Search

Mitochondria are epicentres of eukaryotic metabolism and bioenergetics. Pioneering efforts in recent decades have established the core protein componentry of these organelles(1) and have linked their dysfunction to more than 150 distinct disorders(2,3). Still, hundreds of mitochondrial proteins lack clear functions(4), and the underlying genetic basis for approximately 40\% of mitochondrial disorders remains unresolved(5). Here, to establish a more complete functional compendium of human mitochondrial proteins, we profiled more than 200 CRISPR-mediated HAP1 cell knockout lines using mass spectrometry-based multiomics analyses. This effort generated approximately 8.3 million distinct biomolecule measurements, providing a deep survey of the cellular responses to mitochondrial perturbations and laying a foundation for mechanistic investigations into protein function. Guided by these data, we discovered that PIGY upstream open reading frame (PYURF) is an S-adenosylmethionine-dependent methyltransferase chaperone that supports both complex I assembly and coenzyme Q biosynthesis and is disrupted in a previously unresolved multisystemic mitochondrial disorder. We further linked the putative zinc transporter SLC30A9 to mitochondrial ribosomes and OxPhos integrity and established RAB5IF as the second gene harbouring pathogenic variants that cause cerebrofaciothoracic dysplasia. Our data, which can be explored through the interactive online MITOMICS.app resource, suggest biological roles for many other orphan mitochondrial proteins that still lack robust functional characterization and define a rich cell signature of mitochondrial dysfunction that can support the genetic diagnosis of mitochondrial diseases.

Mass spectrometry (MS) serves as the centerpiece technology for proteome, lipidome, and metabolome analysis. To have a better understanding of the multi-faceted networks of myriad regulatory layers in complex organisms, an integration on different layers of multi-omics is up-and-coming, including joint extraction methods of diverse biomolecular classes and comprehensive data analyses of different omics. Despite the versatility of MS systems, fractured methodology drives nearly all MS laboratories to specialize in analysis of a single ome at the exclusion of the others. Although liquid chromatography-mass spectrometry (LC-MS) analysis is similar for different biomolecular classes, the integration on the instrument level is lagging behind. The recent advancement on high flow proteomics enables us to take a first step on integration of proteins and lipids analysis. Here, we describe a technology to achieve broad and deep coverage of multiple molecular classes simultaneously through multi-omic single-shot technology (MOST) requiring only one column, one LC-MS instrument and a simplified workflow. MOST achieved great robustness and reproducibility. Its application on a Saccharomyces cerevisiae study consisting of 20 conditions revealed 2,842 protein groups and 325 lipids, and potential molecular relationships.

Despite the crucial roles of lipids in metabolism, we are still at the early stages of comprehensively annotating lipid species and their genetic basis. Mass spectrometry-based discovery lipidomics offers the potential to globally survey lipids and their relative abundances in various biological samples. To discover the genetics of lipid features obtained through high-resolution liquid chromatography-tandem mass spectrometry, we analysed liver and plasma from 384 diversity outbred mice, and quantified 3,283 molecular features. These features were mapped to 5,622 lipid quantitative trait loci and compiled into a public web resource termed LipidGenie. The data are cross-referenced to the human genome and offer a bridge between genetic associations in humans and mice. Harnessing this resource, we used genome-lipid association data as an additional aid to identify a number of lipids, for example gangliosides through their association with B4galnt1, and found evidence for a group of sex-specific phosphatidylcholines through their shared locus. Finally, LipidGenie's ability to query either mass or gene-centric terms suggests acyl-chain-specific functions for proteins of the ABHD family.

The molecular bases of how host genetic variation impact gut microbiome remain largely unknown. Here, we used a genetically diverse mouse population and systems genetics strategies to identify interactions between molecular phenotypes, including microbial functions, intestinal transcripts and cecal lipids that influence microbe-host dynamics. Quantitative trait loci (QTL) analysis identified genomic regions associated with variations in bacterial taxa, bacterial functions, including motility, sporulation and lipopolysaccharide production, and levels of bacterial- and host-derived lipids. We found overlapping QTL for the abundance of Akkermansia muciniphila and cecal levels of ornithine lipids (OL). Follow-up studies revealed that A. muciniphila is a major source of these lipids in the gut, provided evidence that OL have immunomodulatory effects and identified intestinal transcripts co-regulated with these traits. Collectively, these results suggest that OL are key players in A. muciniphila-host interactions and support the role of host genetics as a determinant of responses to gut microbes.

