The World In A Candy Bar

To define the geographic theme "movement." To understand the definition of "system." To identify and locate examples of systems on a world map. To understand the interconnectedness of systems throughout the world. To recognize how events in one part of the global system have potential consequences on the workings of the system as a whole.This lesson is from the National Geographic Society Geography Education Program, 198

Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability.

This is the author accepted manuscript. It is currently under an indefinite embargo pending publication by the Public Library of Science.The advancement of high-throughput sequencing (HTS) technologies and the rapid development of numerous analysis algorithms and pipelines in this field has resulted in an unprecedentedly high demand for training scientists in HTS data analysis. Embarking on developing new training materials is challenging for many reasons. Trainers often do not have prior experience in preparing or delivering such materials and struggle to keep them up to date. A repository of curated HTS training materials would support trainers in materials preparation, reduce the duplication of effort by increasing the usage of existing materials, and allow for the sharing of teaching experience among the HTS trainers' community. To achieve this, we have developed a strategy for materials' curation and dissemination. Standards for describing training materials have been proposed and applied to the curation of existing materials. A Git repository has been set up for sharing annotated materials that can now be reused, modified, or incorporated into new courses. This repository uses Git; hence, it is decentralized and self-managed by the community and can be forked/built-upon by all users. The repository is accessible at http://bioinformatics.upsc.se/htmr.COST action SeqAhead (BM1006

Estudio del metaboloma en el antagonismo microbiano a través de cromatografía líquida con algoritmos quimiométricos.

El metaboloma es el conjunto de compuestos orgánicos de bajo peso molecular (metabolitos) producidos por sistemas biológicos. El antagonismo microbiano es una importante fuerza evolutiva, por lo que el análisis de su metaboloma es una herramienta útil para la búsqueda de nuevas moléculas con actividad biológica. El objetivo de este trabajo fue implementar el uso de algoritmos quimiométricos para la identificación de variaciones en el metaboloma del antagonismo microbiano entre Pseudovibrio denitrificans y Vibrio harveyi. Extractos de bacterias y del medio de cultivo usado fueron analizados por cromatografía líquida de ultra alta eficiencia acoplada a un detector de arreglo de iodos (UHPLC-DAD). Además, algoritmos imiométricos fueron aplicados realizando un Análisis de Componentes Principales (PCA) de los cromatogramas obtenidos. Se encontraron tres picos que expresaron una mayor variabilidad entre el metaboloma individual y el metaboloma de la interacción de P. denitrificans y V. harveyi. De esta manera, la metabolómica con UHPLC-DAD y algoritmos quimiométricos demostró ser una herramienta útil para la identificación de picos responsables de las diferencias entre interacciones microbianas.Metabolome is a group of low molecular weight organic compounds (metabolites) produced by biological systems. Bacterial antagonism is an important evolving force, in this sense analysis of its metabolome represents a useful tool for discovering new molecules with biological activity. The objective of this research work was to implement the use of chemometric algorithms for the identification of variations in the metabolome of the microbial antagonism between Pseudovibrio denitrificans and Vibrio harveyi. Extracts from cultured bacteria and used culture media were analyzed by Ultra-high performance liquid chromatography coupled with a diode-array detector (UHPLC-DAD). Additionally, chemometric algorithms were employed, subjecting to Principal Component Analysis (PCA) for the obtained chromatograms. Three peaks were found that express the major variability between the individual metabolome and the metabolome from the interaction of P. denitrificans and V. harveyi. In this manner, metabolomic through UHPLCDAD and chemometric algorithms, showed to be a useful tool to identify the peaks responsible for differences between microbial interactions

Indirect evaluation of Mars Gravity Model 2011 using a replication experiment on Earth

