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1.
Nat Methods ; 21(7): 1349-1363, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38849569

RESUMO

The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.


Assuntos
Perfilação da Expressão Gênica , RNA-Seq , Humanos , Animais , Camundongos , RNA-Seq/métodos , Perfilação da Expressão Gênica/métodos , Transcriptoma , Análise de Sequência de RNA/métodos , Anotação de Sequência Molecular/métodos
2.
PLoS Comput Biol ; 20(3): e1011976, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38483981

RESUMO

The potential effects of conservation actions on threatened species can be predicted using ensemble ecosystem models by forecasting populations with and without intervention. These model ensembles commonly assume stable coexistence of species in the absence of available data. However, existing ensemble-generation methods become computationally inefficient as the size of the ecosystem network increases, preventing larger networks from being studied. We present a novel sequential Monte Carlo sampling approach for ensemble generation that is orders of magnitude faster than existing approaches. We demonstrate that the methods produce equivalent parameter inferences, model predictions, and tightly constrained parameter combinations using a novel sensitivity analysis method. For one case study, we demonstrate a speed-up from 108 days to 6 hours, while maintaining equivalent ensembles. Additionally, we demonstrate how to identify the parameter combinations that strongly drive feasibility and stability, drawing ecological insight from the ensembles. Now, for the first time, larger and more realistic networks can be practically simulated and analysed.


Assuntos
Ecossistema , Método de Monte Carlo , Previsões
3.
Malar J ; 23(1): 96, 2024 Apr 06.
Artigo em Inglês | MEDLINE | ID: mdl-38582837

RESUMO

BACKGROUND: Understanding the dynamics of gametocyte production in polyclonal Plasmodium falciparum infections requires a genotyping method that detects distinct gametocyte clones and estimates their relative frequencies. Here, a marker was identified and evaluated to genotype P. falciparum mature gametocytes using amplicon deep sequencing. METHODS: A data set of polymorphic regions of the P. falciparum genome was mined to identify a gametocyte genotyping marker. To assess marker resolution, the number of unique haplotypes in the marker region was estimated from 95 Malawian P. falciparum whole genome sequences. Specificity of the marker for detection of mature gametocytes was evaluated using reverse transcription-polymerase chain reaction of RNA extracted from NF54 mature gametocytes and rings from a non-gametocyte-producing strain of P. falciparum. Amplicon deep sequencing was performed on experimental mixtures of mature gametocytes from two distinct parasite clones, as well as gametocyte-positive P. falciparum field isolates to evaluate the quantitative ability and determine the limit of detection of the genotyping approach. RESULTS: A 400 bp region of the pfs230 gene was identified as a gametocyte genotyping marker. A larger number of unique haplotypes was observed at the pfs230 marker (34) compared to the sera-2 (18) and ama-1 (14) markers in field isolates from Malawi. RNA and DNA genotyping accurately estimated gametocyte and total parasite clone frequencies when evaluating agreement between expected and observed haplotype frequencies in gametocyte mixtures, with concordance correlation coefficients of 0.97 [95% CI: 0.92-0.99] and 0.92 [95% CI: 0.83-0.97], respectively. The detection limit of the genotyping method for male gametocytes was 0.41 pfmget transcripts/µl [95% CI: 0.28-0.72] and for female gametocytes was 1.98 ccp4 transcripts/µl [95% CI: 1.35-3.68]. CONCLUSIONS: A region of the pfs230 gene was identified as a marker to genotype P. falciparum gametocytes. Amplicon deep sequencing of this marker can be used to estimate the number and relative frequency of parasite clones among mature gametocytes within P. falciparum infections. This gametocyte genotyping marker will be an important tool for studies aimed at understanding dynamics of gametocyte production in polyclonal P. falciparum infections.


