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1.
Cell ; 185(20): 3823-3837.e23, 2022 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-36179672

RESUMO

Biochemical processes often require spatial regulation and specific microenvironments. The general lack of organelles in bacteria limits the potential of bioengineering complex intracellular reactions. Here, we demonstrate synthetic membraneless organelles in Escherichia coli termed transcriptionally engineered addressable RNA solvent droplets (TEARS). TEARS are assembled from RNA-binding protein recruiting domains fused to poly-CAG repeats that spontaneously drive liquid-liquid phase separation from the bulk cytoplasm. Targeting TEARS with fluorescent proteins revealed multilayered structures with composition and reaction robustness governed by non-equilibrium dynamics. We show that TEARS provide organelle-like bioprocess isolation for sequestering biochemical pathways, controlling metabolic branch points, buffering mRNA translation rates, and scaffolding protein-protein interactions. We anticipate TEARS to be a simple and versatile tool for spatially controlling E. coli biochemistry. Particularly, the modular design of TEARS enables applications without expression fine-tuning, simplifying the design-build-test cycle of bioengineering.


Assuntos
Escherichia coli , Organelas , Escherichia coli/genética , Organelas/metabolismo , RNA/metabolismo , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Solventes/análise , Solventes/metabolismo
2.
Am J Hum Genet ; 110(5): 880-894, 2023 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-37105174

RESUMO

Using contemporary people as proxies for ancient communities is a contentious but necessary practice in anthropology. In southern Africa, the distinction between the Cape KhoeSan and eastern KhoeSan remains unclear, as ethnicity labels have been changed through time and most communities were decimated if not extirpated. The eastern KhoeSan may have had genetic distinctions from neighboring communities who speak Bantu languages and KhoeSan further away; alternatively, the identity may not have been tied to any notion of biology, instead denoting communities with a nomadic "lifeway" distinct from African agro-pastoralism. The Baphuthi of the 1800s in the Maloti-Drakensberg, southern Africa had a substantial KhoeSan constituency and a lifeway of nomadism, cattle raiding, and horticulture. Baphuthi heritage could provide insights into the history of the eastern KhoeSan. We examine genetic affinities of 23 Baphuthi to discern whether the narrative of KhoeSan descent reflects distinct genetic ancestry. Genome-wide SNP data (Illumina GSA) were merged with 52 global populations, for 160,000 SNPs. Genetic analyses show no support for a unique eastern KhoeSan ancestry distinct from other KhoeSan or southern Bantu speakers. The Baphuthi have strong affinities with early-arriving southern Bantu-speaking (Nguni) communities, as the later-arriving non-Nguni show strong evidence of recent African admixture possibly related to late-Iron Age migrations. The references to communities as "San" and "Bushman" in historic literature has often been misconstrued as notions of ethnic/biological distinctions. The terms may have reflected ambiguous references to non-sedentary polities instead, as seems to be the case for the eastern "Bushman" heritage of the Baphuthi.


Assuntos
Variação Genética , Genética Populacional , Humanos , África Austral , População Negra/genética , Etnicidade/genética
4.
Proc Natl Acad Sci U S A ; 119(19): e2113701119, 2022 05 10.
Artigo em Inglês | MEDLINE | ID: mdl-35500123

RESUMO

Cnidocytes (i.e., stinging cells) are an unequivocally novel cell type used by cnidarians (i.e., corals, jellyfish, and their kin) to immobilize prey. Although they are known to share a common evolutionary origin with neurons, the developmental program that promoted the emergence of cnidocyte fate is not known. Using functional genomics in the sea anemone, Nematostella vectensis, we show that cnidocytes develop by suppression of neural fate in a subset of neurons expressing RFamide. We further show that a single regulatory gene, a C2H2-type zinc finger transcription factor (ZNF845), coordinates both the gain of novel (cnidocyte-specific) traits and the inhibition of ancestral (neural) traits during cnidocyte development and that this gene arose by domain shuffling in the stem cnidarian. Thus, we report a mechanism by which a truly novel regulatory gene (ZNF845) promotes the development of a truly novel cell type (cnidocyte) through duplication of an ancestral cell lineage (neuron) and inhibition of its ancestral identity (RFamide).


