(Hamilton, 1822) is an economically important food fish species occurring throughout Indian rivers, which also has ornamental value. This study focuses on morphological variations in
from seven river ...basins across India namely; Son, Tons, Ken, Brahmaputra, Ganga, Gomti and Gandak. A truss network was constructed by interconnecting nine landmarks to generate 36 morphometric variables extracted from digital images of specimens sampled from the study locations. Transformed truss measurements were subjected to principal component analysis (PCA), canonical discriminant function analysis (CDFA) and discriminant analyses of principal components (DAPC). DAPC function coefficients performed much better in capturing the variation pattern and discrimination between the rivers which was not achieved using CDFA. Eight truss variables were identified with significant and highest loading for truss variables on principal components and coefficients on discriminant function from DAPC contributing to maximum variation between the rivers. Performance graph and functional distribution of identified truss variables clearly indicated distinction between the rivers. Thin plate spline analysis and procrustes shape analysis further showed the variation in morphology between specimens across the rivers. The significant parameters differentiating specimens from different rivers were linked to dorsal fin origin, the base of the pectoral fin and the perpendicular point on the anal fin from the dorsal fin origin. Variation in the hydrodynamics of the rivers studied might be possibly affecting the fin kinematics and consequently leading to adaption seen as phenotypic variation in
. The results showcased in the present study shall help in better understanding of intra-specific diversity which is significant for management and conservation of a species.
Food and water scarcity in high altitudes of the Trans-Himalayan landscape are being seen as impacts of climate change, which is characterized by prolonged winters with sub-zero temperatures for a ...longer period. Average daily temperature from Oct to Mar (2020-21) ranged from − 6.73 ± 1.55 to 6.85 ± 1.93 °C; however, fluctuates between − 10.5 °C (minimum) and 4.6 °C (maximum) on a typical day. With minimal rainfall, agriculture is limited to one season in these cold deserts thus limiting the land productivity. The changing scenario affects water availability for agriculture and otherwise in the villages located at further high altitudes dependent on snowmelt flow in nearby streams. This study explores the potential of extended cultivation during winters using low-cost inputs by comparing different technological options for temperature retention for vegetable cultivation. It further demonstrates the role of peoples’ participation in developing zero-energy artificial ice reservoirs (water harvesting technology through capturing and storing water in the form of ice) in winters to make water available in the following growing season. With site-specific modifications, an artificial ice reservoir was created by the villagers in 2020-21 which provided additional water for irrigation and was timely available (14 days in advance). Using this additional water, a barren area was brought under the plantation to meet futuristic wood and fodder requirements. Confidence building (knowledge gathered, interventions to solve the major problem of water scarcity) through locally adaptable solutions (portable polyhouse, ice reservoir, increased plant productivity) motivated high altitude villagers in Trans-Himalayan to combat threats of climate change.
Silonia silondia is a commercially important fish distributed in Asian countries, which is under threat due to overexploitation. This study focuses on the morphological analysis and genetic variation ...of S. silondia individuals, through truss network and sequencing of two mitochondrial regions, respectively, from six wild populations of the Ganga and Mahanadi river systems in India. A total of 38 haplotypes was observed by analysing combined mitochondrial genes (cytochrome b + ATPase 6/8) in 247 individuals of S. silondia collected from six populations. Average haplotype and nucleotide diversities were 0.8508 and 0.00231, respectively. Genetic structure analysis showed the predominant cause of genetic variation to be within populations. The two clades were observed among the haplotypes and time of divergence from their most probable ancestor was estimated to be around 0.3949 mya. Analysis of combined mitochondrial genes in six populations of S. silondia resulted into three management units or genetic stocks. The truss network analysis was carried out by interconnecting 12 landmarks from digital images of specimens to identify phenotypic stocks. Sixty‐five truss morphometric variables were analysed for geometric shape variation which revealed morphological divergence in River Son specimens. The present study presents molecular markers and genetic diversity data which can be critical input for conservation and management of differentiated populations and future monitoring of the genetic bottleneck. The morphological shape analysis clearly shows that variation in the insertion of adipose fin is an important parameter influencing the morphological discrimination.
