Transcriptomic basis of sex loss in the pea aphid

BACKGROUND

Transitions from sexual to asexual reproduction are common in eukaryotes, but the underlying mechanisms remain poorly known. The pea aphid-Acyrthosiphon pisum-exhibits reproductive polymorphism, with cyclical parthenogenetic and obligate parthenogenetic lineages, offering an opportunity to decipher the genetic basis of sex loss. Previous work on this species identified a single 840 kb region controlling reproductive polymorphism and carrying 32 genes. With the aim of identifying the gene(s) responsible for sex loss and the resulting consequences on the genetic programs controlling sexual or asexual embryogenesis, we compared the transcriptomic response to photoperiod shortening-the main sex-inducing cue-of a sexual and an obligate asexual lineage of the pea aphid, focusing on heads (where the photoperiodic cue is detected) and embryos (the final target of the cue).

RESULTS

Our analyses revealed that four genes (one expressed in the head, and three in the embryos) of the region responded differently to photoperiod in the two lineages. We also found that the downstream genetic programs expressed during embryonic development of a future sexual female encompass ∼1600 genes, among which miRNAs, piRNAs and histone modification pathways are overrepresented. These genes mainly co-localize in two genomic regions enriched in transposable elements (TEs).

CONCLUSIONS

Our results suggest that the causal polymorphism(s) in the 840 kb region somehow impair downstream epigenetic and post-transcriptional regulations in obligate asexual lineages, thereby sustaining asexual reproduction.

Occurrences of post-traumatic stress disorder, anxiety, depression, and burnout syndrome in ICU staff workers after two-year of the COVID-19 pandemic: the international PSY-CO in ICU study

PURPOSE

The present study aimed at assessing the prevalences of post-traumatic stress disorder (PTSD) (main objective), anxiety, depression, and burnout syndrome (BOS) and their associated factors in intensive care unit (ICU) staff workers in the second year of the COVID-19 pandemic.

MATERIALS AND METHODS

An international cross-sectional multicenter ICU-based online survey was carried out among the ICU staff workers in 20 ICUs across 3 continents. ICUs staff workers (both caregivers and non-caregivers) were invited to complete PCL-5, HADS, and MBI questionnaires for assessing PTSD, anxiety, depression, and the different components of BOS, respectively. A personal questionnaire was used to isolate independent associated factors with these disorders.

RESULTS

PCL-5, HADS, and MBI questionnaires were completed by 585, 570, and 539 responders, respectively (525 completed all questionnaires). PTSD was diagnosed in 98/585 responders (16.8%). Changing familial environment, being a non-caregiver staff worker, having not being involved in a COVID-19 patient admission, having not been provided with COVID-19-related information were associated with PTSD. Anxiety was reported in 130/570 responders (22.8%). Working in a public hospital, being a woman, being financially impacted, being a non-clinical healthcare staff member, having no theoretical or practical training on individual preventive measures, and fear of managing COVID-19 patients were associated with anxiety. Depression was reported in 50/570 responders (8.8%). Comorbidity at risk of severe COVID-19, working in a public hospital, looking after a child, being a non-caregiver staff member, having no information, and a request for moving from the unit were associated with depression. Having received no information and no adequate training for COVID-19 patient management were associated with all 3 dimensions of BOS.

CONCLUSION

The present study confirmed that ICU staff workers, whether they treated COVID-19 patients or not, have a substantial prevalence of psychological disorders.

[Describing and disseminating organizational innovation in public health DINOSP ; guide (Description of Organizational Innovations in Public Health)]

OBJECTIVES

The transition from experimentation to the scaling up of organizational innovations in public health is arduous. The innovation process requires back-up in view of enhancing the chances of success and generalization. The aim of this article is to present the development of a guide to support the description and analysis of organizational innovations in public health.

METHOD

The mobilization of two analysis and description tools, ASTAIRE and TIDIeR, made it possible to select the innovation criteria to be considered for generalization. Collective discussions between actors, decision-makers and researchers and individual interviews with the latter refined and completed the proposed guide, which was reread by experts and tested by project leaders, thereby improving its accuracy and usability.

RESULTS

The guide puts forward a two-step approach: i) to describe innovation at two levels: on the one hand, intervention methods, and on the other hand, interventional, population or contextual components corresponding to 27 criteria and ii) to assess the transferability of the innovation by distinguishing its key functions, its formal elements and the margins of maneuver to be maintained.

DISCUSSION

The guide presents a modular vision of innovations and leaves room for reflection on its mechanisms. It favors the synchronization of innovations with the existing system and their mutualization.

CONCLUSIONS

By putting forward a standardised description of organizational innovations in health and analyzing their effectiveness, the tool can effectively contribute to the development of effective, adaptable and generalizable projects, and thereby contribute to progress in public health.

Prostate cancer brachytherapy: SFRO guidelines 2021

Prostate brachytherapy techniques are described, concerning both permanent seed implant and high dose rate brachytherapy. The following guidelines are presented: brachytherapy indications, implant procedure for permanent low dose rate implants and high dose rate with source projector, as well as dose and dose-constraints objectives, immediate postoperative management, post-treatment evaluation, and long-term follow-up.

Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions

BACKGROUND

Ticks transmit pathogens of medical and veterinary importance and are an increasing threat to human and animal health. Assessing disease risk and developing new control strategies requires identifying members of the tick-borne microbiota as well as their temporal dynamics and interactions.

METHODS

Using high-throughput sequencing, we studied the Ixodes ricinus microbiota and its temporal dynamics. 371 nymphs were monthly collected during three consecutive years in a peri-urban forest. After a Poisson lognormal model was adjusted to our data set, a principal component analysis, sparse network reconstruction, and differential analysis allowed us to assess seasonal and monthly variability of I. ricinus microbiota and interactions within this community.

RESULTS

Around 75% of the detected sequences belonged to five genera known to be maternally inherited bacteria in arthropods and to potentially circulate in ticks: Candidatus Midichloria, Rickettsia, Spiroplasma, Arsenophonus and Wolbachia. The structure of the I. ricinus microbiota varied over time with interannual recurrence and seemed to be mainly driven by OTUs commonly found in the environment. Total network analysis revealed a majority of positive partial correlations. We identified strong relationships between OTUs belonging to Wolbachia and Arsenophonus, evidence for the presence of the parasitoid wasp Ixodiphagus hookeri in ticks. Other associations were observed between the tick symbiont Candidatus Midichloria and pathogens belonging to Rickettsia. Finally, more specific network analyses were performed on TBP-infected samples and suggested that the presence of pathogens belonging to the genera Borrelia, Anaplasma and Rickettsia may disrupt microbial interactions in I. ricinus.

CONCLUSIONS

We identified the I. ricinus microbiota and documented marked shifts in tick microbiota dynamics over time. Statistically, we showed strong relationships between the presence of specific pathogens and the structure of the I. ricinus microbiota. We detected close links between some tick symbionts and the potential presence of either pathogenic Rickettsia or a parasitoid in ticks. These new findings pave the way for the development of new strategies for the control of ticks and tick-borne diseases. Video abstract.

Information Pamphlet Given to Relatives During the End-of-Life Decision in the ICU: An Assessor-Blinded, Randomized Controlled Trial

BACKGROUND

Symptoms of posttraumatic stress disorder (PTSD) are common in family members of patients who have died in the ICU.

RESEARCH QUESTION

Could a pamphlet describing the role of relatives in the end-of-life decision decrease their risk of developing PTSD-related symptoms?

STUDY DESIGN AND METHODS

In this assessor-blinded, randomized controlled trial, 90 relatives of adult patients for whom an end-of-life decision was anticipated were enrolled. Relatives were randomly assigned to receive oral information as well as an information pamphlet explaining that the end-of-life decision is made by physicians (Group 1; n = 45) or oral information alone (Group 2; n = 45). PTSD-related symptoms were blindly assessed at 90 days following the patient's death by using the Impact of Event Scale (scores range from 0 [indicating no symptoms] to 75 [indicating severe symptoms]). Anxiety and depression symptoms were assessed by using the Hospital Anxiety and Depression Scale score (range, 0-21 [higher scores indicate worse symptoms]).

RESULTS

On day 90, the number of relatives with PTSD-related symptoms was significantly lower in Group 1 than in Group 2: 18 of 45 vs 33 of 45 (P = .001). The risk ratio of having PTSD-related symptoms in Group 2 compared with Group 1 was 1.8 (95% CI, 1.2-2.7). The mean Impact of Event Scale and Hospital Anxiety and Depression Scale scores were significantly reduced in Group 1 compared with Group 2: 28 ± 10 vs 38 ± 14 (P < .001) and 13 ± 5 vs 17 ± 8 (P = .023), respectively.

INTERPRETATION

An information pamphlet describing the relatives' role during end-of-life decisions significantly reduced their risk of developing PTSD-related symptoms.

CLINICAL TRIAL REGISTRATION

ClinicalTrials.gov; No.: NCT02329418; URL: www.clinicaltrials.gov).

Genetic gain for rice yield in rainfed environments in India

The complexity of genotype × environment interactions under drought reduces heritability, which determines the effectiveness of selection for drought tolerance and development of drought tolerant varieties. Genetic progress measured through changes in yield performance over time is important in determining the efficiency of breeding programmes in which test cultivars are replaced each year on the assumption that the new cultivars will surpass the older cultivars. The goal of our study was to determine the annual rate of genetic gain for rice grain yield in a drought-prone rainfed system in a series of multi-environment trials conducted from 2005 to 2014 under the Drought Breeding Network of Indian sites in collaboration with the International Rice Research Institute (IRRI). Our results show a positive trend in grain yield with an annual genetic yield increase of about 0.68 % under irrigated control, 0.87 % under moderate reproductive stage drought stress and 1.9 % under severe reproductive stage drought stress due to breeding efforts. The study also demonstrates the effectiveness of direct selection for grain yield under both irrigated control as well as managed drought stress screening to improve yield in typical rainfed systems. IRRI's drought breeding programme has exhibited a significant positive trend in genetic gain for grain yield over the years under both drought stress as well as favorable irrigated control conditions. Several drought tolerant varieties released from the programme have outperformed the currently grown varieties under varied conditions in the rainfed environments on farmers' fields.

