QTL Mapping in New Arabidopsis thaliana Advanced Intercross-Recombinant Inbred Lines

Background

Even when phenotypic differences are large between natural or domesticated strains, the underlying genetic basis is often complex, and causal genomic regions need to be identified by quantitative trait locus (QTL) mapping. Unfortunately, QTL positions typically have large confidence intervals, which can, for example, lead to one QTL being masked by another, when two closely linked loci are detected as a single QTL. One strategy to increase the power of precisely localizing small effect QTL, is the use of an intercross approach before inbreeding to produce Advanced Intercross RILs (AI-RILs).

Methodology/Principal Findings

We present two new AI-RIL populations of Arabidopsis thaliana genotyped with an average intermarker distance of 600 kb. The advanced intercrossing design led to expansion of the genetic map in the two populations, which contain recombination events corresponding to 50 kb/cM in an F₂ population. We used the AI-RILs to map QTL for light response and flowering time, and to identify segregation distortion in one of the AI-RIL populations due to a negative epistatic interaction between two genomic regions.

Conclusions/Significance

The two new AI-RIL populations, EstC and KendC, derived from crosses of Columbia (Col) to Estland (Est-1) and Kendallville (Kend-L) provide an excellent resource for high precision QTL mapping. Moreover, because they have been genotyped with over 100 common markers, they are also excellent material for comparative QTL mapping.     

Effect of large weirs on abundance and diversity of migratory Labeobarbus species in tributaries of Lake Tana,Ethiopia

Lake Tana has a remarkable fish diversity, including 17 endemic Labeobarbus species, of which nine spawn in the inflowing rivers. Three of the migratory species are threatened, namely the endangered Labeobarbus macrophtalmus and the vulnerable L. acutirostris and L. platydorsus. In July–November 2016 during the wet season netting upstream and downstream of large weirs in two rivers and in two undammed rivers showed that weirs had a severe negative effect on migratory Labeobarbus, including the three threatened species. Of eight Labeobarbus species caught below the Gelda River weir, only L. intermedius was recorded above the weir, and in the Shini River, five Labeobarbus species were caught below the weir, but none above it. Labeobarbus diversity below the Gelda River weir (H’?=?1.4) was significantly different to that above the weir (H’?=?0), whereas in the two rivers without any weirs, Labeobarbus diversity downstream (H’?=?1.39 and 1.55) was not significantly different from that upstream (H’?=?1.52 and 1.40). Therefore, specific mitigation measures, such as fishways, need to be designed from the outset of proposed weir and instream dam construction.     

IgE enhances antibody and T cell responses in vivo via CD23+ B cells

IgE Abs, passively administered together with their specific Ag, can enhance the production of Abs recognizing this Ag by >100-fold. IgE-mediated feedback enhancement requires the low affinity receptor for IgE, CD23. One possible mechanism is that B cells take up IgE-Ag via CD23 and efficiently present Ag to Th cells, resulting in better Ab responses. To test whether IgE Abs have an effect on Th cells in vivo, mice were adoptively transferred with CD4+ T cells expressing a transgenic OVA-specific TCR, before immunization with IgE anti-TNP (2,4,6-trinitrophenyl) plus OVA-TNP or with OVA-TNP alone. IgE induced a 6- to 21-fold increase in the number of OVA-specific T cells. These cells acquired an activated phenotype and were visible in splenic T cell zones. The T cell response peaked 3 days after immunization and preceded the OVA-specific Ab response by a few days. Transfer of CD23+ B cells to CD23-deficient mice rescued their ability to respond to IgE-Ag. Interestingly, in this situation also CD23-negative B cells produce enhanced levels of OVA-specific Abs. The data are compatible with the Ag presentation model and suggest that B cells can take up Ag via "unspecific" receptors and activate naive T cells in vivo.     

Determinants of exclusive breastfeeding practice to infants aged less than six months in Offa district,Southern Ethiopia: a cross-sectional study

Background

World Health Organization (WHO) recommends timely initiation of breastfeeding after birth and only feeding breast milk to infants during the first 6 months of life. It was estimated that exclusive breastfeeding can reduce infant deaths by 13%. The practice of exclusive breastfeeding is suboptimal in many parts of Ethiopia to a varied extent. Factors associated with exclusive breastfeeding practice and the proportion of its practice was not well documented in Offa district. Therefore, this study was aimed to assess the determinants of exclusive breastfeeding in the first 6 months of life in Offa district, Southern Ethiopia.

