Review
Biology
Janani Manochkumar, Aswani Kumar Cherukuri, Raju Suresh Kumar, Abdulrahman I. Almansour, Siva Ramamoorthy, Thomas Efferth
Summary: This review provides a comprehensive overview of the -omics and multi-omics approaches used for characterizing marine metabolites, along with the need for data integration and machine learning algorithms. It also discusses the challenges and recommendations for conducting multi-omics studies.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Gastroenterology & Hepatology
Soo Young Cho, Heeyoun Hwang, Yun-Hee Kim, Byong Chul Yoo, Nayoung Han, Sun-Young Kong, Min-Jeong Baek, Kyung-Hee Kim, Mi Rim Lee, Jae Gwang Park, Sung-Sik Han, Woo Jin Lee, Charny Park, Jong Bae Park, Jin Young Kim, Sang-Jae Park, Sang Myung Woo
Summary: Through comprehensive analysis of genomic, transcriptomic, proteomic, and phosphoproteomic data from 102 iCC patients, three clinically supported subtypes were identified (stem-like, poorly immunogenic, and metabolism), and an organoid model was constructed for therapeutic testing. The ALDH1A1 inhibitor NCT-501 showed synergy with nanoparticle albumin-bound-paclitaxel in the organoid model for the stem-like subtype. Dysregulations in oncometabolites were associated with different clinical outcomes in the stem-like and metabolism subtypes. The poorly immunogenic subtype exhibited non-T-cell tumor infiltration. Integrated multiomics analysis reproduced the 3 subtypes and revealed heterogeneity in iCC.
Article
Medicine, Research & Experimental
Chang-Zhu Pei, Lan Jin, Kwang-Hyun Baek
Summary: PCOS is a common gynecological endocrine disease involving multiple genes and pathways, and cannot be explained by a single factor. Omics analysis plays a key role in studying the pathogenesis of PCOS, offering new perspectives for explaining new mechanisms and potential biomarkers discovery.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Article
Biochemical Research Methods
Nathaniel Kwok, Zita Aretz, Sumiko Takao, Zheng Ser, Paolo Cifani, Alex Kentsis
Summary: Recent advances in nucleic acid sequencing and mass spectrometry proteomics have enabled genome-scale analysis of genetic variation and transcription as well as whole proteome-scale studies of protein expression. However, most proteomic studies are limited to canonical protein sequences. Here, we develop ProteomeGenerator2 (PG2), which integrates genome and transcriptome sequencing to incorporate protein variants and other non-canonical features caused by genomic and transcriptomic variation. PG2 has been benchmarked using synthetic data and analysis of human leukemia cells and can be used with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms. It is open-source and available at https://github.com/kentsisresearchgroup/ProteomeGenerator2.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Oncology
Zijian Zou, Wei Sun, Yu Xu, Wanlin Liu, Jingqin Zhong, Xinyi Lin, Yong Chen
Summary: Sarcomas are rare mesenchymal neoplasms with unique genetic characteristics, and their diagnosis relies heavily on pathological examination. Advanced treatments and multi-omics approaches have shown promise in improving outcomes and understanding sarcomas, but further research is needed to optimize their clinical application.
FRONTIERS IN ONCOLOGY
(2022)
Article
Chemistry, Medicinal
Sophie Guillotin, Nicolas Delcourt
Summary: Harmful algal blooms (HAB) and the release of toxic metabolites pose a threat to marine organisms and human health. The consequences of toxin exposure on gene expression, protein profile, and metabolic pathways are still not well understood, but recent OMICS-based research has provided important insights. This review provides a comprehensive overview of the latest research and discusses the use of OMICS datasets to identify new features in ecotoxicology, food safety, and human health. Future perspectives in OMICS studies are also explored.
Review
Biotechnology & Applied Microbiology
Alexander Arsov, Kaloyan Petrov, Penka Petrova
Summary: This article discusses the potential of microbial production of butanol as a new fuel and the challenge of butanol toxicity to microbes. Modern omics approaches have made significant progress in addressing the issue of low butanol tolerance, but a strain capable of both synthesis and tolerance at commercializable concentrations has yet to be discovered or produced.
BIOTECHNOLOGY ADVANCES
(2021)
Review
Food Science & Technology
Karolinny Cristiny de Oliveira Vieira, Hevelin Regiane Augusto da Silva, Isabela Poletto Masselli Rocha, Emmanuel Barboza, Lizziane Kretli Winkelstroter Eller
Summary: Outbreaks and deaths related to Foodborne Diseases (FBD) are constantly occurring worldwide, largely due to consumption of contaminated foodstuffs with pathogens. This review discusses the main omic techniques applied in foodborne pathogens and their potential in ensuring food safety. Omics have been shown to integrate variables that contribute to food safety and improve consumer health, costs, and product quality.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Article
Cell Biology
Linyan Chen, Hao Zeng, Yu Xiang, Yeqian Huang, Yuling Luo, Xuelei Ma
Summary: In this study, machine learning models based on histopathological image features successfully predicted genetic aberrations, transcriptional subtypes, and survival outcomes of LUAD patients. The combination of histopathological image features with single omics data improved the prognostic power for LUAD patients.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Cell Biology
Jia-Chen Liu, Shan-Shan Dong, Hui Shen, Dan-Yue Yang, Bin-Bin Chen, Xue-Ying Ma, Yi-Ran Peng, Hong-Mei Xiao, Hong-Wen Deng
Summary: Sarcopenia is a systemic disease characterized by muscle dysfunction, with its genetic architecture and molecular mechanisms still largely unclear. Recent advancements in multi-omics studies offer new insights into the pathogenesis of sarcopenia and may lead to new clinical applications.
AGEING RESEARCH REVIEWS
(2022)
Review
Biochemistry & Molecular Biology
Huan Li, Muhammad Tahir ul Qamar, Li Yang, Junchao Liang, Jun You, Linhai Wang
Summary: Sesame is an important traditional oil crop with high economic and nutritional value. Advances in high throughput sequencing techniques and bioinformatical methods have led to rapid developments in genomics, methylomics, transcriptomics, proteomics, and metabonomics studies of sesame.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Pharmacology & Pharmacy
Mengyuan Kan, Blanca E. Himes
Summary: Glucocorticoid drugs are widely used in the treatment of diseases, but there is still much to learn about their cell type-specific mechanisms and why patients respond differently. Recent studies have used genomics, transcriptomics, and other omics approaches to address these questions, but there are still knowledge gaps to be filled related to glucocorticoid action mechanisms.
PHARMACOLOGY & THERAPEUTICS
(2021)
Review
Plant Sciences
Yamshi Arif, Priyanka Singh, Andrzej Bajguz, Pravej Alam, Shamsul Hayat
Summary: This review discusses the crucial role of silicon in plant development and stress responses, highlighting its interactions with plant hormones and antioxidants, as well as its application in 'omic approaches. Furthermore, it emphasizes the need for further research on the role of silicon during abiotic stress in plants for a better understanding at a broader level.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Review
Plant Sciences
Vikas Mangal, Milan Kumar Lal, Rahul Kumar Tiwari, Muhammad Ahsan Altaf, Salej Sood, Vijay Gahlaut, Ashish Bhatt, Ajay Kumar Thakur, Ravinder Kumar, Vinay Bhardwaj, Vinod Kumar, Brajesh Singh, Rajender Singh, Devendra Kumar
Summary: Abiotic stresses have a negative impact on vegetable crops, but research on crop genomes can help identify stress-responsive genes. Understanding omics approaches and advanced molecular tools is crucial for studying the biology of abiotic stresses.
Review
Biotechnology & Applied Microbiology
Ranjna Sirohi, Jaemin Joun, Hong Ii Choi, Vivek Kumar Gaur, Sang Jun Sim
Summary: This article discusses the potential of microalgae as an energy feedstock and the efforts to increase microalgae productivity using various omics techniques, with a particular focus on the application of genome sequencing and metabolic engineering in this field.
MICROBIAL CELL FACTORIES
(2021)
Article
Biochemistry & Molecular Biology
Philippe Savarino, Emmanuel Colson, Guillaume Caulier, Igor Eeckhaut, Patrick Flammang, Pascal Gerbaux
Summary: This study focused on the sulfated saponins contained in a sea cucumber from the Indian Ocean, and developed a method to desulfate them using microwave activation under alkaline conditions. The study identified the sulfate function as highly responsible for the saponin toxicity based on a comparison of the hemolytic activities.
Article
Biochemistry & Molecular Biology
Guillaume Caulier, Alexia Lourtie, Lola Brasseur, Jerome Mallefet, Pascal Gerbaux, Patrick Flammang, Igor Eeckhaut
Summary: Quinones in feather stars play a role in providing bright colors and defense. The snapping shrimp Synalpheus stimpsonii uses anthraquinones released by crinoids as chemical stimuli for host selection. These anthraquinones act as kairomones, attracting the shrimp and maintaining the symbiosis between the shrimp and its crinoid hosts.
Article
Chemistry, Medicinal
Philip Bertemes, Alexandra L. Grosbusch, Anik Geschwindt, Bob Kauffmann, Willi Salvenmoser, Birte Mertens, Robert Pjeta, Bernhard Egger, Peter Ladurner
Summary: In this study, we sequenced and assembled the genome and transcriptome of the polyclad Theama mediterranea and identified 15 candidate genes potentially involved in temporary adhesion. We discovered two key components, a Kringle-domain-containing protein and a secreted tyrosinase, which play important roles in the flatworm temporary adhesion system. These findings have implications for the development of reversible synthetic glues for medical and industrial applications.
Article
Biochemistry & Molecular Biology
Marie Bonneel, Elise Hennebert, A. Sesilja Aranko, Dong Soo Hwang, Mathilde Lefevre, Valentine Pommier, Ruddy Wattiez, Jerome Delroisse, Patrick Flammang
Summary: The study reveals the mechanism of Tensilin, a stiffening factor in echinoderm MCTs, in regulating the mechanical properties of collagen fibrils. The researchers identified Hf-(D)Tensilin in the dermis of Holothuria forskali and confirmed its stiffening effect on dermal tissues and aggregation effect on collagen fibrils. Additionally, the study provides insights into the interactions between Tensilin and collagen fibrils.
Article
Multidisciplinary Sciences
Vasileios Papadogiannis, Alessandro Pennati, Hugo J. Parker, Ute Rothbacher, Cedric Patthey, Marianne E. Bronner, Sebastian M. Shimeld
Summary: This study investigates the role of the Hmx gene in the development of sensory ganglia in vertebrates. The results demonstrate the conservation of regulatory and functional properties of Hmx between Ciona and vertebrates, and suggest that bipolar tail neurons might be homologous to cranial sensory ganglia.
Article
Physiology
Valeriya Zabelina, Marketa Vrchotova, Naoyuki Yonemura, Hideki Sezutsu, Toshiki Tamura, Vyacheslav Klymenko, Frantisek Sehnal, Michal Zurovec, Hana Sehadova, Ivo Sauman
Summary: The use of parthenogenetic silkworm strains is useful for maintaining transgenic clonal lines, but the efficiency of downstream transgenesis techniques is relatively low. This study aims to optimize the use of transgenesis in parthenogenetic individuals and found that the timing of embryo microinjection is a crucial parameter. The modification of the original method increased the efficiency of transgene injection and survival rate.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Morgane Algrain, Elise Hennebert, Philip Bertemes, Ruddy Wattiez, Patrick Flammang, Birgit Lengerer
Summary: In this study, the catalog of sea star footprint proteins (Sfps) in Asterias rubens was characterized, revealing their different functions during attachment, including coupling to the surface, providing cohesive strength, and forming a binding matrix.
