Fungal genomes: suffering with functional annotation errors by Tapan Kumar Mohanta, Ahmed Al-Harrasi

“…Results An analysis of proteome sequence data of 689 fungal species (7.15 million protein sequences) was conducted to identify the presence of functional annotation errors. …”
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Wavenumber-dependent transmission of subthreshold waves on electrical synapses network model of Caenorhabditis elegans by Iksoo Chang, Taegon Chung, Sangyeol Kim

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Proteogenomic Analysis Reveals Proteins Involved in the First Step of Adipogenesis in Human Adipose-Derived Stem Cells by Bernardo Bonilauri, Amanda C. Camillo-Andrade, Marlon D. M. Santos, Juliana de S. da G. Fischer, Paulo C. Carvalho, Bruno Dallagiovanna

“…Cells were cultured for 24 hours in adipogenic differentiation medium followed by protein extraction. We used shotgun proteomics to compare the proteomic profile of 24 h-adipogenic, differentiated, and undifferentiated hASC. …”
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Formation mechanisms of ethyl acetate and organic acids in Kluyveromyces marxianus L1-1 in Chinese acid rice soup by Na Liu, Likang Qin, Laili Hu, Song Miao

“…This study aims to explore the formation mechanism of ethyl acetate and organic acids in acid rice soup (rice-acid soup) inoculated with Kluyveromyces marxianus L1-1 through the complementary analysis of transcriptome and proteome. The quantity of K. marxianus L1-1 varied significantly in the fermentation process of rice-acid soup and the first and third days were the two key turning points in the growth phase of K. marxianus L1-1. …”
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The effect of triple CFTR modulator therapy and azithromycin on ion channels and inflammation in cystic fibrosis by Suhad Bani Melhim, Lisa E.J. Douglas, James A. Reihill, Damian G. Downey, S. Lorraine Martin

“…AZ reduced IL-8 in NuLi-1 but not CuFi-1 cells. The Proteome Profiler™ screen identified several disease-relevant cytokines that were modulated by treatment. …”
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iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control by Huanhuan Gao, Yi Zhu, Dongxue Wang, Zongxiang Nie, He Wang, Guibin Wang, Shuang Liang, Yuting Xie, Yingying Sun, Wenhao Jiang, Zhen Dong, Liqin Qian, Xufei Wang, Mengdi Liang, Min Chen, Houqi Fang, Qiufang Zeng, Jiao Tian, Zeyu Sun, Juan Xue, Shan Li, Chen Chen, Xiang Liu, Xiaolei Lyu, Zhenchang Guo, Yingzi Qi, Ruoyu Wu, Xiaoxian Du, Tingde Tong, Fengchun Kong, Liming Han, Minghui Wang, Yang Zhao, Xinhua Dai, Fuchu He, Tiannan Guo

“…Abstract Quality control (QC) in mass spectrometry (MS)-based proteomics is mainly based on data-dependent acquisition (DDA) analysis of standard samples. …”
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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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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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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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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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Hepatic macrophages in liver fibrosis: pathogenesis and potential therapeutic targets by Hai Li, Hong You, Jidong Jia, Xu Fan

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RNA structure in alternative splicing regulation: from mechanism to therapy by Bao Nengcheng, Wang Zhechao, Fu Jiayan, Dong Haiyang, Jin Yongfeng

“…Alternative splicing is a highly intricate process that plays a crucial role in post-transcriptional regulation and significantly expands the functional proteome of a limited number of coding genes in eukaryotes. …”
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Deep phosphoproteomics of Klebsiella pneumoniae reveals HipA-mediated tolerance to ciprofloxacin. by Payal Nashier, Isabell Samp, Marvin Adler, Fiona Ebner, Lisa Thai Lê, Marc Göppel, Carsten Jers, Ivan Mijakovic, Sandra Schwarz, Boris Macek

“…Importantly, HipAkp overproduction leads to increased tolerance against ciprofloxacin, a commonly used antibiotic in the treatment of K. pneumoniae infections. Proteome and phosphoproteome analyses in the absence and presence of ciprofloxacin confirm that HipAkp has Ser/Thr kinase activity, auto-phosphorylates at S150, and shares multiple substrates with HipAec, thereby providing a valuable resource to clarify the molecular basis of tolerance and the role of Ser/Thr phosphorylation in this human pathogen.…”
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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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Activators of the 26S proteasome when protein degradation increases by Donghoon Lee

“…Abstract In response to extra- and intracellular stimuli that constantly challenge and disturb the proteome, cells rapidly change their proteolytic capacity to maintain proteostasis. …”
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Assessment of Salivary Adipokines Resistin, Visfatin, and Ghrelin as Type 2 Diabetes Mellitus Biomarkers by Mythily Srinivasan, Melinda L. Meadows, Lisa Maxwell

“…Human saliva is an easily accessible biospecimen amenable for painless frequent collection and possesses nearly 50% of serum proteome. In this study, we measured the adipokines resistin, visfatin, TNF-α, and ghrelin as markers for T2DM in unstimulated whole saliva (UWS) using specific assay kits. …”
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Phytochemical Evaluation of Moth Bean (Vigna aconitifolia L.) Seeds and Their Divergence by Neha Gupta, Nidhi Shrivastava, Pramod Kumar Singh, Sameer S. Bhagyawant

“…Over 20 individual protein fractions were distributed over the gel as a series of spots in two moth bean accessions. Seed proteome accumulated spots of high intensity over a broad range of pI values of 3–10 in a molecular weight range of 11–170 kDa. …”
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Physicochemical properties and cytochromes P-450 kinetics of the trifluoroacetamido derivative of phenacetin by Hannah L. Cure, Thomas A. Shell

“…Phenacetin and TFA-phenacetin have the same apparent binding affinity for the SD rat liver microsome CYP proteome and undergo CYP catalyzed oxidation at the same rate in the presence of SD rat liver microsomes.…”
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The protein composition of human adenovirus replication compartments by Paloma Hidalgo, Amada Torres, Pierre M. Jean Beltran, Gamaliel López-Leal, Luca D. Bertzbach, Thomas Dobner, S. J. Flint, Ileana M. Cristea, Ramón A. González

“…These findings represent the first analysis of the proteomes of isolated RCs and not only enhance our understanding of nuclear organization during infection but also shed light on the complex interplay between viral and host factors within RCs.…”
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The RNA-dependent association of phosphatidylinositol 4,5-bisphosphate with intrinsically disordered proteins contribute to nuclear compartmentalization. by Martin Sztacho, Jakub Červenka, Barbora Šalovská, Ludovica Antiga, Peter Hoboth, Pavel Hozák

“…In this study, we unveiled the RNA-dependent PIP2-associated (RDPA) nuclear proteome in human cells by mass spectrometry. We found that intrinsically disordered regions (IDRs) with polybasic PIP2-binding K/R motifs are prevalent features of RDPA proteins. …”
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