Assessment of Antioxidant Potential of Lutein, a Retinol Equivalent Carotenoid in Medicinal Landrace of Rice ‘Kavuni’

Background: Indigenous traditional coloured rices are rich in dietary fibre, resistant starch, minerals, bioactive compounds and antioxidants like anthocyanins, luteins and phenols. Kavuni is one such brownish black medical landrace of rice considered as nutrition supplement since 400BC as it cures gastritis, peptic ulcer and also enhances blood circulation and known for its anti diabetic and anti-inflammatory properties. Lutein is the only dietary oxycarotenoid found in both the macula and lens of the human eye, and acts as blocker of blue light damage, quench reactive oxygen species, prevent age related macular degeneration, cataracts, cardiovascular disease and lung cancer. Aim: The objective of the present investigation was to characterize the lutein content and antioxidant potential of Kavuni and released mega varieties of rice (ASD 16, Swarna Sub1) and its derivatives obtained from crosses ASD 16 and Kavuni; Swarna Sub1 and Kavuni. Methodology & Results: It was found that lutein (quantified by HPLC) was much higher in Kavuni (225 µg/100 g) compared with white rice varieties (ASD 16-15 µg/100g and Swarna Sub1-21 µg/100 g) and the DPPH (2, 2-diphenyl-1-picrylhydrazyl) scavenging ability (for quantification of antioxidant potential) were in the order (Kavuni >>ASD16, Swarna Sub1. Pigmented grain genotypes having higher lutein content had higher percentage of free radical scavenging activity of DPPH and lower IC50 values compared to non pigmented genotypes. Conclusion: It is conceivable that the medicinal landraces of rice could be exploited as one of the potential sources for plant - based pharmaceutical products.

Blood CD9+ B cell, a biomarker of bronchiolitis obliterans syndrome after lung transplantation

Bronchiolitis obliterans syndrome is the main limitation for long-term survival after lung transplantation. Some specific B cell populations are associated with long-term graft acceptance. We aimed to monitor the B cell profile during early development of bronchiolitis obliterans syndrome after lung transplantation. The B cell longitudinal profile was analyzed in peripheral blood mononuclear cells from patients with bronchiolitis obliterans syndrome and patients who remained stable over 3 years of follow-up. CD24^hi CD38^hi transitional B cells were increased in stable patients only, and reached a peak 24 months after transplantation, whereas they remained unchanged in patients who developed a bronchiolitis obliterans syndrome. These CD24^hi CD38^hi transitional B cells specifically secrete IL-10 and express CD9. Thus, patients with a total CD9⁺ B cell frequency below 6.6% displayed significantly higher incidence of bronchiolitis obliterans syndrome (AUC = 0.836, PPV = 0.75, NPV = 1). These data are the first to associate IL-10-secreting CD24^hi CD38^hi transitional B cells expressing CD9 with better allograft outcome in lung transplant recipients. CD9-expressing B cells appear as a contributor to a favorable environment essential for the maintenance of long-term stable graft function and as a new predictive biomarker of bronchiolitis obliterans syndrome-free survival.

Persistence of antibody response in chikungunya

Chikungunya is a mosquito-borne viral illness associated with chronic arthritic symptoms that persist for months. The IgM antibody appears within a week post any infection and declines at 2-3 months. The present study was aimed to demonstrate the presence of specific IgM antibody among chikungunya confirmed cases. Blood samples were collected from chikungunya PCR positive patients at the time of diagnosis, at 1-week, 1, 8, 10 and 12 months post infection. All acute and follow-up serum samples were evaluated for chikungunya virus-specific IgM antibodies using ELISA technique. Our findings indicate the persistence of anti-chikungunya IgM up to 10-months post-infection in a majority of chikungunya virus infected persons. Interpretation of results should be carefully done as only IgM ELISA is used to diagnose acute infection, especially post chikungunya outbreak. The presence of IgM antibody does not rule out the absence of any other diagnosis due to its persistence. Thus, we hypothesize that real-time PCR is more reliable for the detection of acute chikungunya cases in endemic areas while IgM detection may be useful in identifying exposure to this disease.

Exudates absorption and proteases trapping in venous leg ulcers

OBJECTIVE

In venous leg ulcer (VLU), the impaired healing has been shown to be associated with excessive levels of protease activities such as matrix metalloproteinases (MMPs) and elastases found in exudates. The present study focused on exudates absorption and proteases trapping capacity of a new generation of polyacrylate superabsorbent, Tegaderm superabsorber (TS), compared with a traditional dressing such as Zetuvit.

