Article
Multidisciplinary Sciences
Kenneth C. Smith, Daniel G. Chawla, Bhavjinder K. Dhillon, Zhou Ji, Randi Vita, Eva C. van der Leest, Jing Yi Jessica Weng, Ernest Tang, Amani Abid, Bjoern Peters, Robert E. W. Hancock, Aris Floratos, Steven H. Kleinstein
Summary: Advancements in high-throughput experiments and systems biology approaches have led to the identification of immune signatures. However, these signatures are often presented in a format that is not suitable for computational processing, hindering our ability to fully utilize this information. In this study, a data model and a web-enabled application were developed to facilitate the access and querying of immune signatures.
Article
Multidisciplinary Sciences
James C. Pino, Alexander L. R. Lubbock, Leonard A. Harris, Danielle B. Gutierrez, Melissa A. Farrow, Nicole Muszynski, Tina Tsui, Stacy D. Sherrod, Jeremy L. Norris, John A. McLean, Richard M. Caprioli, John P. Wikswo, Carlos F. Lopez
Summary: This study demonstrates the use of multi-omics integration to explore the cellular response to bendamustine in HL-60 cells, providing detailed insights into the progression of DNA damage and programmed cell death at molecular, pathway, and process-level resolutions.
Article
Biochemical Research Methods
Gwanghoon Jang, Sungjoon Park, Sanghoon Lee, Sunkyu Kim, Sejeong Park, Jaewoo Kang
Summary: MoAble is a model that can predict the mechanism of actions of drugs without requiring compound signatures. It trains a deep learning-based coembedding model to map compound signatures and structures, and then uses pathway enrichment analysis to predict MoAs. The results show that MoAble is comparable to methods with actual compound signatures in predicting MoAs of novel compounds.
Article
Biochemistry & Molecular Biology
Diego Viasus, Antonella E. F. Simonetti, Lara Nonell, Oscar Vidal, Yolanda Meije, Lucia Ortega, Magdalena Arnal, Marta Bodalo-Torruella, Montserrat Sierra, Alexander Rombauts, Gabriela Abelenda-Alonso, Gemma Blanchart, Carlota Gudiol, Jordi Carratala
Summary: We examined the differences in gene expression profiles in patients with community-acquired pneumonia (CAP) who died during hospitalization and those who survived. Whole blood samples were obtained for genome-expression-profile analysis within 24 hours of admission. The study found significant differences in gene expression at hospital admission between patients who died and those who survived. These findings could help identify potential intervention targets and biomarkers for risk stratification.
Article
Biochemical Research Methods
Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity Law, Sean Davis, Vincent Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Summary: Researchers developed a framework for assessing enrichment methods based on defined criteria, evaluated 10 major enrichment methods using a curated compendium of expression datasets, and provided practical recommendations for efficient interpretation of results when applying these methods.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Diego Viasus, Lara Nonell, Carlos Restrepo, Fabian Figueroa, Carla Donado-Mazarron, Jordi Carratala
Summary: This study summarizes the reported differentially expressed genes (DEGs) in critically ill septic patients with community-acquired pneumonia (CAP) and investigates their functional implications. The results highlight the complexity of immune responses during CAP.
Review
Plant Sciences
Hans-Joerg Mai, Dibin Baby, Petra Bauer
Summary: Cellular homeostasis of iron in plants is tightly regulated by various factors. However, the existing Gene Ontology (GO) terms for iron homeostasis lack consistency and completeness, and do not accurately reflect the known biological functions associated with iron homeostasis. To address this issue, the authors suggest using applicable evidence codes to add missing genes and improve the reliability of iron homeostasis-related GO terms. They also compiled comprehensive gene lists for iron homeostasis research in A. thaliana, which can be used for custom enrichment analysis in transcriptomic or proteomic studies.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Taku Monjo, Masaru Koido, Satoi Nagasawa, Yutaka Suzuki, Yoichiro Kamatani
Summary: Spatial transcriptomics can enhance histological interpretations by predicting gene expression patterns in unmeasured regions and tissues. Researchers developed a deep learning model called DeepSpaCE, which accurately predicts gene expression using spatial transcriptome data and immunohistochemistry images. They also developed a semi-supervised version of DeepSpaCE, which improves imputation accuracy using unlabeled histology images.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Luhong Wang, Yinan Ding, Chuanyong Zhang, Rong Chen
Summary: This study reveals the molecular link between COVID-19 and HCC and proposes potential drugs for HCC patients with COVID-19, providing clinicians with novel therapeutic ideas.
