Deoxycholic Acid-Mediated Sphingosine-1-Phosphate Receptor 2 Signaling Exacerbates DSS-Induced Colitis through Promoting Cathepsin B Release by Shengnan Zhao, Zizhen Gong, Xixi Du, Chunyan Tian, Lingyu Wang, Jiefei Zhou, Congfeng Xu, Yingwei Chen, Wei Cai, Jin Wu

Get full text

Diagnosis of Parasitic Diseases: Old and New Approaches by Momar Ndao

“…These include immunoassays, molecular-based approaches, and proteomics using mass spectrometry platforms technology. …”
Get full text

Investigating the role of intratumoral Streptococcus mitis in gastric cancer progression: insights into tumor microenvironment by Ping Yang, Gaoli Liang, Yangyue Ni, Xiaojie Chu, Xiaoshan Zhang, Zhongyu Wang, Adeel Khan, Fangfang Jin, Han Shen, Miao Li, Zhipeng Xu

“…Here, using 16 S rRNA sequencing, tumor tissue proteomics and serum cytokines analysis, we identified enrichment of specific microbial communities within tumors of gastric cancer patients, possibly affecting the tumor microenvironment by immune modulation, metabolic processes, and inflammatory responses. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

Advances in multi-omics integrated analysis methods based on the gut microbiome and their applications by Dongdong Duan, Mingyu Wang, Jinyi Han, Mengyu Li, Zhenyu Wang, Shenping Zhou, Wenshui Xin, Xinjian Li, Xinjian Li

“…With the emergence of new technologies including next-generation sequencing (NGS) and advanced techniques such as microbial community sequencing, people have begun to explore the interaction mechanisms between microorganisms and hosts at various omics levels such as genomics, transcriptomics, metabolomics, and proteomics. With the enrichment of multi-omics integrated analysis methods based on the microbiome, an increasing number of complex statistical analysis methods have also been proposed. …”
Get full text

Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq by Shintaro Funasaki, Yuri Miyamura, Shunsuke Kamei, Akhinur Rahman, Masaya Yamazaki, Shingo Usuki, Keiichiro Yasunaga, Yorifumi Satou, Hiroto Ohguchi, Takashi Minami

“…This scalable protocol is also applicable to diverse omics studies, including proteomics and metabolomics.For complete details on the use and execution of this protocol, please refer to Miyamura et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.…”
Get full text

APOE Christchurch enhances a disease-associated microglial response to plaque but suppresses response to tau pathology by Kristine M. Tran, Nellie E. Kwang, Claire A. Butler, Angela Gomez-Arboledas, Shimako Kawauchi, Cassandra Mar, Donna Chao, Rocio A. Barahona, Celia Da Cunha, Kate I. Tsourmas, Zechuan Shi, Shuling Wang, Sherilyn Collins, Amber Walker, Kai-Xuan Shi, Joshua A. Alcantara, Jonathan Neumann, Duc M. Duong, Nicholas T. Seyfried, Andrea J. Tenner, Frank M. LaFerla, Lindsay A. Hohsfield, Vivek Swarup, Grant R. MacGregor, Kim N. Green

“…We used immunohistochemical and biochemical analysis along with single-cell spatial omics and bulk proteomics to explore the impact of the ApoeCh variant on AD pathological development and the brain’s response to plaques and tau. …”
Get full text

Trojan-horse silk fibroin nanocarriers loaded with a re-call antigen to redirect immunity against cancer by Luca Mastracci, Patrizio Castagnola, Elia Bari, Francesca Ferrera, Tiziana Altosole, Sara Perteghella, Pierluigi Mauri, Rossana Rossi, Giulia Passignani, Martina Galati, Giuseppina Iliana Astone, Maddalena Mastrogiacomo, Daniela Fenoglio, Dario Di Silvestre, Maria Luisa Torre, Gilberto Filaci

“…Cancer dimensions/survival time were monitored, while, at the molecular level, system biology approaches based on graph theory and experimental proteomic data were performed.Results SFNs were efficiently in vitro uptaken by cancer and dendritic cells. …”
Get full text

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. …”
Get full text

Culturing of Giardia lamblia under microaerobic conditions can impact metronidazole susceptibility by inducing increased expression of antioxidant enzymes by Kateryna Starynets, Ana Paunkov, Anja Wagner, Klaus Kratochwill, Christian Klotz, David Leitsch

Get full text

USP14 is crucial for proteostasis regulation and α-synuclein degradation in human SH-SY5Y dopaminergic cells by Vignesh Srinivasan, Rabah Soliymani, Larisa Ivanova, Ove Eriksson, Nina Peitsaro, Maciej Lalowski, Mati Karelson, Dan Lindholm

Get full text

Genetic context modulates aging and degeneration in the murine retina by Olivia J. Marola, Michael MacLean, Travis L. Cossette, Cory A. Diemler, Amanda A. Hewes, Alaina M. Reagan, Jonathan Nyandu Kanyinda, Daniel A. Skelly, Gareth R. Howell

“…Methods Transcriptomics and proteomics were employed to elucidate retinal aging signatures in nine genetically diverse mouse strains (C57BL/6J, 129S1/SvlmJ, NZO/HlLtJ, WSB/EiJ, CAST/EiJ, PWK/PhK, NOD/ShiLtJ, A/J, and BALB/cJ) across lifespan. …”
Get full text

Gut bacterium Intestinimonas butyriciproducens improves host metabolic health: evidence from cohort and animal intervention studies by Elena Rampanelli, Nadia Romp, Antonio Dario Troise, Jakshana Ananthasabesan, Hao Wu, Ismail Sahin Gül, Sabrina De Pascale, Andrea Scaloni, Fredrik Bäckhed, Vincenzo Fogliano, Max Nieuwdorp, Thi Phuong Nam Bui

Get full text

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). …”
Get full text

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.…”
Get full text

Role of New Biomarkers: Functional and Structural Damage by Evdoxia Tsigou, Vasiliki Psallida, Christos Demponeras, Eleni Boutzouka, George Baltopoulos

“…Innovative technologies such as genomics and proteomics have contributed to the discovery of new biomarkers, such as neutrophil gelatinase-associated lipocalin (NGAL), cystatin C (Cys C), kidney injury molecule-1 (KIM-1), interleukin-18 (IL-18), and liver-type fatty acid binding protein (L-FABP). …”
Get full text

Characterization of extracellular vesicles by capillary zone electrophoresis: A novel concept for characterization of a next-generation drug delivery platform by Aleksandra Steć, Andrea Heinz, Szymon Dziomba

“…According to current recommendations, quantification of EVs, confirmation of their identity, and purity assessment require the use of several analytical techniques, including particle-size distribution analysis, proteomics, and electron microscopy, making the characterization process demanding. …”
Get full text