Review
Biochemistry & Molecular Biology
Bingting Yu, Ruslan Mamedov, Gwenny M. Fuhler, Maikel P. Peppelenbosch
Summary: The liver plays a crucial role in maintaining biochemical balance, and diseases affecting the liver have a significant impact on human health. However, due to the complexity and uniqueness of hepatic kinase activities, there are challenges in studying them comprehensively. Nevertheless, current kinome profiling approaches show great promise for advancing research in this area.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Connor Denomy, Conor Lazarou, Daniel Hogan, Antonio Facciuolo, Erin Scruten, Anthony Kusalik, Scott Napper
Summary: Peptide microarrays with defined phosphorylation target sites are effective for high throughput analysis of cellular kinome activity. The PIIKA software, including the recent version 2.5, provides quality control metrics and a new background correction technique to enhance accuracy and consistency of kinome results. These modifications improve identification and correction of technical issues, leading to better extraction of biological information.
Article
Microbiology
John Osei Sekyere, Ayodeji B. Oyenihi, Jason Trama, Martin E. Adelson
Summary: Since 2005, the pathogen BVAB has been identified in the female vaginal tract using PCR, but its actual species was unknown. Without the full genome of these pathogens, we cannot fully understand their pathogenicity, treatment, resistance, and diagnostics. Through sequence homology and phylogenetics analysis, we have identified the actual species of BVAB-1, -2, and -3 and found them to be anaerobic and uncultured species that can only be identified through metagenomics.
MICROBIOLOGY SPECTRUM
(2023)
Article
Agricultural Engineering
Xinran Chong, Yunlong Li, Minlei Yan, Yue Wang, Mingzhi Li, Yanwei Zhou, Hong Chen, Xiaoqing Lu, Fan Zhang
Summary: The genus Ilex includes economically important ornamental and medicinal plant species. This study describes the complete chloroplast genome sequences of three Ilex species and develops DNA barcodes for species identification. The findings provide resources for further research on the identification, genetic engineering, evolution, and phylogeny of Ilex species.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Microbiology
Kajal Mandal, Subhajeet Dutta, Aditya Upadhyay, Arijit Panda, Sucheta Tripathy
Summary: This study investigates the genomes of 128 Phytophthora species and reveals that their simple sequence repeats follow isolate-specific patterns, with TG/CA dinucleotide repeats being the most abundant. The telomeric repeats and RxLR effectors in Phytophthora show rapid divergence. The analysis also identifies a large number of other virulence genes present in repeat-rich compartments. Whole genome duplication studies suggest a geographic location-specific pattern. Overall, this study sheds light on the adaptive evolution of Phytophthora driven by localized host-mediated selection pressure.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Enda M. Byrne, Zhihong Zhu, Ting Qi, Nathan G. Skene, Julien Bryois, Antonio F. Pardinas, Eli Stahl, Jordan W. Smoller, Marcella Rietschel, Michael J. Owen, James T. R. Walters, Michael C. O'Donovan, John G. McGrath, Jens Hjerling-Leffler, Patrick F. Sullivan, Michael E. Goddard, Peter M. Visscher, Jian Yang, Naomi R. Wray
Summary: Most genetic variants associated with psychiatric disorders show pleiotropic effects, impacting multiple disorders. However, some variants exhibit disorder-specific effects. Differences in gene expression, such as decreased VPS29 expression being linked to increased schizophrenia risk, highlight disorder-specific mechanisms.
MOLECULAR PSYCHIATRY
(2021)
Article
Food Science & Technology
Xinran Xiang, Jiaran Lu, Xiaowei Xu, Xiaogai Hou, Enjie Diao, Shiquan Qian, Huwei Song, Liqin Liang, Yinglong He, Yuting Shang
Summary: In this study, molecular targets specific to four Enterococcus species were screened and a PCR method was established for their rapid detection. The PCR method not only verified the specificity of the molecular targets, but also served as an effective tool for molecular diagnosis. The exploitation of these specific molecular targets and the unambiguous identification of Enterococcus species through PCR are important for determining food contamination and clinical diseases.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Microbiology
Theerapong Krajaejun, Thidarat Rujirawat, Tassanee Lohnoo, Wanta Yingyong, Pattarana Sae-Chew, Onrapak Reamtong, Weerayuth Kittichotirat, Preecha Patumcharoenpol
Summary: This study analyzed the secretome of Pythium insidiosum using proteogenomic analysis and validated its expression in vivo. P. insidiosum may employ an alternative secretory pathway, and its specific secreted/extracellular proteins may be responsible for host-specific infection. Additionally, some proteins that were significantly upregulated at body temperature may contribute to the pathogen's fitness and thermotolerance. Secreted/extracellular proteins, such as urease and chaperones, identified through a microbial virulence database, may play roles in P. insidiosum virulence.