Assuntos
Anêmonas-do-Mar , Animais , Diferenciação Celular , Genes Reguladores , Anêmonas-do-Mar/metabolismo
5.
Biophys J ; 2024 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-38291751

RESUMO

Here we explore the evolutionary origins of fast N-type ball-and-chain inactivation in Shaker (Kv1) K+ channels by functionally characterizing Shaker channels from the ctenophore (comb jelly) Mnemiopsis leidyi. Ctenophores are the sister lineage to other animals and Mnemiopsis has >40 Shaker-like K+ channels, but they have not been functionally characterized. We identified three Mnemiopsis channels (MlShak3-5) with N-type inactivation ball-like sequences at their N termini and functionally expressed them in Xenopus oocytes. Two of the channels, MlShak4 and MlShak5, showed rapid inactivation similar to cnidarian and bilaterian Shakers with rapid N-type inactivation, whereas MlShak3 inactivated ∼100-fold more slowly. Fast inactivation in MlShak4 and MlShak5 required the putative N-terminal inactivation ball sequences. Furthermore, the rate of fast inactivation in these channels depended on the number of inactivation balls/channel, but the rate of recovery from inactivation did not. These findings closely match the mechanism of N-type inactivation first described for Drosophila Shaker in which 1) inactivation balls on the N termini of each subunit can independently block the pore, and 2) only one inactivation ball occupies the pore binding site at a time. These findings suggest classical N-type activation evolved in Shaker channels at the very base of the animal phylogeny in a common ancestor of ctenophores, cnidarians, and bilaterians and that fast-inactivating Shakers are therefore a fundamental type of animal K+ channel. Interestingly, we find evidence from functional co-expression experiments and molecular dynamics that MlShak4 and MlShak5 do not co-assemble, suggesting that Mnemiopsis has at least two functionally independent N-type Shaker channels.

6.
Proteomics ; : e2300397, 2024 Feb 08.
Artigo em Inglês | MEDLINE | ID: mdl-38329168

RESUMO

This Dataset Brief describes the computational prediction of protein structures for the ctenophore Mnemiopsis leidyi. Here, we report the proteome-scale generation of 15,333 protein structure predictions using AlphaFold, as well as an updated implementation of publicly available search, manipulation, and visualization tools for these protein structure predictions through the Mnemiopsis Genome Project Portal (https://research.nhgri.nih.gov/mnemiopsis). The utility of these predictions is demonstrated by highlighting comparisons to experimentally determined structures for the light-sensitive protein mnemiopsin 1 and the ionotropic glutamate receptor (iGluR). The application of these novel protein structure prediction methods will serve to further position non-bilaterian species such as Mnemiopsis as powerful model systems for the study of early animal evolution and human health.

7.
Mol Biol Evol ; 40(6)2023 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-37288606

RESUMO

Differential regulation of gene expression has produced the astonishing diversity of life on Earth. Understanding the origin and evolution of mechanistic innovations for control of gene expression is therefore integral to evolutionary and developmental biology. Cytoplasmic polyadenylation is the biochemical extension of polyadenosine at the 3'-end of cytoplasmic mRNAs. This process regulates the translation of specific maternal transcripts and is mediated by the Cytoplasmic Polyadenylation Element-Binding Protein family (CPEBs). Genes that code for CPEBs are amongst a very few that are present in animals but missing in nonanimal lineages. Whether cytoplasmic polyadenylation is present in non-bilaterian animals (i.e., sponges, ctenophores, placozoans, and cnidarians) remains unknown. We have conducted phylogenetic analyses of CPEBs, and our results show that CPEB1 and CPEB2 subfamilies originated in the animal stem lineage. Our assessment of expression in the sea anemone, Nematostella vectensis (Cnidaria), and the comb jelly, Mnemiopsis leidyi (Ctenophora), demonstrates that maternal expression of CPEB1 and the catalytic subunit of the cytoplasmic polyadenylation machinery (GLD2) is an ancient feature that is conserved across animals. Furthermore, our measurements of poly(A)-tail elongation reveal that key targets of cytoplasmic polyadenylation are shared between vertebrates, cnidarians, and ctenophores, indicating that this mechanism orchestrates a regulatory network that is conserved throughout animal evolution. We postulate that cytoplasmic polyadenylation through CPEBs was a fundamental innovation that contributed to animal evolution from unicellular life.