METHOD

We studied the proteases implicated in VLU (MMP-1, MMP-2, MMP-9 and PMN elastase). Absorption was tested using an artificial exudate like fluid, over 30 minutes. The protein trapping ability was obtained using ELISA assays (enzyme-linked immunosorbent assay) to determine the amount retained by the dressings from spiked fluid samples.

RESULTS

TS had a higher exudate absorption capacity (72.8±1.7%) compared with the standard dressing (36.5±1.6%), and was also able to trap and retain proteases while the standard dressing released them. The difference was shown to be much larger for MMP-2 and PMN elastase.

CONCLUSION

In our knowledge, this is the first comparative in vitro study evaluating absorption capacity as well as protease trapping capacity of a polyacrylate dressing for the four most implicated proteases in VLU. TS could be an appropriate alternative to improve the management of VLU by trapping MMPs and PMN elastse with a particularly high affinity for MMP-2 and PMN elastase.

Development and Genetic Characterization of A Novel Herbicide (Imazethapyr) Tolerant Mutant in Rice (Oryza sativa L.)

BACKGROUND

Increased water and labour scarcity in major rice growing areas warrants a shift towards direct seeded rice cultivation under which management of weeds is a major issue. Use of broad spectrum non-selective herbicides is an efficient means to manage weeds. Availability of rice genotypes with complete tolerance against broad-spectrum non-selective herbicides is a pre-requisite for advocating use of such herbicides. In the present study, we developed an EMS induced rice mutant, 'HTM-N22', exhibiting tolerance to a broad spectrum herbicide, 'Imazethapyr', and identified the mutations imparting tolerance to the herbicide.

RESULTS

We identified a stable and true breeding rice mutant, HTM-N22 (HTM), tolerant to herbicide, Imazethapyr, from an EMS-mutagenized population of approximately 100,000 M2 plants of an upland rice variety, Nagina 22 (N22). Analysis of inheritance of herbicide tolerance in a cross between Pusa 1656-10-61/HTM showed that this trait is governed by a single dominant gene. To identify the causal gene for Imazethapyr tolerance, bulked segregant analysis (BSA) was followed using microsatellite markers flanking the three putative candidate genes viz., an Acetolactate Synthase (ALS) on chromosome 6 and two Acetohydroxy Acid Synthase (AHAS) genes, one on chromosomes 2 and another on chromosome 4. RM 6844 on chromosome 2 located 0.16 Mbp upstream of AHAS (LOC_Os02g30630) was found to co-segregate with herbicide tolerance. Cloning and sequencing of AHAS (LOC_Os02g30630) from the wild type, N22 and the mutant HTM and their comparison with reference Nipponbare sequence revealed several Single Nucleotide Polymorphisms (SNPs) in the mutant, of which eight resulted in non-synonymous mutations. Three of the eight amino acid substitutions were identical to Nipponbare and hence were not considered as causal changes. Of the five putative candidate SNPs, four were novel (at positions 30, 50, 81 and 152) while the remaining one, S627D was a previously reported mutant, known to result in Imidazolinone tolerance in rice. Of the novel ones, G152E was found to alter the hydrophobicty and abolish an N myristoylation site in the HTM compared to the WT, from reference based modeling and motif prediction studies.

CONCLUSIONS

A novel mutant tolerant to the herbicide "Imazethapyr" was developed and characterized for genetic, sequence and protein level variations. This is a HTM in rice without any IPR (Intellectual Property Rights) infringements and hence can be used in rice breeding as a novel genetic stock by the public funded organizations in the country and elsewhere.

Evaluation of the management of pregnancies and infants at risk for congenital syphilis: La Réunion, 2008 to 2014

OBJECTIVE

To evaluate the maternal-fetal management and follow-up of infants at risk for congenital syphilis.

STUDY DESIGN

Monocentric retrospective cohort study at the Félix Guyon Hospital, Saint-Denis, La Réunion between January 2008 and December 2014. Management of 38 pregnancies (35 women, 39 fetuses) with a positive syphilis serology was evaluated according to the Centers for Disease Control and Prevention (CDC) guidelines.

RESULTS

A total of 68% (n=26) of pregnancies were screened before 16 weeks of gestation, and 26% (n=10) had appropriate treatment. Adverse outcomes were noted in 45% of pregnancies. Neonatal serology was not performed in 7 live-born neonates (19%) and 33 infants were classifiable according to the four CDC scenarios. In the infants, adequate complementary evaluation and appropriate treatment were noted in 42% (n=13) and 55% (n=17) of cases, respectively. Rate of infant follow-up was 76% (n=16). No treatment failure was observed in infants.

CONCLUSION

Reinforcement of public health policies and a better sensitization, training and collaboration among perinatal caregivers are warranted given the gaps revealed in our study.

Depth of soil compaction predominantly affects rice yield reduction by reproductive-stage drought at varietal screening sites in Bangladesh, India, and Nepal

AIMS

Drought is the major constraint to rainfed rice productivity in South Asia, but few reports provide detailed characterization of the soil properties related to drought stress severity in the region. The aim of the study was to provide a compilation of drought breeding network sites and their respective levels of drought stress, and to relate soil parameters with yield reduction by drought.