Article
Biochemistry & Molecular Biology
Zongliang Yue, Eric Zhang, Clark Xu, Sunny Khurana, Nishant Batra, Son Do Hai Deng, James J. Cimino, Jake Y. Chen
Summary: PAGER-CoV is a new web-based database that assists biomedical researchers in interpreting coronavirus-related functional genomic study results using a vast collection of PAGs. By exploring relationships between PAGs, users can gain deeper insights into the research information. This database can help researchers find molecular biology mechanisms and tailored therapeutics for treating COVID-19 patients.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Wanshan Ning, Yuxiang Wei, Letian Gao, Cheng Han, Yujie Gou, Shanshan Fu, Dan Liu, Chi Zhang, Xinhe Huang, Sicheng Wu, Di Peng, Chenwei Wang, Yu Xue
Summary: This article introduces the features and advantages of Heml 2.0 software, which can be used for visualization of biomolecular expression data and enrichment analysis. Heml 2.0 offers various clustering methods and distance metrics, and provides multiple export and visualization options, offering users convenient and comprehensive analysis tools.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Nicolas Derian, Hang-Phuong Pham, Djamel Nehar-Belaid, Nicolas Tchitchek, David J. Klatzmann, Vicaut J. Eric, Adrien J. Six
Summary: This study reinvestigated diversity measures commonly used in ecology and evaluated the potential of the Tsallis entropy function to characterize mouse pregnancy microenvironments. The results demonstrate that the Tsallis entropy function provides additional information compared to traditional diversity indices and allows evaluation of the impact of biological stimulus on inter-individual variability. Additionally, a strategy for reducing the complexity of transcriptome datasets using maximization of beta diversity is proposed.
Article
Biochemical Research Methods
Alexander Lachmann, Zhuorui Xie, Avi Ma'ayan
Summary: This paper introduces an algorithm called blitzGSEA, which significantly improves gene set enrichment analysis. Compared to previous methods, blitzGSEA allows for faster calculations and more accurate estimation of small P-values.
Article
Plant Sciences
Jing-xuan Wang, Bo Wang, Lu-bin Cui, Hao Xie, Run-zhi Li, Cheng Wang, Zhang-jie Nan, Yu-shu Liu, Jing-yu Ma, Yun-jin Sun, Wei-yu Li
Summary: This study identified key genes involved in aluminum resistance in soybeans, which are crucial for functions such as cell junction and phenylpropanoid biosynthesis, providing important information for breeding aluminum-resistant varieties.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2021)
Article
Biochemical Research Methods
Chen-An Tsai, James J. Chen
Summary: This study introduces a new gene set analysis framework, GSCoA, which identifies differentially expressed gene sets and highly correlated pathways by simultaneously measuring within and between gene set variation. Co-inertia analysis is applied to compare gene sets in gene expression data and measure the co-structure of expression profiles. Results demonstrate that combining co-inertia analysis and gene set enrichment analysis effectively reveals relationships between gene sets significantly associated with phenotypes.
CURRENT BIOINFORMATICS
(2021)
Article
Food Science & Technology
Martina Colapietro, Andrea Ianni, Francesca Bennato, Giuseppe Martino
Summary: This study investigated the effects of three different light-color temperatures of LEDs (Neutral, Cool, and Warm) on the attributes of chicken breast meat. The results showed that the LEDs caused changes in the physical and chemical characteristics of the meat. Specifically, significant variations were observed in the fatty acid profiles and accumulation of volatile compounds in the meat. These findings highlight the potential impact of LED lighting on the quality of chicken breast meat.
