Characterizing Antimicrobial Effects of Radiation and Antibiotic Interactions on <i>Staphylococcus aureus</i> and <i>Escherichia coli</i> Using MALDI-TOF MS by Ali Haider, Renáta Homlok, Csilla Mohácsiné Farkas, Tamás Kocsis

“…The findings highlight MALDI-TOF MS as a valuable tool in detecting proteomic biomarkers linked to bacterial resistance and stress adaptation.…”
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Polygenic prediction of human longevity on the supposition of pervasive pleiotropy by M. Reza Jabalameli, Jhih-Rong Lin, Quanwei Zhang, Zhen Wang, Joydeep Mitra, Nha Nguyen, Tina Gao, Mark Khusidman, Sanish Sathyan, Gil Atzmon, Sofiya Milman, Jan Vijg, Nir Barzilai, Zhengdong D. Zhang

“…Together, our approach demonstrates a promising framework for polygenic modeling of additive liability conferred by ARTs in defining exceptional longevity and assisting the identification of individuals at a higher risk of mortality for targeted lifestyle modifications earlier in life. Furthermore, the proteomic signature associated with iLGS highlights the functional pathway upstream of the PI3K-Akt that can be effectively targeted to slow down aging and extend lifespan.…”
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RECONSTRUCTION OF AMINO ACID SEQUENCES OF CYCLIC PEPTIDES FROM THEIR MASS SPECTRA by E. S. Fomin

“…Mass spectrometry is a physical method, which can be applied to the investigation of proteomes of different organisms. It allows us both to solve the problem of identification of biological macromolecules and to sequence peptide chains in cases where information on the genomes is scarce or absent. …”
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Single-Cell Sequencing in Cancer: Recent Applications to Immunogenomics and Multi-omics Tools by Michael C. Sierant, Jungmin Choi

“…The application of single-cell sequencing, in concert with existing genomics methods, has enabled high-resolution interrogation of the genome, transcriptome, epigenome, and proteome. Applied to cancers, these single-cell multi-omics methods bypass previous limitations on data resolution and have enabled a more nuanced understanding of the evolutionary dynamics of tumor progression, immune evasion, metastasis, and treatment resistance. …”
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Sodium butyrate is incorporated into central metabolism in fly head while inducing oxygen consumption increase. by Annika Müller-Eigner, Benedikt Gille, Frederik Dethloff, Chen Meng, Christina Ludwig, John T Heiker, Patrick Giavalisco, Shahaf Peleg

“…Here we show that while head oxygen consumption is increased by the addition of butyrate, no apparent changes are observed on the proteome and acetylome. Instead, we show that butyrate is metabolized and incorporated into the tricarboxylic acid (TCA) cycle. …”
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The mitochondrial genome of Carex pseudochinensis H. Lév. & Vaniot, an endemic sedge in Korea by Jieun Lee, Sang Chul Choi, Sangtae Kim

“…Phylogenetic analysis based on mitochondrial proteomes, including those from ten species of related taxa, confirmed a close phylogenetic relationship between C. breviculmis and C. pseudochinensis.…”
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Alu Mobile Elements: From Junk DNA to Genomic Gems by Sami Dridi

“…Alu RNAs embedded in Pol II transcripts can promote evolution and proteome diversity, which further indicates that these mobile retroelements are in fact genomic gems rather than genomic junks.…”
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Alcohol intake exacerbates experimental autoimmune prostatitis through activating PI3K/AKT/mTOR pathway-mediated Th1 differentiation by Shun Xu, Shun Xu, Shun Xu, Jing Chen, Jing Chen, Jing Chen, Shaoyu Yue, Shaoyu Yue, Shaoyu Yue, Yifan Zhang, Yifan Zhang, Yifan Zhang, Shengyu Zhao, Shengyu Zhao, Shengyu Zhao, Yongtao Hu, Yongtao Hu, Yongtao Hu, Cheng Zhang, Cheng Zhang, Cheng Zhang, Wenrui Guan, Wenrui Guan, Wenrui Guan, Li Zhang, Li Zhang, Li Zhang, Ligang Zhang, Ligang Zhang, Ligang Zhang, Chaozhao Liang, Chaozhao Liang, Chaozhao Liang

“…Proteomic and KEGG pathway analyses showed that abnormal Th1 differentiation and PI3K/AKT/mTOR pathway were significantly enriched. …”
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Karyopherin Alpha 2-Expressing Pancreatic Duct Glands and Intra-Islet Ducts in Aged Diabetic C414A-Mutant-CRY1 Transgenic Mice by Satoshi Okano, Akira Yasui, Shin-ichiro Kanno, Kennichi Satoh, Masahiko Igarashi, Osamu Nakajima

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Cervical mucus in linked human Cervix and Vagina Chips modulates vaginal dysbiosis by Ola Gutzeit, Aakanksha Gulati, Zohreh Izadifar, Anna Stejskalova, Hassan Rhbiny, Justin Cotton, Bogdan Budnik, Sanjid Shahriar, Girija Goyal, Abidemi Junaid, Donald E. Ingber

