Interventions to reduce camel and small ruminant young stock morbidity and mortality in Ethiopia.

Morbidity and mortality of young stock is a challenge for livestock producers globally. In Ethiopia, where camels and small ruminants (sheep and goats) are essential smallholder and pastoral livestock, young stock losses can cause severe consequences to livelihoods. This pilot study, part of a Government-led Young Stock Mortality Reduction Consortium project, was undertaken to identify and evaluate interventions to reduce young stock mortality in mixed crop-livestock and pastoral production systems in Ethiopia. Pastoralists and mixed crop-livestock farmers were enrolled by convenience sampling across four regions. Households were sampled with questionnaire surveys to establish baseline mortality risk and prevalence of diarrhoea and respiratory disease in animals younger than one year, and followed longitudinally over a one-year period, with final evaluations conducted from March to July 2020. Mortality risk and prevalence of diarrhoea and respiratory disease before and after implementation were compared using Poisson regression models including household as random effect. Prior to intervention, median camel mortality, prevalence of diarrhoea, and respiratory disease across production systems in the different households was 0.4, 0.44 and 0.2, respectively. This compared to median pastoralist small ruminant mortality risk and prevalence of diarrhoea and respiratory disease of 0.45, 0.32 and 0.18, respectively. Post-intervention, median camel mortality, prevalence of diarrhoea and respiratory disease dropped to 0.1, 0.08 and 0. Similarly, more than half of the small ruminant households reported no mortality, and no cases of diarrhoea or respiratory disease. In camels, rate ratios of mortality risk, prevalence of diarrhoea, and respiratory disease post-intervention compared to the baseline were 0.41, 0.41 and 0.37. In small ruminants, rate ratios were 0.33, 0.35 and 0.46. All reductions were statistically significant (p < 0.01). Generally, pastoralists experienced higher mortality and disease prevalence compared to mixed crop-livestock smallholders, and the effect of intervention was slightly higher in pastoralist households. The pilot study findings demonstrated highly significant reductions in mortality and risk of diarrhoea and respiratory disease post-interventions. However, not all households benefitted from the interventions, with a few households reporting increased mortality and morbidity. Many households had very few animals which made it challenging to measure impact and the study was conducted over a single year, without a control group, so between year effects could not be accounted for in the reductions observed. These findings should contribute to improved livestock productivity in Ethiopia.

Mitochondrial DNA population variation is not associated with Alzheimer's in the Japanese population: A consistent finding across global populations.

Several mitochondrial DNA (mtDNA) haplogroup association studies have suggested that common mtDNA variants are associated with multifactorial diseases, including Alzheimer's disease (AD). However, such studies have also produced conflicting results. A new mtDNA association model, the 'variant load model' (VLM), has been applied to multiple disease phenotypes. Application of the VLM in a 2017 study failed to find different variant loads in AD patients compared to controls, in two cohorts of European origin. The study also suggested a lower variant load in healthy elderly individuals, but could offer no replicate cohort to support this observation. Here, the VLM is applied to Japanese mtDNA sequences; in doing so, we explored the role of mtDNA variation in AD and ageing in a different global population. Consistent with the previous findings using the VLM in two populations of European origin, we found no evidence for an association between rarer, non-haplogroup associated variation and the development of AD. However, the result in the context of ageing that suggested those with fewer mildly deleterious mutations might undergo healthier ageing, was not replicated. In contrast to our previous study, our present results suggest that those living to advanced old age may harbour more mildly deleterious mtDNA variations. Importantly our analysis showed this finding is not primarily being driven by many rare population variants dispersed across the mtDNA, but by a few more frequent variants with high MutPred scores. It is suggested the variants in question do not exert a mildly deleterious effect in their most frequent haplogroup context.

Use of a cow-side oestrus detection test for fertility management in Kenyan smallholder dairy herds.