Article
Agriculture, Dairy & Animal Science
Andrea Ianni, Francesca Bennato, Camillo Martino, Alessio Di Luca, Giuseppe Martino
Summary: This study aimed to characterize the qualitative aspects of Teramana goat meat, an indigenous breed from Abruzzo, Italy. The results showed differences in color, fatty acid profile, and antioxidant properties compared to the local breed. The findings highlight the potential value of Teramana goat meat.
Article
Food Science & Technology
Andrea Ianni, Francesca Bennato, Camillo Martino, Maurizio Odoardi, Agostino Sacchetti, Giuseppe Martino
Summary: This study characterized the qualitative properties of commercial meat obtained from the Nero d'Abruzzo pig breed. The results showed that the Nero d'Abruzzo meat had higher fat content, higher concentration of alpha-linolenic acid, and higher Coenzyme Q10 content compared to meat from hybrid pigs. The Nero d'Abruzzo meat also exhibited better oxidative stability and reduced accumulation of hexanal.
Article
Food Science & Technology
Francesca Bennato, Andrea Ianni, Lisa Grotta, Giuseppe Martino
Summary: This study investigated the effects of red grape pomace dietary supplementation on the chemical quality of whey and Ricotta obtained from ewes. The results showed that the supplementation did not affect the lipid content of whey and Ricotta, but significant variations were observed in color. The fatty acid profile of whey and Ricotta was modified, while the protein profile of whey protein remained unchanged. Overall, the inclusion of red grape pomace in the ewes' diet did not have negative effects on the characteristics and quality of dairy by-products.
FOOD SCIENCE OF ANIMAL RESOURCES
(2022)
Article
Agriculture, Dairy & Animal Science
Andrea Ianni, Francesca Bennato, Veronica Di Gianvittorio, Marco Di Domenico, Camillo Martino, Martina Colapietro, Cesare Camma, Giuseppe Martino
Summary: This study characterized the fecal microbiota of broiler chickens reared under different shades of LED lights and correlated it with biochemical and molecular evidence. The findings suggest a potential positive effect of neutral LED lighting on animal welfare.
Article
Food Science & Technology
Francesca Bennato, Andrea Ianni, Marco Florio, Lisa Grotta, Francesco Pomilio, Maria Antonietta Saletti, Giuseppe Martino
Summary: The present study evaluated the effects of grape pomace on milk yield, chemical-nutritional characteristics, antioxidant activity, fatty acids, and protein profile of dairy ewe's milk. The results showed that adding 10% grape pomace did not affect milk yield and composition, but significantly changed the fatty acid composition.
Article
Agronomy
Marco Florio, Claudia Giannone, Andrea Ianni, Francesca Bennato, Lisa Grotta, Giuseppe Martino
Summary: This study aimed to investigate the variations in cow milk composition based on different breeding systems and seasonal changes. The results showed that milk samples from outdoor grazing had lower concentrations of saturated fatty acids and higher concentrations of rumenic, vaccenic, and oleic acids, as well as a greater presence of specific caseins. In contrast, intensive farming showed the opposite results. The concentration of retinol significantly increased during summer in both breeding systems.
