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1.
Nature ; 626(8001): 948-951, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38409541
2.
Bioessays ; 44(9): e2200098, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35832007

RESUMO

A closer look at Wilhelm Ostwald's articles that originally proposed the concept of autocatalysis reveals that he accepted reactants, not just products, as potential autocatalysts. Therefore, that a process is catalyzed by some of its products, which is the common definition of autocatalysis, is only a proper subset of what Ostwald meant by "Autokatalyse." As a result, it is necessary to reconsider the definition of autocatalysis, which is especially important for origins-of-life research because autocatalysis provides an abiotic mechanism that yields reproduction-like dynamics. Here, we translate and briefly review the two key publications on autocatalysis by Ostwald to revive his understanding of autocatalysis, and we introduce the concepts of recessive and expansive autocatalysis. Then we discuss the twofold significance of such a revival: first, facilitating the search for candidate processes underlying the origins of life, and second, updating our view of autocatalysis in complex reaction networks and metabolism.


Assuntos
Catálise
3.
J Low Genit Tract Dis ; 27(2): 125-130, 2023 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-36794761

RESUMO

OBJECTIVE: This study aimed to analyze which clinical characteristics are associated with recurrence and progression of vulvar high-grade squamous intraepithelial lesion (vHSIL). MATERIALS AND METHODS: This was a retrospective cohort study, including all women with vHSIL followed in 1 center between 2009 and 2021. Women with a concomitant diagnosis of invasive vulvar cancer were excluded. Medical records were reviewed for demographic factors, clinical data, treatment type, histopathologic results, and follow-up information. RESULTS: A total of 30 women were diagnosed with vHSIL. The median follow-up time was 4 years (range = 1-12 years). More than half of the women (56.7% [17/30]) underwent excisional treatment, whereas 26.7% (8/30) underwent combined (excisional plus medical) treatment, and 16.7% (5/30) only had medical treatment (imiquimod). Six women had recurrence of vHSIL (20% [6/30]), with a mean time to recurrence of 4.7 ± 2.88 years. The progression rate to invasive vulvar cancer was 13.3% (4/30), with a mean time to progression of 1.8 ± 0.96 years. Multifocal disease was associated with progression to vulvar cancer ( p = .035). We did not identify other variables associated with progression; no differences were found between women with and without recurrences. CONCLUSIONS: Multifocality of the lesions was the only variable associated with progression to vulvar cancer. This reinforces the idea that these lesions are a challenge in both treatment and surveillance, involving a more difficult therapeutic decision with greater associated morbidity.


Assuntos
Carcinoma in Situ , Neoplasias Cutâneas , Lesões Intraepiteliais Escamosas , Neoplasias Vulvares , Feminino , Humanos , Neoplasias Vulvares/diagnóstico , Neoplasias Vulvares/epidemiologia , Neoplasias Vulvares/patologia , Estudos Retrospectivos , Carcinoma in Situ/patologia , Vulva/patologia , Lesões Intraepiteliais Escamosas/epidemiologia
4.
Philos Trans A Math Phys Eng Sci ; 380(2227): 20210244, 2022 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-35599556

RESUMO

Life and the genetic code are self-referential and so are autocatalytic networks made of simpler, small molecules. Several origins of life theories postulate autocatalytic chemical networks preceding the primordial genetic code, yet demonstration with biochemical systems is lacking. Here, small-molecule reflexively autocatalytic food-generated networks (RAFs) ranging in size from 3 to 619 reactions were found in all of 6683 prokaryotic metabolic networks searched. The average maximum RAF size is 275 reactions for a rich organic medium and 93 for a medium with a single organic cofactor, NAD. In the rich medium, all universally essential metabolites are produced with the exception of glycerol-1-p (archaeal lipid precursor), phenylalanine, histidine and arginine. The 300 most common reactions, present in at least 2732 RAFs, are mostly involved in amino acid biosynthesis and the metabolism of carbon, 2-oxocarboxylic acid and purines. ATP and NAD are central in generating network complexity, and because ATP is also one of the monomers of RNA, autocatalytic networks producing redox and energy currencies are a strong candidate niche of the origin of a primordial information-processing system. The wide distribution of small-molecule autocatalytic networks indicates that molecular reproduction may be much more prevalent in the Universe than hitherto predicted. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.


