Determinants of above-ground carbon stocks and productivity in secondary forests along a 3000-m elevation gradient in the Ecuadorian Andes

Background: Secondary montane forests, covering 30% of forested lands in the Andes, play a crucial role in mitigating the impact of carbon release. However, the mechanisms responsible for carbon sequestration in the above-ground biomass of these forests are not well quantified. Aims: Understanding the determinants of above-ground carbon (AGC) dynamics in secondary forests along a 3000-m elevational gradient in the Andes to assess their mitigation potential. Methods: We assessed how abiotic and biotic conditions and past human disturbances were related to forest structure and composition, AGC stocks and productivity within sixteen 0.36-ha plots established in secondary forest stands of 30–35 years of age. Results: Structural equation models revealed that changes in temperature conditions along the elevation gradient shaped leaf functional composition, which in turn controlled AGC dynamics. Productivity and temperature decreased with increasing elevation and decreased tree community leaf area. Disturbance legacy (Tree mortality) increased with competitive thinning and low soil fertility. Conclusions: We show that temperature drives AGC dynamics by changing the functional trait composition. This highlights the importance of preserving these forests along elevation gradients and implies potentially strong future changes due to global warming.</p

Estudio Preliminar Sobre La Decoloración Del Residual Líquido De La Producción De Papel Mediante Ozonización

Preliminarily, the relationship between Color Reduction (%RC), Total Suspended Solids concentration (SST), and as independent variable, the time of Ozone Oxidation Process, was evaluated with reference values of DQO of the black liquor adjusting its concentration from SST to 300 and 50mg/dm3. A batch reactor of 12,60dm3, an effective height of 3,2dm and an ozone generating device from SEFILTRA company (air flow of 2dm3/min, c(O3) of 9,50mg/dm3 with a O3(g) production 19mg/min) was used. The polynomic correlation was determined from 192 data sets with satisfactory adjustment level (R=0,92; p &lt;0,001). Although, preliminarily, the DQO reduction (%RDQO) was not included in the polynomial relationship, it can be concluded that: a) The %RC and %RDQO is reduced when color and DQO increases from the ozonized sample at same time intervals; this reduction is greater when the SST levels of the ozonized sample increases. b) The %RC and %RDQO decrease when the SST level of the ozonized sample increases. c) Depending on the initial color, of the DQO and of the SST level of the sample, values from 10 to 53 %Rc were obtained after 10 min, and of 66 to 94 %Rc after 60 min

Estudio descriptivo del patrón de dieta y adherencia a la Dieta Mediterránea en pacientes con Enfermedad de Alzheimer prodrómica en La Rioja

Trabajo presentado en la Reunión Anual de la Sociedad de Neurología del País Vasco, celebrada en San Sebastián (España), los días 3 y 4 de marzo de 202

Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning.

BACKGROUND: TFIIS stimulates RNA cleavage by RNA polymerase II and promotes the resolution of backtracking events. TFIIS acts in the chromatin context, but its contribution to the chromatin landscape has not yet been investigated. Co-transcriptional chromatin alterations include subtle changes in nucleosome positioning, like those expected to be elicited by TFIIS, which are elusive to detect. The most popular method to map nucleosomes involves intensive chromatin digestion by micrococcal nuclease (MNase). Maps based on these exhaustively digested samples miss any MNase-sensitive nucleosomes caused by transcription. In contrast, partial digestion approaches preserve such nucleosomes, but introduce noise due to MNase sequence preferences. A systematic way of correcting this bias for massively parallel sequencing experiments is still missing. RESULTS: To investigate the contribution of TFIIS to the chromatin landscape, we developed a refined nucleosome-mapping method in Saccharomyces cerevisiae. Based on partial MNase digestion and a sequence-bias correction derived from naked DNA cleavage, the refined method efficiently mapped nucleosomes in promoter regions rich in MNase-sensitive structures. The naked DNA correction was also important for mapping gene body nucleosomes, particularly in those genes whose core promoters contain a canonical TATA element. With this improved method, we analyzed the global nucleosomal changes caused by lack of TFIIS. We detected a general increase in nucleosomal fuzziness and more restricted changes in nucleosome occupancy, which concentrated in some gene categories. The TATA-containing genes were preferentially associated with decreased occupancy in gene bodies, whereas the TATA-like genes did so with increased fuzziness. The detected chromatin alterations correlated with functional defects in nascent transcription, as revealed by genomic run-on experiments. CONCLUSIONS: The combination of partial MNase digestion and naked DNA correction of the sequence bias is a precise nucleosomal mapping method that does not exclude MNase-sensitive nucleosomes. This method is useful for detecting subtle alterations in nucleosome positioning produced by lack of TFIIS. Their analysis revealed that TFIIS generally contributed to nucleosome positioning in both gene promoters and bodies. The independent effect of lack of TFIIS on nucleosome occupancy and fuzziness supports the existence of alternative chromatin dynamics during transcription elongation