Assuntos
Malária Falciparum , Plasmodium falciparum , Masculino , Feminino , Humanos , Plasmodium falciparum/genética , Genótipo , Malária Falciparum/parasitologia , RNA , Sequenciamento de Nucleotídeos em Larga Escala
4.
J Fish Biol ; 104(6): 1667-1674, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38553910

RESUMO

Mathematical and statistical models underlie many of the world's most important fisheries management decisions. Since the 19th century, difficulty calibrating and fitting such models has been used to justify the selection of simple, stationary, single-species models to aid tactical fisheries management decisions. Whereas these justifications are reasonable, it is imperative that we quantify the value of different levels of model complexity for supporting fisheries management, especially given a changing climate, where old methodologies may no longer perform as well as in the past. Here we argue that cost-benefit analysis is an ideal lens to assess the value of model complexity in fisheries management. While some studies have reported the benefits of model complexity in fisheries, modeling costs are rarely considered. In the absence of cost data in the literature, we report, as a starting point, relative costs of single-species stock assessment and marine ecosystem models from two Australian organizations. We found that costs varied by two orders of magnitude, and that ecosystem model costs increased with model complexity. Using these costs, we walk through a hypothetical example of cost-benefit analysis. The demonstration is intended to catalyze the reporting of modeling costs and benefits.


Assuntos
Análise Custo-Benefício , Ecossistema , Pesqueiros , Pesqueiros/economia , Austrália , Animais , Conservação dos Recursos Naturais/economia , Modelos Biológicos , Peixes , Modelos Teóricos
5.
bioRxiv ; 2024 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-38352519

RESUMO

Generating an accurate and complete genome annotation for an organism is complex because the cells within each tissue can express a unique set of transcript isoforms from a unique set of genes. A comprehensive genome annotation should contain information on what tissues express what transcript isoforms at what level. This tissue-level isoform information can then inform a wide range of research questions as well as experiment designs. Long-read sequencing technology combined with advanced full-length cDNA library preparation methods has now achieved throughput and accuracy where generating these types of annotations is achievable. Here, we show this by generating a genome annotation of the mouse (Mus musculus). We used the nanopore-based R2C2 long-read sequencing method to generate 64 million highly accurate full length cDNA consensus reads - averaging 5.4 million reads per tissue for a dozen tissues. Using the Mandalorion tool we processed these reads to generate the Tissue-level Atlas of Mouse Isoforms (TAMI - available at https://genome.ucsc.edu/s/vollmers/TAMI) which we believe will be a valuable complement to conventional, manually curated reference genome annotations.

6.
Environ Pollut ; 351: 123941, 2024 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-38614427

RESUMO

Urbanization has numerous benefits to human society, but some aspects of urban environments, such as air pollution, can negatively affect human health. Two major air pollutants, particulate matter (PM) and polycyclic aromatic hydrocarbons (PAH), have been classified as carcinogens by the International Agency for Research on Cancer. Here, we answer two questions: (1) What are the carcinogenic effects of PM and PAH exposure? (2) How does carcinogenic risk vary across geographical regions? We performed a comprehensive literature search of peer-reviewed published studies examining the link between air pollution and human cancer rates. Focusing on studies published since 2014 when the last IARC monograph on air pollution was published, we converted the extracted data into relative risks and performed subgroup analyses. Exposure to PM2.5 (per 10 µg/m3) resulted in an 8.5% increase in cancer incidence when all cancer types were combined, and risk for individual cancer types (i.e. lung cancer and adenocarcinoma) was also elevated. PM2.5 was also associated with 2.5% higher mortality due to cancer when all types of cancer were combined, and for individual cancer types (i.e., lung and breast cancer). Exposure to PM2.5 and PM10 posed the greatest risk to lung cancer incidence and mortality in Europe (PM2.5 RR 2.15; PM10 RR 1.26); the risk in Asia and the Americas was also elevated. Exposure to PAH and benzo[a]pyrene significantly increased the pooled risk of cancer incidence (10.8% and 8.0% respectively) at the highest percentile of exposure concentration. Our meta-analyses of studies over the past decade shows that urban air pollution in the form of PM2.5, PM10, and PAH all elevate the incidence and mortality of cancer. We discuss the possible mechanisms of carcinogenesis of PM and PAH. These results support World Health Organization's conclusion that air pollution poses among the greatest health risks to humans living in cities.