Assuntos
Fósseis , NAD , Trifosfato de Adenosina , Catálise , RNA
5.
PLoS Genet ; 14(8): e1007518, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-30114187

RESUMO

All known life forms trace back to a last universal common ancestor (LUCA) that witnessed the onset of Darwinian evolution. One can ask questions about LUCA in various ways, the most common way being to look for traits that are common to all cells, like ribosomes or the genetic code. With the availability of genomes, we can, however, also ask what genes are ancient by virtue of their phylogeny rather than by virtue of being universal. That approach, undertaken recently, leads to a different view of LUCA than we have had in the past, one that fits well with the harsh geochemical setting of early Earth and resembles the biology of prokaryotes that today inhabit the Earth's crust.


Assuntos
Evolução Molecular , Filogenia , Archaea/genética , Bactérias/genética , Eucariotos/genética , Transferência Genética Horizontal , Código Genético , Genoma , Mitocôndrias/genética , Conformação de Ácido Nucleico , Origem da Vida , Células Procarióticas
6.
Proc Biol Sci ; 287(1922): 20192377, 2020 03 11.
Artigo em Inglês | MEDLINE | ID: mdl-32156207

RESUMO

Modern cells embody metabolic networks containing thousands of elements and form autocatalytic sets of molecules that produce copies of themselves. How the first self-sustaining metabolic networks arose at life's origin is a major open question. Autocatalytic sets smaller than metabolic networks were proposed as transitory intermediates at the origin of life, but evidence for their role in prebiotic evolution is lacking. Here, we identify reflexively autocatalytic food-generated networks (RAFs)-self-sustaining networks that collectively catalyse all their reactions-embedded within microbial metabolism. RAFs in the metabolism of ancient anaerobic autotrophs that live from H2 and CO2 provided with small-molecule catalysts generate acetyl-CoA as well as amino acids and bases, the monomeric components of protein and RNA, but amino acids and bases without organic catalysts do not generate metabolic RAFs. This suggests that RAFs identify attributes of biochemical origins conserved in metabolic networks. RAFs are consistent with an autotrophic origin of metabolism and furthermore indicate that autocatalytic chemical networks preceded proteins and RNA in evolution. RAFs uncover intermediate stages in the emergence of metabolic networks, narrowing the gaps between early Earth chemistry and life.


Assuntos
Evolução Biológica , Redes e Vias Metabólicas , Catálise , Fenômenos de Química Orgânica
7.
BMC Evol Biol ; 19(1): 24, 2019 01 16.
Artigo em Inglês | MEDLINE | ID: mdl-30651060

RESUMO

BACKGROUND: Knowledge about the distribution of the genetic variation of marine species is fundamental to address species conservation and management strategies, especially in scenarios with mass mortalities. In the Mediterranean Sea, Petrosia ficiformis is one of the species most affected by temperature-related diseases. Our study aimed to assess its genetic structure, connectivity, and bottleneck signatures to understand its evolutionary history and to provide information to help design conservation strategies of sessile marine invertebrates. RESULTS: We genotyped 280 individuals from 19 locations across the entire distribution range of P. ficiformis in the Atlanto-Mediterranean region at 10 microsatellite loci. High levels of inbreeding were detected in most locations (especially in the Macaronesia and the Western Mediterranean) and bottleneck signatures were only detected in Mediterranean populations, although not coinciding entirely with those with reported die-offs. We detected strong significant population differentiation, with the Atlantic populations being the most genetically isolated, and show that six clusters explained the genetic structure along the distribution range of this sponge. Although we detected a pattern of isolation by distance in P. ficiformis when all locations were analyzed together, stratified Mantel tests revealed that other factors could be playing a more prominent role than isolation by distance. Indeed, we detected a strong effect of oceanographic barriers impeding the gene flow among certain areas, the strongest one being the Almeria-Oran front, hampering gene flow between the Atlantic Ocean and the Mediterranean Sea. Finally, migration and genetic diversity distribution analyses suggest a Mediterranean origin for the species. CONCLUSIONS: In our study Petrosia ficiformis showed extreme levels of inbreeding and population differentiation, which could all be linked to the poor swimming abilities of the larva. However, the observed moderate migration patterns are highly difficult to reconcile with such poor larval dispersal, and suggest that, although unlikely, dispersal may also be achieved in the gamete phase. Overall, because of the high genetic diversity in the Eastern Mediterranean and frequent mass mortalities in the Western Mediterranean, we suggest that conservation efforts should be carried out specifically in those areas of the Mediterranean to safeguard the genetic diversity of the species.