Mass spectrometry (MS) serves as the centerpiece technology for proteome, lipidome, and metabolome analysis. Despite the versatility of MS systems, fractured methodology drives nearly all MS laboratories to specialize in analysis of a single ome at the exclusion of the others. We describe a technology to achieve broad and deep coverage of multiple molecular classes simultaneously through multi-omic single-shot technology (MOST) requiring only one column, one LC-MS instrument and a simplified workflow.

We performed RNA-Seq and high-resolution mass spectrometry on 128 blood samples from COVID-19 positive and negative patients with diverse disease severities and outcomes. Quantified transcripts, proteins, metabolites, and lipids were associated with clinical outcomes in a curated relational database, uniquely enabling systems analysis and cross-ome correlations to molecules and patient prognoses. We mapped 219 molecular features with high significance to COVID-19 status and severity, many involved in complement activation, dysregulated lipid transport, and neutrophil activation. We identified sets of covarying molecules, e.g., protein gelsolin and metabolite citrate or plasmalogens and apolipoproteins, offering pathophysiological insights and therapeutic suggestions. The observed dysregulation of platelet function, blood coagulation, acute phase response, and endotheliopathy further illuminated the unique COVID-19 phenotype. We present a web-based tool (covid-omics.app) enabling interactive exploration of our compendium and illustrate its utility through a machine learning approach for prediction of COVID-19 severity., Graphical Abstract, Highlights · We surveyed biomolecules in 102 COVID-19 and 26 non-COVID-19 patient blood samples · We found 219 biomolecules strongly associated with COVID-19 status and severity · We observed pronounced dysregulation of lipid transport and neutrophil degranulation · Our resource of measurements and patient data is located at https://covid-omics.app, Leukocyte mRNA expression and plasma protein, metabolite, and lipid levels were measured in 102 COVID-19 and 26 non-COVID patient samples. 219 diverse biomolecules were strongly associated with COVID-19 status and severity and pointed to dysregulation of processes related to lipid transport, blood coagulation, acute phase response, endotheliopathy, and neutrophil degranulation in this disease.

Resumo Neste artigo, apresentamos a proposta teórico-metodológica de, ao contrário do que usualmente se faz, não tomarmos apenas as formas finais das pinturas e gravuras rupestres como objeto de análise. Propomos que se considere o processo de construção gráfica das figuras como objeto de estudo, colocando esse processo como algo em si relevante, e não apenas como meio para a forma final. A proposta é apresentada a partir de uma leitura teórica crítica (combinada a fontes etnográficas e arqueológicas) e por meio de exemplos concretos de análises que desenvolvemos, sob essa perspectiva, em diferentes áreas de Minas Gerais. Tomamos também como tema a construção de painéis, uma vez que percebemos que o processo de construção de figuras envolveu, muitas vezes, relações com figuras que já ocupavam os suportes. Abstract In this paper, we present a theoretical and methodological proposal that goes beyond analysing the final shape of paintings or carvings and instead considers the process of making figures and their graphic composition, viewing the production process itself as relevant and not just the means of achieving the final product. We start from theoretical discussions (combined with ethnographic and archaeological sources) and present examples from different areas of Minas Gerais (central Brazil) from this perspective. We also examine the construction of rock art panels, since we noticed that the process of constructing figures often involved relations with figures that already existed in these areas.