“…By integrating human Cervix and Vagina Chips, we demonstrated that cervical mucus significantly reduces inflammation and epithelial damage caused by a dysbiotic microbiome commonly associated with BV. Proteomic analysis of the Vagina Chip, following exposure to mucus from the Cervix Chip, revealed differentially abundant proteins, suggesting potential biomarkers and therapeutic targets for BV management. …”
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Helicobacter pylori: Genomic Insight into the Host-Pathogen Interaction by Kathryn P. Haley, Jennifer A. Gaddy

“…Infectious disease research in particular has experienced an explosion of bacterial genomic, transcriptomic, and proteomic data complementing the phenotypic methods employed in traditional bacteriology. …”
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Alternative Splicing and Its Impact as a Cancer Diagnostic Marker by Yun-Ji Kim, Heui-Soo Kim

“…Genome instability and flexible proteomes by alternative splicing could affect cancer cells to grow and survive, leading to metastasis. …”
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State of the interactomes: an evaluation of molecular networks for generating biological insights by Sarah N Wright, Scott Colton, Leah V Schaffer, Rudolf T Pillich, Christopher Churas, Dexter Pratt, Trey Ideker

“…Abstract Advancements in genomic and proteomic technologies have powered the creation of large gene and protein networks (“interactomes”) for understanding biological systems. …”
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Why cutting respiratory CO2 loss from crops is possible, practicable, and prudential by Jaya Joshi, Jeffrey S. Amthor, Donald R. McCarty, Carlos D. Messina, Mark A. Wilson, A. Harvey Millar, Andrew D. Hanson

“…Conceptual and technical advances, particularly in protein turnover and directed enzyme evolution, have now opened ways to trim the large fraction of respiration that fuels proteome maintenance by lowering the breakdown and resynthesis rates of enzymes and other proteins. …”
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NEAT1 regulates BMSCs aging through disruption of FGF2 nuclear transport by Zifei Wang, Wenyu Zhen, Qing Wang, Yuqiang Sun, Siyu Jin, Sensen Yu, Xing Wu, Wenhao Zhang, Yulong Zhang, Fei Xu, Rui Wang, Yuxuan Xie, Wansu Sun, Jianguang Xu, Hengguo Zhang

“…Subsequent RNA pulldown and proteomic analyses, along with single-cell analysis, immunofluorescence, RNA immunoprecipitation (RIP), and co-immunoprecipitation (Co-IP), were conducted to investigate that NEAT1 impairs the nuclear transport of mitotic FGF2 and contributes to BMSCs aging. …”
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Chromosome-level genome assembly of Monolepta hieroglyphica, two-spotted leaf beetle (Coleoptera: Chrysomelidae) by Hao He, Yongxin Zhao, Dengyu Zheng, Huiyun Kuang, Fei Shen, Kang He, Haiyan Zhang, Changjiang Zhao, Lu Jiang, Da Xiao, Su Wang, Zhenying Wang, Shuai Zhan, Jianhua Wei, Xiaozeng Yang, Zhongyi Wu, Chun Zhang

“…The completeness of the final reported genome and proteome were assessed by BUSCO and show high values of 99.4% and 95.2%, respectively. …”
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Two-Component Signal Transduction System SaeRS Positively Regulates Staphylococcus epidermidis Glucose Metabolism by Qiang Lou, Yijun Qi, Yuanfang Ma, Di Qu

“…In this study, we performed a proteomic analysis of differences in expression between the S. epidermidis 1457 wild-type and saeRS mutant to identify candidates regulated by saeRS using two-dimensional gel electrophoresis (2-DE) combined with matrix-assisted laser desorption/lonization mass spectrometry (MALDI-TOF-MS). …”
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Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink by Lejla Gul, Anna Julia Elias, Tanvi Tambaku, Marton Olbei, Emily Watters, Balazs Bohar, Dezso Modos, Matthew Madgwick, Tamas Korcsmaros

“…We describe steps for setting up the environment, installing software, and preparing human transcriptomic and bacterial proteomic data. The protocol outlines procedures for predicting protein-protein interactions through domain-motif interactions, integrating multi-omic datasets to map downstream effects, performing network analyses to identify key regulatory pathways, and visualizing multi-layered networks for systems-level data interpretation.For complete details on the use and execution of this protocol, please refer to Gul et al.1 and Poletti et al.2 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.…”
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The Problem of Abnormal Body Weight and Dyslipidemia as Risk Factors for Cardiovascular Diseases in Children and Adolescents with Type 1 Diabetes by Katarzyna Noras, Ewa Rusak, Przemysława Jarosz-Chobot

“…Recently, a new look at the vasoprotective effect of HDL has appeared, which due to its dysfunctional form in type 1 diabetes may not protect against cardiovascular risk. The HDL proteome in type 1 diabetes has an altered protein composition compared to the healthy population. …”
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Amyloids in bladder cancer hijack cancer-related proteins and are positive correlated to tumor stage by Diego Alem, César X. García-Laviña, Francisco Garagorry, Dardo Centurión, Joaquina Farias, Hany Pazos-Espinosa, María Noel Cuitiño-Mendiberry, Carolina Villadóniga, Susana Castro-Sowinski, Martín Fló, Federico Carrión, Brenda Iglesias, Kevin Madauss, Lucía Canclini

“…Subsequently, the amyloid proteome of the RT4 non-invasive and HT1197 invasive bladder cancer cell lines was identified and included oncogenes, tumor suppressors, and highly expressed cancer-related proteins. …”
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