Assuntos
Fluxo Gênico , Variação Genética , Petrosia/genética , Migração Animal/fisiologia , Animais , Organismos Aquáticos/genética , Oceano Atlântico , Genética Populacional , Genótipo , Geografia , Mar Mediterrâneo , Densidade Demográfica
8.
PLoS Comput Biol ; 14(11): e1006556, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30444863

RESUMO

Essential metabolic reactions are shaping constituents of metabolic networks, enabling viable and distinct phenotypes across diverse life forms. Here we analyse and compare modelling predictions of essential metabolic functions with experimental data and thereby identify core metabolic pathways in prokaryotes. Simulations of 15 manually curated genome-scale metabolic models were integrated with 36 large-scale gene essentiality datasets encompassing a wide variety of species of bacteria and archaea. Conservation of metabolic genes was estimated by analysing 79 representative genomes from all the branches of the prokaryotic tree of life. We find that essentiality patterns reflect phylogenetic relations both for modelling and experimental data, which correlate highly at the pathway level. Genes that are essential for several species tend to be highly conserved as opposed to non-essential genes which may be conserved or not. The tRNA-charging module is highlighted as ancestral and with high centrality in the networks, followed closely by cofactor metabolism, pointing to an early information processing system supplied by organic cofactors. The results, which point to model improvements and also indicate faults in the experimental data, should be relevant to the study of centrality in metabolic networks and ancient metabolism but also to metabolic engineering with prokaryotes.


Assuntos
Archaea/genética , Bactérias/genética , Metabolismo Energético , Genes Essenciais , Modelos Biológicos , Genoma , Redes e Vias Metabólicas , Filogenia , RNA de Transferência/genética
9.
Metab Eng ; 39: 200-208, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-27939572

RESUMO

The composition of a cell in terms of macromolecular building blocks and other organic molecules underlies the metabolic needs and capabilities of a species. Although some core biomass components such as nucleic acids and proteins are evident for most species, the essentiality of the pool of other organic molecules, especially cofactors and prosthetic groups, is yet unclear. Here we integrate biomass compositions from 71 manually curated genome-scale models, 33 large-scale gene essentiality datasets, enzyme-cofactor association data and a vast array of publications, revealing universally essential cofactors for prokaryotic metabolism and also others that are specific for phylogenetic branches or metabolic modes. Our results revise predictions of essential genes in Klebsiella pneumoniae and identify missing biosynthetic pathways in models of Mycobacterium tuberculosis. This work provides fundamental insights into the essentiality of organic cofactors and has implications for minimal cell studies as well as for modeling genotype-phenotype relations in prokaryotic metabolic networks.


Assuntos
Bactérias/metabolismo , Proteínas de Bactérias/metabolismo , Mapeamento Cromossômico/métodos , Coenzimas/metabolismo , Redes e Vias Metabólicas/fisiologia , Metaboloma/fisiologia , Modelos Biológicos , Bactérias/genética , Proteínas de Bactérias/genética , Biomassa , Coenzimas/genética , Simulação por Computador , Análise do Fluxo Metabólico/métodos , Integração de Sistemas
10.
Nucleic Acids Res ; 42(Web Server issue): W154-60, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24852251

RESUMO

Stem cells are characterized by their potential for self-renewal and their capacity to differentiate into mature cells. These two key features emerge through the interplay of various factors within complex molecular networks. To provide researchers with a dedicated tool to investigate these networks, we have developed StemCellNet, a versatile web server for interactive network analysis and visualization. It rapidly generates focused networks based on a large collection of physical and regulatory interactions identified in human and murine stem cells. The StemCellNet web-interface has various easy-to-use tools for selection and prioritization of network components, as well as for integration of expression data provided by the user. As a unique feature, the networks generated can be screened against a compendium of stemness-associated genes. StemCellNet can also indicate novel candidate genes by evaluating their connectivity patterns. Finally, an optional dataset of generic interactions, which provides large coverage of the human and mouse proteome, extends the versatility of StemCellNet to other biomedical research areas in which stem cells play important roles, such as in degenerative diseases or cancer. The StemCellNet web server is freely accessible at http://stemcellnet.sysbiolab.eu.


