11 research outputs found
Increasing efficiency and reducing bias in the sampling of seed-dispersal interactions based on mist-netted birds
Efficient and unbiased sampling of ecological interactions is essential to our understanding of the functions they mediate. Seed dispersal by frugivorous birds is a key mutualism for plant regeneration and community dynamics. Mist-netting is one of the most widely used methods to sample avian seed dispersal through the identification of seeds in droppings of captured birds kept inside cloth bags. However, birds may drop seeds on the ground before being extracted from the net, leading to a fraction of missing information due to ineffective sampling. Worryingly, this fraction could be unevenly distributed across bird and plant species, leading to sampling biases. Here, we assess the effectiveness of using a 1-m wide mesh below mist nets to sample seeds dropped by entangled birds. We used data from birds mist-netted during one-year-round. We sampled nearly 50% of interaction events and 75% of dispersed seeds on the mesh band below the mist nets (i.e. lost information without this optimization). The proportion of seeds sampled on the mesh bands was not evenly distributed among bird species but strongly related to bird size, ranging from 57â63% in warblers to 84â94% in thrushes. Moreover, the proportion of seeds sampled on the mesh was negatively related to seed size, although this relationship was weaker. We also evaluated accumulation curves of species and pairwise interactions with increasing sampling effort, both with and without using the mesh bands. The number of seed species sampled increased by 21% when using the mesh bands and the number of pairwise interactions by 36%. Our findings provide strong evidence on how inefficient and biased traditional mist-netting can be for sampling community-wide seedâdispersal interactions. We thus urge the use of mesh bands in future studies to increase sampling effectiveness and avoid biases, which will ultimately improve our understanding of the seed dispersal function
SARS-CoV-2 mutant spectra reveal differences between COVID-19 severity categories
Trabajo presentado en el XVI Congreso Nacional de VirologĂa, celebrado en MĂĄlaga (España) del 06 al 09 de septiembre de 2022.RNA virus populations are composed of complex mixtures of genomes that are termed mutant spectra. SARS-CoV-2 replicates as a viral quasispecies, and mutations that are detected at low frequencies in a host can be dominant in subsequent variants. We have studied mutant spectrum complexities of SARS-CoV-2 populations derived from thirty nasopharyngeal swabs of patients infected during the first wave (April 2020) in the Hospital Universitario FundaciĂłn JimĂ©nez DĂaz. The patients were classified according to the COVID-19 severity in mild (non-hospitalized), moderate (hospitalized) and exitus (hospitalized with ICU admission and who passed away due to COVID-19). Using ultra-deep sequencing technologies (MiSeq, Illumina), we have examined four amplicons of the nsp12 (polymerase)-coding region and two amplicons of the spike-coding region. Ultra-deep sequencing data were analyzed with different cut-off frequency for mutation detection. Average number of different point mutations, mutations per haplotype and several diversity indices were significantly higher in SARS-CoV-2 isolated from patients who developed mild disease. A feature that we noted in the SARS-CoV-2 mutant spectra from diagnostic samples is the remarkable absence of mutations at intermediate frequencies, and an overwhelming abundance of mutations at frequencies lower than 10%. Thus, the decrease of the cut-off frequency for mutation detection from 0.5% to 0.1% revealed an increasement (50- to 100 fold) in the number of different mutations. The significantly higher frequency of mutations in virus from patients displaying mild than moderate or severe disease was maintained with the 0.1% cut- off frequency. To evaluate whether the frequency repertoire of amino acid substitutions differed between SARS-CoV-2 and the well characterized hepatitis C virus (HCV), we performed a comparative study of mutant spectra from infected patients using the same bioinformatics pipelines. HCV did not show the deficit of intermediate frequency substitutions that was observed with SARS-CoV-2. This difference was maintained when two functionally equivalent proteins, the corresponding viral polymerases, were compared. In conclusion, SARS-CoV-2 mutant spectra are rich reservoirs of mutants, whose complexity is not uniform among clinical isolates. Virus from patients who developed mild disease may be a source of new variants that may acquire epidemiological relevance.This work was supported by Instituto de Salud Carlos III, Spanish Ministry of Science and In-novation (COVID-19 Research Call COV20/00181), and co-financed by European Development Regional Fund âA way to achieve Europeâ. The work was also supported by grants CSIC-COV19-014 from Consejo Superior de Investigaciones CientĂficas (CSIC), project 525/C/2021 from FundaciĂł La MaratĂł de TV3, PID2020-113888RB-I00 from Ministerio de Ciencia e InnovaciĂłn, BFU2017-91384-EXP from Ministerio de Ciencia, InnovaciĂłn y Universidades (MCIU), PI18/00210 and PI21/00139 from Instituto de Salud Carlos III, and S2018/BAA-4370 (PLATESA2 from Comunidad de Madrid/FEDER). C.P., M.C., and P.M. are supported by the Miguel Servet programme of the Instituto de Salud Carlos III (CPII19/00001, CPII17/00006, and CP16/00116, respectively) co-financed by the European Regional Development Fund (ERDF). CIBERehd (Centro de Investi-gaciĂłn en Red de Enfermedades HepĂĄticas y Digestivas) is funded by Instituto de Salud Carlos III. Institutional grants from the FundaciĂłn RamĂłn Areces and Banco Santander to the CBMSO are also acknowledged. The team at CBMSO belongs to the Global Virus Network (GVN). B.M.-G. is supported by predoctoral contract PFIS FI19/00119 from Instituto de Salud Carlos III (Ministerio de Sanidad y Consumo) cofinanced by Fondo Social Europeo (FSE). R.L.-V. is supported by predoctoral contract PEJD-2019-PRE/BMD-16414 from Comunidad de Madrid. C.G.-C. is sup-ported by predoctoral contract PRE2018-083422 from MCIU. BS was supported by a predoctoral research fellowship (Doctorados Industriales, DI-17-09134) from Spanish MINECO
SARS-CoV-2 Point Mutation and Deletion Spectra, and Their Association with Different Disease Outcome
Mutant spectra of RNA viruses are important to understand viral pathogenesis, and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultra-deep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of thirty nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19.This work was supported by Instituto de Salud Carlos III, Spanish Ministry of Science and Innovation (COVID-19 Research Call COV20/00181), and coâfinanced by European Development Regional Fund âA way to achieve Europeâ. The work was also supported by grants CSIC-COV19-014 from Consejo Superior de Investigaciones CientĂficas (CSIC), project 525/C/2021 from FundaciĂł La MaratĂł de TV3, PID2020-113888RB-I00 from Ministerio de Ciencia e InnovaciĂłn, BFU2017-91384-EXP from Ministerio de Ciencia, InnovaciĂłn y Universidades (MCIU), PI18/00210 and PI21/00139 from Instituto de Salud Carlos III and S2018/BAA-4370 (PLATESA2 from Comunidad de Madrid/FEDER). C.P., M.C. and P.M. are supported by the Miguel Servet programme of the Instituto de Salud Carlos III (CPII19/00001, CPII17/00006 and CP16/00116, respectively) cofinanced by the European Regional Development Fund (ERDF). CIBERehd (Centro de InvestigaciĂłn en Red de Enfermedades HepĂĄticas y Digestivas) is funded by Instituto de Salud Carlos III. Institutional grants from the FundaciĂłn RamĂłn Areces and Banco Santander to the CBMSO are also acknowledged. The team at CBMSO belongs to the Global Virus Network (GVN). B.M.-G. is supported by predoctoral contract PFIS FI19/00119 from Instituto de Salud Carlos III (Ministerio de Sanidad y Consumo) cofinanced by Fondo Social Europeo (FSE). R.L.- V. is supported by predoctoral contract PEJD-2019-PRE/BMD-16414 from Comunidad de Madrid. C.G.-C. is supported by predoctoral contract PRE2018-083422 from MCIU. BS was supported by a predoctoral research fellowship (Doctorados Industriales, DI-17- 09134) from Spanish MINECON
SARS-CoV-2 Point Mutation and Deletion Spectra and Their Association with Different Disease Outcomes