Background: The use of artificial insemination (AI) has great potential to improve smallholder dairy herds in Africa, however poor success and, in some situations, high costs in Kenya, have been discouraging.  Effective AI requires accurate oestrus detection and the measurement of progesterone (P4) can be used to indicate oestrus as well as non-pregnancy.  A cow-side progesterone lateral flow test, P4 Rapid, was evaluated as an aid to detect oestrus and non-pregnancy in Kenyan dairy cows, and assessed for association with AI efficiency.  Methods: A total of 527 cows were enrolled in the study, from two counties in central and southern Kenya.  Cattle in the test group (n = 308) were presented when suspected to be in oestrus and tested with the P4 Rapid (low P4 = oestrus, medium P4 = inconclusive, high P4 = not in oestrus/pregnant).  Cattle with low P4 were inseminated.  Cattle in the control group (n = 219) were inseminated when oestrus behaviour was detected i.e. standard practice. Results: Of the total P4 Rapid tests performed (n = 745), 1.5% were inconclusive, with the true accuracy of the test between 87-97%.  Conception rates were not significantly higher in the test group (83.9%) compared to the control group (77.9%). Abortion rates were not significantly different between the control (9.5%) and test groups (8.2%).  In the test group, 6.2% (19/308) cows showed a medium or high P4 level on day 0 and nine of these were subsequently found to have been already pregnant. Conclusions: The data indicated that the P4 Rapid test can be a useful tool to assist farmer decision-making in the confirmation of correct timing for AI, and importantly may avoid unnecessary inseminations in pregnant animals, thus reducing the risk of AI-induced abortion.

Reducing Calf Mortality in Ethiopia.

Morbidity and mortality of young stock present economic and production challenges to livestock producers globally. In Ethiopia, calf morbidity and mortality rates, particularly due to diarrhea and respiratory disease, are high, limiting production, incomes, and the ability of farmers to improve their livelihoods. In this paper, we present findings from the combined experience of the Young Stock Mortality Reduction Consortium, which conducted epidemiological and intervention testing in calves across three production systems. This innovative alliance identified Cryptosporidium parvum and E. Coli K99 as the most common causes of diarrhea in pastoral and peri-urban calves; Strongyloides spp. as the most common fecal parasite in mixed crop-livestock and peri-urban calves; and bovine adenovirus, parainfluenza virus-3, and bovine respiratory syncytial virus as the most common respiratory pathogens in peri-urban calves. Furthermore, by improving producer knowledge with respect to fundamental livestock husbandry, feeding, housing, and neonatal care practices, calf mortality risk across production systems was reduced by 31.4 to 71.4% compared to baseline (between 10.5 and 32.1%), whereas risk of diarrhea was reduced by 52.6-75.3% (baseline between 11.4 and 30.4%) and risk of respiratory disease was reduced by 23.6-80.8% (baseline between 3.3 and 16.3%). These findings have informed scaling strategies and can potentially contribute to improved livestock productivity and human livelihoods in Ethiopia.

Refining livestock mortality indicators: a systematic review.

Background: Livestock mortality impacts farmer livelihoods and household nutrition. Capturing trends in livestock mortality at localised or national levels is essential to planning, monitoring and evaluating interventions and programs aimed at decreasing mortality rates. However, livestock mortality data is disparate, and indicators used have not been standardised. This review aims to assess livestock mortality indicator definitions reported in literature, and define the ages where mortality has greatest impact. Methods: A systematic review was conducted, limited to articles focussed on mortality of cattle, sheep and goats. Peer-reviewed articles in Web of Science until year 2020 were assessed for inclusion of age-based definitions for mortality indicators and data on age distribution of mortality. Indicator definitions for each species were collated and similar terms and age groups most targeted were compared. The cumulative distribution of age at mortality was compared across studies graphically where possible; otherwise, age patterns for mortality were collated. Results: Most studies reported mortality risk rather than rate, and there was little agreement between indicator definitions used in the literature. The most common indicators reported were perinatal and neonatal mortality in cattle, and for perinatal, neonatal and pre-weaning mortality indicators for sheep and goats. Direct comparison of age distribution of mortality was only possible for cattle, which found that approximately 80% of all mortalities within the first 12 months had occurred by six months of age. A significant finding of the study is the variation in age groups for which mortality is reported, which impedes the comparison of mortality risk across studies, particularly for sheep and goats. Conclusions: This study demonstrates the importance and value of standardising mortality risk indicators for general use, including a young stock mortality risk indicator measuring mortality in the highest risk period of birth to six months of age in cattle, sheep and goats.

A study of the effectiveness of a detergent-based California mastitis test (CMT), using Ethiopian and Nigerian domestic detergents, for the detection of high somatic cell counts in milk and their reliability compared to the commercial UK CMT.

Background:  The California mastitis test (CMT) is a simple cow-side indicator of the somatic cell count (SCC) in milk, providing a useful tool in identifying cases of subclinical mastitis in cattle. Mastitis, and in particular subclinical mastitis, is a major concern in Ethiopia and Nigeria, yet detection is challenging due to cost and access to commercial CMT reagents. Methods: Commercially available domestic detergents from Ethiopia and Nigeria were compared (n = 3 for each country) with the UK commercial CMT reagent in their ability to detect high SCC (>400,000 cells/ml milk).  Sensitivity and specificity of the CMT test were calculated for the different detergents and positive and negative predictive values were established. Results:  The average sensitivities of the tests ranged from 28-75% for the Ethiopian detergents and 68-80% for the Nigerian detergents, compared to 76% for the UK domestic detergent.  Test specificities were 84-98%, 93-97% and 96%, respectively. Conclusions:  Overall, the detergents demonstrated higher specificity than sensitivity.   Nigerian detergents performed better than the Ethiopian products, however, the study identified suitable domestic detergents from both Ethiopia and Nigeria, comparable to the UK commercial CMT reagent, and we recommend their use as alternative CMT reagents for livestock-keepers to aid in cost-effective diagnosis of mastitis.

Participatory Epidemiology: Principles, Practice, Utility, and Lessons Learnt.

Participatory epidemiology (PE) evolved as a branch of veterinary epidemiology and has been largely employed for the control and early warning of infectious diseases within resource-limited settings. It was originally based on combining practitioner communication skills with participatory methods to facilitate the involvement of animal caretakers and owners (embracing their knowledge, experience, and motivations) in the identification and assessment of animal disease problems, including in the design, implementation, monitoring and evaluation of disease control programs, policies, and strategies. With the importance of understanding social perceptions and drivers receiving increasing recognition by epidemiologists, PE tools are being adapted for an increasingly wide range of settings and endeavors. More recently, PE tools have been adapted for use in food and nutrition security programs, One Health activities, wildlife disease surveillance and as part of mixed-methods research across a range of socio-economic settings. This review describes the evolution of PE (in relation to veterinary epidemiology and briefly in relation to public health epidemiology), the underpinning philosophy and principles essential to its effective application and the importance of gender-sensitive approaches and data triangulation, including conventional confirmatory testing. The article also provides illustrative examples highlighting the diversity of approaches and applications of PE, hallmarks of successful PE initiatives and the lessons we can learn when these are missing. Finally, we look forward, describing the particular utility of PE for dealing with emerging infectious diseases, gaining attention of field-level cross-sector officials who can escalate concerns to a higher level and for continuing to raise the voices of those less-heard (such as women, minority groups, and remote communities with limited exposure to formal education) in defining the problems and planning activities that will likely impact directly on their well-being and livelihoods.

Comparative metabolomics implicates threitol as a fungal signal supporting colonization of Armillaria luteobubalina on eucalypt roots.

Armillaria root rot is a fungal disease that affects a wide range of trees and crops around the world. Despite being a widespread disease, little is known about the plant molecular responses towards the pathogenic fungi at the early phase of their interaction. With recent research highlighting the vital roles of metabolites in plant root-microbe interactions, we sought to explore the presymbiotic metabolite responses of Eucalyptus grandis seedlings towards Armillaria luteobuablina, a necrotrophic pathogen native to Australia. Using a metabolite profiling approach, we have identified threitol as one of the key metabolite responses in E. grandis root tips specific to A. luteobubalina that were not induced by three other species of soil-borne microbes of different lifestyle strategies (a mutualist, a commensalist, and a hemi-biotrophic pathogen). Using isotope labelling, threitol detected in the Armillaria-treated root tips was found to be largely derived from the fungal pathogen. Exogenous application of d-threitol promoted microbial colonization of E. grandis and triggered hormonal responses in root cells. Together, our results support a role of threitol as an important metabolite signal during eucalypt-Armillaria interaction prior to infection thus advancing our mechanistic understanding on the earliest stage of Armillaria disease development. Comparative metabolomics of eucalypt roots interacting with a range of fungal lifestyles identified threitol enrichment as a specific characteristic of Armillaria pathogenesis. Our findings suggest that threitol acts as one of the earliest fungal signals promoting Armillaria colonization of roots.

