Cross-amplification of ungulate microsatellite markers in the endemic Indian antelope or blackbuck (Antilope cervicapra) for population monitoring and conservation genetics studies in south Asia

The Indian antelope or blackbuck (Antilope cervicapra) is endemic to the Indian subcontinent, inhabiting scrublands and dry grasslands. Most of the blackbuck populations are small, isolated, and threatened by habitat fragmentation and degradation. Management of such disjunct populations requires genetic characterization, which is critical for assessing hazards of stochastic events and inbreeding. Addressing the scarcity of such information on the blackbuck, we describe a novel panel of microsatellite markers that could be used to monitor blackbuck demography and population genetic parameters using non-invasive faecal sampling. We screened microsatellites (n?=?40) that had been reported to amplify in bovid and cervid species using faecal samples of the blackbuck collected from Kaimoor Wildlife Sanctuary, Uttar Pradesh, India and its vicinities. We selected 12 markers for amplification using faecal DNA extracts (n?=?140) in three multiplex reactions. We observed a mean amplification success rate of 72.4% across loci (92.1–25.7%) with high allele diversity (mean number of alleles/locus?=?8.67?±?1.03). Mean genotyping error rates across the markers were low to moderate (allelic drop-out rate?=?0.09; false allele rate?=?0.11). The proportions of first- and second-order relatives in the study population were 0.69% and 6.21%, respectively. Based on amplification success, genotyping error rates and the probability of identity (P_ID), we suggest (i) a panel of five microsatellite markers (cumulative P_ID?=?1.24?×?10^–5) for individual identification and population monitoring and (ii) seven additional markers for conservation genetics studies. This study provides essential tools capable of augmenting blackbuck conservation strategies at the landscape level, integral to protecting the scrubland-grassland ecosystem.

     

Focus: Preventive Medicine: Variation in Non-external and External Causes of Death in Peru in Relation to the COVID-19 Lockdown

Introduction: Lockdowns are designed to slow COVID-19 transmission, but they may have unanticipated relationships with other aspects of public health. Assessing the overall pattern in population health as a country implements and relaxes a lockdown is relevant, as these patterns may not necessarily be symmetric. We aimed to estimate the changing trends in cause-specific mortality in relation to the 2020 COVID-19 related lockdowns in Peru. Methods: Based on data from the Peruvian National Death Information System (SINADEF), we calculated death rates per 10 million population to assess the trends in mortality rates for non-external and external causes of death (suicides, traffic accidents, and homicides). We compared these trends to 2018-2019, before, during, and after the lockdown, stratified by sex, and adjusted by Peruvian macro-region (Lima & Callao (capital region), Coast, Highland, and Jungle). Results: Non-external deaths presented a distinctive pattern among macro-regions, with an early surge in the Jungle and a later increase in the Highland. External deaths dropped during the lockdown, however, suicides and homicides returned to previous levels in the post-lockdown period. Deaths due to traffic accidents dropped during the lockdown and returned to pre-pandemic levels by December 2020. Conclusions: We found a sudden drop in external causes of death, with suicides and homicides returning to previous levels after the lifting of the lockdown. Non-external deaths showed a differential pattern by macro-region. A close monitoring of these trends could help identify early spikes among these causes of death and take action to prevent a further increase in mortality indirectly affected by the pandemic.     

Synergistic influence of CuO nanoparticles and spectral lights transforms biomass,antioxidative response,and antioxidants in Brassica nigra

Some nanoparticles (NPs) have photocatalytic and photodynamic properties that change on variation in wavelength of light carrying different energies. To access photo-dynamic toxicity of CuO NPs, Brassica nigra seeds were in vitro grown on CuO NPs supplemented media under the exposure of five different spectral lights (white, blue, red, yellow and green). Light wavelength significantly affected shoot and root length and fresh weight of B. nigra and CuO NPs exerted different level of toxicity under these lights. Noteworthy variations were observed in free radical scavenging activity, total antioxidantive response and total reducing power potential when plants were grown in presence of NPs and spectral lights. Significant variations in total phenolics and flavonoids contents were observed in shoots as compared with roots. HPLC analysis presented variation in phenolics in shoots extracts under synergistic influence of NPs and light regime. The study shows that nanoparticles exert different level of toxicity under different wavelengths of lights. Resultantly plants show variations in morphological and biochemical responses. Consequently secondary metabolites produce in plants at varying concentrations to mitigate nanotoxicity under photodynamic response.

     

A comparative study on the effects of selected pesticides on hemato-biochemistry and tissue histology of freshwater fish Cirrhinus mrigala (Hamilton, 1822)

The aim of the present study was to investigate the comparative effects of pesticides Chlorfenapyr, Dimethoate and Acetamiprid on the health of Cirrhinus mrigala under long term exposure. Eighty C. mrigala were divided in four equal groups; one control and three treated groups. The blood was collected from both control and treated groups at intervals of 10th, 20th and 30th days for hemato-biochemistry and histopathological alterations. The result indicates significant difference (P < 0.05) in RBCs, Hb, PCV and MCHC whereas elevation in WBCs and Platelets counts were recorded. In 10th day sampling, MCV value of Dimethoate and Acetamiprid treatment had no difference in comparison with the control group, however it is significantly increased (P < 0.05) in rest of sampling. The MCH value of exposed fish showed significant increased (P < 0.05) after 20th and 30th days for Chlorfenapyr and after 30th days for Acetamiprid exposure while insignificantly increased for rest of sampling. It was also found that these pesticides significantly decrease (p < 0.05) the T3 and T4 levels while increase in the TSH, cortical, ALP, AST, ALT and LDH levels in the serum of the treated fishes in contrast to control group. Similarly, histopathological analysis of gills and liver showed significant alterations in all the treated groups. Toxicity trends of these pesticides was ranked as Chlorfenapyr > Acetamiprid > Dimethoate. It is concluded that indiscriminate use of such pesticides poses a noxious threat to non-target organisms, harm the ecosystems and jeopardizes human health.     