Assuntos
Redes Reguladoras de Genes , Software , Células-Tronco/metabolismo , Animais , Expressão Gênica , Humanos , Internet , Camundongos , Mapeamento de Interação de Proteínas , Proteoma
11.
Mar Drugs ; 14(10)2016 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-27727161

RESUMO

Among marine organisms, sponges are the richest sources of pharmacologically-active compounds. Stemming from a previous lead discovery program that gathered a comprehensive library of organic extracts of marine sponges from the off-shore region of Portugal, crude extracts of Erylus cf. deficiens collected in the Gorringe Bank (Atlantic Ocean) were tested in the innovative high throughput screening (HTS) assay for inhibitors of indoleamine 2,3-dioxygenase (IDO) and showed activity. Bioassay guided fractionation of the dichloromethane extract led to the isolation of four new glycolipids, named erylusamide A-D. The structures of the isolated compounds were established by 1D and 2D nuclear magnetic resonance (NMR) spectroscopy, high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) and chemical derivatization. The metabolites shared a pentasaccharide moiety constituted by unusual highly acetylated ᴅ-glucose moieties as well as ᴅ-xylose and ᴅ-galactose. The aglycones were unprecedented long chain dihydroxyketo amides. Erylusamides A, B and D differ in the length of the hydrocarbon chain, while erylusamide C is a structural isomer of erylusamide B.


Assuntos
Glicolipídeos/química , Animais , Oceano Atlântico , Células COS/efeitos dos fármacos , Chlorocebus aethiops , Glicolipídeos/farmacologia , Poríferos , Portugal , Relação Estrutura-Atividade
12.
Ann Rheum Dis ; 74(3): 618-24, 2015 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24326010

RESUMO

OBJECTIVES: To identify new susceptibility loci for Behçet's disease (BD), we performed a genome-wide association study (GWAS) using DNA pooling. METHODS: Two replicate pools of 292 Iranian BD cases and of 294 age- and sex-matched controls were allelotyped in quadruplicate on the Affymetrix Genome-Wide Human SNP Array 6.0. Of the 51 top markers, 47 were technically validated through individually genotyping. Replication of validated single nucleotide polymorphisms (SNPs) was performed in an independent Iranian dataset (684 cases and 532 controls). RESULTS: In addition to the well-established HLA-B locus, rs7528842 in a gene desert on chromosome 1p21.2, and rs632111 at the 3'UTR of FUT2 were associated in both the discovery and replication datasets (individually and in combination). However, only the FUT2 SNP was associated in a previous GWAS for BD in Turkish people. Fine-mapping of FUT2 in the full Iranian dataset showed additional associations in five coding SNPs (2.97E-06

Assuntos
Síndrome de Behçet/genética , Cromossomos Humanos Par 1/genética , Fucosiltransferases/genética , Antígenos HLA-B/genética , Regiões 3' não Traduzidas/genética , Adulto , Estudos de Casos e Controles , Feminino , Estudo de Associação Genômica Ampla , Humanos , Irã (Geográfico) , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único , População Branca/genética , Galactosídeo 2-alfa-L-Fucosiltransferase
13.
J R Soc Interface ; 21(214): 20230732, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38774958

RESUMO

The concept of an autocatalytic network of reactions that can form and persist, starting from just an available food source, has been formalized by the notion of a reflexively autocatalytic and food-generated (RAF) set. The theory and algorithmic results concerning RAFs have been applied to a range of settings, from metabolic questions arising at the origin of life, to ecological networks, and cognitive models in cultural evolution. In this article, we present new structural and algorithmic results concerning RAF sets, by studying more complex modes of catalysis that allow certain reactions to require multiple catalysts (or to not require catalysis at all), and discuss the differing ways catalysis has been viewed in the literature. We also focus on the structure and analysis of minimal RAFs and derive structural results and polynomial-time algorithms. We then apply these new methods to a large metabolic network to gain insights into possible biochemical scenarios near the origin of life.