Mutant spectra of RNA viruses are important to understand viral pathogenesis and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultradeep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of 30 nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low-frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype, and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three-dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19.Peer reviewe
SARS-CoV-2 Mutant Spectra at Different Depth Levels Reveal an Overwhelming Abundance of Low Frequency Mutations
Populations of RNA viruses are composed of complex and dynamic mixtures of variant genomes that are termed mutant spectra or mutant clouds. This applies also to SARS-CoV-2, and mutations that are detected at low frequency in an infected individual can be dominant (represented in the consensus sequence) in subsequent variants of interest or variants of concern. Here we briefly review the main conclusions of our work on mutant spectrum characterization of hepatitis C virus (HCV) and SARS-CoV-2 at the nucleotide and amino acid levels and address the following two new questions derived from previous results: (i) how is the SARS-CoV-2 mutant and deletion spectrum composition in diagnostic samples, when examined at progressively lower cut-off mutant frequency values in ultra-deep sequencing; (ii) how the frequency distribution of minority amino acid substitutions in SARS-CoV-2 compares with that of HCV sampled also from infected patients. The main conclusions are the following: (i) the number of different mutations found at low frequency in SARS-CoV-2 mutant spectra increases dramatically (50- to 100-fold) as the cut-off frequency for mutation detection is lowered from 0.5% to 0.1%, and (ii) that, contrary to HCV, SARS-CoV-2 mutant spectra exhibit a deficit of intermediate frequency amino acid substitutions. The possible origin and implications of mutant spectrum differences among RNA viruses are discussed.This work was supported by Instituto de Salud Carlos III, Spanish Ministry of Science and
Innovation (COVID-19 Research Call COV20/00181), and co-financed by European Development
Regional Fund âA way to achieve Europeâ. The work was also supported by grants CSIC-COV19-014
from Consejo Superior de Investigaciones CientĂficas (CSIC), project 525/C/2021 from FundaciĂł La
MaratĂł de TV3, PID2020-113888RB-I00 from Ministerio de Ciencia e InnovaciĂłn, BFU2017-91384-EXP
from Ministerio de Ciencia, InnovaciĂłn y Universidades (MCIU), PI18/00210 and PI21/00139 from
Instituto de Salud Carlos III, and S2018/BAA-4370 (PLATESA2 from Comunidad de Madrid/FEDER).
C.P., M.C., and P.M. are supported by the Miguel Servet programme of the Instituto de Salud Carlos III (CPII19/00001, CPII17/00006, and CP16/00116, respectively) cofinanced by the European Regional
Development Fund (ERDF). CIBERehd (Centro de InvestigaciĂłn en Red de Enfermedades HepĂĄticas y
Digestivas) is funded by Instituto de Salud Carlos III. Institutional grants from the FundaciĂłn RamĂłn
Areces and Banco Santander to the CBMSO are also acknowledged. The team at CBMSO belongs to
the Global Virus Network (GVN). B.M.-G. is supported by predoctoral contract PFIS FI19/00119 from
Instituto de Salud Carlos III (Ministerio de Sanidad y Consumo) cofinanced by Fondo Social Europeo
(FSE). R.L.-V. is supported by predoctoral contract PEJD-2019-PRE/BMD-16414 from Comunidad de
Madrid. C.G.-C. is supported by predoctoral contract PRE2018-083422 from MCIU. P.S. is supported
by postdoctoral contract âMargarita Salasâ CA1/RSUE/2021 from MCIU. B.S. was supported by a
predoctoral research fellowship (Doctorados Industriales, DI-17-09134) from Spanish MINECO.Peer reviewe
Outcomes from elective colorectal cancer surgery during the SARS-CoV-2 pandemic
This study aimed to describe the change in surgical practice and the impact of SARS-CoV-2 on mortality after surgical resection of colorectal cancer during the initial phases of the SARS-CoV-2 pandemic
GestiĂłn del conocimiento: perspectiva multidisciplinaria. Volumen 11
El libro âGestiĂłn del Conocimiento. Perspectiva Multidisciplinariaâ, Volumen 11, de la ColecciĂłn UniĂłn Global, es resultado de investigaciones. Los capĂtulos del libro, son resultados de investigaciones desarrolladas por sus autores. El libro cuenta con el apoyo de los grupos de investigaciĂłn: Universidad Sur del Lago âJesĂșs MarĂa SemprĂșmâ (UNESUR), Zulia â Venezuela; Universidad PolitĂ©cnica Territorial de FalcĂłn Alonso Gamero (UPTAG), FalcĂłn â Venezuela; Universidad PolitĂ©cnica Territorial de MĂ©rida Kleber RamĂrez (UPTM), MĂ©rida â Venezuela;
Universidad Guanajuato (UG) - Campus Celaya - Salvatierra - Cuerpo AcadĂ©mico de Biodesarrollo y BioeconomĂa en las Organizaciones y PolĂticas PĂșblicas (C.A.B.B.O.P.P), Guanajuato â MĂ©xico; Centro de Altos Estudios de Venezuela (CEALEVE), Zulia â Venezuela, Centro Integral de FormaciĂłn Educativa Especializada del Sur (CIFE - SUR) - Zulia - Venezuela, Centro de Investigaciones Internacionales SAS (CIN), Antioquia - Colombia.y diferentes grupos de investigaciĂłn del ĂĄmbito nacional e internacional que hoy se unen para estrechar vĂnculos investigativos, para que sus aportes cientĂficos formen parte de los libros que se publiquen en formatos digital e impreso
Metabolic Disturbance of High-Saturated Fatty Acid Diet in Cognitive Preservation
Aging continues to be the main cause of the development of Alzheimerâs, although it has been described that certain chronic inflammatory pathologies can negatively influence the progress of dementia, including obesity and hyperlipidemia. In this sense, previous studies have shown a relationship between low-density lipoprotein receptor (LDLR) and the amyloid-beta (AÎČ) binding activity, one of the main neuropathological features of Alzheimerâs disease (AD). LDLR is involved in several processes, including lipid transport, regulation of inflammatory response and lipid metabolism. From this perspective, LDLRâ/â mice are a widely accepted animal model for the study of pathologies associated with alterations in lipid metabolism, such as familial hypercholesterolemia, cardiovascular diseases, metabolic syndrome, or early cognitive decline. In this context, we induced hyperlipidemia in LDLRâ/â mice after feeding with a high-saturated fatty acid diet (HFD) for 44 weeks. LDLRâ/â-HFD mice exhibited obesity, hypertriglyceridemia, higher glucose levels, and early hepatic steatosis. In addition, HFD increased plasmatic APOE and ubiquitin 60S levels. These proteins are related to neuronal integrity and health maintenance. In agreement, we detected mild cognitive dysfunctions in mice fed with HFD, whereas LDLRâ/â-HFD mice showed a more severe and evident affectation. Our data suggest central nervous system dysfunction is associated with a well-established metabolic syndrome. As a late consequence, metabolic syndrome boots many behavioral and pathological alterations recognized in dementia, supporting that the control of metabolic parameters could improve cognitive preservation and prognosis
Del presente y del pasado: enfoques cientĂficos en la antropologĂa, historia y arqueologĂa de MĂ©xico. Num. 32 (2004) Vol. 11 septiembre-diciembre. Cuicuilco Revista de la Escuela Nacional de AntropologĂa e Historia
- PresentaciĂłn, Patricia Fournier - MiscelĂĄnea: - La civilizaciĂłn maya de las tierras bajas: los lĂmites de una forma social de explotaciĂłn, por Miguel Ăngel HernĂĄndez GarcĂa - Religiosidad e identidad en una comunidad de pequeños horticultores del altiplano potosino, por Micaela GarcĂa Bravo Orta y Javier Fortanelli MartĂnez - El saber antropolĂłgico: sobre la experiencia de campo, por Michel Duquesnoy - De moral y regeneraciĂłn: el programa de âingenierĂa social" posrevolucionario visto a travĂ©s de las revistas masĂłnicas mexicanas, 1930-1945, por Beatriz UrĂas Horcasitas - Del desamparo a la protecciĂłn. Ideas, instituciones y prĂĄcticas de la asistencia social en la ciudad de MĂ©xico, 1861-1910, por Antonio Padilla Arroyo - InvestigaciĂłn diagnĂłstica sobre las misiones jesuitas en la Sierra Tarahumara, por Esperanza Penagos Belman - Estudios microscĂłpicos de huellas de uso en artefactos lĂticos: algunas observaciones teĂłricas y metodolĂłgicas, por Stephen Castillo Bernal - Reseñas: - Miguel BartolomĂ©, Librar el camino. Relatos sobre antropologĂa y alteridad, por SaĂșl MillĂĄn - Whaley Lindsay, Introduction to Typology. The Unity and Diversity of Language, por Martha Islas