Article
Biochemical Research Methods
Giorgio Saluti, Matteo Ricci, Federica Castellani, Maria Novella Colagrande, Gabriella Di Bari, Michele Podaliri Vulpiani, Francesco Cerasoli, Giovanni Savini, Giampiero Scortichini, Nicola D'Alterio
Summary: Comparing the hair cortisol concentrations (HCC) of 47 horses under different managements, this study found that liquid chromatography coupled to hybrid high-resolution mass spectrometry (LC-HRMS/MS) provided more accurate results compared to the enzyme-linked immunosorbent assay (ELISA), which may overestimate the HCC. This finding is of significance in the development of accurate and reliable methods for monitoring stress in animals.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Agriculture, Dairy & Animal Science
Marco Florio, Costanza Cimini, Andrea Ianni, Francesca Bennato, Lisa Grotta, Luca Valbonetti, Giuseppe Martino
Summary: In this study, milk and cheese from the native Teramana goat breed were analysed and compared with those from the intensive Saanen breed. The Teramana breed showed higher levels of certain fatty acids, especially linoleic acid, in its milk and cheese. The Teramana cheeses also exhibited better oxidative stability during ripening due to lower levels of ketones and esters and higher levels of carboxylic acids. These findings highlight the importance of preserving and promoting native goat breeds.
Article
Agriculture, Dairy & Animal Science
Alessio Di Luca, Andrea Ianni, Francesca Bennato, Camillo Martino, Michael Henry, Paula Meleady, Giuseppe Martino
Summary: This study compared the proteomic differences between Nero d'Abruzzo and commercial-hybrid pigs, revealing significant differences in the protein expression of a large pool of proteins. Certain proteins, such as fatty acid synthase, catalase, and glutathione peroxidase, were found to be differentially expressed and may contribute to the phenotypic differences between the pigs. This work has identified potential proteins that could be useful for new applications in pig breeding programs.
Article
Biochemistry & Molecular Biology
Francesca Bennato, Andrea Ianni, Eleonora Oliva, Nicola Franceschini, Lisa Grotta, Manuel Sergi, Giuseppe Martino
Summary: The aim of this study was to evaluate the effect of grape pomace (GP) in the diet of dairy ewes on the content of phenolic compounds (PCs) in milk and its anti-inflammatory and antioxidative status. The results showed that the use of GP increased the concentration of phenolic compounds in milk, but had minimal impact on its antioxidant and inflammatory status.
Article
Food Science & Technology
Francesca Bennato, Camillo Martino, Andrea Ianni, Claudia Giannone, Giuseppe Martino
Summary: The study aimed to evaluate the effects of grape pomace supplementation on lambs' diets. The results showed that the supplementation improved the fatty acid composition and oxidative stability of lamb meat. Therefore, using grape pomace as a research focus in animal nutrition can enhance the quality of animal products.
Article
Agriculture, Dairy & Animal Science
Alessio Di Luca, Francesca Bennato, Andrea Ianni, Lisa Grotta, Michael Henry, Paula Meleady, Giuseppe Martino
Summary: In this study, proteomic technologies were used to compare the milk proteome of two goat breeds, Teramana and Saanen. The analysis identified 29 proteins that could discriminate between the two breeds. This research contributes to our understanding of the goat milk proteome and provides important information for future studies on goat milk proteins.
Article
Biotechnology & Applied Microbiology
Francesca Bennato, Marco Di Domenico, Andrea Ianni, Luigina Di Gialleonardo, Cesare Camma, Giuseppe Martino
Summary: The objective of this research was to evaluate the development of volatile organic compounds (VOCs) and the accumulation of biogenic amines (BAs) in cheese and their relationship with microbial population composition. The results showed that diet had an impact on the microbial composition and compound levels in the cheese, and there were significant positive correlations between certain bacterial families and compound formation.
FERMENTATION-BASEL
(2022)
Article
Veterinary Sciences
Francesca Bennato, Camillo Martino, Marco Di Domenico, Andrea Ianni, Benli Chai, Lisa Di Marcantonio, Cesare Camma, Giuseppe Martino
Summary: The aim of this study was to examine the effects of feeding olive leaves on the rumen microbiota and volatile organic compounds (VOCs) in Saanen goat kids. The results showed that feeding olive leaves influenced the microbial community in the rumen, increasing the abundance of cellulolytic bacteria. In addition, the analysis of VOCs in the rumen highlighted differences related to the diet and the presence of compounds indicative of health status.
VETERINARY SCIENCES
(2022)