The microbial communities that inhabit the distal gut of humans and other mammals exhibit large inter-individual variation. While host genetics is a known factor that influences gut microbiota composition, the mechanisms underlying this variation remain largely unknown. Bile acids (BAs) are hormones that are produced by the host and chemically modified by gut bacteria. BAs serve as environmental cues and nutrients to microbes, but they can also have antibacterial effects. We hypothesized that host genetic variation in BA metabolism and homeostasis influence gut microbiota composition. To address this, we used the Diversity Outbred (DO) stock, a population of genetically distinct mice derived from eight founder strains. We characterized the fecal microbiota composition and plasma and cecal BA profiles from 400 DO mice maintained on a high-fat high-sucrose diet for ∼22 weeks. Using quantitative trait locus (QTL) analysis, we identified several genomic regions associated with variations in both bacterial and BA profiles. Notably, we found overlapping QTL forTuricibacter sp.and plasma cholic acid, which mapped to a locus containing the gene for the ileal bile acid transporter,Slc10a2. Mediation analysis and subsequent follow-up validation experiments suggest that differences inSlc10a2gene expression associated with the different strains influences levels of both traits and revealed novel interactions betweenTuricibacterand BAs. This work illustrates how systems genetics can be utilized to generate testable hypotheses and provide insight into host-microbe interactions.Author summaryInter-individual variation in the composition of the intestinal microbiota can in part be attributed to host genetics. However, the specific genes and genetic variants underlying differences in the microbiota remain largely unknown. To address this, we profiled the fecal microbiota composition of 400 genetically distinct mice, for which genotypic data is available. We identified many loci of the mouse genome associated with changes in abundance of bacterial taxa. One of these loci is also associated with changes in the abundance of plasma bile acids—metabolites generated by the host that influence both microbiota composition and host physiology. Follow up validation experiments provide mechanistic insights linking host genetic differences, with changes in ileum gene expression, bile acid-bacteria interactions and bile acid homeostasis. Together, this work demonstrates how genetic approaches can be used to generate testable hypothesis to yield novel insight into how host genetics shape gut microbiota composition.

The biosynthesis of coenzyme Q presents a paradigm for how cells surmount hydrophobic barriers in lipid biology. In eukaryotes, CoQ precursors—among nature’s most hydrophobic molecules—must somehow be presented to a series of enzymes peripherally associated with the mitochondrial inner membrane. Here, we reveal that this process relies on custom lipid-binding properties of COQ9. We show that COQ9 repurposes the bacterial TetR fold to bind aromatic isoprenes with high specificity, including CoQ intermediates that likely reside entirely within the bilayer. We reveal a process by which COQ9 associates with cardiolipin-rich membranes and warps the membrane surface to access this cargo. Finally, we identify a molecular interface between COQ9 and the hydroxylase COQ7, motivating a model whereby COQ9 presents intermediates directly to CoQ enzymes. Overall, our results provide a mechanism for how a lipid binding protein might access, select, and deliver specific cargo from a membrane to promote biosynthesis.

The purpose of this work was to investigate new bone formation in macroporous iron foams coated with strontium (FeSr) or bisphosphonate (FeBiP) compared to plain iron foam (Fe) and empty defect in a critical size metaphyseal bone defect model in ovariectomized rats. 60 female rats were subjected to bilateral ovariectomy and multi-deficient diet for 3 months. A 4 mm wedge shaped metaphyseal osteotomy was created, fixed with a mini-plate and subsequently filled with Fe, FeSr, FeBiP or left empty. After 6 weeks, mCt analysis revealed a statistically significant increased bone formation at the implant interface in FeSr compared to FeBiP (p = 0.035) and Fe (p = 0.002), respectively. Increased mineralized tissue was also seen within the pores in FeSr (p = 0.023) compared to Fe. Histomorphometry revealed significantly increased bone formation at the implant interface in FeSr (p < 0.001) and FeBiP (p = 0.006) compared to plain Fe with increased osteoblast and decreased osteoclast activity in combination with increased BMP2 and decreased RANKL/OPG in immunohistochemistry. ToF-SIMS analysis showed overlapping Ca signals with Fe for both FeSr and FeBiP thereby indicating tissue in-growth into the scaffolds. In conclusion, iron foam with strontium or bisphosphonate coating are of further interest in metaphyseal fracture defects in osteopenic bone.

