Article
Genetics & Heredity
Ana Karen Sandoval-Talamantes, Jair Antonio Tenorio-Castano, Fernando Santos-Simarro, Carmen Adan, Maria Fernandez-Elvira, Laura Garcia-Fernandez, Yolanda Munoz, Pablo Lapunzina, Julian Nevado
Summary: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by deficiencies in communication, social interaction, and repetitive and restrictive behaviors. The discovery of genetic involvement in ASD has made genome-based diagnostic tests possible. By implementing a personalized NGS panel for autism (AutismSeq), we were able to detect important genetic variations in individuals with ASD, highlighting the high genetic and clinical heterogeneity of the disorder, and demonstrating the practicality and cost-effectiveness of NGS panels in diagnosis.
Article
Biochemistry & Molecular Biology
Fernando Mora-Marquez, Victor Chano, Jose Luis Vazquez-Poletti, Unai Lopez de Heredia
Summary: TOA is a user-friendly open source application designed for functional annotation in non-model plant species, outperforming other software in terms of number of annotated sequences and accuracy of the annotation.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Jinjun Gao, Xinlei Sheng, Jianfeng Du, Di Zhang, Chang Han, Yue Chen, Chu Wang, Yingming Zhao
Summary: We developed a new database search strategy called CHiMA, which uses 50% matched fragment ions as the key criterion to identify high-confidence PSMs. Compared to conventional methods, CHiMA identified twice as many histone modification sites in benchmark datasets. Reanalysis of previous proteomics data using CHiMA led to the discovery of 113 new histone marks, almost doubling the number of previously reported marks. This tool not only offers a valuable approach for identifying histone modifications but also greatly expands the repertoire of histone marks.
Article
Food Science & Technology
Roberta Piredda, Anna Mottola, Giulia Cipriano, Roberto Carlucci, Giuseppina Ciccarese, Angela Di Pinto
Summary: The multi-species fish products market is growing rapidly due to urbanization, modern lifestyles, and new technologies. These products lack species-related morphological traits and may contain fish waste, making them susceptible to substitution fraud. New molecular tools, such as metabarcoding, can be used to trace species in complex food matrices.
Article
Biochemical Research Methods
Husen M. Umer, Enrique Audain, Yafeng Zhu, Julianus Pfeuffer, Timo Sachsenberg, Janne Lehtio, Rui Branca, Yasset Perez-Riverol
Summary: The pypgatk package and pgdb workflow have been implemented to create proteogenomics databases based on ENSEMBL resources. The tools can generate protein sequences from different types of transcripts and take into account the impact of genomic variants on protein sequences. Using these tools, researchers have reanalyzed public datasets and identified a significant number of novel protein sequences.
Article
Oncology
Shuchen Chen, Wanyi Huang, Zhenzhen Liu, Meizi Jin, Jielin Li, Lihui Meng, Ting Li, Yuzhu Diao, Hong Gao, Chengyu Hong, Jian Zheng, Fei Li, Yue Zhang, Dan Bi, Lin Teng, Xiaoling Li
Summary: This study identifies nine mutant genes and smoking history associated with organ tropism metastases of NSCLC and provides three models for predicting metastatic organs.
Article
Chemistry, Applied
Nan Wang, Ran-Ran Xing, Meng-Yue Zhou, Rui-Xue Sun, Jian-Xun Han, Jiu-Kai Zhang, Wen-Jie Zheng, Ying Chen
Summary: This study tested the feasibility of next-generation sequencing in identifying mixed salmon products and found that 50% of the commercial salmon food products surveyed were mislabelled. DNA barcoding and metabarcoding methods are useful for the identification of salmon species in food and can be used for quality control of various types of salmon products.
FOOD ADDITIVES AND CONTAMINANTS PART A-CHEMISTRY ANALYSIS CONTROL EXPOSURE & RISK ASSESSMENT
(2021)
Article
Chemistry, Multidisciplinary
Bhuvana K. Shanbhag, Chang Liu, G. C. Pradeep, Tayyaba Younas, Kevin K. Y. Hu, Alex J. Fulcher, Weston B. Struwe, David Steer, Geoff Dumsday, Ian S. Harper, Philipp Kukura, Victoria S. Haritos, Lizhong He
Summary: The authors have developed a versatile protein assembling method to create customized protein particles for various applications, such as biocatalysis, sensing, and labeling. They have successfully demonstrated the co-assembly of two functional proteins within a single particle. This strategy provides a reliable way to fabricate protein particles with new functionalities on demand.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Microbiology
Suwanna Chaorattanakawee, Achareeya Korkusol, Bousaraporn Tippayachai, Sommai Promsathaporn, Betty K. Poole-Smith, Ratree Takhampunya
Summary: Through NGS technology, a study was successfully conducted on samples of rodents and host animals from different regions of Thailand, which found the highest percentage of Rickettsia DNA in fleas, primarily from dogs. The study also showed that Ctenocephalides felis orientis is the most common host with a high positivity rate, and identified the risk of tick-borne Spotted Fever Group rickettsiosis and flea-borne murine typhus transmission in certain provinces of Thailand.