Cytogenetic and genomic analysis of a patient with turner syndrome and t(2;12): a case report

Background: Turner syndrome is a genetic disorder that afects women. It is caused by an absent or incomplete X chromosome, which can be presented in mosaicism or not. There are 12 cases of Turner syndrome patients who present structural alterations in autosomal chromosomes. Case presentation: The present case report describes a patient with a reciprocal, maternally inherited translocation between chromosomes 2 and 12 with a mosaicism of X monosomy 45,X,t(2;12)(p13;q24)[95]/46,XX,t(2;12)(p13;q24) [5]. Through genetic mapping arrays, altered genes in the patient were determined within the 23 chromosome pairs. These genes were associated with the patient’s clinical features using a bioinformatics tool Conclusion: To our knowledge, this is the frst case in which a translocation (2;12) is reported in a patient with Turner syndrome and confrmed by conventional cytogenetics, FISH and molecular genetics. Clinical features of our patient are closely related with the loss of one X chromosome, however mild intellectual disability can be likely explained by autosomal genes. The presence of familial translocations was a common fnding, thus emphasizing the need for familiar testing for further genetic counselling

A Quick Guide for Using Microsoft Onenote as an Electronic Laboratory Notebook

[Abstract] Scientific data recording and reporting systems are of a great interest for endorsing reproducibility and transparency practices among the scientific community. Current research generates large datasets that can no longer be documented using paper lab notebooks (PLNs). In this regard, electronic laboratory notebooks (ELNs) could be a promising solution to replace PLNs and promote scientific reproducibility and transparency. We previously analyzed five ELNs and performed two survey-based studies to implement an ELN in a biomedical research institute. Among the ELNs tested, we found that Microsoft OneNote presents numerous features related to ELN best functionalities. In addition, both surveyed groups preferred OneNote over a scientifically designed ELN (PerkinElmer Elements). However, OneNote remains a general note-taking application and has not been designed for scientific purposes. We therefore provide a quick guide to adapt OneNote to an ELN workflow that can also be adjusted to other nonscientific ELNs

USO DE MICROSOFT ONENOTE COMO CUADERNO ELECTRÓNICO DE LABORATORIO

Los sistemas de registro y de reporte de datos son de gran interés, puesto que respaldan la reproducibilidad y transparencia científica. La investigación actual genera una gran cantidad de datos que ya no se pueden documentar utilizando cuadernos de laboratorio de papel (CLP). Los cuadernos electrónicos de laboratorio (CEL) podrían ser una solu-ción prometedora para reemplazar los CLP y promover la reproducibilidad científica y su transparencia. Anteriormente analizamos cinco CEL y realizamos dos encuestas para implementar un CEL en un instituto de investigación biomédica. Entre los CEL proba-dos, encontramos que Microsoft OneNote presenta numerosas características relacio-nadas con las mejores funcionalidades del CEL. Además, ambos grupos encuestados prefirieron OneNote sobre un CEL científico (Elements de PerkinElmer). Sin embargo, OneNote es una aplicación general para tomar notas que no ha sido diseñada para fi-nes científicos. Por lo tanto, en este trabajo proporcionamos varias pautas para adaptar OneNote a un flujo de trabajo experimental

