Conventionally, plant genetic transformation has relied on time-consuming, costly, and technically demanding procedures, such as electroporation and chimeric viruses or biolistic methods, which usually yield variable transformation efficiencies. …”
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Bacterial community assembly of specific pathogen-free neonatal mice by Elizabeth A. Kennedy, James S. Weagley, Andrew H. Kim, Avan Antia, Anna L. DeVeaux, Megan T. Baldridge

“…Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species. …”
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A ribodepletion and tagging protocol to multiplex samples for RNA-seq based virus detection: application to the cassava virome by Daniel H. Otron, Justin S. Pita, Murielle Hoareau, Fidèle Tiendrébéogo, Jean-Michel Lett, Pierre Lefeuvre

“…After confirming that the protocol was suitable for ribodepletion, we demonstrated it was possible to detect RNA and DNA viruses via identification of near full-size genomes. Additional phylogenetic analyses confirmed the presence of begomoviruses and ipomoviruses responsible for CMD and CBSD, respectively. …”
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WNT3A promotes the cementogenic differentiation of dental pulp stem cells through the FOXO1 signaling pathway by Dongmei Cheng, Yang Bao, Xue Wang, Haidong Xiang, Tianyuan Guo, Yong Du, Zhiyong Zhang, Han Guo

“…Pathway enrichment exploration was conducted utilizing gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), and Metascape tools. …”
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Identification and functional analysis of energy metabolism and pyroptosis-related genes in diabetic nephropathy by Shan He, Jian Ye, Yu Wang, Lu yang Xie, Si Yi Liu, Qin kai Chen

“…Subsequent analyses included Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, Gene Set Enrichment Analysis (GSEA), and Protein-Protein Interaction (PPI) network analysis. …”
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New insights into the mechanism of triphenyl phosphate and its metabolite diphenyl phosphate in diabetic kidney disease by Ting Fang, Qiaoyan Liu, Xinxin Huangfu, Hongkai Zhu, Hongwen Sun, Liming Chen

“…Additionally, the study explored the targets of action for TPHP and DPHP using network toxicity analysis, conducted protein interaction analysis, and explored the functional aspects of action through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Furthermore, the study identified key proteins involved in the action and conducted experimental verification by treating cells with TPHP and DPHP. …”
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