Root renovation: how an improved understanding of basic root biology could inform the development of elite crops that foster sustainable soil health.

A major goal in agricultural research is to develop 'elite' crops with stronger, resilient root systems. Within this context, breeding practices have focussed on developing plant varieties that are, primarily, able to withstand pathogen attack and, secondarily, able to maximise plant productivity. Although great strides towards breeding disease-tolerant or -resistant root stocks have been made, this has come at a cost. Emerging studies in certain crop species suggest that domestication of crops, together with soil management practices aimed at improving plant yield, may hinder beneficial soil microbial association or reduce microbial diversity in soil. To achieve more sustainable management of agricultural lands, we must not only shift our soil management practices but also our breeding strategy to include contributions from beneficial microbes. For this latter point, we need to advance our understanding of how plants communicate with, and are able to differentiate between, microbes of different lifestyles. Here, we present a review of the key findings on belowground plant-microbial interactions that have been made over the past decade, with a specific focus on how plants and microbes communicate. We also discuss the currently unresolved questions in this area, and propose plausible ways to use currently available research and integrate fast-emerging '-omics' technologies to tackle these questions. Combining past and developing research will enable the development of new crop varieties that will have new, value-added phenotypes belowground.

QTLs Regulating the Contents of Antioxidants, Phenolics, and Flavonoids in Soybean Seeds Share a Common Genomic Region.

Soybean seeds are a rich source of phenolic compounds, especially isoflavonoids, which are important nutraceuticals. Our study using 14 wild- and 16 cultivated-soybean accessions shows that seeds from cultivated soybeans generally contain lower total antioxidants compared to their wild counterparts, likely an unintended consequence of domestication or human selection. Using a recombinant inbred population resulting from a wild and a cultivated soybean parent and a bin map approach, we have identified an overlapping genomic region containing major quantitative trait loci (QTLs) that regulate the seed contents of total antioxidants, phenolics, and flavonoids. The QTL for seed antioxidant content contains 14 annotated genes based on the Williams 82 reference genome (Gmax1.01). None of these genes encodes functions that are related to the phenylpropanoid pathway of soybean. However, we found three putative Multidrug And Toxic Compound Extrusion (MATE) transporter genes within this QTL and one adjacent to it (GmMATE1-4). Moreover, we have identified non-synonymous changes between GmMATE1 and GmMATE2, and that GmMATE3 encodes an antisense transcript that expresses in pods. Whether the polymorphisms in GmMATE proteins are major determinants of the antioxidant contents, or whether the antisense transcripts of GmMATE3 play important regulatory roles, awaits further functional investigations.

Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods.

To survive under abiotic stresses in the environment, plants trigger a reprogramming of gene expression, by transcriptional regulation or translational regulation, to turn on protective mechanisms. The current focus of research on how plants cope with abiotic stresses has transitioned from transcriptomic analyses to small RNA investigations. In this review, we have summarized and evaluated the current methodologies used in the identification and validation of small RNAs and their targets, in the context of plant responses to abiotic stresses.

Using RNA-Seq Data to Evaluate Reference Genes Suitable for Gene Expression Studies in Soybean.

Differential gene expression profiles often provide important clues for gene functions. While reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an important tool, the validity of the results depends heavily on the choice of proper reference genes. In this study, we employed new and published RNA-sequencing (RNA-Seq) datasets (26 sequencing libraries in total) to evaluate reference genes reported in previous soybean studies. In silico PCR showed that 13 out of 37 previously reported primer sets have multiple targets, and 4 of them have amplicons with different sizes. Using a probabilistic approach, we identified new and improved candidate reference genes. We further performed 2 validation tests (with 26 RNA samples) on 8 commonly used reference genes and 7 newly identified candidates, using RT-qPCR. In general, the new candidate reference genes exhibited more stable expression levels under the tested experimental conditions. The three newly identified candidate reference genes Bic-C2, F-box protein2, and VPS-like gave the best overall performance, together with the commonly used ELF1b. It is expected that the proposed probabilistic model could serve as an important tool to identify stable reference genes when more soybean RNA-Seq data from different growth stages and treatments are used.