Assuntos
Poluentes Atmosféricos , Carcinógenos , Neoplasias , Material Particulado , Hidrocarbonetos Policíclicos Aromáticos , Humanos , Poluição do Ar/estatística & dados numéricos , Carcinógenos/toxicidade , Exposição Ambiental/estatística & dados numéricos , Neoplasias/induzido quimicamente , Neoplasias/epidemiologia , Hidrocarbonetos Policíclicos Aromáticos/toxicidade
7.
Health Place ; 87: 103214, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38520992

RESUMO

The COVID-19 pandemic has disproportionately affected immigrant and racialized communities globally and revealed another public health crisis - structural racism. While structural racism is known to foster discrimination via mutually reinforcing systems, the unevenness of COVID-19 infections, hospitalizations, and deaths across societies has precipitated attention to the impacts of structural racism. Research highlights the inequitable burden of COVID-19 among immigrant and racialized groups; however, little is known about the synergistic impacts of structural racism and COVID-19 on the health and wellbeing of these groups. Fewer studies examine how structural racism and COVID-19 intersect within neighbourhoods to co-produce landscapes of disease exposure and management. This article examines the pathways through which structural racism shapes access, use, and control of environmental resources among immigrant and racialized individuals in the neighbourhoods of the Peel Region and how they converged to shape health and disease dynamics during the height of Canada's COVID-19 pandemic. Findings from in-depth interviews reveal that mutually reinforcing inequitable systems created environments for COVID-19 to reinscribe disparities in access, use, and control of key resources needed to manage health and disease, and created new forms of disparities and landscapes of inequality for immigrants and racialized individuals. We close with a discussion on the impacts for policy and practice.


Assuntos
COVID-19 , Emigrantes e Imigrantes , Racismo , Humanos , COVID-19/epidemiologia , COVID-19/etnologia , Canadá/epidemiologia , Emigrantes e Imigrantes/psicologia , Feminino , Masculino , Características de Residência , Disparidades nos Níveis de Saúde , Adulto , Pandemias , Desigualdades de Saúde , SARS-CoV-2 , Pessoa de Meia-Idade
8.
Int J Retina Vitreous ; 10(1): 49, 2024 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-39039572

RESUMO

BACKGROUND AND OBJECTIVE: Lens feathering due to intraocular gas may cause significant challenges with intraoperative visualization during posterior segment surgery. Herein, we describe an intraoperative technique for improving posterior segment visualization impacted by lens feathering. METHODS: New technique to improve visualization in vitrectomy from gas-induced cataract. RESULTS: The light pipe is used to gently massage posterior subcapsular lens vacuoles to improve the surgical view intraoperatively. CONCLUSION: We report an effective and efficient technique to improve lens feathering during vitreoretinal surgery without need for cataract extraction.

9.
NPJ Syst Biol Appl ; 10(1): 44, 2024 Apr 27.
Artigo em Inglês | MEDLINE | ID: mdl-38678051

RESUMO

Malaria vaccine development is hampered by extensive antigenic variation and complex life stages of Plasmodium species. Vaccine development has focused on a small number of antigens, many of which were identified without utilizing systematic genome-level approaches. In this study, we implement a machine learning-based reverse vaccinology approach to predict potential new malaria vaccine candidate antigens. We assemble and analyze P. falciparum proteomic, structural, functional, immunological, genomic, and transcriptomic data, and use positive-unlabeled learning to predict potential antigens based on the properties of known antigens and remaining proteins. We prioritize candidate antigens based on model performance on reference antigens with different genetic diversity and quantify the protein properties that contribute most to identifying top candidates. Candidate antigens are characterized by gene essentiality, gene ontology, and gene expression in different life stages to inform future vaccine development. This approach provides a framework for identifying and prioritizing candidate vaccine antigens for a broad range of pathogens.