Curtin University’s Mars Gravity Model 2011 (MGM2011) is a high-resolution composite set of gravity field functionals that uses topography-implied gravity effects at medium- and short-scales (~125 km to ~3 km) to augment the space-collected MRO110B2 gravity model. Ground-truth gravity observations that could be used for direct validation of MGM2011 are not available on Mars’s surface. To indirectly evaluate MGM2011 and its modelling principles, an as-close-as-possible replication of the MGM2011 modelling approach was performed on Earth as the planetary body with most detailed gravity field knowledge available. Comparisons among six ground-truth data sets (gravity disturbances, quasigeoid undulations and vertical deflections) and the MGM2011-replication over Europe and North America show unanimously that topography-implied gravity information improves upon space-collected gravity models over areas with rugged terrain. The improvements are ~55% and ~67% for gravity disturbances, ~12% and ~47% for quasigeoid undulations, and ~30% to ~50% for vertical deflections. Given that the correlation between space-collected gravity and topography is higher for Mars than Earth at spatial scales of a few 100 km, topography-implied gravity effects are more dominant on Mars. It is therefore reasonable to infer that the MGM2011 modelling approach is suitable, offering an improvement over space-collected Martian gravity field models

HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens

Humanity is currently facing the challenge of two devastating pandemics caused by two very different RNA viruses: HIV-1, which has been with us for decades, and SARS-CoV-2, which has swept the world in the course of a single year. The same evolutionary strategies that drive HIV-1 evolution are at play in SARS-CoV-2. Single nucleotide mutations, multi-base insertions and deletions, recombination, and variation in surface glycans all generate the variability that, guided by natural selection, enables both HIV-1’s extraordinary diversity and SARS-CoV-2’s slower pace of mutation accumulation. Even though SARS-CoV-2 diversity is more limited, recently emergent SARS-CoV-2 variants carry Spike mutations that have important phenotypic consequences in terms of both antibody resistance and enhanced infectivity. We review and compare how these mutational patterns manifest in these two distinct viruses to provide the variability that fuels their evolution by natural selection.Fil: Fischer, Will. Los Alamos National Laboratory; Estados Unidos. New Mexico Consortium; MéxicoFil: Giorgi, Elena E.. New Mexico Consortium; México. Los Alamos National Laboratory; Estados UnidosFil: Chakraborty, Srirupa. Center For Nonlinear Studies; Estados Unidos. Los Alamos National Laboratory; Estados UnidosFil: Nguyen, Kien. Los Alamos National Laboratory; Estados UnidosFil: Bhattacharya, Tanmoy. Los Alamos National Laboratory; Estados UnidosFil: Theiler, James. Los Alamos National Laboratory; Estados UnidosFil: Goloboff, Pablo Augusto. American Museum of Natural History; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; ArgentinaFil: Yoon, Hyejin. Los Alamos National Laboratory; Estados UnidosFil: Abfalterer, Werner. Los Alamos National Laboratory; Estados UnidosFil: Foley, Brian T.. Los Alamos National Laboratory; Estados UnidosFil: Tegally, Houriiyah. University Of Kwazulu-natal; SudáfricaFil: San, James Emmanuel. University Of Kwazulu-natal; SudáfricaFil: de Oliveira, Tulio. University of KwaZulu-Natal; SudáfricaFil: Gnanakaran, Sandrasegaram. Los Alamos National Laboratory; Estados UnidosFil: Korber, Bette. Los Alamos National Laboratory; Estados Unidos. New Mexico Consortium; Méxic

Widespread shortfalls in protected area resourcing undermine efforts to conserve biodiversity

Protected areas (PAs) are a key tool in efforts to safeguard biodiversity against increasing anthropogenic threats. As signatories to the 2011–2020 Strategic Plan for Biodiversity, 196 nations pledged support for expansion in the extent of the global PA estate and the quality of PA management. While this has resulted in substantial increases in PA designations, many sites lack the resources needed to guarantee effective biodiversity conservation. Using management reports from 2167 PAs (with an area representing 23% of the global terrestrial PA estate), we demonstrate that less than a quarter of these PAs report having adequate resources in terms of staffing and budget. Using data on the geographic ranges of the 11,919 terrestrial vertebrate species overlapping our sample of PAs, we estimate that only 4–9% of terrestrial amphibians, birds, and mammals are sufficiently represented within the existing global PA estate, when only adequately resourced PAs are considered. While continued expansion of the world's PAs is necessary, a shift in emphasis from quantity to quality is critical to effectively respond to the current biodiversity crisis.</jats:p

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.

Among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (i) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (ii) interactions of Spike with ACE2 receptors, and (iii) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any genomes within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron over all previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected