Maximizing genetic representation in seed collections from populations of self and cross-pollinated banana wild relatives

Background: Conservation of plant genetic resources, including the wild relatives of crops, plays an important and well recognised role in addressing some of the key challenges faced by humanity and the planet including ending hunger and biodiversity loss. However, the genetic diversity and representativeness of ex situ collections, especially that contained in seed collections, is often unknown. This limits meaningful assessments against conservation targets, impairs targeting of future collecting and limits their use. We assessed genetic representation of seed collections compared to source populations for three wild relatives of bananas and plantains. Focal species and sampling regions were M. acuminata subsp. banksii (Papua New Guinea), M. balbisiana (Viet Nam) and M. maclayi s.l. (Bougainville, Papua New Guinea). We sequenced 445 samples using suites of 16–20 existing and newly developed taxon-specific polymorphic microsatellite markers. Samples of each species were from five populations in a region; 15 leaf samples from different individuals and 16 seed samples from one infructescence (‘bunch’) were analysed for each population. Results: Allelic richness of seeds compared to populations was 51, 81 and 93% (M. acuminata, M. balbisiana and M. maclayi respectively). Seed samples represented all common alleles in populations but omitted some rarer alleles. The number of collections required to achieve the 70% target of the Global Strategy for Plant Conservation was species dependent, relating to mating systems. Musa acuminata populations had low heterozygosity and diversity, indicating self-fertilization; many bunches were needed (> 15) to represent regional alleles to 70%; over 90% of the alleles from a bunch are included in only two seeds. Musa maclayi was characteristically cross-fertilizing; only three bunches were needed to represent regional alleles; within a bunch, 16 seeds represent alleles. Musa balbisiana, considered cross-fertilized, had low genetic diversity; seeds of four bunches are needed to represent regional alleles; only two seeds represent alleles in a bunch. Conclusions: We demonstrate empirical measurement of representation of genetic material in seeds collections in ex situ conservation towards conservation targets. Species mating systems profoundly affected genetic representation in seed collections and therefore should be a primary consideration to maximize genetic representation. Results are applicable to sampling strategies for other wild species

Drying banana seeds for ex situ conservation

The ability of seeds to withstand drying is fundamental to ex situ seed conservation but drying responses are not well known for most wild species including crop wild relatives. We look at drying responses of seeds of Musa acuminata and Musa balbisiana, the two primary wild relatives of bananas and plantains, using the following four experimental approaches: (i)We equilibrated seeds to a range of relative humidity (RH) levels using non-saturated lithium chloride solutions and subsequently measured moisture content (MC) and viability. At each humidity levelwe tested viability using embryo rescue (ER), tetrazolium chloride staining and germination in an incubator.We found that seed viabilitywas not reduced when seedswere dried to 4% equilibrium relative humidity (eRH; equating to 2.5% MC). (ii)We assessed viability ofmature and less mature seeds using ER and germination in the soil and tested responses to drying. Findings showed that seeds must be fully mature to germinate and immature seeds had negligible viability. (iii) We dried seeds extracted from ripe/unripe fruit to 35–40% eRH at different rates and tested viability with germination tests in the soil. Seeds from unripe fruit lost viability when dried and especially when dried faster; seeds from ripe fruit only lost viability when fast dried. (iv) Finally, we dried and re-imbibed mature and less mature seeds and measured embryo shrinkage and volume change using X-ray computer tomography. Embryos of less mature seeds shrank significantly when dried to 15% eRH from 0.468 to 0.262 mm3, but embryos of mature seeds did not. Based on our results, mature seeds from ripe fruit are desiccation tolerant to moisture levels required for seed genebanking but embryos from immature seeds are mechanistically less able to withstand desiccation, especially when water potential gradients are high

A novel diagnostic model for tuberculous meningitis using Bayesian latent class analysis

Background Diagnosis of tuberculous meningitis (TBM) is hampered by the lack of a gold standard. Current microbiological tests lack sensitivity and clinical diagnostic approaches are subjective. We therefore built a diagnostic model that can be used before microbiological test results are known. Methods We included 659 individuals aged ≥ 16 years with suspected brain infections from a prospective observational study conducted in Vietnam. We fitted a logistic regression diagnostic model for TBM status, with unknown values estimated via a latent class model on three mycobacterial tests: Ziehl–Neelsen smear, Mycobacterial culture, and GeneXpert. We additionally re-evaluated mycobacterial test performance, estimated individual mycobacillary burden, and quantified the reduction in TBM risk after confirmatory tests were negative. We also fitted a simplified model and developed a scoring table for early screening. All models were compared and validated internally. Results Participants with HIV, miliary TB, long symptom duration, and high cerebrospinal fluid (CSF) lymphocyte count were more likely to have TBM. HIV and higher CSF protein were associated with higher mycobacillary burden. In the simplified model, HIV infection, clinical symptoms with long duration, and clinical or radiological evidence of extra-neural TB were associated with TBM At the cutpoints based on Youden’s Index, the sensitivity and specificity in diagnosing TBM for our full and simplified models were 86.0% and 79.0%, and 88.0% and 75.0% respectively. Conclusion Our diagnostic model shows reliable performance and can be developed as a decision assistant for clinicians to detect patients at high risk of TBM. Summary Diagnosis of tuberculous meningitis is hampered by the lack of gold standard. We developed a diagnostic model using latent class analysis, combining confirmatory test results and risk factors. Models were accurate, well-calibrated, and can support both clinical practice and research

