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Item type:Publication, From the Andes to the desert: First overview of the bacterial community in the Rimac river, the main source of water for Lima, Peru(Cold Spring Harbor Laboratory, 2020-08-16)Abstract Background The Rimac river is the main source of water for Lima, Peru’s capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. We aim to produce the first characterization of bacterial communities in the Rimac river using a 16S rRNA amplicon sequencing approach which would be useful to identify bacterial diversity and potential understudied pathogens. Results We report a higher diversity in bacterial communities from the Upper and, especially, Middle Rimac compared to the Lower Rimac (Metropolitan zone). Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility, quorum sensing and xenobiotics metabolism. Additional metabolomic analyses showed the presence natural flavonoids and antibiotics in the Upper Rimac, and herbicides in the Lower Rimac. Conclusions The dominance in the Metropolitan area of Arcobacter cryaerophilus , an emergent pathogen associated with fecal contamination and antibiotic multiresistance, but that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Coincidence detection of mitogenic signals via cytosolic pH regulates Cyclin D1 expression(Cold Spring Harbor Laboratory, 2020-07-16)Abstract Enhanced cell growth and proliferation are accompanied by profound changes in cellular metabolism. Originally identified as the Warburg effect in cancer, such metabolic changes are also common under physiological conditions and include increased fermentation and elevated cytosolic pH (pHc) 1,2 . However, how these changes contribute to enhanced cell growth and proliferation is unclear. Here, we demonstrate that elevated pHc specifically orchestrates an E2F-dependent transcriptional program to drive cell proliferation by promoting Cyclin D1 expression. pHc-dependent transcription of Cyclin D1 requires the transcription factors CREB1/ATF1 and ETS1 and the Histone Acetyltransferases p300/CBP. Interestingly, biochemical characterization revealed that the CREB1-p300/CBP interaction acts as a pH-sensor and coincidence detector linking different mitotic signals to Cyclin D1 transcription. We also show that elevated pHc contributes to increased Cyclin D1 expression in Malignant Pleural Mesotheliomas (MPMs) and renders them hypersensitive to pharmacological reduction of pHc. Taken together, these data demonstrate that elevated pHc is a critical cellular signal regulating G1 progression and provide a mechanism linking elevated pHc to oncogenic activation of Cyclin D1 in MPMs and possibly other Cyclin D1-dependent tumors. Thus, an increase of pHc may represent a functionally important, early event in the etiology of cancer amenable to therapeutic intervention. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, The Influence of Taxonomy and Environment on Leaf Trait Variation Along Tropical Abiotic Gradients(Frontiers Media S.A., 2020-03-03)Deconstructing functional trait variation and co-variation across a wide range of environmental conditions should increase the mechanistic understanding of community assembly processes and improve current parameterization of dynamic vegetation models. Here, we present a study that deconstructs leaf trait variation and co-variation to iithin-species, taxonomic-interspecific, and plot-environment components comparing three tropical environmental gradients in Peru, Brazil and Ghana. We measured photosynthetic, chemical and structural leaf traits using a standardized sampling protocol, totalling more than 1,000 individuals belonging to 367 species sampled. Variation associated with the whole interspecific taxonomic component (species+genus+family) for most traits was relatively consistent across environmental gradients, but intra-specificwithin-species variation and the plot-environment variation was strongly dependent on the environmental gradient. Trait-trait co-variation was also strongly linked to the environmental gradient where the traits were measured, although some traits had consistent co-variation components irrespective of environmental gradient. Our results demonstrate that filtering along gradients is mostly expressed through trait intra- and interspecifictaxonomic variation, but that trait co-variation is strongly dependent on the local environment, and thus global trait co-variation relationships might not always apply at smaller scales. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Cytosolic pH regulates proliferation and tumour growth by promoting expression of cyclin D1(Nature Research, 2020-11-01)Enhanced growth and proliferation of cancer cells are accompanied by profound changes in cellular metabolism. These metabolic changes are also common under physiological conditions, and include increased glucose fermentation accompanied by elevated cytosolic pH (pHc)1,2. However, how these changes contribute to enhanced cell growth and proliferation is unclear. Here, we show that elevated pHc specifically orchestrates an E2F-dependent transcriptional programme to drive cell proliferation by promoting cyclin D1 expression. pHc-dependent transcription of cyclin D1 requires the transcription factors CREB1, ATF1 and ETS1, and the histone acetyltransferases p300 and CBP. Biochemical characterization revealed that the CREB1–p300/CBP interaction acts as a pH sensor and coincidence detector, integrating different mitotic signals to regulate cyclin D1 transcription. We also show that elevated pHc contributes to increased cyclin D1 expression in malignant pleural mesotheliomas (MPMs), and renders these cells hypersensitive to pharmacological reduction of pHc. Taken together, these data demonstrate that elevated pHc is a critical cellular signal regulating G1 progression, and provide a mechanism linking elevated pHc to oncogenic activation of cyclin D1 in MPMs, and possibly other cyclin D1~dependent tumours. Thus, an increase of pHc may represent a functionally important, early event in the aetiology of cancer that is amenable to therapeutic intervention. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Changes in oak (Quercus robur) photosynthesis after winter moth (Operophtera brumata) herbivory are not explained by changes in chemical or structural leaf traits(Public Library of Science, 2020-01-01)Insect herbivores have the potential to change both physical and chemical traits of their host plant. Although the impacts of herbivores on their hosts have been widely studied, experiments assessing changes in multiple leaf traits or functions simultaneously are still rare. We experimentally tested whether herbivory by winter moth (Operophtera brumata) caterpillars and mechanical leaf wounding changed leaf mass per area, leaf area, leaf carbon and nitrogen content, and the concentrations of 27 polyphenol compounds on oak (Quercus robur) leaves. To investigate how potential changes in the studied traits affect leaf functioning, we related the traits to the rates of leaf photosynthesis and respiration. Overall, we did not detect any clear effects of herbivory or mechanical leaf damage on the chemical or physical leaf traits, despite clear effect of herbivory on photosynthesis. Rather, the trait variation was primarily driven by variation between individual trees. Only leaf nitrogen content and a subset of the studied polyphenol compounds correlated with photosynthesis and leaf respiration. Our results suggest that in our study system, abiotic conditions related to the growth location, variation between tree individuals, and seasonal trends in plant physiology are more important than herbivory in determining the distribution and composition of leaf chemical and structural traits. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures(Oxford University Press, 2020-11-20)The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classification scheme. The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class > Topology > Fold) with two new levels (Clan > Family) requiring sequence similarity and describing repeat motifs in collaboration with Pfam. Data growth has been addressed with improved mechanisms for browsing the classification hierarchy. A new UniProt-centric view unifies the increasingly frequent annotation of structures from identical or similar sequences. This update of RepeatsDB aligns with our commitment to develop a resource that extracts, organizes and distributes specialized information on tandem repeat protein structures. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, A Paleogenomic Reconstruction of the Deep Population History of the Andes(Cell Press, 2020-05-28)There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000–500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. Video Abstract: [Figure presented] Genome-wide data from 89 ancient humans illuminates the changes to the genetic landscape in the Central Andes over 9,000 years, revealing large-scale gene flow and cosmopolitan societies in the Tiwanaku and Inca polities. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Gut microbiota and Parkinson's disease(2021-12-01)It is possible for the non-motor symptoms (NMS) of Parkinson's disease (PD), which include constipation, sleep difficulties, and olfactory impairments, to appear up to 20 years before the motor symptoms of the disease. There is a growing body of research that suggests the pathology of Parkinson's disease may begin in the gastrointestinal tract and progress to the brain. Numerous studies provide credence to the idea that the microbiota in one's gut communicates with one's brain in Parkinson's disease (PD) via way of the immune system, a certain amino acid metabolism, and the neurological system. Through what has become known as the "gut microbiota-brain axis" (GMBA), the gut microbiota is thought to play an important part in the modulation of several neurochemical pathways.In the process of mediating the crosstalk between the gut microbiota and the physiology of the host, many of the metabolites produced by the gut microbiota, such as fatty acids, amino acids, and bile acids, carry signaling activities. In Parkinson's disease (PD), the quantity of amino acids and species-specific alterations of amino acids, such as glutamate and tryptophan, may interfere with the signaling transmission between nerve cells and disrupt the normal operation of the basal ganglia. Certain amino acids and the receptors that bind to them are being looked at as new possible targets for the treatment of PD. The of the current investigation was to compile and analyze all of the evidence that is currently available on the gut microbiota-derived amino acid metabolic changes that are related with PD. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Innova Biology Sciences. Revista científica de biología y conservación. Vol. 1, n.° 2 (2021). Número completo(European Organization for Nuclear Research, 2021-12-31)Entre las principales causas que favorecen el incremento de la contaminación ambiental se encuentran la falta de educación y de concientización ambiental, así como un deficiente sistema de información acerca de este tema, sobre todo, a nivel de publicaciones científicas. Por tal motivo, esta segunda edición de la revista Innova Biology Sciences gira en torno a la contaminación ambiental y los posibles efectos negativos que esta tiene en los ecosistemas y los seres vivos que habitan en ellos. Los artículos presentados en este número abordan distintos tipos de contaminación y los analizan desde diversos enfoques, con la intención de generar una reflexión acerca de los mismos. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Variation of non-structural carbohydrates across the fast-slow continuum in Amazon forest canopy trees(Wiley, 2021-11-20)Tropical tree species span a range of life‐history strategies within a fast–slow continuum. The position of a species within this continuum is thought to reflect a negative relationship between growth and storage, with fast‐growing species allocating more carbon to growth and slow‐growing species investing more in storage. For tropical species, the relationship between storage and life‐history strategies has been largely studied on seedlings and less so in adult trees. We evaluated how stored non‐structural carbohydrates (NSC) vary across adult trees spanning the fast–slow continuum in the Peruvian Amazon by: (a) analysing whole‐tree NSC in two species of contrasting growth and (b) investigating the relationships with key life‐history traits across a broader set of species. Our results are consistent with a growth–storage trade‐off. The analysis of whole‐tree NSC revealed that the slow‐growing Eschweilera coriacea stored about 2.7 times as much NSC as the fast‐growing Bixa arborea due to markedly higher storage in woody stems and roots. B. arborea also had higher seasonality in NSC, reflecting its strong seasonality in stem growth. Across a range of species, stem starch was negatively related to species growth rate and positively related to wood density. Given the role of NSC in mediating plants' response to stress, our results suggest that slow‐growing species with greater storage reserves may be more resilient to drought than fast‐growing species.