Article
Biochemistry & Molecular Biology
Milos Avramov, Eva Schad, Agnes Revesz, Lilla Turiak, Iva Uzelac, Agnes Tantos, Laszlo Drahos, Zeljko D. Popovic
Summary: This study utilizes wet lab methods and bioinformatics tools to analyze intrinsically disordered proteins in a cold-hardy insect species. The results suggest that these proteins play important roles in the insect's adaptive mechanisms to extreme temperatures.
Article
Medicine, General & Internal
Justyna Dabrowska, Barbara Biedziak, Agnieszka Bogdanowicz, Adrianna Mostowska
Summary: This study aimed to detect low-frequency variants implicated in the aetiology of ns-CP in the Polish population. Through screening coding regions of 423 genes associated with orofacial cleft anomalies and/or facial development, eight novel and four known rare variants that may influence ns-CP risk were identified. Seven of these alterations were located in novel candidate genes for ns-CP, while the remaining risk variants were found within genes previously linked to ns-CP.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Biochemical Research Methods
Leonard A. Daly, Dominic P. Byrne, Simon Perkins, Philip J. Brownridge, Euan Mcdonnell, Andrew R. Jones, Patrick A. Eyers, Claire E. Eyers
Summary: In this study, a MS-based workflow for sY-peptide characterization was developed, allowing systematic investigation of the sulfome. The key for distinguishing sulfated peptides from phosphopeptides was low collision energy-induced neutral loss. Applying this workflow identified 21 new sulfotyrosine-containing proteins and revealed new interplay between enzymes relevant to both protein and glycan sulfation.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Ecology
Congtian Lin, Xiongwei Huang, Jiangning Wang, Tianyu Xi, Liqiang Ji
Summary: Species identification is crucial in ecological research. NicheNet, a method combining ecological niche model and image-based deep learning model, significantly improves accuracy and robustness compared to image-only models. The introduction of a new criterion "Near Error Rate" shows the superior performance of NicheNet in distinguishing similar species when compared to image-only models.
ECOLOGICAL INFORMATICS
(2021)
Article
Biodiversity Conservation
Romain Gastineau, Chahinez Hamedi, Mohammed Bey Baba Hamed, Sidi-Mohammed El-Amine Abi-Ayad, Malgorzata Bak, Claude Lemieux, Monique Turmel, Slawomir Dobosz, Rafal J. Wrobel, Agnieszka Kierzek, Horst Lange-Bertalot, Andrzej Witkowski
Summary: The study successfully identified diatom specimens from deep Sahara using modern taxonomical tools, demonstrating the possibility of cultivating such material in laboratories for biogeographical and bioindication experiments. The results suggest that European identification keys can be effective when applied to diatoms from the Sahara.
ECOLOGICAL INDICATORS
(2021)
Article
Biochemistry & Molecular Biology
Justyna Dabrowska, Barbara Biedziak, Anna Szponar-Zurowska, Margareta Budner, Pawel P. Jagodzinski, Rafal Ploski, Adrianna Mostowska
Summary: This study investigates the potential role of rare and private variants in the risk of non-syndromic cleft lip with or without cleft palate (ns-CL/P). The results indicate that rare coding variants may contribute to the genetic architecture of ns-CL/P. Additionally, the study suggests a common genetic link between orofacial clefts and dental abnormalities.
