brainlife.io: a decentralized and open-source cloud platform to support neuroscience research.

Neuroscience is advancing standardization and tool development to support rigor and transparency. Consequently, data pipeline complexity has increased, hindering FAIR (findable, accessible, interoperable and reusable) access. brainlife.io was developed to democratize neuroimaging research. The platform provides data standardization, management, visualization and processing and automatically tracks the provenance history of thousands of data objects. Here, brainlife.io is described and evaluated for validity, reliability, reproducibility, replicability and scientific utility using four data modalities and 3,200 participants.

brainlife.io: A decentralized and open source cloud platform to support neuroscience research.

Neuroscience research has expanded dramatically over the past 30 years by advancing standardization and tool development to support rigor and transparency. Consequently, the complexity of the data pipeline has also increased, hindering access to FAIR data analysis to portions of the worldwide research community. brainlife.io was developed to reduce these burdens and democratize modern neuroscience research across institutions and career levels. Using community software and hardware infrastructure, the platform provides open-source data standardization, management, visualization, and processing and simplifies the data pipeline. brainlife.io automatically tracks the provenance history of thousands of data objects, supporting simplicity, efficiency, and transparency in neuroscience research. Here brainlife.io's technology and data services are described and evaluated for validity, reliability, reproducibility, replicability, and scientific utility. Using data from 4 modalities and 3,200 participants, we demonstrate that brainlife.io's services produce outputs that adhere to best practices in modern neuroscience research.

Meiotic cells escape prolonged spindle checkpoint activity through kinetochore silencing and slippage.

To prevent chromosome mis-segregation, a surveillance mechanism known as the spindle checkpoint delays the cell cycle if kinetochores are not attached to spindle microtubules, allowing the cell additional time to correct improper attachments. During spindle checkpoint activation, checkpoint proteins bind the unattached kinetochore and send a diffusible signal to inhibit the anaphase promoting complex/cyclosome (APC/C). Previous work has shown that mitotic cells with depolymerized microtubules can escape prolonged spindle checkpoint activation in a process called mitotic slippage. During slippage, spindle checkpoint proteins bind unattached kinetochores, but the cells cannot maintain the checkpoint arrest. We asked if meiotic cells had as robust of a spindle checkpoint response as mitotic cells and whether they also undergo slippage after prolonged spindle checkpoint activity. We performed a direct comparison between mitotic and meiotic budding yeast cells that signal the spindle checkpoint through two different assays. We find that the spindle checkpoint delay is shorter in meiosis I or meiosis II compared to mitosis, overcoming a checkpoint arrest approximately 150 minutes earlier in meiosis than in mitosis. In addition, cells in meiosis I escape spindle checkpoint signaling using two mechanisms, silencing the checkpoint at the kinetochore and through slippage. We propose that meiotic cells undertake developmentally-regulated mechanisms to prevent persistent spindle checkpoint activity to ensure the production of gametes.

Meiotic Cells Escape Prolonged Spindle Checkpoint Activity Through Premature Silencing and Slippage.

