Structure of the lectin mannose 6-phosphate receptor homology (MRH) domain of glucosidase II an enzyme that regulates glycoprotein folding quality control in the endoplasmic reticulum

Here we report for the first time the three-dimensional structure of a mannose 6-phosphate receptor homology (MRH) domain present in a protein with enzymatic activity, glucosidase II (GII). GII is involved in glycoprotein folding in the endoplasmic reticulum. GII removes the two innermost glucose residues from the Glc3Man9GlcNAc2 transferred to nascent proteins and the glucose added by UDP-Glc:glycoprotein glucosyltransferase. GII is composed of a catalytic GIIα subunit and a regulatory GIIβ subunit. GIIβ participates in the endoplasmic reticulum localization of GIIα and mediates in vivo enhancement of N-glycan trimming by GII through its C-terminal MRH domain. We determined the structure of a functional GIIβ MRH domain by NMR spectroscopy. It adopts a β-barrel fold similar to that of other MRH domains, but its binding pocket is the most shallow known to date as it accommodates a single mannose residue. In addition, we identified a conserved residue outside the binding pocket (Trp-409) present in GIIβ but not in other MRHs that influences GII glucose trimming activity.Fil: Olson, Linda J.. Medical College Of Wisconsin; Estados UnidosFil: Orsi, Ramiro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Alculumbre, Solana G.. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Peterson, Francis C.. Medical College Of Wisconsin; Estados UnidosFil: Stigliano, Ivan Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Parodi, Armando Jose A.. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: D'alessio, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Universidad de Buenos Aires; ArgentinaFil: Dahms, Nancy M.. Medical College Of Wisconsin; Estados Unido

Pingu virus : a new picornavirus in penguins from Antarctica

Picornaviridae family comprises single-stranded, positive-sense RNA viruses distributed into forty-seven genera. Picornaviruses have a broad host range and geographic distribution in all continents. In this study, we applied a high-throughput sequencing approach to examine the presence of picornaviruses in penguins from King George Island, Antarctica. We discovered and characterized a novel picornavirus from cloacal swab samples of gentoo penguins (Pygoscelis papua), which we tentatively named Pingu virus. Also, using RT-PCR we detected this virus in 12.9 per cent of cloacal swabs derived from P. papua, but not in samples from adelie penguins (Pygoscelis adeliae) or chinstrap penguins (Pygoscelis antarcticus). Attempts to isolate the virus in a chicken cell line and in embryonated chicken eggs were unsuccessful. Our results expand the viral diversity, host range, and geographical distribution of the Picornaviridae52FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP13/14929-1; 17/13981-0; 12/24150-9; 15/05778-5; 14/20851-8, 16/01414-1; 06/00572-0This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo, Brazil (Grant no. 13/14929-1, and Scholarships nos. 17/13981-0; 12/24150-9; 15/05778-5; 14/20851-8; 16/01414-1; 06/00572-0). P.R.M. was supported by the Medical Research Council of the UK (Grant no. MC_UU_120/14/9

Three bird species new to Brazil from the serra da mocidade, a remote mountain in Roraima

From 15 January to 06 February 2016, we conducted an expedition to the Serra da Mocidade, a remote and previously unexplored mountain range in extreme northern Amazonian Brazil. There we encountered three bird species never before documented in Brazilian territory: Grallaria guatimalensis (Grallariidae) was photographed, audio recorded, video recorded and a single specimen collected; Catharus aurantiirostris (Turdidae) was similarly documented and a series of specimens collected; and a single individual of Parkesia motacilla (Parulidae) was photographed. All were found in the understory of montane forest at 1000–1550 m elevation. We interpret each of these as most likely representing a regularly occurring population on Mocidade. However, each had probably been overlooked in Brazil for a different reason and represents a distinct distributional pattern. Adding these novelties to Brazil's previously published total of 1919 species clearly expresses the country's position among the most bird-rich in the world, perhaps the richest, and suggests that further exploration of Brazil's Amazonian mountains will yield more discoveries. © 2019, Sociedade Brasileira de Ornitologia. All rights reserved

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

Crystal Structure and Functional Analyses of the Lectin Domain of Glucosidase II: Insights into Oligomannose Recognition

N-Glycans are modified as part of a quality control mechanism during glycoprotein folding in the endoplasmic reticulum (ER). Glucosidase II (GII) plays a critical role by generating monoglucosylated glycans that are recognized by lectin chaperones, calnexin and calreticulin. To understand how the hydrolytic activity of GIIα is enhanced by the mannose 6-phosphate receptor (MPR) homology domain (MRH domain) of its β subunit, we now report a 1.6 Å resolution crystal structure of the MRH domain of GIIβ bound to mannose. A comparison of ligand-bound and unbound structures reveals no major difference in their overall fold, but rather a repositioning of side chains throughout the binding pocket, including Y372. Mutation of Y372 inhibits GII activity, demonstrating an important role for Y372 in regulating GII activity. Comparison of the MRH domains of GIIβ, MPRs, and the ER lectin OS-9 identified conserved residues that are critical for the structural integrity and architecture of the carbohydrate binding pocket. As shown by nuclear magnetic resonance spectroscopy, mutations of the primary binding pocket residues and adjacent W409, all of which inhibit the activity of GII both in vitro and in vivo, do not cause a significant change in the overall fold of the GIIβ MRH domain but impact locally the stability of the binding pocket. W409 does not directly contact mannose; rather, its indole ring is stabilized by binding into a hydrophobic pocket of an adjacent crystallographic neighbor. This suggests that W409 interacts with a hydrophobic region of the GIIβ or GIIα subunit to modulate its effect on GII activityFil: Olson, Linda J.. Medical College Of Wisconsin; Estados UnidosFil: Orsi, Ramiro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. Fundación Instituto Leloir; ArgentinaFil: Peterson, Francis C.. Medical College Of Wisconsin; Estados UnidosFil: Parodi, Armando Jose A.. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. Fundación Instituto Leloir; ArgentinaFil: Kim, Jung Ja. Medical College Of Wisconsin; Estados UnidosFil: D'alessio, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. Fundación Instituto Leloir; Argentina. Universidad de Buenos Aires. Departamento de Ciencias Exactas; ArgentinaFil: Dahms, Nancy M.. Medical College Of Wisconsin; Estados Unido

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

11 pages, 7 figures, 2 tablesFlagellated heterotrophic microeukaryotes have key roles for the functioning of marine ecosystems as they channel large amounts of organic carbon to the upper trophic levels and control the population sizes of bacteria and archaea. Still, we know very little on the diversity patterns of most groups constituting this evolutionary heterogeneous assemblage. Here, we investigate 11 groups of uncultured flagellates known as MArine STramenopiles (MASTs). MASTs are ecologically very important and branch at the base of stramenopiles. We explored the diversity patterns of MASTs using pyrosequencing (18S rDNA) in coastal European waters. We found that MAST groups range from highly to lowly diversified. Pyrosequencing (hereafter ‘454’) allowed us to approach to the limits of taxonomic diversity for all MAST groups, which varied in one order of magnitude (tens to hundreds) in terms of operational taxonomic units (98% similarity). We did not evidence large differences in activity, as indicated by ratios of DNA:RNA-reads. Most groups were strictly planktonic, although we found some groups that were active in sediments and even in anoxic waters. The proportion of reads per size fraction indicated that most groups were composed of very small cells (~2–5 μm). In addition, phylogenetically different assemblages appeared to be present in different size fractions, depths and geographic zones. Thus, MAST diversity seems to be highly partitioned in spatial scales. Altogether, our results shed light on these ecologically very important but poorly known groups of uncultured marine flagellatesFinancial support for this work has been provided by a Marie Curie Intra-European Fellowship grant (PIEF-GA-2009-235365) to RL and by projects BioMarKs (2008-6530, ERA-net Biodiversa, EU) and FLAME (CGL2010-16304, MICINN, Spain) to RM. Large-scale computing resources were provided by the Canarian Institute of Astrophysics (www.iac.es), through the Barcelona Supercomputer Center and the Spanish Network of Supercomputing (grants BCV-2010-3-0003 and 2011-2-0003/3-0005 to RL and RM). We thank the BioMarKs consortium for undertaking the sampling and performing the initial laboratory processing of the samples, in particular Sarah Romac. We thank Hiroyuki Ogata and Jean-Michel Claverie for the implementation of bioinformatics tools through a BioMarKs grant and a project from the French National Research Agency (ANR-08-BDVA-003) to Jean-Michel Claverie. Javier del Campo is thanked for providing curated Sanger sequences of Ochrophyta. Berit Kaasa at the University of Oslo is thanked for running the nutrient analyses. We thank the three reviewers and the editor who helped to improve this workPeer reviewe

O ESPAÇO TERRITORIAL COMO REFERÊNCIA PARA A CONSTRUÇÃO DA CIDADANIA: UMA REFLEXÃO GEOGRÁFICA INTRODUTÓRIA SOBRE O PROBLEMA DAS DEMARCAÇÕES DE TERRAS DE POPULAÇÕES “REMANESCENTES”

Territorially, the Brazilian history is loaded with conflicts and antagonisms. The modernization towards the cities and expansion of the internal market of consumption, national foundations of the new order, conflicts, not a few times, with interests of local collectivities. The deliberate design of the state to achieve new levels of production, with the expansion of production and flow in the territory, has not been accompanied by a similar policy of effective recognition of the different "nations" that formed the national population. More recently, the surface is the discussion on the "remnants", new creations of social emerge where new political subjects. The recognition of these multiple subject presents a reality in which differ widely among themselves. Regarding the territorial quilombola, is the clear differentiation of strong socio-stamp this area both with regard to the origins and ownership of the land, about the events of this (cultural, religious, located in the national territory, the type of housing and size of the community, use of resources, training and recognition in the fight, and so on.). Before this destruction, the rearrangement of productive activities and cultural, produces new relationships that can be considered hybrid. This hybridization, however, follows the logic, it seems, apart from the inclusion.Territorialmente, a história brasileira é carregada de conflitos e antagonismos. A modernização rumo às cidades e a ampliação do mercado interno de consumo, alicerces da nova ordem nacional, conflita, não poucas vezes, com interesses de coletividades locais. O projeto deliberado do Estado de alcançar novos níveis produtivos, com a ampliação da produção e da fluidez dentro do território, não foi acompanhado de uma política semelhante de reconhecimento efetivo dos diferentes “povos” que compunham a população nacional. Mais recentemente, vem a tona a discussão sobre os “remanescentes”, novas criações sociais de onde emergem novos sujeitos políticos. O reconhecimento desses sujeitos apresenta uma realidade múltipla em que diferem bastante entre si. No que se refere à territorialidade quilombola, são nítidas as diferenciações de forte cunho sócio-territorial presente tanto no que diz respeito às origens e posse da terra, quanto às manifestações do presente (culturais, religiosas, de localização no território nacional, do tipo de habitação e tamanho da coletividade, uso dos recursos, estágio na luta e reconhecimento, etc.). Diante desta desestruturação, o rearranjo das atividades produtivas e culturais, produz novas relações que podem ser consideradas híbridas. Esta hibridização, no entanto, obedece a uma lógica, ao que parece, distante da inclusão