Assuntos
Ctenóforos , Anêmonas-do-Mar , Animais , Filogenia , Poliadenilação , Ctenóforos/genética , Anêmonas-do-Mar/genética
8.
Mol Biol Evol ; 40(2)2023 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-36740225

RESUMO

Innexins facilitate cell-cell communication by forming gap junctions or nonjunctional hemichannels, which play important roles in metabolic, chemical, ionic, and electrical coupling. The lack of knowledge regarding the evolution and role of these channels in ctenophores (comb jellies), the likely sister group to the rest of animals, represents a substantial gap in our understanding of the evolution of intercellular communication in animals. Here, we identify and phylogenetically characterize the complete set of innexins of four ctenophores: Mnemiopsis leidyi, Hormiphora californensis, Pleurobrachia bachei, and Beroe ovata. Our phylogenetic analyses suggest that ctenophore innexins diversified independently from those of other animals and were established early in the emergence of ctenophores. We identified a four-innexin genomic cluster, which was present in the last common ancestor of these four species and has been largely maintained in these lineages. Evidence from correlated spatial and temporal gene expression of the M. leidyi innexin cluster suggests that this cluster has been maintained due to constraints related to gene regulation. We describe the basic electrophysiological properties of putative ctenophore hemichannels from muscle cells using intracellular recording techniques, showing substantial overlap with the properties of bilaterian innexin channels. Together, our results suggest that the last common ancestor of animals had gap junctional channels also capable of forming functional innexin hemichannels, and that innexin genes have independently evolved in major lineages throughout Metazoa.


Assuntos
Ctenóforos , Animais , Ctenóforos/genética , Filogenia , Transdução de Sinais , Genoma , Comunicação Celular/fisiologia
9.
J Cell Sci ; 135(13)2022 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-35662333

RESUMO

Cells exist in an astonishing range of volumes across and within species. However, our understanding of cell size control remains limited, owing in large part to the challenges associated with accurate determination of cell volume. Much of our comprehension of size regulation derives from yeast models, but even for these morphologically stereotypical cells, assessment of cell volume has mostly relied on proxies and extrapolations from two-dimensional measurements. Recently, the fluorescence exclusion method (FXm) was developed to evaluate the size of mammalian cells, but whether it could be applied to smaller cells remained unknown. Using specifically designed microfluidic chips and an improved data analysis pipeline, we show here that FXm reliably detects subtle differences in the volume of fission yeast cells, even for those with altered shapes. Moreover, it allows for the monitoring of dynamic volume changes at the single-cell level with high time resolution. Collectively, our work highlights how the coupling of FXm with yeast genetics will bring new insights into the complex biology of cell growth.


Assuntos
Saccharomyces cerevisiae , Schizosaccharomyces , Animais , Ciclo Celular , Tamanho Celular , Mamíferos , Microfluídica , Saccharomyces cerevisiae/genética
10.
Proc Natl Acad Sci U S A ; 118(14)2021 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-33753556

RESUMO

Oil and gas wells with compromised integrity are a concern because they can potentially leak hydrocarbons or other fluids into groundwater and/or the atmosphere. Most states in the United States require some form of integrity testing, but few jurisdictions mandate widespread testing and open reporting on a scale informative for leakage risk assessment. In this study, we searched 33 US state oil and gas regulatory agency databases and identified records useful for evaluating well integrity in Colorado, New Mexico, and Pennsylvania. In total, we compiled 474,621 testing records from 105,031 wells across these states into a uniform dataset. We found that 14.1% of wells tested prior to 2018 in Pennsylvania exhibited sustained casing pressure (SCP) or casing vent flow (CVF)-two indicators of compromised well integrity. Data from different hydrocarbon-producing regions within Colorado and New Mexico revealed a wider range (0.3 to 26.5%) of SCP and/or CVF occurrence than previously reported, highlighting the need to better understand regional trends in well integrity. Directional wells were more likely to exhibit SCP and/or CVF than vertical wells in Colorado and Pennsylvania, and their installation corresponded with statewide increases in SCP and/or CVF occurrence in Colorado (2005 to 2009) and Pennsylvania (2007 to 2011). Testing the ground around wells for indicators of gas leakage is not a widespread practice in the states considered. However, 3.0% of Colorado wells tested and 0.1% of New Mexico wells tested exhibited a degree of SCP sufficient to potentially induce leakage outside the well.

11.
Rev Endocr Metab Disord ; 24(6): 1075-1088, 2023 12.
Artigo em Inglês | MEDLINE | ID: mdl-37439960

RESUMO

BACKGROUND AND AIMS: Bariatric surgery is the most effective treatment in individuals with obesity to achieve remission of type 2 diabetes. Post-bariatric surgery hypoglycaemia occurs frequently, and management remains suboptimal, because of a poor understanding of the underlying pathophysiology. The glucoregulatory hormone responses to nutrients in individuals with and without post-bariatric surgery hypoglycaemia have not been systematically examined. MATERIALS AND METHODS: The study protocol was prospectively registered with PROSPERO. PubMed, EMBASE, Web of Science and the Cochrane databases were searched for publications between January 1990 and November 2021 using MeSH terms related to post-bariatric surgery hypoglycaemia. Studies were included if they evaluated individuals with post-bariatric surgery hypoglycaemia and included measurements of plasma glucagon-like peptide-1 (GLP-1), glucose-dependent insulinotropic polypeptide (GIP), insulin, C-peptide and/or glucagon concentrations following an ingested nutrient load. Glycated haemoglobin (HbA1c) was also evaluated. A random-effects meta-analysis was performed, and Hedges' g (standardised mean difference) and 95% confidence intervals were reported for all outcomes where sufficient studies were available. The τ2 estimate and I2 statistic were used as tests for heterogeneity and a funnel plot with the Egger regression-based test was used to evaluate for publication bias. RESULTS: From 377 identified publications, 12 were included in the analysis. In all 12 studies, the type of bariatric surgery was Roux-en-Y gastric bypass (RYGB). Comparing individuals with and without post-bariatric surgery hypoglycaemia following an ingested nutrient load, the standardised mean difference in peak GLP-1 was 0.57 (95% CI, 0.32, 0.82), peak GIP 0.05 (-0.26, 0.36), peak insulin 0.84 (0.44, 1.23), peak C-peptide 0.69 (0.28, 1.1) and peak glucagon 0.05 (-0.26, 0.36). HbA1c was less in individuals with hypoglycaemia - 0.40 (-0.67, -0.12). There was no evidence of substantial heterogeneity in any outcome except for peak insulin: τ2 = 0.2, I2 = 54.3. No publication bias was evident. CONCLUSION: Following RYGB, postprandial peak plasma GLP-1, insulin and C-peptide concentrations are greater in individuals with post-bariatric surgery hypoglycaemia, while HbA1c is less. These observations support the concept that antagonism of GLP-1 would prove beneficial in the management of individuals with hypoglycaemia following RYGB.PROSPERO Registration Number: CRD42021287515.