In present study, single molecule-real time sequencing technology was used to obtain a validated set of microsatellite markers for application in population genetics of the primitive fish,
Chitala ...chitala
. Assembly of circular consensus sequencing reads resulted into 1164 sequences which contained 2005 repetitive motifs. A total of 100 sequences were used for primer designing and amplification yielded a set of 28 validated polymorphic markers. These loci were used to genotype n = 72 samples from three distant riverine populations of India, namely Son, Satluj and Brahmaputra, for determining intraspecific genetic variation. The microsatellite loci exhibited high level of polymorphism with PIC values ranging from 0.281 to 0.901. The genetic parameters revealed that mean heterozygosity ranged from 0.6802 to 0.6826 and the populations were found to be genetically diverse (F
st
0.03–0.06). This indicated the potential application of these microsatellite marker set that can used for stock characterization of
C. chitala
, in the wild. These newly developed loci were assayed for cross transferability in another notopterid fish,
Notopterus notopterus
.
Tor tor (Hamilton 1922), a natural polyploid fish species, is commonly known as the red-fin or deep bodied mahseer and is the type species of the Tor genus. It was assessed as ‘Near Threatened’ in ...the IUCN Red List, due to rapidly declining populations in wild and recently reassessed as Data Deficient. To generate the genetic structure information in this species, co-dominant markers face polyploidy specific hitches in genotyping, such as auto/tetrasomy, double reduction and missing dosage information.
In the present study, a total of 25 polymorphic microsatellite loci was developed through long- read single molecule, real time (SMRT) sequencing technology, to genotype 139 T. tor samples from six natural riverine populations of India, to determine intra-specific genetic variation in this species.
Upon sequencing 1.5 kb SMRT bell library, the clustering and assembly of high-quality CCS reads resulted into 9746 contigs and 2129 contained repeat sequences. The majority of repeats were dinucleotide (67.8%), followed by trinucleotide (21.4%) and tetranucleotide (10.7%). Out a total of 118 SSR loci primers designed, 25 loci showed polymorphism. The microsatellite genotype analyses with these loci indicated T. tor as an auto-tetraploid, with tetrasomy segregation and occurrence of double reduction. The microsatellite loci identified were highly polymorphic (average PIC 0.6687).. The genetic diversity parameters, observed and expected heterozygosities ranged from 0.1268 to 0.5047 and from 0.4989 to 0.9212, respectively, whereas inbreeding (FIS) values from 0.2334 to 0.8379. The average ρ statistics value of 0.0739 (p = 0.00) indicated the presence of genetic structure in the natural population, and along with pair-wise ρ statistics and DAPC analysis pointed to the occurrence of three genetic stocks.
The identified microsatellite loci were found to be useful in generating information on genetic diversity and fine scale population structure of tetraploid T. tor, which would be valuable for conservation and management of this threatened species.
Tor tor, Tor mahseer, an endangered cyprinid species, is important as a sport fish. Genetic divergence in natural populations of T. tor was investigated using two mitochondrial genes, Cytb ...(Cytochrome b) and ATPase6/8. Analysis of 140 sequences of Cytb (1121 bp) and ATPase6/8 (842 bp) genes revealed 12 and 7 haplotypes, respectively, whereas 23 haplotypes were found in concatenated sequences (1963 bp). Sequence analysis of mitochondrial regions revealed balancing selection and displayed low nucleotide and moderate haplotype diversities. Mantel tests identified a positive relationship between pairwise geographical and genetic distances for the study region. Results of AMOVA based on genes pointed out that the genetic variations were mainly due to variation in within populations (ATPase6/8: 62.73%, Cytb: 42.13%, concatenated sequences: 48.31%). The total Fst was found to be significant in both genes with a value of 0.5787 (p <0 .05) and 0.3726 (p <0 .05) for Cytb and ATPase6/8genes respectively, whereas 0.51687 (p <0 .05) was found in combined sequences, which revealed sub-structuring in the T. tor natural populations. Population pair-wise Fst ranged from 0.00901– to 0.85631 for Cytb and 0.09910– to 0.64731 for ATPase6/8genes, whereas 0.02039 to 0.85436 in combined sequences. Results indicated the presence of four genetic stocks in the populations studied. The baseline information about stock characterisation in this study would be applicable for planning strategies for conservation, management and sustainable fisheries of this species.
