Molecular Markers and Their Optimization: Addressing the Problems of Nonhomology Using Decapod COI Gene

Advancements in DNA sequencing and computational technologies influenced almost all areas of biological sciences. DNA barcoding technology employed for generating nucleotide sequences (DNA barcodes) from standard gene region(s) is capable of resolving the complexities caused due to morphological characters. Thus, they complement taxonomy, population analysis, and phylogenetic and evolutionary studies. DNA barcodes are also utilized for species identification from eggs, larvae, and commercial products. Sequence similarity search using Basic Local Alignment Search Tool (BLAST) is the most reliable and widely used strategy for characterizing newly generated sequences. Similarity searches identify “homologous” gene sequence(s) for query sequence(s) by statistical calculations and provide identity scores. However, DNA barcoding relies on diverse DNA regions which differ considerably among taxa. Even, region-specific variations within barcode sequences from a single gene leading to “nonhomology” have been reported. This causes complications in specimen identification, population analysis, phylogeny, evolution, and allied studies. Hence, the selection of appropriate barcode region(s) homologous to organism of interest is inevitable. Such complications could be avoided using standardized barcode regions sequenced using optimized primers. This chapter discusses about the potential problems encountered due to the unknown/unintentional/intentional use of nonhomologous barcode regions and the need for primer optimization

Real Time PCR detection of Macrobrachium rosenbergii (de Man, 1879) larvae with emphasis to their ecology

Species specific identification of early larval stages of many decapod crustaceans sampled from plankton collections remains cumbersome owing to lack of distinguishable characteristics, where DNA based molecular methods provide accurate results without taxonomic ambiguities. In the present study, an attempt was made to detect temporal occurrence of early zoea of freshwater prawn Macrobrachium rosenbergii (de Man) using real-time PCR assays in polyhaline, mesohaline and oligohaline areas of a tropical positive estuary, the Vembanad lake (S. India). High caridean larval abundance could be recorded in polyhaline areas in all seasons while it could be recorded in monsoon season in mesohaline and oligohaline areas. 113 DNA isolations were successfully made from morphologically identified taxonomic units (MOTU) and SYBR Green based RT-PCR amplifications using designed primer for M. rosenbergii yielded positive detections in 38 samples (34%) representing all seasons in all three zones. Positive detections could be recorded in all months except May in mesohaline areas and differed significantly (F = 17.2 p < 0.01) with the same in polyhaline and oligohaline areas. The present results of molecular detection of M. rosenbergii larvae extend confirmation of its breeding ground in Vembanad lake where appropriate management strategies could be enforced for stock conservation of this species

Ecological implications of unintentional aquaculture escapees: an overview of risks, remediation strategies and knowledge gaps in the aquaculture sector of India and riparian East African countries

The global expansion of aquaculture has driven significant technological advancements, including raceways, Integrated Multitrophic Aquaculture (IMTA) and marine offshore cages. However, unregulated aquaculture escapees pose a severe threat to aquatic biodiversity, acting as a potential time bomb for the entire ecosystem. Addressing this issue requires a comprehensive understanding of the impact of unintentional escapees on aquatic ecosystems, particularly in India and riparian East African countries (Kenya, Uganda, and Tanzania). Using an exploratory research design drawing from various peer-reviewed sources, this study outlines the dynamic growth of aquaculture in these countries, identifies high-impact escape incidents, and correlates risks and remedies with global cases, especially in regions such as Norway, Scotland, Ireland, Colombia, and the United States, where serious incidents of aquaculture escapees have been reported. The research categorizes aquaculture development trends, discusses mechanisms of escapee impact, proposes remedies, assesses methods and inferential strength, and highlights gaps in the existing literature. The study revealed complex ecological shifts caused by aquaculture escapees from invasive non-native fish species, affecting predation, competition, and genetic diversity. Escaped fish from aquaculture facilities pose a significant threat to aquatic biodiversity, especially in the study regions. The escalating risk of unintentional escapes was highlighted in India and three East African countries. To mitigate this, the study proposes integrating escapee management into national fisheries systems, amending fisheries laws, holding fish farmers accountable for aquaculture system failure, and developing comprehensive regulations for non-native species in aquaculture within the study regions. It is recommended to standardize the planning for aquaculture facilities and implement emergency plans, training, local mobilization and further research on the impact thresholds of aquaculture escapees in the study regions. Ecological education in aquaculture communities and the recognition of the role of translational scientists are crucial for the dissemination of knowledge. Urgent government action is needed to address unreported aquaculture escapes, preventing further ecosystem degradation and ensuring global aquaculture sustainability