Assuntos
Diabetes Mellitus Tipo 2 , Derivação Gástrica , Hipoglicemia , Humanos , Peptídeo 1 Semelhante ao Glucagon , Derivação Gástrica/métodos , Glucagon , Diabetes Mellitus Tipo 2/cirurgia , Peptídeo C , Glicemia , Hipoglicemia/etiologia , Hipoglicemia/cirurgia , Insulina , Polipeptídeo Inibidor Gástrico
12.
Chem Rev ; 121(20): 12327-12383, 2021 10 27.
Artigo em Inglês | MEDLINE | ID: mdl-34259500

RESUMO

High-level radioactive waste is accumulating at temporary storage locations around the world and will eventually be placed in deep geological repositories. The waste forms and containers will be constructed from glass, crystalline ceramic, and metallic materials, which will eventually come into contact with water, considering that the period of performance required to allow sufficient decay of dangerous radionuclides is on the order of 105-106 years. Corrosion of the containers and waste forms in the aqueous repository environment is therefore a concern. This Review describes the recent advances of the field of materials corrosion that are relevant to fundamental materials science issues associated with the long-term performance assessment and the design of materials with improved performance, where performance is defined as resistance to aqueous corrosion. Glass, crystalline ceramics, and metals are discussed separately, and the near-field interactions of these different material classes are also briefly addressed. Finally, recommendations for future directions of study are provided.


Assuntos
Resíduos Radioativos , Corrosão , Resíduos Radioativos/análise
13.
Fam Pract ; 2023 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-37410016

RESUMO

BACKGROUND: Palatability is a key element of paediatric acceptability for medicines. Many patient and drug factors are considered when choosing an antibiotic for a child. Pharmacists report that they receive questions about the palatability of oral liquid antibiotics for children. This study aimed to explore the experiences of GPs and pharmacists concerning palatability of oral liquid antibiotics for children. METHODS: A questionnaire about the impact of palatability on the choice of antibiotic formulation for children was emailed to all community pharmacists in Ireland and to GPs and trainee GPs in the Cork region and posted on social media. Survey items were not compulsory; therefore, percentage responses were calculated based on the number of responses to that item. GP and pharmacist responses were analysed independently. RESULTS: Responses were received from 244 participants (59 GPs, 185 pharmacists). Clinical guidelines and availability of supply were the most important factors considered when choosing an oral liquid antibiotic formulation for children by GP (79.7%) and pharmacist (66.5%) respondents respectively. Forty GP respondents (76.9%) reported ensuring adherence was the most common palatability-related reason leading to deviation from guidelines. Pharmacist respondents (52%) reported advising a parent/caregiver to manipulate the required antibiotic dose to improve acceptability. The least palatable oral liquid antibiotics reported were flucloxacillin (16% GPs, 18% pharmacists) and clarithromycin (17% of each profession). CONCLUSION: This study identified palatability issues associated with oral liquid antibiotics for children reported by GPs and pharmacists. Pharmaceutical approaches to adapting oral liquid antibiotic formulations must be developed to improve palatability and thus paediatric acceptability.

14.
Health Expect ; 26(1): 119-131, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36333948

RESUMO

BACKGROUND: Critical care bed capacity per capita in Ireland is among the lowest in Europe. The COVID-19 pandemic has put additional strain on an over-stretched healthcare system. COVID-19 community assessment hubs (CAHs) were established to prevent unnecessary admission to acute hospitals and to reduce infection spread. OBJECTIVE: The aim of this study was to assess the effectiveness and acceptability of CAHs and identify how the service might be improved or adapted for possible future use. DESIGN: This was a mixed methods study, incorporating co-design with clinical stakeholders. Data collection was via an online survey and semistructured telephone interviews with staff and patients conducted between January and May 2021. SETTING AND PARTICIPANTS: Thirty-one patients completed the survey and nine were interviewed. Twenty interviews were conducted with staff. RESULTS: The findings suggest that the CAH model was successful in providing a dedicated pathway for assessing patients with COVID-19 symptoms, whilst mitigating the risk of infection. Patients were particularly positive about the timely, comprehensive and holistic care they received, as well as the accessibility of the clinics and the friendly attitudes of the staff. Staff welcomed the training and clinical protocols which contributed to their feelings of safety and competency in delivering care to this cohort of patients. They also highlighted the benefits of working in a multidisciplinary environment. Both staff and patients felt that the hubs could be repurposed for alternative use, including the treatment of chronic diseases. DISCUSSION: This study describes staff and patients' experiences of these hubs. An unexpected outcome of this study is its demonstration of the true value of effective multidisciplinary working, not only for the staff who were deployed to this service but also for the patients in receipt of care in these hubs. CONCLUSION: This multidisciplinary patient-centred service may provide a useful model for the delivery of other services currently delivered in hospital settings. PATIENT OR PUBLIC CONTRIBUTION: An earlier phase of this study involved interviews with COVID-19-positive patients on a remote monitoring programme. The data informed this phase. Several of the authors had worked in the CAHs and provided valuable input into the design of the staff and patient interviews.


Assuntos
COVID-19 , Humanos , Irlanda , Pandemias , Atenção à Saúde , Pacientes
15.
J Appl Res Intellect Disabil ; 36(5): 1169-1178, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37417242

RESUMO

BACKGROUND: Individuals with intellectual disabilities need continued supports in completing daily living tasks to increase the likelihood of achieving independence. Fortunately, research has shown that assistive technology, and particularly video prompting helps support independent living for individuals with intellectual disabilities. AIMS: This study investigated the efficacy of a highly customizable task analysis smartphone application in assisting three young adults with intellectual disabilities learn how to cook three different multistep recipes. MATERIALS & METHODS: Three young adults with intellectual disabilities enrolled in a four-year postsecondary education program (PSE) participated in a multiple probe design across participants to examine the effect of a Task Analysis app on the participants' completion of three cooking tasks. RESULTS: In this present study, the use of video prompting to teach a daily living skill resulted in large and meaningful effect size gains of 99%-100% for all three participants, as measured by Tau-U. DISCUSSION: Video prompting is an effective instructional strategy which allows the user to self-prompt and manage their ability to successfully complete daily living skills. In this current study, video prompting made a substantial difference in the safety of participants. CONCLUSION: The use of video prompting can decrease the reliance on others (e.g., teachers and caregivers), improve self-confidence of the user, and improve the user's level of autonomy.


Assuntos
Deficiência Intelectual , Smartphone , Adulto Jovem , Humanos , Aprendizagem , Vida Independente
16.
Syst Biol ; 70(6): 1200-1212, 2021 10 13.
Artigo em Inglês | MEDLINE | ID: mdl-33837789

RESUMO

Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of six-state recoding approaches by comparing the performance of analyses on recoded and non-recoded data sets that have been simulated under gradients of compositional heterogeneity or saturation. In our simulation analyses, non-recoding approaches consistently outperform six-state recoding approaches. Our results suggest that six-state recoding strategies are not effective in the face of high saturation. Furthermore, while recoding strategies do buffer the effects of compositional heterogeneity, the loss of information that accompanies six-state recoding outweighs its benefits. In addition, we evaluate recoding schemes with 9, 12, 15, and 18 states and show that these consistently outperform six-state recoding. Our analyses of other recoding schemes suggest that under conditions of very high compositional heterogeneity, it may be advantageous to apply recoding using more than six states, but we caution that applying any recoding should include sufficient justification. Our results have important implications for the more than 90 published papers that have incorporated six-state recoding, many of which have significant bearing on relationships across the tree of life. [Compositional heterogeneity; Dayhoff 6-state recoding; S&R 6-state recoding; six-state amino acid recoding; substitution saturation.].


Assuntos
Aminoácidos , Filogenia
17.
Environ Sci Technol ; 56(23): 17227-17235, 2022 12 06.
Artigo em Inglês | MEDLINE | ID: mdl-36379467

RESUMO

Fluids leaked from oil and gas wells often originate from their surface casing─a steel pipe installed beneath the deepest underlying source of potable groundwater that serves as the final barrier around the well system. In this study, we analyze a regulatory dataset of surface casing geochemical samples collected from 2573 wells in northeastern Colorado─the only known publicly available dataset of its kind. Thermogenic gas was present in the surface casings of 96.2% of wells with gas samples. Regulatory records indicate that 73.3% of these wells were constructed to isolate the formation from which the gas originated with cement. This suggests that gas migration into the surface casing annulus predominantly occurs through compromised barriers (e.g., steel casings or cement seals), indicative of extensive integrity issues in the region. Water was collected from 22.6% of sampled surface casings. Benzene, toluene, ethylbenzene, and xylenes were detected in 99.7% of surface casing water samples tested for these compounds, which may be due to the presence of leaked oil, natural gas condensate, or oil-based drilling mud. Our findings demonstrate the value of incorporating surface casing geochemical analysis in well integrity monitoring programs to identify integrity issues and focus leak mitigation efforts.