Thyroid dysfunction is one of the most common endocrine disorders in people living with HIV (PLHIV). The abnormality in thyroid function has been linked with the adverse effects of prolonged ...antiretroviral therapy (ART) in PLHIV, but its prevalence remains obscure. The present study aimed to determine the prevalence of impaired thyroid function and its relationship to ART duration in Nepalese people living with HIV.
This cross-sectional clinical laboratory based study was conducted at SRL Diagnostics Nepal, Pvt. Ltd. from October 2021 to May 2022. Two hundred and three HIV-seropositive patients enrolled at Tribhuvan University Teaching Hospital (TUTH) in Kathmandu, Nepal were examined for their thyroid function test (TFT) by analyzing the serum T3, T4, and TSH concentrations using a fully automated COBAS e411 analyzer (Roche Diagnostics, USA) based on the electrochemiluminescence assay (ECLIA).
Out of 203 PLHIV, 22 (10.83%) had a thyroid disorder, with subclinical hypothyroidism (
= 16, 72.73%) being the most common, followed by subclinical hyperthyroidism (
= 3, 13.63%). Thyroid dysfunction had no significant correlation with HIV/ART duration (
= 0.304) and sex (
= 0.419), whereas, the risk of thyroid dysfunction was induced with the rise in the age of the PLHIV (
= 0.002, ϕ = 0.274). There were no significant differences in the mean serum T3, T4 and TSH values among different sexes and the HIV/ART duration, however a significant difference in the mean values of TSH (F (3, 199) = 3.231,
= 0.023) and T3 (F (3, 199) = 4.587,
= 0.004) among the different age-groups were shown. The mean T3 values also indicated a gradual decrease with increasing age.
The study revealed subclinical hypothyroidism as the prevailing thyroid disorder associated with PLHIV. The risk of thyroid dysfunction in PLHIV was neither gender specific nor being attributed by the ART duration in Nepalese population; however, elderly PLHIV were highly susceptible to the risk of thyroid disorder.
Hepatitis C Virus (HCV) co-infection and its genotypic distribution in people living with Human Immunodeficiency Virus (HIV) show global inconsistency. Therefore, the present study aimed to ...investigate the prevalence and genotypic distribution patterns of HCV, along with viral load, in people living with HIV. This cross-sectional study was conducted at SRL Diagnostics Nepal, Pvt. Ltd. in 203 HIV-seropositive patients attending the Tribhuvan University Teaching Hospital (TUTH), Maharajgunj, Kathmandu, Nepal from October 2021 to May 2022. The viral load and HCV genotypes were estimated from RNA extracted from the blood sample (plasma) of PLHIV by using a standard Q-PCR protocol. HCV infection was considered as a core variable, whereas covariates used for this study were duration of HIV infection, age, sex, and ART regimen. Out of total 203 PLHIV, the estimated prevalence of HCV co-infection was 115 (56.6%). Male gender was a unique characteristic associated with a high prevalence of HCV co-infection compared to females. The HCV viral load among PLHIV ranged from 34 to 3,000,000 IU/mL. Among HCV co-infected PLHIV, 56 (48.69%) had a low level of HCV viral load. Interestingly, only 3 (2.6%) patients had an HCV viral load higher than 3,000,000 IU/mL. Diverse HCV genotypes were found in the population, including genotypes 1, 1a, 3a, 5a, and 6. However, genotype 3 was the most prevalent HCV variant among HCV-co-infected PLHIV, with a distribution of 36 (61.1%) and viral load ranging from 34 to 3000 IU/mL. HCV coinfection is frequent in the Nepalese population of people living with HIV, particularly due to HCV genotypic variant 3. The findings of this study could be useful for the management and clearance of the HCV co-infection in PLHIV, aiming to provide a good quality of life.
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