METHODS

This study characterized levels of drought stress and soil nutrient and physical properties at 18 geographically distributed research station sites involved in rice varietal screening in Bangladesh, India, and Nepal, as well as at farmers' fields located near the research stations.

RESULTS

Based on soil resistance to penetration profiles, a hardpan was surprisingly absent at about half of the sites characterized. Significant relationships of depth of compaction and yield reduction by drought indicated the effects of soil puddling on susceptibility to cracking, rather than water retention by hardpans, on plant water availability in this region. The main difference between research stations and nearby farmers' fields was in terms of soil compaction.

CONCLUSIONS

These results present an initiative for understanding the range of severities of reproductive-stage drought stress in drought-prone rainfed lowland rice-growing areas in South Asia.

Exact distribution of word occurrences in a random sequence of letters

The study of the distribution of the distance between words in a random sequence of letters is interesting in view of application in genome sequence analysis. In this paper we give the exact distribution probability and cumulative distribution function of the distances between two successive occurrences of a given word and between the nth and the (n+m)th occurrences under three models of generation of the letters: i.i.d. with the same probability for each letter, i.i.d. with different probabilities and Markov process. The generating function and the first two moments are also given. The point of studying the distances instead of the counting process is that we get some knowledge not only about the frequency of a word but also about its longitudinal distribution in the sequence.

Evaluation of virus resistance and agronomic performance of rice cultivar ASD 16 after transfer of transgene against Rice tungro bacilliform virus by backcross breeding

Severe losses of rice yield in south and southeast Asia are caused by Rice tungro disease (RTD) induced by mixed infection of Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). In order to develop transgene-based resistance against RTBV, one of its genes, ORF IV, was used to generate transgenic resistance based on RNA-interference in the easily transformed rice variety Pusa Basmati-1, and the transgene was subsequently introgressed to rice variety ASD 16, a variety popular in southern India, using transgene marker-assisted selection. Here, we report the evaluation of BC3F4 and BC3F5 generation rice plants for resistance to RTBV as well as for agronomic traits under glasshouse conditions. The BC3F4 and BC3F5 generation rice plants tested showed variable levels of resistance, which was manifested by an average of twofold amelioration in height reduction, 1.5-fold decrease in the reduction in chlorophyll content, and 100- to 10,000-fold reduction in the titers of RTBV, but no reduction of RTSV titers, in three backcrossed lines when compared with the ASD 16 parent. Agronomic traits of some of the backcrossed lines recorded substantial improvements when compared with the ASD 16 parental line after inoculation by RTBV and RTSV. This work represents an important step in transferring RTD resistance to a susceptible popular rice variety, hence enhancing its yield in areas threatened by the disease.

Advances in the metabolic profiling of acidic compounds in children's urines achieved by comprehensive two-dimensional gas chromatography

The main objective of this work was to evaluate a comprehensive two-dimensional gas chromatographic (GCxGC) coupled to quadrupole mass spectrometry (qMS) method in the field of biomarker candidates' discovery. To this purpose we developed a GCxGC-qMS method suitable for the separation of organic acids and other classes of compounds with silylable polar hydrogen such as sugars, amino-acids, and vitamins. As compared to those obtained by a widely used 1D-GC method, the urinary chromatographic profiles performed by the proposed 2D-GC method exhibit higher resolution and sensitivity, leading to the detection of up to 92 additional compounds in some urine samples including some well-known biomarkers. In order to validate the proposed method we focused on three metabolites of interest with various functional groups and polarities including CH3-malonic acid (MMA: biomarker of methylmalonic acidemia), 3-hydroxy-3-methyl-glutaric acid (3-OHMGA: biomarker of 3-hydroxy-3-methylglutaric acidemia), and phenylpiruvic acid (PhPA: marker of phenylketonuria). While these three metabolites can be considered as representative of organic acids classically determined by 1D-GC, they cannot be representative of new detected metabolites. Thus, we also focused on quinolic acid (QUIN), taken as an example of biomarker not detected at basal levels with the classical 1D GC-qMS method. In order to obtain sufficient recoveries for all tested compounds, we developed a sample preparation protocol including a step of urea removal followed by two extraction steps using two solvents of different polarity and selectivity. Recoveries with the proposed method reached more than 80% for all targeted compounds and the linearity was satisfactory up to 50μmol/L. The CVs of the within-run and within-laboratory precisions were less than 8% for all tested compounds. The limits of quantification (LOQs) were 0.6μmol/L for MMA, 0.4μmol/L for 3-OHMGA, 0.7μmol/L for PhPA, and 1μmol/L for QUIN. The LOQs of these metabolites obtained by a classical GC-MS method under the same chromatographic conditions were 5μmol/L for MMA, 4μmol/L for 3-OHMGA, 6μmol/L for PhPA while QUIN was below the limit of detection. As compared to 1D-GC, these results highlight the enhanced detectability of urine metabolites by the 2D-GC technique. Our results also show that for each new detected compound it is necessary to develop and validate an appropriate sample preparation procedure.