Assuntos
Água Subterrânea , Poluentes Químicos da Água , Poluentes Químicos da Água/análise , Poços de Água , Água Subterrânea/química , Campos de Petróleo e Gás , Gás Natural/análise , Aço/análise , Água , Monitoramento Ambiental
18.
Nature ; 531(7596): 637-641, 2016 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-26886793

RESUMO

Animals are grouped into ~35 'phyla' based upon the notion of distinct body plans. Morphological and molecular analyses have revealed that a stage in the middle of development--known as the phylotypic period--is conserved among species within some phyla. Although these analyses provide evidence for their existence, phyla have also been criticized as lacking an objective definition, and consequently based on arbitrary groupings of animals. Here we compare the developmental transcriptomes of ten species, each annotated to a different phylum, with a wide range of life histories and embryonic forms. We find that in all ten species, development comprises the coupling of early and late phases of conserved gene expression. These phases are linked by a divergent 'mid-developmental transition' that uses species-specific suites of signalling pathways and transcription factors. This mid-developmental transition overlaps with the phylotypic period that has been defined previously for three of the ten phyla, suggesting that transcriptional circuits and signalling mechanisms active during this transition are crucial for defining the phyletic body plan and that the mid-developmental transition may be used to define phylotypic periods in other phyla. Placing these observations alongside the reported conservation of mid-development within phyla, we propose that a phylum may be defined as a collection of species whose gene expression at the mid-developmental transition is both highly conserved among them, yet divergent relative to other species.


Assuntos
Padronização Corporal , Desenvolvimento Embrionário , Filogenia , Animais , Padronização Corporal/genética , Sequência Conservada/genética , Desenvolvimento Embrionário/genética , Evolução Molecular , Regulação da Expressão Gênica no Desenvolvimento , Redes Reguladoras de Genes , Genes Controladores do Desenvolvimento/genética , Modelos Biológicos , Fenótipo , Especificidade da Espécie , Transcriptoma/genética
19.
Nucleic Acids Res ; 48(D1): D668-D675, 2020 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-31680137

RESUMO

ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.


Assuntos
Bases de Dados Genéticas , Perfilação da Expressão Gênica , Genoma , Software , Urocordados/genética , Animais , Sítios de Ligação , Cefalocordados/genética , Gráficos por Computador , Simulação por Computador , Equinodermos/genética , Evolução Molecular , Ordem dos Genes , Genômica , Hibridização In Situ , Internet , Anotação de Sequência Molecular , Filogenia , Linguagens de Programação , RNA-Seq , Sintenia , Interface Usuário-Computador , Vertebrados/genética
20.
Nat Mater ; 19(3): 310-316, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31988512

RESUMO

The US plan for high-level nuclear waste includes the immobilization of long-lived radionuclides in glass or ceramic waste forms in stainless-steel canisters for disposal in deep geological repositories. Here we report that, under simulated repository conditions, corrosion could be significantly accelerated at the interfaces of different barrier materials, which has not been considered in the current safety and performance assessment models. Severe localized corrosion was found at the interfaces between stainless steel and a model nuclear waste glass and between stainless steel and a ceramic waste form. The accelerated corrosion can be attributed to changes of solution chemistry and local acidity/alkalinity within a confined space, which significantly alter the corrosion of both the waste-form materials and the metallic canisters. The corrosion that is accelerated by the interface interaction between dissimilar materials could profoundly impact the service life of the nuclear waste packages, which, therefore, should be carefully considered when evaluating the performance of waste forms and their packages. Moreover, compatible barriers should be selected to further optimize the performance of the geological repository system.

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