To prevent chromosome mis-segregation, a surveillance mechanism known as the spindle checkpoint delays the cell cycle if kinetochores are not attached to spindle microtubules, allowing the cell additional time to correct improper attachments. During spindle checkpoint activation, checkpoint proteins bind the unattached kinetochore and send a diffusible signal to inhibit the anaphase promoting complex/cyclosome (APC/C). Previous work has shown that mitotic cells with depolymerized microtubules can escape prolonged spindle checkpoint activation in a process called mitotic slippage. During slippage, spindle checkpoint proteins bind unattached kinetochores, but the cells cannot maintain the checkpoint arrest. We asked if meiotic cells had as robust of a spindle checkpoint response as mitotic cells and whether they also undergo slippage after prolonged spindle checkpoint activity. We performed a direct comparison between mitotic and meiotic budding yeast cells that signal the spindle checkpoint due to a lack of either kinetochore-microtubule attachments or due to a loss of tension-bearing attachments. We find that the spindle checkpoint is not as robust in meiosis I or meiosis II compared to mitosis, overcoming a checkpoint arrest approximately 150 minutes earlier in meiosis. In addition, cells in meiosis I escape spindle checkpoint signaling using two mechanisms, silencing the checkpoint at the kinetochore and through slippage. We propose that meiotic cells undertake developmentally-regulated mechanisms to prevent persistent spindle checkpoint activity to ensure the production of gametes. AUTHOR SUMMARY: Mitosis and meiosis are the two major types of cell divisions. Mitosis gives rise to genetically identical daughter cells, while meiosis is a reductional division that gives rise to gametes. Cell cycle checkpoints are highly regulated surveillance mechanisms that prevent cell cycle progression when circumstances are unfavorable. The spindle checkpoint promotes faithful chromosome segregation to safeguard against aneuploidy, in which cells have too many or too few chromosomes. The spindle checkpoint is activated at the kinetochore and then diffuses to inhibit cell cycle progression. Although the checkpoint is active in both mitosis and meiosis, most studies involving checkpoint regulation have been performed in mitosis. By activating the spindle checkpoint in both mitosis and meiosis in budding yeast, we show that cells in meiosis elicit a less persistent checkpoint signal compared to cells in mitosis. Further, we show that cells use distinct mechanisms to escape the checkpoint in mitosis and meiosis I. While cells in mitosis and meiosis II undergo anaphase onset while retaining checkpoint proteins at the kinetochore, cells in meiosis I prematurely lose checkpoint protein localization at the kinetochore. If the mechanism to remove the checkpoint components from the kinetochore is disrupted, meiosis I cells can still escape checkpoint activity. Together, these results highlight that cell cycle checkpoints are differentially regulated during meiosis to avoid long delays and to allow gametogenesis.

Use of Time-Lapse Microscopy and Stage-Specific Nuclear Depletion of Proteins to Study Meiosis in S. Cerevisiae.

Time-lapse fluorescence microscopy has revolutionized the understanding of meiotic cell-cycle events by providing temporal and spatial data that is often not seen by imaging fixed cells. Budding yeast has proved to be an important model organism to study meiotic chromosome segregation because many meiotic genes are highly conserved. Time-lapse microscopy of meiosis in budding yeast allows the monitoring of different meiotic mutants to show how the mutation disrupts meiotic processes. However, many proteins function at multiple points in meiosis. The use of loss-of-function or meiotic null mutants can therefore disrupt an early process, blocking or disturbing the later process and making it difficult to determine the phenotypes associated with each individual role. To circumvent this challenge, this protocol describes how the proteins can be conditionally depleted from the nucleus at specific stages of meiosis while monitoring meiotic events using time-lapse microscopy. Specifically, this protocol describes how the cells are synchronized in prophase I, how the anchor away technique is used to deplete proteins from the nucleus at specific meiotic stages, and how time-lapse imaging is used to monitor meiotic chromosome segregation. As an example of the usefulness of the technique, the kinetochore protein Ctf19 was depleted from the nucleus at different time points during meiosis, and the number of chromatin masses was analyzed at the end of meiosis II. Overall, this protocol can be adapted to deplete different nuclear proteins from the nucleus while monitoring the meiotic divisions.

Viruses Infecting Greenhood Orchids (Pterostylidinae) in Eastern Australia.

The Australasian biogeographic realm is a major centre of diversity for orchids, with every subfamily of the Orchidaceae represented and high levels of endemism at the species rank. It is hypothesised that there is a commensurate diversity of viruses infecting this group of plants. In this study, we have utilised high-throughput sequencing to survey for viruses infecting greenhood orchids (Pterostylidinae) in New South Wales and the Australian Capital Territory. The main aim of this study was to characterise Pterostylis blotch virus (PtBV), a previously reported but uncharacterised virus that had been tentatively classified in the genus Orthotospovirus. This classification was confirmed by genome sequencing, and phylogenetic analyses suggested that PtBV is representative of a new species that is possibly indigenous to Australia as it does not belong to either the American or Eurasian clades of orthotospoviruses. Apart from PtBV, putative new viruses in the genera Alphaendornavirus, Amalgavirus, Polerovirus and Totivirus were discovered, and complete genome sequences were obtained for each virus. It is concluded that the polerovirus is likely an example of an introduced virus infecting a native plant species in its natural habitat, as this virus is probably vectored by an aphid, and Australia has a depauperate native aphid fauna that does not include any species that are host-adapted to orchids.