Physiological, anatomical and transcriptional alterations in a rice mutant leading to enhanced water stress tolerance

Water stress is one of the most severe constraints to crop productivity. Plants display a variety of physiological and biochemical responses both at the cellular and whole organism level upon sensing water stress. Leaf rolling, stomatal closure, deeper root penetration, higher relative water content (RWC) and better osmotic adjustment are some of the mechanisms that plants employ to overcome water stress. In the current study, we report a mutant, enhanced water stress tolerant1 (ewst1) with enhanced water stress tolerance, identified from the ethyl methanesulfonate-induced mutant population of rice variety Nagina22 by field screening followed by withdrawal of irrigation in pots and hydroponics (PEG 6000). Though ewst1 was morphologically similar to the wild type (WT) for 35 of the 38 morphological descriptors (except chalky endosperm/expression of white core, decorticated grain colour and grain weight), it showed enhanced germination in polyethylene glycol-infused medium. It exhibited increase in maximum root length without any significant changes in its root weight, root volume and total root number on crown when compared with the WT under stress in PVC tube experiment. It also showed better performance for various physiological parameters such as RWC, cell membrane stability and chlorophyll concentration upon water stress in a pot experiment. Root anatomy and stomatal microscopic studies revealed changes in the number of xylem and phloem cells, size of central meta-xylem and number of closed stomata in ewst1. Comparative genome-wide transcriptome analysis identified genes related to exocytosis, secondary metabolites, tryptophan biosynthesis, protein phosphorylation and other signalling pathways to be playing a role in enhanced response to water stress in ewst1. The possible involvement of a candidate gene with respect to the observed morpho-physiological and transcriptional changes and its role in stress tolerance are discussed. The mutant identified and characterized in this study will be useful for further dissection of water stress tolerance in rice.

Two-dimensional segmentation for analyzing Hi-C data

MOTIVATION

The spatial conformation of the chromosome has a deep influence on gene regulation and expression. Hi-C technology allows the evaluation of the spatial proximity between any pair of loci along the genome. It results in a data matrix where blocks corresponding to (self-)interacting regions appear. The delimitation of such blocks is critical to better understand the spatial organization of the chromatin. From a computational point of view, it results in a 2D segmentation problem.

RESULTS

We focus on the detection of cis-interacting regions, which appear to be prominent in observed data. We define a block-wise segmentation model for the detection of such regions. We prove that the maximization of the likelihood with respect to the block boundaries can be rephrased in terms of a 1D segmentation problem, for which the standard dynamic programming applies. The performance of the proposed methods is assessed by a simulation study on both synthetic and resampled data. A comparative study on public data shows good concordance with biologically confirmed regions.

AVAILABILITY AND IMPLEMENTATION

The HiCseg R package is available from the Comprehensive R Archive Network and from the Web page of the corresponding author.

Transcriptome analysis of salinity responsiveness in contrasting genotypes of finger millet (Eleusine coracana L.) through RNA-sequencing

Finger millet (Eleusine coracana L.) is a hardy cereal known for its superior level of tolerance against drought, salinity, diseases and its nutritional properties. In this study, attempts were made to unravel the physiological and molecular basis of salinity tolerance in two contrasting finger millet genotypes viz., CO 12 and Trichy 1. Physiological studies revealed that the tolerant genotype Trichy 1 had lower Na(+) to K(+) ratio in leaves and shoots, higher growth rate (osmotic tolerance) and ability to accumulate higher amount of total soluble sugar in leaves under salinity stress. We sequenced the salinity responsive leaf transcriptome of contrasting finger millet genotypes using IonProton platform and generated 27.91 million reads. Mapping and annotation of finger millet transcripts against rice gene models led to the identification of salinity responsive genes and genotype specific responses. Several functional groups of genes like transporters, transcription factors, genes involved in cell signaling, osmotic homeostasis and biosynthesis of compatible solutes were found to be highly up-regulated in the tolerant Trichy 1. Salinity stress inhibited photosynthetic capacity and photosynthesis related genes in the susceptible genotype CO 12. Several genes involved in cell growth and differentiation were found to be up-regulated in both the genotypes but more specifically in tolerant genotype. Genes involved in flavonoid biosynthesis were found to be down-regulated specifically in the salinity tolerant Trichy 1. This study provides a genome-wide transcriptional analysis of two finger millet genotypes differing in their level of salinity tolerance during a gradually progressing salinity stress under greenhouse conditions.

Common mental disorders: a challenge among people living with human immunodeficiency virus infection/acquired immunodeficiency syndrome in udupi, India

BACKGROUND

Globally, the prevalence of common mental disorders (CMD) is greater among people living with human immunodeficiency virus/acquired immunodeficiency syndrome (PLHA) as opposed to the general population. There is relatively limited research on mental health in PLHA in India and this study seeks to gain insight in this area.

AIM

The aim of this study is to find the prevalence of CMD among PLHA in Udupi district.