Conservation status assessment of banana crop wild relatives using species distribution modelling

Aim: Crop wild relatives (CWR) are an essential source of genetic material for the improvement of certain traits in related crop species. Despite their importance, increasing public, scientific and political support, large gaps exist in the amount of genetic material collected and conserved of many CWR. Here, we construct a dataset on the distribution of wild banana species (Musa spp.) and assess their risk and conservation status. We deal with the following questions: (a) What areas are potentially suitable for wild banana species? (b) How much of the wild banana diversity is currently at risk or insufficiently conserved ex and in situ? Location: Native distribution area of wild banana species, ranging from the northeastern states of India to north-eastern Australia. Methods: We assessed the potential environmental range of wild species using a species distribution modelling approach with MaxEnt. Extinction risk was evaluated following IUCN criterion B, and the ex and in situ conservation status was assessed using an indicator for biodiversity and sustainable development targets. Results: We found that 11 out of 59 assessed species can be considered as vulnerable and nine as endangered. Highest species richness was found along the border of south China and northern Vietnam, in the north-eastern states of India and on the Malayan peninsula. Our distribution modelling approach indicates that the northern Indo-Burmese region has the highest environmental suitability for most wild banana species and that lowland rain forests in general are highly suitable for bananas. Assessment of in and ex situ conservation status indicates that 56 out of 59 assessed species are currently insufficiently conserved ex situ and that 49 are of high priority for further conservation. Additional in situ conservation is of high priority for six species and of medium priority for 40 species. Main conclusions: To date, little of the banana CWR are sufficiently conserved both in and ex situ

Effectiveness and safety of in vitro maturation of oocytes versus in vitro fertilisation in women with high antral follicle count : Study protocol for a randomised controlled trial

This work was supported by Ferring grant number 000323 and sponsored by My Duc Hospital.Peer reviewedPublisher PD

Online physical exercise intervention in older adults during lockdown: Can we improve the recipe?

peer reviewed[en] BACKGROUND: Recorded and live online physical exercise (PE) interventions are known to provide health benefits. However, the effects of prioritizing the number of live or recorded sessions remain unclear. AIMS: To explore which recorded-live sessions ratio leads to the best implementation and benefits in older adults. METHODS: Forty-six community-dwelling adults (> 60y.o.) were randomized into two groups completing a 12-week online PE intervention. Each group had a different ratio of live-recorded online sessions as follows: Live-Recorded-Live sessions (LRL; n = 22) vs. Recorded-Live-Recorded sessions (RLR; n = 24). RESULTS: Drop-out rates did not reach significance (LRL:14% vs. RLR: 29%, p = 0.20), and adherence was similar (> 85%) between groups. Both groups reported similar levels of satisfaction (> 70%), enjoyment (> 75%), and perceived exertion (> 60%). Both groups increased physical health and functional capacities, with greater improvements in muscle power (LRL: LRL: + 35 ± 16.1% vs. RLR: + 7 ± 13.9%; p = 0.010) and endurance (LRL: + 34.7 ± 15.4 vs. RLR: + 27.0 ± 26.5, p < 0.001) in the LRL group. DISCUSSION: Both online PE intervention modalities were adapted to the participants' capacities and led to a high level of enjoyment and retention. The greater physical improvements observed in the LRL group are likely due to the higher presence of the instructor compared to the RLR group. Indeed, participants received likely more feedback to appropriately adjust postures and movements, increasing the quality of the exercises. CONCLUSION: When creating online PE interventions containing both recorded and live sessions, priority should be given to maximizing the number of live sessions and not the number of recorded sessions

Burden of injuries in Vietnam: emerging trends from a decade of economic achievement

BACKGROUND: Vietnam has been one of the fastest-growing world economies in the past decade. The burden of injuries can be affected by economic growth given the increased exposure to causes of injury as well as decreased morbidity and mortality of those that experience injury. It is of interest to evaluate the trends in injury burden that occurred alongside Vietnam's economic growth in the past decade. METHODS: Results from Global Burden of Disease 2017 were obtained and reviewed. Estimates of incidence, cause-specific mortality, years lived with disability, years of life lost, disability-adjusted life years were analysed and reported for 30 causes of injury in Vietnam from 2007 to 2017. RESULTS: Between 2007 and 2017, the age-standardised incidence rate of all injuries increased by 14.6% (11.5%-18.2%), while the age-standardised mortality rate decreased by 11.6% (3.0%-20.2%). Interpersonal violence experienced the largest increase in age-standardised incidence (28.3% (17.6%-40.1%)), while exposure to forces of nature had the largest decrease in age-standardised mortality (47.1% (37.9%-54.6%)). The five leading causes of injury in both 2007 and 2017 were road injuries, falls, exposure to mechanical forces, interpersonal violence and other unintentional injuries, all of which increased in incidence from 2007 to 2017. Injury burden varied markedly by age and sex. CONCLUSIONS: The rapid expansions of economic growth in Vietnam as well as improvements in the Sociodemographic Index have occurred alongside dynamic patterns in injury burden. These results should be used to develop and implement prevention and treatment programme