Article
Biochemistry & Molecular Biology
Lenka Rouhova, Hana Sehadova, Lucie Pauchova, Miluse Hradilova, Martina Zurovcova, Michal Sery, Michal Rindos, Michal Zurovec
Summary: This study described the silk glands of P. conspersa and used multi-omics methods to obtain a complete picture of the fiber composition. The approach allows for comparing the overall composition of silk with other insect species and helps distinguish between the basic components of all silks and proteins that represent the adaptation of the fibers for specific purposes or environments.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jack F. Cazet, Stefan Siebert, Hannah Morris Little, Philip Bertemes, Abby S. Primack, Peter Ladurner, Matthias Achrainer, Mark T. Fredriksen, R. Travis Moreland, Sumeeta Singh, Suiyuan Zhang, Tyra G. Wolfsberg, Christine E. Schnitzler, Andreas D. Baxevanis, Oleg Simakov, Bert Hobmayer, Celina E. Juliano
Summary: The stem cells of the freshwater polyp Hydra are well-studied and provide insights into cell type evolution and stemness in animals. However, the regulatory mechanisms that maintain these stem cells and give rise to different cell types are poorly understood. To address this, extensive resources were generated, including new genome assemblies, single-cell RNA-seq atlas, and genome-wide maps of chromatin interactions, accessibility, sequence conservation, and histone modifications. These resources revealed the existence of large chromatin interaction domains containing co-regulated genes and identified novel regulators of cell type-specific transcription.
Article
Entomology
Peter Kmet, Lucie Kucerova, Hana Sehadova, Bulah Chia-hsiang Wu, Yueh-Lung Wu, Michal Zurovec
Summary: Silk produced by caterpillars consists of insoluble filamentous proteins forming a silk core and soluble coat proteins secreted by silk glands. Through the analysis of a silk gland-specific transcriptome, we identified major silk components and confirmed their homology with known silk proteins. Phylogenetic analysis revealed the evolutionary relationships among silk proteins in the Bombycoidea. Our study provides important information for the annotation and future functional studies of silk proteins.
JOURNAL OF INSECT PHYSIOLOGY
(2023)
Article
Chemistry, Medicinal
Ines Ventura, Victoria Harman, Robert J. Beynon, Romana Santos
Summary: Biomedical adhesives still struggle with strong adhesion in wet environments. Marine invertebrates' biological adhesives show promising characteristics for underwater biomimetic adhesives. Through analysis of sea urchin Paracentrotus lividus adhesive proteins, researchers identified glycosylated protein candidates. The deeper characterization of these adhesive glycoproteins advances the development of sea urchin-inspired bioadhesives.
Article
Engineering, Environmental
Henk A. M. Ketelaars, Arco J. Wagenvoort, Marjolein C. F. M. Peters, Julia Wunderer, Wim A. M. Hijnen
Summary: Invertebrates such as rotifers, copepods, and cladocerans are commonly found in drinking water distribution systems. A study conducted in the Netherlands over eight years investigated the biomass and composition of invertebrates in the finished water of nine treatment plants. The study found that surface water treatment plants had higher invertebrate biomass due to higher nutrient levels in the source water.
Article
Zoology
Isabel L. Dittmann, Alexandra L. Grosbusch, Philip Bertemes, Bernhard Egger
Summary: We described a new species of polyclad flatworm, Cycloporus pinkipus, from the Adriatic coast of Croatia, using various methods such as live images, histological sections, and molecular marker. This species is the fifteenth described species of Cycloporus and the second in the Mediterranean. It is characterized by its small oval body, tentacular bumps, and marginal pores.
Letter
Developmental Biology
Ute Rothbacher