Real Time PCR detection of

Species specific identification of early larval stages of many decapod crustaceans sampled from plankton collections remains cumbersome owing to lack of distinguishable characteristics, where DNA based molecular methods provide accurate results without taxonomic ambiguities. In the present study, an attempt was made to detect temporal occurrence of early zoea of freshwater prawn Macrobrachium rosenbergii (de Man) using real-time PCR assays in polyhaline, mesohaline and oligohaline areas of a tropical positive estuary, the Vembanad lake (S. India). High caridean larval abundance could be recorded in polyhaline areas in all seasons while it could be recorded in monsoon season in mesohaline and oligohaline areas. 113 DNA isolations were successfully made from morphologically identified taxonomic units (MOTU) and SYBR Green based RT-PCR amplifications using designed primer for M. rosenbergii yielded positive detections in 38 samples (34%) representing all seasons in all three zones. Positive detections could be recorded in all months except May in mesohaline areas and differed significantly (F = 17.2 p < 0.01) with the same in polyhaline and oligohaline areas. The present results of molecular detection of M. rosenbergii larvae extend confirmation of its breeding ground in Vembanad lake where appropriate management strategies could be enforced for stock conservation of this species

Fish stock demographics of skipjack tuna (Katsuwonus pelamis) from Kavaratti in Lakshadweep, Southern Arabian Sea

Marine fish stocks are depleting at an alarming rate. Skipjack tuna, Katsuwonus pelamis has been exploited in Lakshadweep Island area in the Indian Ocean mainly by pole and line fishery which constituted one-third of its production in the country. Age, growth, demographics and stock assessment of this species were investigated from the Lakshadweep waters. The von Bertalanffy growth factors were estimated as asymptotic length 72.5 cm, growth constant 0.480 and the theoretical age at zero-length as –0.1097. This study showed that skipjack grows from 30 to 68.26 cm from first to sixth year. The natural mortality, fishing mortality and total mortality were 0.82, 1.51 and 2.33 respectively. The exploitation ratio was 0.65, while the exploitation which maximises relative yield per recruit (Emax) was 1.0.&nbsp; Recruitment pattern showed that young recruits entered the fishing grounds in most months, with peaks during June–July. Length based Virtual Population Analysis indicated that the major loss in its stock up to 22 cm was due to natural causes. At the same time, higher fishing mortality was registered in 40–60 cm length group. The present study provides knowledge on the demographics of K. pelamis, pertinent for formulating an effective fisheries management in the region

Clinical profile and outcomes of pediatric hypertrophic cardiomyopathy in a South Indian tertiary care cardiac center: a three decade experience

Abstract Introduction Although much research has been done on adult hypertrophic cardiomyopathy, data on pediatric hypertrophic cardiomyopathy is still limited. Methods and results The study enrolled all patients with cardiomyopathy who presented to us between 1990 to 2020 and were younger than 18 yrs. During the thirty-year study period, we identified 233 cases of pediatric cardiomyopathy. Sixty-three cases (27%) had hypertrophic cardiomyopathy. Out of the 63 HCM cases, 12% presented in the neonatal period and 37% presented in the first year of life. The median age of presentation was 7 yrs (Range 0.1–18 yrs). Sixteen patients had proven syndromic, metabolic, or genetic disease (25%). LV outflow obstruction was present in 30 patients (47%). Noonan syndrome was present in 9 of the 63 patients (14%). Dyspnea on exertion was the most common mode of presentation. Cardiac MRI was done in 28 patients, out of which 17 had late gadolinium enhancement (LGE). Mid myocardial enhancement was the most common pattern. Four patients had LGE of more than 15%. Over a mean follow-up period of 5.6 years (0.1–30 years), twenty-one were lost to follow-up (33%). Among the patients whose outcome was known, eleven died (26%), and thirty-one (73%) were alive. The 5-year survival rate of HCM patients was 82%, and the 10-year survival rate was 78%. Seven died of sudden cardiac death, three from heart failure, and one from ventricular arrhythmias. Sustained ventricular arrhythmias were seen in three patients and atrial arrhythmias in two. First-degree AV block was seen in 10 patients (15%) and bundle branch blocks (BBB) in five (8%). Eight patients required ICD or transplant (12.7%). Two patients underwent ICD for primary prevention, and one underwent PPI for distal AV conduction disease. Among the various clinical, echocardiographic, and radiological risk factors studied, only consanguinity showed a trend towards higher events of death or ventricular arrhythmias (P-value 0.08). Conclusion More than one-third of our HCM cohort presented in infancy. LV outflow tract obstruction is common (47%). Mid myocardial enhancement was the most common pattern of late gadolinium enhancement. SCD was the most common cause of death. The outcome in our HCM cohort is good and similar to other population cohorts. Only Consanguinity showed a trend towards higher events of death or ventricular arrhythmias