Assuntos
Algoritmos , Catálise , Modelos Biológicos , Bioquímica , Origem da Vida
14.
Arthritis Rheum ; 64(8): 2761-72, 2012 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-22378604

RESUMO

OBJECTIVE: Independent replication of the findings from genome-wide association studies (GWAS) remains the gold standard for results validation. Our aim was to test the association of Behçet's disease (BD) with the interleukin-10 gene (IL10) and the IL-23 receptor-IL-12 receptor ß2 (IL23R-IL12RB2) locus, each of which has been previously identified as a risk factor for BD in 2 different GWAS. METHODS: Six haplotype-tagging single-nucleotide polymorphisms (SNPs) in IL10 and 42 in IL23R-IL12RB2 were genotyped in 973 Iranian patients with BD and 637 non-BD controls. Population stratification was assessed using a panel of 86 ancestry-informative markers. RESULTS: Subtle evidence of population stratification was found in our data set. In IL10, rs1518111 was nominally associated with BD before and after adjustment for population stratification (odds ratio [OR] for T allele 1.20, 95% confidence interval [95% CI] 1.02-1.40, unadjusted P [P(unadj) ] = 2.53 × 10(-2) ; adjusted P [P(adj) ] = 1.43 × 10(-2) ), and rs1554286 demonstrated a trend toward association (P(unadj) = 6.14 × 10(-2) ; P(adj) = 3.21 × 10(-2) ). Six SNPs in IL23R-IL12RB2 were found to be associated with BD after Bonferroni correction for multiple testing, the most significant of which were rs17375018 (OR for G allele 1.51, 95% CI 1.27-1.78, P(unadj) = 1.93 × 10(-6) ), rs7517847 (OR for T allele 1.48, 95% CI 1.26-1.74, P(unadj) = 1.23 × 10(-6) ), and rs924080 (OR for T allele 1.29, 95% CI 1.20-1.39, P = 1.78 × 10(-5) ). SNPs rs10489629, rs1343151, and rs1495965 were also significantly associated with BD in all tests performed. Results of meta-analyses of our data combined with data from other populations further confirmed the role of rs1518111, rs17375018, rs7517847, and rs924080 in the risk of BD, but no epistatic interactions between IL10 and IL23R-IL12RB2 were detected. Results of imputation analysis highlighted the importance of IL23R regulatory regions in the susceptibility to BD. CONCLUSION: These findings independently confirm, extend, and refine the association of BD with IL10 and IL23R-IL12RB2. These associations warrant further validation and investigation in patients with BD, as they may have implications for the development of novel therapies (e.g., immunosuppressive therapy targeted at IL-23p19).


Assuntos
Síndrome de Behçet/etnologia , Síndrome de Behçet/genética , Interleucina-10/genética , Receptores de Interleucina-12/genética , Receptores de Interleucina/genética , Adulto , Alelos , Síndrome de Behçet/epidemiologia , Estudos de Casos e Controles , Feminino , Estudo de Associação Genômica Ampla , Haplótipos/genética , Humanos , Irã (Geográfico)/epidemiologia , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único/genética , Fatores de Risco
15.
Front Med (Lausanne) ; 10: 907310, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36844231

RESUMO

Background: Cardiovascular diseases are still a significant cause of death and hospitalization. In 2019, circulatory diseases were responsible for 29.9% of deaths in Portugal. These diseases have a significant impact on the hospital length of stay. Length of stay predictive models is an efficient way to aid decision-making in health. This study aimed to validate a predictive model on the extended length of stay in patients with acute myocardial infarction at the time of admission. Methods: An analysis was conducted to test and recalibrate a previously developed model in the prediction of prolonged length of stay, for a new set of population. The study was conducted based on administrative and laboratory data of patients admitted for acute myocardial infarction events from a public hospital in Portugal from 2013 to 2015. Results: Comparable performance measures were observed upon the validation and recalibration of the predictive model of extended length of stay. Comorbidities such as shock, diabetes with complications, dysrhythmia, pulmonary edema, and respiratory infections were the common variables found between the previous model and the validated and recalibrated model for acute myocardial infarction. Conclusion: Predictive models for the extended length of stay can be applied in clinical practice since they are recalibrated and modeled to the relevant population characteristics.