Traditionally regarded to coordinate movement, the cerebellum also exerts non-motor functions including the regulation of cognitive and behavioral processing, suggesting a potential role in neurodegenerative conditions affecting cognition, such as Alzheimer's disease (AD). This study aims to investigate neuropathology and AD-related molecular changes within the neocerebellum using post-mortem human brain tissue microarrays (TMAs). Immunohistochemistry was conducted on neocerebellar paraffin-embedded TMAs from 24 AD and 24 matched control cases, and free-floating neocerebellar sections from 6 AD and 6 controls. Immunoreactivity was compared between control and AD groups for neuropathological hallmarks (amyloid-β, tau, ubiquitin), Purkinje cells (calbindin), microglia (IBA1, HLA-DR), astrocytes (GFAP) basement-membrane associated molecules (fibronectin, collagen IV), endothelial cells (CD31/PECAM-1) and mural cells (PDGFRβ, αSMA). Amyloid-β expression (total immunolabel intensity) and load (area of immunolabel) was increased by >4-fold within the AD cerebellum. Purkinje cell counts, ubiquitin and tau immunoreactivity were unchanged in AD. IBA1 expression and load was increased by 91% and 69%, respectively, in AD, with no change in IBA1-positive cell number. IBA1-positive cell process length and branching was reduced by 22% and 41%, respectively, in AD. HLA-DR and GFAP immunoreactivity was unchanged in AD. HLA-DR-positive cell process length and branching was reduced by 33% and 49%, respectively, in AD. Fibronectin expression was increased by 27% in AD. Collagen IV, PDGFRβ and αSMA immunoreactivity was unchanged in AD. The number of CD31-positive vessels was increased by 98% in AD, suggesting the increase in CD31 expression and load in AD is due to greater vessel number. The PDGFRβ/CD31 load ratio was reduced by 59% in AD. These findings provide evidence of molecular changes affecting microglia and the neurovasculature within the AD neocerebellum. These changes, occurring without overt neuropathology, support the hypothesis of microglial and neurovascular dysfunction as drivers of AD, which has implications on the neocerebellar contribution to AD symptomatology and pathophysiology.

Ao longo de aproximados quarenta anos de pesquisas arqueológicas no Centro e Norte de Minas Gerais, nos quais os grafismos rupestres foram contemplados, criou-se um cenário de um quase contínuo de áreas pesquisadas. Nestas as pesquisas dos vestígios gráficos parietais foram organizados em conjuntos, utilizando-se das grandes unidades classificatórias usuais na Arqueologia, dialogando com os conceitos de estilo e tradição. Esta pesquisa comparou os conjuntos gráficos de algumas regiões do centro e norte de Minas Gerais a partir de análises tipológicas e de associação temática a fim de se discutir as atribuições dos conjuntos em categorias classificatórias amplas e o delineamento de possíveis territórios. Para tanto se utilizou de conjuntos de dados primários e secundários, os últimos disponíveis das dissertações, teses, artigos e acervos do Museu de História Natural da UFMG e de diálogos entre o conceito de estilo, e próprios da reflexão metodológica, buscando uma aproximação entre a produção bibliográfica arqueológica e antropológica. In a forty years period of archeological researches in the Center and in the North of Minas Gerais, in which rock art was contemplated, a scenario of an almost uninterrupted researched areas was created. In these areas, the parietal graphics traces were organized in sets, using the great classificatory unities, usual in archaeology, communicating with the notions of style and tradition. This research compared the graphical sets of some regions of the north and center of Minas Gerais, making use of typological analyses and thematic associations, aiming to discuss the filiations of the sets in wide classificatory categories and the design of some possible territories. In order to achieve it, sets of primary and secondary data were utilized, the ones that are available in the dissertations, thesis, articles and collections of Museu de História Natural da Universidade Federal de Minas Gerais and in dialogs between concept and style, and others associated to the methodological reflection, sighting an approach between the anthropological and archaeological bibliographic production.

O trabalho não tem resumo

Resumo: a Lapa do Caboclo, em Diamantina (Minas Gerais), apresenta em suas ocupações do Holoceno Superior, quatro estruturas funerárias, correspondendo a sepultamentos secundários de composição sofisticada. Apresentamos os estudos bioarqueológicos, elementos do processo de escavação e características das estruturas (constituídas por estojos de cascas de árvores, com ossos recobertos de pigmentos, resina, penas e couro), construindo interpretações sobre as práticas funerárias. Palavras-chave: Sepultamentos secundários. Holoceno Superior. Serra do Espinhaço. Horticultores. Arqueologia Pré-histórica.