Article
Biochemistry & Molecular Biology
Chang Lu, Bastian Greshake Tzovaras, Julian Gough
Summary: The rapid growth of human genetic data is driven by medical research and direct-to-consumer sequencing companies. A review of over 7000 genomes is provided, along with a toolkit for preparing consumer DNA datasets for research purposes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Lei Ji, Zhi-Xiang Li, Dong-Bing Cheng, Xue-Hao Zhang, Junan Liu, Zixin Yang, Zeng-Ying Qiao, Hao Wang
Summary: Chemotherapy is a main approach in clinical cancer treatment, but the delivery of drugs remains a challenge. This study presents a reactive oxygen species (ROS)-responsive peptide-drug conjugate (PDC) system that targets mitochondria for drug release, leading to enhanced therapeutic effects by inducing cell apoptosis.
Article
Cell Biology
Yasutaka Kakui, Christopher Barrington, Yoshiharu Kusano, Rahul Thadani, Todd Fallesen, Toru Hirota, Frank Uhlmann
Summary: Mitotic chromosomes in different organisms have various dimensions, which may be related to chromatin contacts, thickness, and species-specific organizing principles.
Article
Plant Sciences
Consolata Nanjala, Vincent Okelo Wanga, Wyclif Odago, Elizabeth Syowai Mutinda, Emmanuel Nyongesa Waswa, Millicent Akinyi Oulo, Elijah Mbandi Mkala, Josiah Kuja, Jia-Xin Yang, Xiang Dong, Guang-Wan Hu, Qing-Feng Wang
Summary: This study investigated the complete plastomes of 6 Calanthe and 2 Phaius species, revealing their structural characteristics. The results showed highly conserved plastomes among the species, with some non-coding regions having more sequence repeats important for DNA barcoding. Phylogenetic analysis revealed a paraphyletic relationship in the Calanthe group and confirmed the position of Phaius delavayi within the genus Calanthe.
Article
Biochemistry & Molecular Biology
Min-Min Chen, Miao Zhang, Zong-Suo Liang, Qiu-Ling He
Summary: This study investigated the evolutionary relationships and germplasm identification of the Uncaria genus, a traditional Chinese medicine. The researchers sequenced and annotated the chloroplast genomes of various Uncaria species, identifying highly variable loci and SSRs that can be used as molecular markers. Phylogenetic analysis revealed the relationships between five Uncaria species. This research provides valuable insights for identifying genuine Uncaria species and their counterfeits.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Haruna Nakamura, Mitsuto Aibara, Rei Kajitani, Hillary D. J. Mrosso, Semvua Mzighani, Atsushi Toyoda, Takehiko Itoh, Norihiro Okada, Masato Nikaido
Summary: The cichlids of Lake Victoria exhibit rapid adaptive radiation, with low genetic differentiation among species and highly differentiated genes related to vision playing a crucial role in speciation. Comparative genomic analyses of three Lake Victoria cichlid species in different habitats revealed distinct patterns of population history and identified novel adaptive candidate genes, some with long divergent haplotypes between species, indicating selective sweep events. Phylogenetic analyses showed that much of the allelic diversity among Lake Victoria cichlids originated from standing genetic variation before the adaptive radiation. The study uncovered the species-specific adaptation processes and complex genomic substrate that facilitated this adaptation.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Yuheng Huang, Harsh Shukla, Yuh Chwen G. Lee
Summary: Transposable elements (TEs) are selfish genetic parasites that increase their copy number at the expense of host fitness. The abundance of TEs differs greatly between species, and this study explores the role of TE-mediated local enrichment of repressive marks in determining genomic TE abundance. The results show that the TE-mediated effect varies across and even within species, and the transcription of neighboring genes can impact this spreading. This multi-species analysis highlights the importance of host chromatin landscapes in shaping genome evolution through the epigenetic effects of TEs.