المؤلفون: Arturo Becerra, Israel Muñoz-Velasco, Abelardo Aguilar-Cámara, Wolfgang Cottom-Salas, Adrián Cruz-González, Alberto Vázquez-Salazar, Ricardo Hernández-Morales, Rodrigo Jácome, José Alberto Campillo-Balderas, Antonio Lazcano

المصدر: Scientific Reports, Vol 12, Iss 1, Pp 1-8 (2022)

مصطلحات موضوعية: Medicine, Science

الوصف: Abstract Low complexity regions (LCRs) are protein sequences formed by a set of compositionally biased residues. LCRs are extremely abundant in cellular proteins and have also been reported in viruses, where they may partake in evasion of the host immune system. Analyses of 28,231 SARS-CoV-2 whole proteomes and of 261,051 spike protein sequences revealed the presence of four extremely conserved LCRs in the spike protein of several SARS-CoV-2 variants. With the exception of Iota, where it is absent, the Spike LCR-1 is present in the signal peptide of 80.57% of the Delta variant sequences, and in other variants of concern and interest. The Spike LCR-2 is highly prevalent (79.87%) in Iota. Two distinctive LCRs are present in the Delta spike protein. The Delta Spike LCR-3 is present in 99.19% of the analyzed sequences, and the Delta Spike LCR-4 in 98.3% of the same set of proteins. These two LCRs are located in the furin cleavage site and HR1 domain, respectively, and may be considered hallmark traits of the Delta variant. The presence of the medically-important point mutations P681R and D950N in these LCRs, combined with the ubiquity of these regions in the highly contagious Delta variant opens the possibility that they may play a role in its rapid spread.

وصف الملف: electronic resource

Relation: https://doaj.org/toc/2045-2322

URL الوصول: https://doaj.org/article/4862fc21befd4a6e99eb04702176ac49

المؤلفون: Bárbara Moguel, Liseth Pérez, Luis D. Alcaraz, Jazmín Blaz, Margarita Caballero, Israel Muñoz-Velasco, Arturo Becerra, Juan P. Laclette, Beatriz Ortega-Guerrero, Claudia S. Romero-Oliva, Luis Herrera-Estrella, Socorro Lozano-García

المصدر: Scientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)

مصطلحات موضوعية: Medicine, Science

الوصف: Abstract Metagenomic and traditional paleolimnological approaches are suitable to infer past biological and environmental changes, however, they are often applied independently, especially in tropical regions. We combined both approaches to investigate Holocene Prokaryote and Eukaryote diversity and microbial metabolic pathways in ancient Lake Chalco, Mexico. Here, we report on diversity among a large number of lineages (36,722 OTUs) and functional diversity (27,636,243 non-clustered predicted proteins, and 6,144 annotated protein-family genes). The most abundant domain is Bacteria (81%), followed by Archaea (15%) and Eukarya (3%). We also determined the diversity of protein families and their relationship to metabolic pathways. The early Holocene (> 11,000 cal years BP) lake was characterized by cool, freshwater conditions, which later became warmer and hyposaline (11,000–6,000 cal years BP). We found high abundances of cyanobacteria, and fungi groups associated with mature forests in these sediments. Bacteria and Archaea include mainly anaerobes and extremophiles that are involved in the sulfur, nitrogen, and carbon cycles. We found evidence for early human impacts, including landscape modifications and lake eutrophication, which began ~ 6,000 cal years BP. Subsaline, temperate conditions were inferred for the past 5,000 years. Finally, we found nitrogen-fixing bacteria and protein-family genes that are linked to contaminated environments, as well as several fungal pathogens of crops in near-surface sediments.

وصف الملف: electronic resource

Relation: https://doaj.org/toc/2045-2322

URL الوصول: https://doaj.org/article/d52295b99e1b4a91974cc15243ad056f

المؤلفون: Socorro Lozano-García, Israel Muñoz-Velasco, Arturo Becerra, Bárbara Moguel, Beatriz Ortega-Guerrero, Juan Pedro Laclette, Jazmín Blaz, Claudia S. Romero-Oliva, Luis David Alcaraz, Margarita Caballero, Luis Herrera-Estrella, Liseth Pérez

المصدر: Scientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
Scientific Reports

مصطلحات موضوعية: 0301 basic medicine, Cyanobacteria, Geologic Sediments, Nitrogen, Science, 030106 microbiology, Article, Carbon Cycle, 03 medical and health sciences, Limnology, Temperate climate, Humans, Extremophile, Mexico, Phylogeny, Holocene, Tropical Climate, Multidisciplinary, Ecology, Bacteria, Ancient lake, biology, Microbiota, Prokaryote, biology.organism_classification, Archaea, Environmental sciences, Lakes, 030104 developmental biology, Metagenomics, Metagenome, Medicine

الوصف: Metagenomic and traditional paleolimnological approaches are suitable to infer past biological and environmental changes, however, they are often applied independently, especially in tropical regions. We combined both approaches to investigate Holocene Prokaryote and Eukaryote diversity and microbial metabolic pathways in ancient Lake Chalco, Mexico. Here, we report on diversity among a large number of lineages (36,722 OTUs) and functional diversity (27,636,243 non-clustered predicted proteins, and 6,144 annotated protein-family genes). The most abundant domain is Bacteria (81%), followed by Archaea (15%) and Eukarya (3%). We also determined the diversity of protein families and their relationship to metabolic pathways. The early Holocene (> 11,000 cal years BP) lake was characterized by cool, freshwater conditions, which later became warmer and hyposaline (11,000–6,000 cal years BP). We found high abundances of cyanobacteria, and fungi groups associated with mature forests in these sediments. Bacteria and Archaea include mainly anaerobes and extremophiles that are involved in the sulfur, nitrogen, and carbon cycles. We found evidence for early human impacts, including landscape modifications and lake eutrophication, which began ~ 6,000 cal years BP. Subsaline, temperate conditions were inferred for the past 5,000 years. Finally, we found nitrogen-fixing bacteria and protein-family genes that are linked to contaminated environments, as well as several fungal pathogens of crops in near-surface sediments.

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4b9bb417e3bcbc8cdf9ff47ab2258087
https://doaj.org/article/d52295b99e1b4a91974cc15243ad056f