SUBJECTS AND METHODS

In this cross-sectional study, 227 PLHA were selected using a convenience sampling method and interviewed at a district antiretroviral treatment center. The Kessler Psychological Distress Scale (K10 scale) and the General Health Questionnaire (GHQ-12) were used to measure distress and stress, respectively to assess CMD. Statistical analysis was performed with categorical variables expressed as frequencies and percentages. Continuous variables were measured using mean and standard deviation. Univariate and multivariate analyses using binomial logistic regression was carried out. SPSS version 15 (SPSS Inc., Chicago, IL, USA) was used to analyze the data.

RESULTS

The K10 Psychological Distress Scale indicated that 78.9% (n = 179/227) of participants suffered from mild to severe mental disorder and it was higher among divorced, separated or widowed PLHA followed by the married participants versus unmarried individuals. The GHQ-12 scale showed 68.3% (n = 155/227) suffering from mild to severe mental stress with the female gender developing stress 2.3 times more often.

CONCLUSION

High levels of distress were seen among PLHA. They should be periodically screened for CMD and provided early psychological intervention at the point of contact with health professionals. Psychological care needs to be integrated along with the clinical care.

Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought

Background

Rice (Oryza sativa L.) is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL) that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge.

Methodology/Principal Findings

Two pairs of backcross inbred lines (BILs) from a cross between drought-tolerant donor Aday Sel and high-yielding but drought-susceptible rice variety IR64 were produced. From six BC₄F₃ mapping populations produced by crossing the +QTL BILs with the −QTL BILs and IR64, four major-effect QTL - one each on chromosomes 2, 4, 9, and 10 - were identified. Meta-analysis of transcriptome data from the +QTL/−QTL BILs identified differentially expressed genes (DEGs) significantly associated with QTL on chromosomes 2, 4, 9, and 10. Physiological characterization of BILs showed increased water uptake ability under drought. The enrichment of DEGs associated with root traits points to differential regulation of root development and function as contributing to drought tolerance in these BILs. BC₄F₃-derived lines with the QTL conferred yield advantages of 528 to 1875 kg ha⁻¹ over IR64 under reproductive-stage drought stress in the targeted ecosystems of South Asia.

Conclusions/Significance

Given the importance of rice in daily food consumption and the popularity of IR64, the BC₄F₃ lines with multiple QTL could provide higher livelihood security to farmers in drought-prone environments. Candidate genes were shortlisted for further characterization to confirm their role in drought tolerance. Differential yield advantages of different combinations of the four QTL reported here indicate that future research should include optimizing QTL combinations in different genetic backgrounds to maximize yield advantage under drought.

Drought yield index to select high yielding rice lines under different drought stress severities

BACKGROUND

Drought is the most severe abiotic stress reducing rice yield in rainfed drought prone ecosystems. Variation in intensity and severity of drought from season to season and place to place requires cultivation of rice varieties with different level of drought tolerance in different areas. Multi environment evaluation of breeding lines helps breeder to identify appropriate genotypes for areas prone to similar level of drought stress. From a set of 129 advanced rice (Oryza sativa L.) breeding lines evaluated under rainfed drought-prone situations at three locations in eastern India from 2005 to 2007, a subset of 39 genotypes that were tested for two or more years was selected to develop a drought yield index (DYI) and mean yield index (MYI) based on yield under irrigated, moderate and severe reproductive-stage drought stress to help breeders select appropriate genotypes for different environments.

RESULTS

ARB 8 and IR55419-04 recorded the highest drought yield index (DYI) and are identified as the best drought-tolerant lines. The proposed DYI provides a more effective assessment as it is calculated after accounting for a significant genotype x stress-level interaction across environments. For rainfed areas with variable frequency of drought occurrence, Mean yield index (MYI) along with deviation in performance of genotypes from currently cultivated popular varieties in all situations helps to select genotypes with a superior performance across irrigated, moderate and severe reproductive-stage drought situations. IR74371-70-1-1 and DGI 75 are the two genotypes identified to have shown a superior performance over IR64 and MTU1010 under all situations.

CONCLUSION

For highly drought-prone areas, a combination of DYI with deviation in performance of genotypes under irrigated situations can enable breeders to select genotypes with no reduction in yield under favorable environments compared with currently cultivated varieties. For rainfed areas with variable frequency of drought stress, use of MYI together with deviation in performance of genotypes under different situations as compared to presently cultivated varieties will help breeders to select genotypes with superior performance under all situations.

[Severe forms of chikungunya virus infection in a pediatric intensive care unit on Reunion Island]

In 2005-2006, an unexpected, massive outbreak of chikungunya occurred on Reunion Island, a French overseas territory in the Indian Ocean. This arboviral infection transmitted by a mosquito of the Aedes genus is usually benign. A surprising feature of the Reunion Island epidemic was the occurrence of rare severe forms involving adults as well as children.

OBJECTIVES

The purpose of this report is to describe severe forms of chikungunya observed in children hospitalized in a pediatric intensive care unit.