16.
J Gynecol Obstet Hum Reprod ; 52(9): 102649, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37611747

RESUMO

INTRODUCTION: The aim of this study was to compare the effectiveness of a combined misoprostol-Foley catheter induction of labor protocol against the current guidelines of our department. MATERIAL AND METHODS: A randomized trial was conducted comparing two cervical ripening study groups: combined misoprostol-cervical Foley and the current department practice (misoprostol alone or dinoprostone alone). Women were stratified randomly according to parity for the two intervention groups. The primary outcome was defined as time to delivery (in hours). Secondary outcomes were cesarean delivery rate, time to active labor (defined as dilatation 6 cm or greater), delivery within 12 h, delivery within 24 h, maternal length of stay and indication for cesarean delivery. A composite of maternal morbidity and neonatal morbidity were also analyzed. RESULTS: 142 women were randomized into one of the two groups (74 for treatment group and 68 for control group). Demographic and clinical characteristics were similar among the two groups. The primary outcome, the average time to delivery, was faster in the treatment group (22.7 h vs 27.2 h, p = 0.03) and this difference was higher in the nulliparous subgroup (24.2 h vs 29.2 h, p = 0.03). Active phase of labor was achieved faster in the treatment group (17.9 h vs 22.7 h, p = 0.008). The risk for cesarean section was similar in both groups (OR 0.801 (0.527-1.217) vs OR 1.203 (0.871-1.662), p = 0.278). CONCLUSIONS: Our study suggests that the combined method of cervical Foley with vaginal misoprostol for women presenting to induction of labor with unfavorable Bishop scores reduces time to delivery safely. The risk for cesarean section was similar in both groups.


Assuntos
Misoprostol , Ocitócicos , Recém-Nascido , Gravidez , Feminino , Humanos , Cesárea , Trabalho de Parto Induzido/métodos , Dinoprostona
17.
Mar Pollut Bull ; 191: 114902, 2023 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-37058834

RESUMO

Industrial deep-sea mining will release plumes containing metals that may disperse over long distances; however, there is no general understanding of metal effects on marine ecosystems. Thus, we conducted a systematic review in search of models of metal effects on aquatic biota with the future perspective to support Environmental Risk Assessment (ERA) of deep-sea mining. According to results, the use of models to study metal effects is strongly biased towards freshwater species (83% freshwater versus 14% marine); Cu, Hg, Al, Ni, Pb, Cd and Zn are the best-studied metals, and most studies target few species rather than entire food webs. We argue that these limitations restrain ERA on marine ecosystems. To overcome this gap of knowledge, we suggest future research directions and propose a modelling framework to predict the effects of metals on marine food webs, which in our view is relevant for ERA of deep-sea mining.


Assuntos
Metais Pesados , Poluentes Químicos da Água , Cadeia Alimentar , Ecossistema , Monitoramento Ambiental , Poluentes Químicos da Água/análise , Metais , Metais Pesados/análise
18.
PeerJ ; 11: e16024, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37846312

RESUMO

Management of deep-sea fisheries in areas beyond national jurisdiction by Regional Fisheries Management Organizations/Arrangements (RFMO/As) requires identification of areas with Vulnerable Marine Ecosystems (VMEs). Currently, fisheries data, including trawl and longline bycatch data, are used by many RFMO/As to inform the identification of VMEs. However, the collection of such data creates impacts and there is a need to collect non-invasive data for VME identification and monitoring purposes. Imagery data from scientific surveys satisfies this requirement, but there currently is no established framework for identifying VMEs from images. Thus, the goal of this study was to bring together a large international team to determine current VME assessment protocols and establish preliminary global consensus guidelines for identifying VMEs from images. An initial assessment showed a lack of consistency among RFMO/A regions regarding what is considered a VME indicator taxon, and hence variability in how VMEs might be defined. In certain cases, experts agreed that a VME could be identified from a single image, most often in areas of scleractinian reefs, dense octocoral gardens, multiple VME species' co-occurrence, and chemosynthetic ecosystems. A decision flow chart is presented that gives practical interpretation of the FAO criteria for single images. To further evaluate steps of the flow chart related to density, data were compiled to assess whether scientists perceived similar density thresholds across regions. The range of observed densities and the density values considered to be VMEs varied considerably by taxon, but in many cases, there was a statistical difference in what experts considered to be a VME compared to images not considered a VME. Further work is required to develop an areal extent index, to include a measure of confidence, and to increase our understanding of what levels of density and diversity correspond to key ecosystem functions for VME indicator taxa. Based on our results, the following recommendations are made: 1. There is a need to establish a global consensus on which taxa are VME indicators. 2. RFMO/As should consider adopting guidelines that use imagery surveys as an alternative (or complement) to using bycatch and trawl surveys for designating VMEs. 3. Imagery surveys should also be included in Impact Assessments. And 4. All industries that impact the seafloor, not just fisheries, should use imagery surveys to detect and identify VMEs.