MOLECULAR GENETICS AND GENOMICS
(2022)
Article
Biochemistry & Molecular Biology
Pamela Gonzalez-Maldonado, Nelson Alvarenga, Alberto Burgos-Edwards, Ma. Eugenia Flores-Giubi, Javier E. Barua, Ma. Cristina Romero-Rodriguez, Ricardo Soto-Rifo, Fernando Valiente-Echeverria, Patricia Langjahr, Guadalupe Cantero-Gonzalez, Pablo H. Sotelo
Summary: The COVID-19 pandemic has prompted the search for new molecules that can inhibit the SARS-CoV-2 virus. One of the main targets for inhibiting this infection is the entry of the virus into cells. Natural products offer a potential source of new therapeutic alternatives. The use of pseudotyped viruses allows for the screening of a large number of antiviral candidates in a safe and efficient manner.
Editorial Material
Plant Sciences
Andres D. D. Sanabria-Velazquez, Alberto Cubilla, Maria Eugenia Flores-Giubi, Javier E. E. Barua, Cristina Romero-Rodriguez, Guillermo A. A. Enciso-Maldonado, LindseyD D. Thiessen, H. David Shew
Article
Multidisciplinary Sciences
Adriana Orrego, Maria Cecilia Gavilan, Anibal Arevalos, Belen Ortiz, Belen Gaete Humada, Amiliana Pineda-Fretez, Maria Cristina Romero-Rodriguez, Maria Eugenia Flores Giubi, Man Mohan Kohli, Julio C. M. Iehisa
Summary: This study evaluated the suitability of 12 candidate reference genes for gene expression analysis of M. phaseolina and identified CYP1 as the best reference gene. The findings provide valuable references for gene expression analysis during host infection with M. phaseolina.
Review
Biochemistry & Molecular Biology
Ana Maria Maldonado-Alconada, Maria angeles Castillejo, Maria-Dolores Rey, Monica Labella-Ortega, Marta Tienda-Parrilla, Tamara Hernandez-Lao, Irene Honrubia-Gomez, Javier Ramirez-Garcia, Victor M. Guerrero-Sanchez, Cristina Lopez-Hidalgo, Luis Valledor, Rafael M. Navarro-Cerrillo, Jesus V. Jorrin-Novo
Summary: This study explores the molecular biology characteristics of the holm oak and its potential for dietary diversification and sustainable food production. The research team conducted various omics studies and discussed molecular markers related to variety selection, biotic and abiotic stresses, and seed maturation and germination. The findings of this study are important for the conservation of holm oak genetic resources and the development of agrosilvopastoral industries.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Engineering, Environmental
Erna Karalija, Maria Carbo, Andrea Coppi, Ilaria Colzi, Marco Dainelli, Mateo Gasparovic, Tine Grebenc, Cristina Gonnelli, Vassilis Papadakis, Selma Pilic, Natasa Sibanc, Luis Valledor, Anna Poma, Federico Martinelli
Summary: Recent research has shown that plants can absorb plastic particles, providing a new approach to removing plastic pollution from water and soil systems. While microplastics are usually unable to be taken up by plant roots, nanoparticles can enter the root system and be transported to upper plant parts via xylem. Algae can degrade plastic particles in water systems through enzyme-facilitated degradation processes, but precautions should be taken to avoid causing algal blooming during the degradation process.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Plant Sciences
Victor Roces, Laura Lamelas, Luis Valledor, Maria Carbo, Maria Jesus Canal, Monica Meijon
Summary: This study investigates the response and memory of alternative splicing (AS) under heat stress in conifers using a systems biology approach. The findings reveal that intron retention may not be the most prevalent AS type in conifers, unlike in angiosperms, and that splicing is the main source of variation during the response. Furthermore, while the mechanism of acquired splicing memory seems to be conserved in seed plants, the dynamics of AS are divergent.
Review
Plant Sciences
Joana Amaral, Luis Valledor, Artur Alves, Jorge Martin-Garcia, Gloria Pinto
Summary: This review examines the knowledge regarding pine pitch canker (PPC), particularly focusing on the response of pines with different susceptibility levels to PPC infection. The integration of research findings from various disciplines can elucidate the mechanisms behind PPC susceptibility/resistance and aid in the development of control strategies.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Lara Garcia-Campa, Luis Valledor, Jesus Pascual
Summary: To improve the quality of reference databases and their annotations, researchers combined full-length isoform sequencing (Iso-Seq) with short-read transcriptomics and proteomics. By including Oxford Nanopore Technologies Direct RNA Sequencing (ONT-DRS) data, they enhanced the identification and discovery of proteoforms in Arabidopsis MS proteomics data. This approach offers unprecedented opportunities for investigating biological systems, but also presents challenges for existing protein searching algorithms.