PATIENTS AND METHODS

This retrospective single-center study was conducted from January 1st to April 30th, 2006. Children between 1 month and 15 years admitted to the pediatric intensive care unit with proven chikungunya infection were included.

RESULTS

A total of 9 children were included. The main manifestations were extensive skin blisters in 5 cases, neurological symptoms (encephalopathy) in 4, cardiac complications (myocarditis, hemodynamic disorders) in 5 and bleeding in 1. Two children died. The causes of death were circulatory failure associated with coma and massive hemorrhage in one case and post-infectious encephalitis in the other. Three survivors present long-term neurologic or dermatologic sequels.

DISCUSSION

Severe cases of chikungunya in children provide a stark reminder of the cardiac and neurological tropism of the virus and its hemorrhagic forms with high potential mortality and morbidity. These cases underline the need for personal protection measures and for research to develop specific antiviral therapy and vaccines to prevent potentially lethal forms of the disease.

P4-09-01: Identification of Poor Prognosis T1T2N0 Luminal ERBB2-ve Breast Carcinomas

Background: To identify ER+ve ERBB2-ve ductal T1T2N0 carcinomas associated with a poor prognosis remains challenging. We have previously demonstrated that the number of chromosomal breakpoints assessed by CGH could be a marker of worse outcome for breast carcinomas. Our aim was to validate the CGH based signature in a series of luminal ductal and T1T2 N0 carcinoma patients with long-term clinical follow-up. Patients and methods: We analyzed 214 patients treated for an invasive ductal ER+ve ERBB2-ve carcinomas, smaller than 30mm. The training set was composed of 109 patients (10.9 years of median follow-up; 30 cases associated with a metastatic event within less than 4 years/79 control cases with no metastastic event at 5 years) and the validation set of 105 patients (10.5 years of median follow-up; 30 relapses including contra-lateral breast carcinomas, loco-regional relapses and 8 metastatic events). None of the patient received adjuvant chemotherapy. 16 received an adjuvant hormonotherapy (10 in the training and 6 in the validation groups). We genotyped the sample set with the SNP6.0 affymetrix array. After RMA normalisation using Genotyping console, segmentation was performed according to the Zhang and Siegmund maximum method. In the training data set, the number of breakpoints was assessed, linked to outcome and the threshold optimising the sensitivity and specificity was determined (ROC curve). The threshold prognostic value was then tested on the validation series (Kaplan Meier analysis, log rank test, determination of relative risk and its confidence interval with a Cox model). Results: In the training set, median numbers of breakpoints were 7 in cases that experienced a metastatic event after more than 5 years and 40.5 in cases that experienced a metastatic event in less than 4 years. The threshold (Younden index ) was 34 breakpoints with a sensitivity of 0.57 and a specificity of 0.94 (AUC: 0.81[0.71;0.91]). In the validation set, the outcome of patients with more than 34 breakpoints was poorer than that of patients with less than 34 breakpoints (&lt;34 breakpoints: 19 events in out of 83 patients; &gt;34 breakpoints: 11 events out of 22 patients with a median time to progression of 108 months; p&lt;0.001 (logrank test); RR: 3.7 [1.73; 7.92]). In multivariate analysis, the number of breakpoints (&gt;34 versus &lt;34) remained the only significant parameter for prediction of outcome (RR: 3.12, CI[1.33; 7.31], p= 0.009). Histopronostic grade, significant in univariate analysis, was not significant in multivariate analysis but was correlated with the number of breakpoints. The number of breakpoints was statistically significant for prediction of metastatic free interval (&lt;34 breakpoints: 4 events in out of 83 patients; &gt;34 breakpoints: 4 events out of 22 patients with a median time to progression of 108 months; p=0.009 (logrank test); RR: 5.29 [1.32; 21.26]). Conclusion: We demonstated that patients with T1T2 (&lt;3cm) N0 ER+Ve ERBB2-ve invasive ductal carcinomas harboured a shorter disease free and metastatic free intervals based on genomic profiles assessed by SNP6.0 with a threshold of more than 34 breakpoints. This new approach to assess prognosis in luminal carcinomas is based on a single genomic platform, could allow identification of future therapeutic targets.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P4-09-01.

Analysis of the complete DNA sequence of rice tungro bacilliform virus from southern India indicates it to be a product of recombination

The complete nucleotide sequence of an isolate of rice tungro bacilliform virus (RTBV), collected from Kanyakumari, India, where RTBV was reported recently for the first time, has been analyzed. Sequence comparison revealed that the RTBV isolate from Kanyakumari (RTBV-KK) has a high degree of identity to the two previously reported RTBV sequences from India, RTBV-AP and RTBV-WB, which had been collected from field locations about 10 years ago and 1000-2000 km away from the collection site of RTBV-KK. Most of the sequence domains reported previously in other RTBV isolates were found to be conserved in RTBV-KK. Closer inspection revealed RTBV-KK to be a possible recombinant between RTBV-AP and RTBV-WB in the genomic region encompassing the coat protein gene.