Assuntos
Conservação dos Recursos Naturais , Ecossistema , Conservação dos Recursos Naturais/métodos , Pesqueiros
19.
Eur J Cancer ; 172: 146-157, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35772352

RESUMO

INTRODUCTION: Translation of genome-wide association study (GWAS) findings into preventive approaches is challenged by the identification of the causal risk variants and the understanding of the biological mechanisms by which they act. We present using allelic expression (AE) ratios to perform quantitative case-control analysis as a novel approach to identify risk associations, causal regulatory variants, and target genes. METHODS: Using the breast cancer (BC) risk locus 17q22 to validate this approach, we measured AE ratios in normal breast tissue samples from controls and cases, as well as from unmatched blood samples. Then we used in-silico and in-vitro analysis to map and functionally characterised candidate causal variants. RESULTS: We found a significant shift in the AE patterns of STXBP4 (rs2628315) and COX11 (rs17817901) in the normal breast tissue of cases and healthy controls. Preferential expression of the G-rs2628315 and A-rs17817901 alleles, more often observed in cases, was associated with an increased risk for BC. Analysis of blood samples from cases and controls found a similar association. Furthermore, we identified two putative cis-regulatory variants - rs17817901 and rs8066588 - that affect a miRNA and a transcription factor binding site, respectively. CONCLUSION: We propose causal variants and target genes for the 17q22 BC risk locus and show that using AE ratios in case-control association studies is helpful in identifying risk and mapping causal variants.


Assuntos
Neoplasias da Mama , Estudo de Associação Genômica Ampla , Alelos , Neoplasias da Mama/genética , Proteínas de Transporte de Cobre , Complexo de Proteínas da Cadeia de Transporte de Elétrons , Feminino , Predisposição Genética para Doença , Células Germinativas , Humanos , Proteínas Mitocondriais , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Proteínas de Transporte Vesicular/genética
20.
PeerJ ; 10: e13394, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35726260

RESUMO

The Ægir Ridge System (ARS) is an ancient extinct spreading axis in the Nordic seas extending from the upper slope east of Iceland (∼550 m depth), as part of its Exclusive Economic Zone (EEZ), to a depth of ∼3,800 m in the Norwegian basin. Geomorphologically a rift valley, the ARS has a canyon-like structure that may promote increased diversity and faunal density. The main objective of this study was to characterize benthic habitats and related macro- and megabenthic communities along the ARS, and the influence of water mass variables and depth on them. During the IceAGE3 expedition (Icelandic marine Animals: Genetics and Ecology) on RV Sonne in June 2020, benthic communities of the ARS were surveyed by means of a remotely-operated vehicle (ROV) and epibenthic sledge (EBS). For this purpose, two working areas were selected, including abyssal stations in the northeast and bathyal stations in the southwest of the ARS. Video and still images of the seabed were usedtoqualitatively describebenthic habitats based on the presence of habitat-forming taxa and the physical environment. Patterns of diversity and community composition of the soft-sediment macrofauna, retrieved from the EBS, were analyzed in a semiquantitative manner. These biological data were complemented by producing high-resolution bathymetric maps using the vessel's multi-beam echosounder system. As suspected, we were able to identify differences in species composition and number of macro- and megafaunal communities associated with a depth gradient. A biological canyon effect became evident in dense aggregates of megafaunal filter feeders and elevated macrofaunal densities. Analysis of videos and still images from the ROV transects also led to the discovery of a number ofVulnerable Marine Ecosystems (VMEs) dominated by sponges and soft corals characteristic of the Arctic region. Directions for future research encompass a more detailed, quantitative study of the megafauna and more coherent sampling over the entire depth range in order to fully capture the diversity of the habitats and biota of the region. The presence of sensitive biogenic habitats, alongside seemingly high biodiversity and naturalness are supportive of ongoing considerations of designating part of the ARS as an "Ecologically and Biologically Significant Area" (EBSA).


Assuntos
Biodiversidade , Ecossistema , Oceanos e Mares , Biota , Noruega
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