Phytochemical Fingerprints and Bioactivities of Ripe Disseminules (Fruit-Seeds) of Seventeen Gundelia (Kenger-Kereng Dikeni) Species from Anatolia with Chemometric Approach

Gundelia species are known as “Kenger-kereng dikeni” in Anatolia, and their aerial parts are consumed as food. Also, roots and seeds (disseminules) of the Gundelia species are used to prepare gum and coffee. The chemical contents of ethanol and hexane extracts of disseminules of 17 Gundelia species, 13 of them are endemic, were studied using LC/MS/MS and GC/MS. Additionally, their antioxidant potential and enzyme inhibitory capacity against acetyl- and butyryl-cholinesterase, urease, and tyrosinase were determined. The unsaturated fatty acid ratios of Gundelia species were higher than their saturated fatty acid ratio. The highest sum of oleic and linoleic acid was detected in G. tournefortii var. tenuisecta (70.42 %). β-Sitosterol, α-amyrin, 3-acetyllupeol were identified in 17 Gundelia species by GC/MS, while chlorogenic acid and luteolin by LC/MS/MS as major compounds. The ethanol and hexane extracts of G. siirtica, G. rosea, and G. mesopotamica indicated good cholinesterase inhibitory activity. Among all species, ethanol extract of G. colemerikensis exhibited the best activity in ABTS (IC₅₀: 32.30±0.98 μg/mL), DPPH (IC₅₀: 59.91±0.89 μg/mL), and CUPRAC (A_0.5: 57.41±1.03 μg/mL) assays. Ethanol extract of G. colemerikensis also displayed the highest inhibitory activity against butyrylcholinesterase (51.14±0.25 % at 200 μg/mL), urease (51.71±1.75 % at 200 μg/mL), and tyrosinase (39.50±0.85 % at 200 μg/mL) enzymes. According to the chemometric analysis of fatty acids, four groups were observed. Therefore, it is suggested that G. colemerikensis can be used in the pharmaceutical, food, and cosmetic industries due to its antioxidant and enzyme inhibition properties.     

Association studies using family pools of outcrossing crops based on allele-frequency estimates from DNA sequencing

Key message

We propose a method in which GBS data can be conveniently analyzed without calling genotypes.

Abstract

F2 families are frequently used in breeding of outcrossing species, for instance to obtain trait measurements on plots. We propose to perform association studies by obtaining a matching “family genotype” from sequencing a pooled sample of the family, and to directly use allele frequencies computed from sequence read-counts for mapping. We show that, under additivity assumptions, there is a linear relationship between the family phenotype and family allele frequency, and that a regression of family phenotype on family allele frequency will estimate twice the allele substitution effect at a locus. However, medium-to-low sequencing depth causes underestimation of the true allele substitution effect. An expression for this underestimation is derived for the case that parents are diploid, such that F2 families have up to four dosages of every allele. Using simulation studies, estimation of the allele effect from F2-family pools was verified and it was shown that the underestimation of the allele effect is correctly described. The optimal design for an association study when sequencing budget would be fixed is obtained using large sample size and lower sequence depth, and using higher SNP density (resulting in higher LD with causative mutations) and lower sequencing depth. Therefore, association studies using genotyping by sequencing are optimal and use low sequencing depth per sample. The developed framework for association studies using allele frequencies from sequencing can be modified for other types of family pools and is also directly applicable for association studies in polyploids.     

Positive selection and intragenic recombination contribute to high allelic diversity in effector genes of Mycosphaerella fijiensis,causal agent of the black leaf streak disease of banana

Previously, we have determined the nonhost‐mediated recognition of the MfAvr4 and MfEcp2 effector proteins from the banana pathogen Mycosphaerella fijiensis in tomato, by the cognate Cf‐4 and Cf‐Ecp2 resistance proteins, respectively. These two resistance proteins could thus mediate resistance against M. fijiensis if genetically transformed into banana (Musa spp.). However, disease resistance controlled by single dominant genes can be overcome by mutated effector alleles, whose products are not recognized by the cognate resistance proteins. Here, we surveyed the allelic variation within the MfAvr4, MfEcp2, MfEcp2‐2 and MfEcp2‐3 effector genes of M. fijiensis in a global population of the pathogen, and assayed its impact on recognition by the tomato Cf‐4 and Cf‐Ecp2 resistance proteins, respectively. We identified a large number of polymorphisms that could reflect a co‐evolutionary arms race between host and pathogen. The analysis of nucleotide substitution patterns suggests that both positive selection and intragenic recombination have shaped the evolution of M. fijiensis effectors. Clear differences in allelic diversity were observed between strains originating from South‐East Asia relative to strains from other banana‐producing continents, consistent with the hypothesis that M. fijiensis originated in the Asian‐Pacific region. Furthermore, transient co‐expression of the MfAvr4 effector alleles and the tomato Cf‐4 resistance gene, as well as of MfEcp2, MfEcp2‐2 and MfEcp2‐3 and the putative Cf‐Ecp2 resistance gene, indicated that effector alleles able to overcome these resistance genes are already present in natural populations of the pathogen, thus questioning the durability of resistance that can be provided by these genes in the field.