Methods

A community-based cross-sectional study was carried out in 396 mothers of infants younger than 6 months using random sampling. Data were collected from mothers of the infants by trained interviewers. Exclusive breastfeeding was measured by the history of infant feeding in the prior 24 h. Pretested and structured questionnaires adopted from standard questionnaires and Ethiopia linkages modules were used. Multivariate logistic regression was used to identify factors significantly influencing exclusive breastfeeding practice.

Results

Based on findings of this study of 396 participants, the proportion of exclusive breastfeeding was 78.0% and awareness of exclusive breastfeeding and bottle feeding were 85.6 and 6.1% respectively. About 6% of infants were given prelacteal feeds. The number of infants fed cow milk was 12.9%, formula 7.8%, water 8.5%, fruits and semisolids 1.5%, over 24 h prior to the survey. The initiation of breastfeeding within one h (AOR 2.2; 95% CI 1.1, 4.27), attending formal education (AOR 4; 95% CI 2.20, 7.25), having an awareness on the benefits of exclusive breastfeeding (AOR 6; 95% CI 3.10, 11.70) and knowledge of colostrum feeding (AOR 2.1; 95% CI 1.11, 4.27) had a statistically significant association with exclusive breastfeeding in the study area.

Conclusions

The practice of exclusive breastfeeding as well as awareness was worthy in Offa district. Additionally the proportion of bottle feeding use was small. However, feeding other than breast milk was associated with the perception that breast milk alone was insufficient for their child. Strategies on promoting exclusive breastfeeding practice must focus on strengthening women’s education and awareness creation activities further.

     

Affordable artificial intelligence-based digital pathology for neglected tropical diseases: A proof-of-concept for the detection of soil-transmitted helminths and Schistosoma mansoni eggs in Kato-Katz stool thick smears

BackgroundWith the World Health Organization’s (WHO) publication of the 2021–2030 neglected tropical diseases (NTDs) roadmap, the current gap in global diagnostics became painfully apparent. Improving existing diagnostic standards with state-of-the-art technology and artificial intelligence has the potential to close this gap.Methodology/Principal findingsWe prototyped an artificial intelligence-based digital pathology (AI-DP) device to explore automated scanning and detection of helminth eggs in stool prepared with the Kato-Katz (KK) technique, the current diagnostic standard for diagnosing soil-transmitted helminths (STHs; Ascaris lumbricoides, Trichuris trichiura and hookworms) and Schistosoma mansoni (SCH) infections. First, we embedded a prototype whole slide imaging scanner into field studies in Cambodia, Ethiopia, Kenya and Tanzania. With the scanner, over 300 KK stool thick smears were scanned, resulting in total of 7,780 field-of-view (FOV) images containing 16,990 annotated helminth eggs (Ascaris: 8,600; Trichuris: 4,083; hookworms: 3,623; SCH: 684). Around 90% of the annotated eggs were used to train a deep learning-based object detection model. From an unseen test set of 752 FOV images containing 1,671 manually verified STH and SCH eggs (the remaining 10% of annotated eggs), our trained object detection model extracted and classified helminth eggs from co-infected FOV images in KK stool thick smears, achieving a weighted average precision (± standard deviation) of 94.9% ± 0.8% and a weighted average recall of 96.1% ± 2.1% across all four helminth egg species.Conclusions/SignificanceWe present a proof-of-concept for an AI-DP device for automated scanning and detection of helminth eggs in KK stool thick smears. We identified obstacles that need to be addressed before the diagnostic performance can be evaluated against the target product profiles for both STH and SCH. Given that these obstacles are primarily associated with the required hardware and scanning methodology, opposed to the feasibility of AI-based results, we are hopeful that this research can support the 2030 NTDs road map and eventually other poverty-related diseases for which microscopy is the diagnostic standard.     

Successful Treatment of Human Visceral Leishmaniasis Restores Antigen-Specific IFN-γ, but not IL-10 Production

One of the key immunological characteristics of active visceral leishmaniasis (VL) is a profound immunosuppression and impaired production of Interferon-γ (IFN-γ). However, recent studies from Bihar in India showed using a whole blood assay, that whole blood cells have maintained the capacity to produce IFN-γ. Here we tested the hypothesis that a population of low-density granulocytes (LDG) might contribute to T cell responses hyporesponsiveness via the release of arginase. Our results show that this population is affected by the anticoagulant used to collect blood: the frequency of LDGs is significantly lower when the blood is collected with heparin as compared to EDTA; however, the anticoagulant does not impact on the levels of arginase released. Next, we assessed the capacity of whole blood cells from patients with active VL to produce IFN-γ and IL-10 in response to antigen-specific and polyclonal activation. Our results show that whole blood cells produce low or levels below detection limit of IFN-γ and IL-10, however, after successful treatment of VL patients, these cells gradually regain their capacity to produce IFN-γ, but not IL-10, in response to activation. These results suggest that in contrast to VL patients from Bihar, India, whole blood cells from VL patients from Gondar, Ethiopia, have lost their ability to produce IFN-γ during active VL and that active disease is not associated with sustained levels of IL-10 production following stimulation.     