Metabolism of no-carrier-added 2-[18F]fluoro-L-tyrosine in rats

Background: Several fluorine-18 labelled fluoroamino acids have been evaluated as tracers for the quantitative assessment of cerebral protein synthesis in vivo by positron emission tomography (PET). Among these, 2-[18F]fluoro-L-tyrosine (2-[18F]Tyr) has been studied in mice at a low specific activity. Its incorporation into proteins is fast and metabolism via other pathways is limited. The present in vivo study was carried out in normal awake rats using no-carrier-added 2-[18F]Tyr. Under normal physiological conditions, we have studied the incorporation into proteins and the metabolism of the tracer in different brain areas. Methods: No-carrier-added 2-[18F]Tyr was administered to awake rats equipped with chronic arterial and venous catheters. The time course of the plasma activity was studied by arterial blood sampling. The biodistribution of the activity in the main organs was studied at the end of the experiment. The distribution of radioactive species in plasma and brain regions was studied by acidic precipitation of the proteins and HPLC analysis of the supernatant. Results: The absolute uptake of radioactivity in brain regions was homogenous. In awake rats, nocarrier-added 2-[18F]Tyr exhibits a fast and almost quantitative incorporation into the proteins fractions of cerebellum and cortex. In striatum, this incorporation into proteins and the unchanged fraction of the tracer detected by HPLC could be lower than in other brain regions. Conclusion: This study confirms the potential of 2-[18F]fluoro-L-tyrosine as a tracer for the assessment of the rate of protein synthesis by positron emission tomography. The observed metabolism suggests a need for a correction for the appearance of metabolites, at least in plasma

TIAToolbox as an end-to-end library for advanced tissue image analytics

Background: Computational pathology has seen rapid growth in recent years, driven by advanced deep-learning algorithms. Due to the sheer size and complexity of multi-gigapixel whole-slide images, to the best of our knowledge, there is no open-source software library providing a generic end-to-end API for pathology image analysis using best practices. Most researchers have designed custom pipelines from the bottom up, restricting the development of advanced algorithms to specialist users. To help overcome this bottleneck, we present TIAToolbox, a Python toolbox designed to make computational pathology accessible to computational, biomedical, and clinical researchers. Methods: By creating modular and configurable components, we enable the implementation of computational pathology algorithms in a way that is easy to use, flexible and extensible. We consider common sub-tasks including reading whole slide image data, patch extraction, stain normalization and augmentation, model inference, and visualization. For each of these steps, we provide a user-friendly application programming interface for commonly used methods and models. Results: We demonstrate the use of the interface to construct a full computational pathology deep-learning pipeline. We show, with the help of examples, how state-of-the-art deep-learning algorithms can be reimplemented in a streamlined manner using our library with minimal effort. Conclusions: We provide a usable and adaptable library with efficient, cutting-edge, and unit-tested tools for data loading, pre-processing, model inference, post-processing, and visualization. This enables a range of users to easily build upon recent deep-learning developments in the computational pathology literature

CD27− B-Cells Produce Class Switched and Somatically Hyper-Mutated Antibodies during Chronic HIV-1 Infection

Class switch recombination and somatic hypermutation occur in mature B-cells in response to antigen stimulation. These processes are crucial for the generation of functional antibodies. During HIV-1 infection, loss of memory B-cells, together with an altered differentiation of naïve B-cells result in production of low quality antibodies, which may be due to impaired immunoglobulin affinity maturation. In the current study, we evaluated the effect of HIV-1 infection on class switch recombination and somatic hypermutation by studying the expression of activation-induced cytidine deaminase (AID) in peripheral B-cells from a cohort of chronically HIV-1 infected patients as compared to a group of healthy controls. In parallel, we also characterized the phenotype of B-cells and their ability to produce immunoglobulins in vitro. Cells from HIV-1 infected patients showed higher baseline levels of AID expression and increased IgA production measured ex-vivo and upon CD40 and TLR9 stimulation in vitro. Moreover, the percentage of CD27−IgA+ and CD27−IgG+ B-cells in blood was significantly increased in HIV-1 infected patients as compared to controls. Interestingly, our results showed a significantly increased number of somatic hypermutations in the VH genes in CD27− cells from patients. Taken together, these results show that during HIV-1 infection, CD27− B-cells can also produce class switched and somatically hypermutated antibodies. Our data add important information for the understanding of the mechanisms underlying the loss of specific antibody production observed during HIV-1 infection