A seasonal comparison of trace metal concentrations in the tissues of Arctic charr (Salvelinus alpinus) in Northern Québec, Canada.

Ecotoxicological research detailing trace metal contamination and seasonal variation in the tissues of northern fishes such as Arctic charr (Salvelinus alpinus) has been poorly represented in the literature beyond examination of mercury. In an effort to address this, anadromous Arctic charr were collected from the Deception River watershed in the late summer and post-winter season, before quantifying seasonal and organotropic variations in dorsal muscle and liver concentrations of arsenic, cadmium, chromium, copper, nickel, lead, and zinc. Potential linkages with biological variables (fork length, age, and somatic condition) and indicators of feeding behavior (δ13C and δ15N) were also assessed. Trace metal organotropism favouring elevation in liver tissue concentrations was exhibited by cadmium, copper, nickel and zinc, while arsenic, chromium and lead exhibited no significant organotropic variation. Seasonal differences in concentrations were metal and tissue dependent, but generally increased in tissues collected from post-winter sampled Arctic charr. Significant correlations with biological and trophic descriptors were also determined to be element and tissue dependent. These parameters, in addition to season, were incorporated into multi-predictor variable models, where variations in trace metal concentration data were often best explained when season, somatic condition, and trophic descriptors were included. These variables were also of greatest relative importance across all considered trace metals and tissue types. These findings suggest that seasonally linked processes have the greatest influence on trace metal concentrations in anadromous Arctic charr. Future metal-related research on Arctic charr and other northern fish species should further consider these variables when evaluating elemental accumulation.

CDK Regulation of Meiosis: Lessons from S. cerevisiae and S. pombe.

Meiotic progression requires precise orchestration, such that one round of DNA replication is followed by two meiotic divisions. The order and timing of meiotic events is controlled through the modulation of the phosphorylation state of proteins. Key components of this phospho-regulatory system include cyclin-dependent kinase (CDK) and its cyclin regulatory subunits. Over the past two decades, studies in budding and fission yeast have greatly informed our understanding of the role of CDK in meiotic regulation. In this review, we provide an overview of how CDK controls meiotic events in both budding and fission yeast. We discuss mechanisms of CDK regulation through post-translational modifications and changes in the levels of cyclins. Finally, we highlight the similarities and differences in CDK regulation between the two yeast species. Since CDK and many meiotic regulators are highly conserved, the findings in budding and fission yeasts have revealed conserved mechanisms of meiotic regulation among eukaryotes.

Seasonal variation of total mercury and condition indices of Arctic charr (Salvelinus alpinus) in Northern Québec, Canada.

The winter ecology of anadromous Arctic charr, an important fish species for Indigenous populations, has remained poorly detailed in the literature beyond descriptions of seasonal fasting and resulting declines in condition. However, prolonged periods of reduced feeding can have significant consequences for other variables, such as tissue contaminant levels. To more thoroughly detail seasonal changes, biological information (fork length, total weight, age, sex, somatic condition), stable isotopes (δ13C, % carbon, δ15N, % nitrogen), dorsal muscle % lipid, caloric densities, and total mercury (THg) concentrations were assessed in anadromous Arctic charr collected from Deception Bay, Canada, during the summer and over-wintering periods. Significant reductions in somatic condition, total weight, and % nitrogen, consistent with prolonged periods of fasting, were found for post-winter captured Arctic charr, but % lipid and caloric densities were significantly higher in these fish. THg also varied seasonally and was significantly higher in summer collected tissue. When tested individually via linear regression, significant relationships were seasonally dependent, but limited in number. All previously mentioned parameters were then incorporated into multi-variable models which better explained variations in the data. While there was no clear best model for explaining the % lipid values, caloric densities, and THg, season, condition, and stable isotope values (% carbon and % nitrogen) were the best indicators of % lipid content and caloric densities. THg concentrations were best explained by total weight, somatic condition, and δ13C. Seasonal variation in fish condition measures and THg may be indicative of condition selective mortality that yields apparent improvement through the disproportionate removal of poorer conditioned fish from the population during the over-wintering period. This hypothesis was further supported by mortality estimates and the results of the multi-predictor variable models. Collectively, this research highlights the importance of understanding seasonal dynamics for anadromous Arctic charr populations.