Larval experience of stable fly,Stomoxys calcitrans Linneaus, 1758 (Diptera: Muscidae) does not influence oviposition preference in gravid females

1. Hopkins' host selection principle (HHSP) proposes that, in holometabolous insects, gravid females prefer to oviposit on their developmental substrate. This hypothesis is widely explored in phytophagous insects, but few studies have considered blood‐feeding insects. In this study, the HHSP was tested using the haematophagous stable fly, Stomoxys calcitrans (Diptera: Muscidae). Using no‐choice and two‐choice tests, the study first sought to demonstrate whether S. calcitrans larvae recognise their rearing substrate. 2. It was found that when a rearing substrate is offered to S. calcitrans larvae singly (no‐choice) or associated with a non‐rearing substrate (two‐choice), they were able to recognise the substrate in which they developed. This ability disappeared when larvae were transferred to another substrate for 5 h. 3. Next, using oviposition bioassays, it was investigated whether information gathered by pre‐imaginal stages during their development can persist into the adult stages after metamorphosis. It was hypothesised that gravid females emerging from clean and uncleaned pupae reared on sheep and camel dung would still prefer to lay on their rearing substrate. The results revealed that gravid females did not prefer to oviposit on their developmental substrate. In addition, failure to recognise and prefer their developmental substrate was found in gravid females that had emerged from puparia that were cleaned as well as those contaminated with sheep dung. 4. It is concluded that S. calcitrans adult preference is not influenced by their offspring's experience. Overall, the HHSP was not supported by our study, suggesting that this principle may not apply to generalist insects characterised by high plasticity in oviposition substrate acceptance.     

Occurrence of Antimicrobial-Resistant Escherichia coli and Salmonella enterica in the Beef Cattle Production and Processing Continuum

Specific concerns have been raised that third-generation cephalosporin-resistant (3GC^r) Escherichia coli, trimethoprim-sulfamethoxazole-resistant (COT^r) E. coli, 3GC^r Salmonella enterica, and nalidixic acid-resistant (NAL^r) S. enterica may be present in cattle production environments, persist through beef processing, and contaminate final products. The prevalences and concentrations of these organisms were determined in feces and hides (at feedlot and processing plant), pre-evisceration carcasses, and final carcasses from three lots of fed cattle (n = 184). The prevalences and concentrations were further determined for strip loins from 103 of the carcasses. 3GC^r Salmonella was detected on 7.6% of hides during processing and was not detected on the final carcasses or strip loins. NAL^r S. enterica was detected on only one hide. 3GC^r E. coli and COT^r E. coli were detected on 100.0% of hides during processing. Concentrations of 3GC^r E. coli and COT^r E. coli on hides were correlated with pre-evisceration carcass contamination. 3GC^r E. coli and COT^r E. coli were each detected on only 0.5% of final carcasses and were not detected on strip loins. Five hundred and 42 isolates were screened for extraintestinal pathogenic E. coli (ExPEC) virulence-associated markers. Only two COT^r E. coli isolates from hides were ExPEC, indicating that fed cattle products are not a significant source of ExPEC causing human urinary tract infections. The very low prevalences of these organisms on final carcasses and their absence on strip loins demonstrate that current sanitary dressing procedures and processing interventions are effective against antimicrobial-resistant bacteria.     

Structural basis for cytokinin recognition by Arabidopsis thaliana histidine kinase 4

Cytokinins are classic hormones that orchestrate plant growth and development and the integrity of stem cell populations. Cytokinin receptors are eukaryotic sensor histidine kinases that are activated by both naturally occurring adenine-type cytokinins and urea-based synthetic compounds. Crystal structures of the Arabidopsis thaliana histidine kinase 4 sensor domain in complex with different cytokinin ligands now rationalize the hormone-binding specificity of the receptor and may spur the design of new cytokinin ligands.