Article
Plant Sciences
Cristina Lopez-Hidalgo, Laura Lamelas, Maria Jesus Canal, Luis Valledor, Monica Meijon
Summary: Climate change has resulted in more intense and prolonged heat waves and drought stresses, exceeding the adaptative capacity of trees. This research focuses on the metabolic responses of maritime pine to different intensities of combined stresses, revealing the importance of considering multiple stresses and intensities for understanding plant responses.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2023)
Article
Mycology
Amiliana Pineda-Fretez, Adriana Orrego, Julio Cesar Masaru Iehisa, Maria Eugenia Flores-Giubi, Javier E. Barua, Rosa Sanchez-Lucas, Jesus Jorrin-Novo, Maria Cristina Romero-Rodriguez
Summary: A proteomic analysis of the proteins secreted by M. phaseolina in soybean leaf infusion culture media was conducted. The analysis revealed a large number of hydrolytic enzymes, as well as plant cell wall degrading enzymes and peptidases possibly involved in the infection process. Putative effector proteins that could induce plant cell death or suppress plant immune response, some of which shared similarities with known fungal virulence factors, were also identified. Expression analysis suggested that selected protein-coding genes are induced during host tissue infection and may participate in the infection process. The identification of secreted proteins of M. phaseolina can contribute to understanding the biology and pathogenesis of this fungus, but further studies are needed to investigate the changes induced during the natural infection process.
Article
Engineering, Environmental
Maria Carbo, Palak Chaturvedi, Ana Alvarez, Daniela Pineda-Cevallos, Arindam Ghatak, Pablo Rodriguez Gonzalez, Maria Jesus Canal, Wolfram Weckwerth, Luis Valledor
Summary: Microplastics, including Bisphenol A (BPA), are major pollutants in aquatic environments. BPA, one of the most abundant and dangerous components, can lead to endocrine disorders and cancer in mammals. This study aimed to understand the molecular-level effects of BPA on plants and microalgae, specifically Chlamydomonas reinhardtii. The findings revealed that BPA disrupts iron and redox homeostasis, leading to cell dysfunction and ferroptosis. Interestingly, the microalgae showed recovery at both molecular and physiological levels, with starch accumulation after 72 hours of BPA exposure. This study provides valuable insights into BPA toxicology, ferroptosis in microalgae, and potential target genes for microplastic bioremediation.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Review
Forestry
Noor Muhammad, Maria Angeles Castillejo, Maria-Dolores Rey, Jesus V. Jorrin-Novo
Summary: This article introduces the formation of broad-leaved evergreen forests by Quercus spp. in the Hindu Kush and Himalayan regions of Pakistan. Seven species of Quercus genus have been identified, but they have received little attention in terms of their economic value and bioactivity evaluation. Quercus spp. show promise for commercial applications, but are currently threatened by human activities and climate change. This review highlights the importance of these forgotten species and discusses various aspects of their distribution, morphology, traditional uses, phytochemical constituents, and threats. The lack of molecular studies on populations of these species in Pakistan is a critical gap that needs to be addressed for conservation and management strategies. Future research directions in molecular approaches for Quercus are also discussed.
Article
Agronomy
Jose G. Vazquez-Garcia, Joel Torra, Candelario Palma-Bautista, Fernando Bastida, Ricardo Alcantara-de la Cruz, Joao Portugal, Jesus V. Jorrin-Novo, Rafael De Prado
Summary: In recent decades, direct sowing in cereal agriculture in Spain has led to increased use of herbicides, such as glyphosate, and the emergence of weedy species from the genus Avena. This study taxonomically characterized different accessions of Avena fatua, Avena byzantina, and Avena sterilis and found that one A. fatua accession had evolved resistance to glyphosate. The study also revealed that A. byzantina and A. sterilis had low susceptibility to glyphosate and showed limited foliar uptake and movement of the herbicide. Enzyme activity and affinity measurements suggested that a non-target site mechanism may be involved in glyphosate susceptibility differences.
Article
Plant Sciences
Xiangxiang Meng, Lu Li, Jesus Pascual, Moona Rahikainen, Changyu Yi, Ricarda Jost, Cunman He, Alexandre Fournier-Level, Justin Borevitz, Saijaliisa Kangasjarvi, James Whelan, Oliver Berkowitz
Summary: The mitochondrial ACONITASE3 (ACO3) plays a crucial role in the acclimation to submergence stress by regulating carbon and nitrogen metabolism and stress signaling pathways in plants.
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)