In vitro and in vivo activity of voriconazole and benznidazole combination on trypanosoma cruzi infection models.

Combination therapy has been proposed as an ideal strategy to reduce drug toxicity and improve treatment efficacy in Chagas disease. Previously, we demonstrated potent in vivo anti-Trypanosoma cruzi activity of voriconazole. In this work, we aimed to study the synergistic effect of voriconazole (VCZ) and benznidazole (BZ) both in vitro and in vivo models of T. cruzi infection using the Tulahuen strain. Combining VCZ and BZ at fixed concentrations, the inhibitory concentration 50% (IC50) on amastigotes was lower than the obtained IC50 for BZ alone and the Fractional Inhibitory Concentration Index (∑FIC) suggested an in vitro additive effect on T. cruzi amastigotes inhibition at concentrations devoid of cytotoxic effects. Treatment response in the in vivo model was evaluated by comparing behavior and physical aspects, parasitemia and mortality of mice infected with Tulahuen strain. VCZ and BZ treatments alone or in combination were well tolerated. All treated animals displayed significantly lower mean peak parasitemia and mortality compared to infected non-treated controls (p< 0.05). However, VCZ + BZ combination elicited no additional benefits over BZ monotherapy. VCZ efficacy was not enhanced by combination therapy with BZ at the doses studied, requiring further and astringent non-clinical studies to establish the VCZ efficacy and eventually moving forward to clinical trials.

Differential requirement for Bub1 and Bub3 in regulation of meiotic versus mitotic chromosome segregation.

Accurate chromosome segregation depends on the proper attachment of kinetochores to spindle microtubules before anaphase onset. The Ipl1/Aurora B kinase corrects improper attachments by phosphorylating kinetochore components and so releasing aberrant kinetochore-microtubule interactions. The localization of Ipl1 to kinetochores in budding yeast depends upon multiple pathways, including the Bub1-Bub3 pathway. We show here that in meiosis, Bub3 is crucial for correction of attachment errors. Depletion of Bub3 results in reduced levels of kinetochore-localized Ipl1 and concomitant massive chromosome missegregation caused by incorrect chromosome-spindle attachments. Depletion of Bub3 also results in shorter metaphase I and metaphase II due to premature localization of protein phosphatase 1 (PP1) to kinetochores, which antagonizes Ipl1-mediated phosphorylation. We propose a new role for the Bub1-Bub3 pathway in maintaining the balance between kinetochore localization of Ipl1 and PP1, a balance that is essential for accurate meiotic chromosome segregation and timely anaphase onset.

Intimate partner violence in the Canadian territorial north: perspectives from a literature review and a media watch.

INTRODUCTION: Family violence is a complex, multidimensional and pervasive presence in many Aboriginal communities. Although practitioners acknowledge that intimate partner violence (IPV) is a grave concern in the North, as in other jurisdictions in Canada, there is a paucity of literature about IPV and the local response to that violence. OBJECTIVE: The purpose of this study is to report on a synthesis of Northern Territorial literature and a 3-year media watch conducted in the Canadian territories. DESIGN: This review is part of a multidisciplinary 5-year study occurring in the Northwest Territories (NT) and northern regions of the Prairie Provinces of Canada. The methods included a review of the literature through CINAHL, PubMed, Academic Search Complete, Social Sciences Index and JSTOR (1990-2012) combined with a media watch from 2009 to 2012. A thematic content analysis was completed. RESULTS: THEMES INCLUDED: colonization; alcohol and substance use; effects of residential schooling; housing inadequacies; help-seeking behaviors; and gaps within the justice system. Identified themes from the media watch were: murders from IPV; reported assaults and criminal charges; emergency protection orders; and awareness campaigns and prevention measures. CONCLUSION: When synthesized, the results of the literature review and media surveillance depict a starting context and description of IPV in the Canadian territories. There are many questions left unanswered which build support for the necessity of the current research, outline the public outcry for action in local media and identify the current published knowledge about IPV.

The enigmatic genome of Chara australis virus.