Assuntos
Antígenos de Protozoários , Vacinas Antimaláricas , Malária Falciparum , Plasmodium falciparum , Plasmodium falciparum/imunologia , Plasmodium falciparum/genética , Vacinas Antimaláricas/imunologia , Antígenos de Protozoários/imunologia , Antígenos de Protozoários/genética , Malária Falciparum/imunologia , Malária Falciparum/prevenção & controle , Aprendizado de Máquina , Humanos , Proteômica/métodos , Desenvolvimento de Vacinas/métodos , Proteínas de Protozoários/imunologia , Proteínas de Protozoários/genética , Biologia Computacional/métodos
10.
Trop Med Health ; 52(1): 22, 2024 Mar 08.
Artigo em Inglês | MEDLINE | ID: mdl-38459581

RESUMO

BACKGROUND: Due to the low prevalence of clinically suspected malaria among pregnant women in Myanmar, little is known about its impact on mothers and newborns. Helminth and Human Immuno-deficiency Virus (HIV) co-infections cause anemia in pregnant women. This study assessed the prevalence of subclinical malaria and co-infections among pregnant women, and its association with adverse outcomes of pregnancy in the presence of infection. METHODS: A prospective longitudinal study was conducted in 12 villages in two townships in Myanmar between 2013 to 2015. A total of 752 pregnant women, with a mean age of 27 years, were enrolled and followed up once a month until six weeks after childbirth. Prevalence ratio was calculated in the multivariable analysis. RESULTS: The prevalence of subclinical malaria as measured by nested PCR was 5.7% for either P. falciparum or P. vivax, 2.7% prevalence of P. falciparum and 2.8% prevalence of P. vivax. Helminth infections were prevalent in 17% of women, and one woman with an HIV infection was found in our study. The burden of anemia was high, with an overall prevalence of 37% with or without helminth infection, 42% of the women were malaria positive and 43% had dual infections (both malaria and helminth). Only 11 abnormal pregnancy outcomes (7 stillbirths, 2 premature, 2 twins) were identified. Poisson regression showed that women in their first trimester had a 2.9 times higher rate of subclinical malaria compared to women in the third trimester (PR:2.9, 95%CI 1.19, 7.31, p = 0.019), women who were enrolled during the wet season were 2.5 times more likely to be malaria positive than the women enrolled in the dry season (PR: 2.5, 95%CI 1.27, 4.88, p = 0.008), and the malaria positivity rate decreased by 5% when increased in one year of woman's age (PR:0.95, 95%CI 0.91, 0.99, p = 0.02). In the multivariable regression, the age of respondents was the only significant factor associated with subclinical malaria in pregnancy. CONCLUSIONS: A comprehensive approach of integrating interventions for malaria, anemia, and helminths should be delivered during antenatal care services for pregnant women in rural areas of Myanmar.

11.
Artigo em Inglês | MEDLINE | ID: mdl-39078321

RESUMO

The development of small-diameter vascular grafts requires testing in large animal models before advancing to clinical trials. Vascular graft interposition implantation in sheep carotid arteries (CAs) is the most widely used model, but ovine CAs are prone to severe spasm following surgical manipulation, potentially impairing graft performance assessment. There is a paucity in the literature on reducing sheep CA spasm using effective vasodilator therapeutic protocols. In this study, four healthy Merino cross White Suffolk wethers (1-2 years, 52.1 ± 0.8 kg) underwent CT angiography and CA graft surgery. CT angiography using iodinated contrast agent was performed with innominate artery access via the CA or ascending aortic arch access via the femoral artery. Sheep were randomly allocated to then underwent right CA sham surgery or left CA vascular graft implantation. A variety of vasodilators, including papaverine, sodium nitroprusside, verapamil and their combination, were tested for preventing or treating CA spasms intraoperatively. Blood flow was reassessed immediately after CA surgery using CT angiography. The results showed that innominate artery access via the CA for CT angiography in sheep induced pre-surgical CA spasm with reduced arterial flow. Conversely, ascending aortic arch access via the femoral artery for CT angiography did not cause CA spasm and maintained arterial flow. During CA graft surgery, surgical trauma induced CA spasm, which was prevented by localised intraarterial administration of vasodilators papaverine hydrochloride and verapamil prior to significant surgical manipulation.

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