Campo das Flores se localiza na bacia do rio Araçuaí, entre os municípios de Senador Modestino Gonçalves e Itamarandiba-MG, no Alto Jequitinhonha. Esta pesquisa teve como preocupação investigar quais as relações que podem ser tecidas entre os sítios com registro rupestre; entre os suportes pintados e não pintados. Buscou-se observar se houve escolhas ou padrão (es) de inserção desses sítios na paisagem e se eles foram ocupados diacronicamente ou sincronicamente no espaço. Para atender o objetivo proposto, embarcou-se na corrente Arqueologia da paisagem, abordou-se a área de forma espacial (inter-sítio) e ao mesmo tempo intra-sítio, observou-se as particularidades de cada sítio e também dos lugares potenciais que aparentemente não apresentou registros rupestres visíveis hoje, mas que podem ter sido ocupados ou participado de processos seletivos de qual lugar pintar. A metodologia utilizada, se respalda em intensivos trabalhos de campo, aplicação de fichas de análise, calque em plástico, consulta a literatura, processamentos de imagens no CorelDraw®, processamento de dados no SPSS® e levantamentos cartográficos por meio do ArcGis®.Os resultados obtidos nesta dissertação destinam-se a oferecer informações da Arqueologia local, para as próprias comunidades que ali estão e somar forças, com outras pesquisas que têm sido desenvolvidas nesta área pelo LAEP/UFVJM e com o Setor de Arqueologia da UFMG na região de Diamantina-MG. Field of Flowers is located in the Araçuaí River basin, between the municipalities Senador Modestino Gonçalves and Itamarandiba-MG in Upper Jequitinhonha. This research had the concern investigate the relations which we can weave between sites with rock record; between the painted and unpainted supports. It sought to observe if there was choices or pattern (s) of insertion of these sites in the landscape and if they were occupied diachronically or synchronically in space.To cater the proposed objective, embarked if on flowing archeology of the landscape, addressing the area of spatial form (inter-site) and at the same intra-site time, it was observed the particularities of each site and also the potential places that seemingly show no visible rock records today, but that may have been occupied or participated in 'selective processes' of which place to paint. The methodology used, if endorses in intensive fieldwork, application of analysis tokens, plastic calque, consultation the literature, image processing in CorelDraw®, data processing in SPSS and cartographic surveys through the ArcGis®. The results obtained in this dissertation it is intended to offer information of the local archeology, to the communities that are there and join forces with other research that has been developed in this area by LAEP / UFVJM and by the UFMG Archaeology Sector in the region of Diamantina-MG.

A região de Diamantina (MG) tem sido alvo de esforços múltiplos em pesquisas arqueológicas, sobretudo aquelas relacionadas a seu passado pré-colonial. Esta pesquisa se insere em um contexto onde diversos levantamentos arqueológicos e questionamentosrelativos às diferentes ocupações grupos pré-coloniais se fazem presentes. O trabalho abordará os registros rupestres de 24 sítios arqueológicos localizados no alto curso do rio Pardo Pequeno, afluente do rio São Francisco. As análises tiveram como norte teóricometodológico conceitos de como paisagem e estilo, entendidos como peculiares a cada formação sociocultural. Estes conceitos foram apropriados na pesquisa em função da necessidade de se compreender as formas particulares que sugerem as diferentes temáticas, inserções dos sítios na paisagem bem como as possíveis relações estabelecidas entre eles e as figurações. Na caracterização das figuras foram priorizadas análises que incorporaram diferentes critérios estilísticos e cronológicosarticulados com os atributos que compõem a paisagem. Os resultados da pesquisa indicam a presença de distintos conjuntos rupestres com diferentes intencionalidades, escolhas, relações estabelecidas com a paisagem e com figurasprecedentes The region of Diamantina (MG) has been the subject of multiple efforts in archaeological research, especially those related to its pre-colonial past. This research is part of a context where several archaeological surveys and inquiries for the various pre-colonial occupations groups are present. The work will approach to the rock art of 24 archaeological sites in the upper course of the river Pardo Pequeno,tributary of the São Francisco river. The analysis had as theoretical and methodological north concepts as landscape and style, perceived as peculiar to each socio-cultural formation. These concepts were appropriate in the function research due to the need to understand the particular forms that suggest different themes, insertions of the sites in the landscape as well as possible relations established between them and the figurations. In the characterization of the figures were prioritized analyzes that incorporatedvarious stylistic and chronological criteria articulated with the attributes that compose the landscape. The survey results indicate the presence of different rock sets with different intentions, choices, relations with the landscape and with previous figures.