Most of the genomic sequence of Chara australis virus (CAV), previously called Chara corallina virus, has been determined. It is a ssRNA molecule of 9065 nt with at least four ORFs. At its 5' end is an ORF encoding a protein of 227 kDa, distantly homologous to the multifunctional replicases of benyviruses and rubiviruses. Next is an ORF encoding a protein of 44 kDa, homologous to the helicases of pestiviruses. The third ORF encodes an unmatched protein of 38 kDa that is probably a movement protein. The fourth and 3'-terminal ORF encodes a protein of 17.7 kDa homologous to the coat proteins of tobamoviruses. The short methyltransferase region of the CAV replicase matches only the C-terminal motif of benyvirus methyltransferases. This and other clues indicate that approximately 11% and 2% of the 5' and 3' termini of the complete CAV genome, respectively, are missing from the sequence. The aligned amino acid sequences of the CAV proteins and their nearest homologues contain many gaps but relationships inferred from them were little affected by removal of these gaps. Sequence comparisons show that three of the CAV genes may have diverged from the most closely related genes of other viruses 250-450 million years ago, and the sister relationship between the genes of CAV and those of benyviruses and tobamoviruses, mirroring the ancient sister relationship between charophytes (i.e. the algal host of CAV) and embryophytes (i.e. the plant hosts of tobamoviruses and benyviruses), is congruent with this possibility.

Isolation and characterisation of a high-efficiency desaturase and elongases from microalgae for transgenic LC-PUFA production.

The production of long-chain polyunsaturated fatty acids from precursor molecules linoleic acid (LA; 18:2omega6) and alpha-linolenic acid (ALA; 18:3omega3) is catalysed by sequential desaturase and elongase reactions. We report the isolation of a front-end Delta6-desaturase gene from the microalgae Ostreococcus lucimarinus and two elongase genes, a Delta6-elongase and a Delta5-elongase, from the microalga Pyramimonas cordata. These enzymes efficiently convert their respective substrates when transformed in yeast (39-75% conversion for omega3 substrate fatty acids), and the Delta5-elongase in particular displays higher elongation efficiency (75% for conversion of eicosapentaenoic acid (20:5omega3) to docosapentaenoic acid (22:5omega3)) than previously reported genes. In addition, the Delta6-desaturase is homologous with acyl-CoA desaturases and shows a strong preference for the omega3 substrate ALA.

Correlates of functional limitations in older Chinese patients with chronic obstructive pulmonary disease in Hong Kong.

BACKGROUND: Few studies have examined functional limitations in Chinese elders with chronic obstructive pulmonary disease (COPD). OBJECTIVES: The objective was to describe the functional limitations, respiratory status, and psychologic status of Chinese elders with COPD; to examine the relationships between functional limitations and selected variables including age, gender, duration of COPD, and hospital readmission history; and to identify the variables that predict functional limitations in Chinese elders with COPD. METHOD: A correlational predictive study was performed with a sample of 97 Chinese elders with COPD. The subjects were 65 years or older and recruited from two hospitals in Hong Kong. Data were individually collected on the day the individual was to be discharged from the hospital, by using the Barthel Index for functional limitations, forced expiratory volume in 1 second percent predicted for respiratory status, and General Health Questionnaire (28 items) for psychologic status. Information on age, gender, duration of COPD, and hospital readmission history were also identified from the medical record. RESULTS: Functional limitations in Chinese elders with COPD were significantly correlated with poorer respiratory status and more depressive symptoms. Multiple regression analysis indicated that depressive symptoms were a significant predictor of functional limitations after controlling for the effect of respiratory status. DISCUSSION: The results of this study demonstrate that depressive symptoms to some extent predict functional limitations in Chinese elders with COPD. Investigation of the effect of appropriate screening and interventions for depressive symptoms on preventing, delaying, or reducing functional limitations in this patient group is suggested.

The 'potyvirid primers' will probably provide phylogenetically informative DNA fragments from all species of Potyviridae.

A survey of gene sequences of species of Potyviridae, the most numerous family of plant viruses, has shown that the -GNNS- encoding region of the NIb gene is present in all c. 300 publicly available sequences of that region. We also report that relationships inferred from the sequence of the 1.6-2.1 kb portion of the genome between the -GNNS- encoding region and its 3' terminus reflect those of the remainder of the genome. Thus, the use for RT-PCR tests of the 'potyvirid primers' based on the -GNNS- encoding region and the 3' terminal poly-A region of the genome, will yield DNA fragments, the sequences of which are very likely to correctly identify viruses from which they were obtained.