Amerindian Helicobacter pylori Strains Go Extinct, as European Strains Expand Their Host Range

We studied the diversity of bacteria and host in the H. pylori-human model. The human indigenous bacterium H. pylori diverged along with humans, into African, European, Asian and Amerindian groups. Of these, Amerindians have the least genetic diversity. Since niche diversity widens the sets of resources for colonizing species, we predicted that the Amerindian H. pylori strains would be the least diverse. We analyzed the multilocus sequence (7 housekeeping genes) of 131 strains: 19 cultured from Africans, 36 from Spanish, 11 from Koreans, 43 from Amerindians and 22 from South American Mestizos. We found that all strains that had been cultured from Africans were African strains (hpAfrica1), all from Spanish were European (hpEurope) and all from Koreans were hspEAsia but that Amerindians and Mestizos carried mixed strains: hspAmerind and hpEurope strains had been cultured from Amerindians and hpEurope and hpAfrica1 were cultured from Mestizos. The least genetically diverse H. pylori strains were hspAmerind. Strains hpEurope were the most diverse and showed remarkable multilocus sequence mosaicism (indicating recombination). The lower genetic structure in hpEurope strains is consistent with colonization of a diversity of hosts. If diversity is important for the success of H. pylori, then the low diversity of Amerindian strains might be linked to their apparent tendency to disappear. This suggests that Amerindian strains may lack the needed diversity to survive the diversity brought by non-Amerindian hosts

A Proof-Of-Principle Study of Epigenetic Therapy Added to Neoadjuvant Doxorubicin Cyclophosphamide for Locally Advanced Breast Cancer

BACKGROUND: Aberrant DNA methylation and histone deacetylation participate in cancer development and progression; hence, their reversal by inhibitors of DNA methylation and histone deacetylases (HDACs) is at present undergoing clinical testing in cancer therapy. As epigenetic alterations are common to breast cancer, in this proof-of-concept study demethylating hydralazine, plus the HDAC inhibitor magnesium valproate, were added to neoadjuvant doxorubicin and cyclophosphamide in locally advanced breast cancer to assess their safety and biological efficacy. METHODOLOGY: This was a single-arm interventional trial on breast cancer patients (ClinicalTrials.gov Identifier: NCT00395655). After signing informed consent, patients were typed for acetylator phenotype and then treated with hydralazine at 182 mg for rapid-, or 83 mg for slow-acetylators, and magnesium valproate at 30 mg/kg, starting from day –7 until chemotherapy ended, the latter consisting of four cycles of doxorubicin 60 mg/m(2) and cyclophosphamide 600 mg/m(2) every 21 days. Core-needle biopsies were taken from primary breast tumors at diagnosis and at day 8 of treatment with hydralazine and valproate. MAIN FINDINGS: 16 patients were included and received treatment as planned. All were evaluated for clinical response and toxicity and 15 for pathological response. Treatment was well-tolerated. The most common toxicity was drowsiness grades 1–2. Five (31%) patients had clinical CR and eight (50%) PR for an ORR of 81%. No patient progressed. One of 15 operated patients (6.6%) had pathological CR and 70% had residual disease <3 cm. There was a statistically significant decrease in global 5(m)C content and HDAC activity. Hydralazine and magnesium valproate up- and down-regulated at least 3-fold, 1,091 and 89 genes, respectively. CONCLUSIONS: Hydralazine and magnesium valproate produce DNA demethylation, HDAC inhibition, and gene reactivation in primary tumors. Doxorubicin and cyclophosphamide treatment is safe, well-tolerated, and appears to increase the efficacy of chemotherapy. A randomized phase III study is ongoing to support the efficacy of so-called epigenetic or transcriptional cancer therapy

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome