Sharks have thrived in the oceans for 400 million years, experienced five extinctions and evolved into today's apex predators. However, enormous genome size, poor karyotyping and limited tissue ...sampling options are the bottlenecks in shark research. Sharks of the family Orectolobiformes act as model species in transcriptome research with exceptionally high reproductive fecundity, catch prominence and oviparity. The present study illustrates a de novo transcriptome for an adult grey bamboo shark, Chiloscyllium griseum (Chondrichthyes; Hemiscyllidae) using paired-end RNA sequencing. Around 150 million short Illumina reads were obtained from five different tissues and assembled using the Trinity assembler. 70,647 hits on Uniprot by BLASTX was obtained after the transcriptome annotation. The data generated serve as a basis for transcriptome-based population genetic studies and open up new avenues in the field of comparative transcriptomics and conservation biology.
Nemipterus randalli, commonly known as Randall's threadfin bream, is a commercially important marine finfish. Understanding its genetic structure is critical to effective management and conservation ...efforts. Previous investigations on population structure in this species were limited by geographic coverage. In this study, we utilized the mitochondrial Cytochrome b gene and nuclear Ribosomal protein gene intron Rp S7 sequences to investigate the population genetic structure, demography and genetic diversity of N. randalli along Indian waters. Our results revealed high haplotype diversity but low nucleotide diversity. AMOVA revealed that the variation among the population was highly significant. Hierarchical AMOVA provided further evidence of significant genetic differentiation between the west and east coasts, which was corroborated by the Bayesian tree and the median-joining network diagram. The mtDNA sequences revealed significant genetic structure between populations based on fixation index analysis following the isolation-by-distance model. Furthermore, the neutrality test and mismatch analysis suggest that N. randalli populations may have experienced a population expansion. However, nuclear marker RpS7, showed a high level of polymorphism, which obscured the population structuring observed with the mitochondrial marker. Consequently, concordant results were not obtained when comparing the mitochondrial and nuclear DNA sequences. The strong genetic differentiation between the east and west coast observed using mitochondrial marker could be attributed to a combination of geographic and environmental factors. These findings lay the groundwork for developing effective conservation and management strategies for N. randalli, considering its genetic structure.
Dynamical systems can undergo critical transitions where the system suddenly shifts from one stable state to another at a critical threshold called the tipping point. The decrease in recovery rate to ...equilibrium (critical slowing down) as the system approaches the tipping point can be used to identify the proximity to a critical transition. Several measures have been adopted to provide early indications of critical transitions that happen in a variety of complex systems. In this study, we use early warning indicators to predict subcritical Hopf bifurcation occurring in a thermoacoustic system by analyzing the observables from experiments and from a theoretical model. We find that the early warning measures perform as robust indicators in the presence and absence of external noise. Thus, we illustrate the applicability of these indicators in an engineering system depicting critical transitions.
Genetic stock structure and historical demography of Indian oil sardine, a commercially and ecologically important small pelagic fish, was studied using mitochondrial control region and Cytochrome C ...Oxidase I (COI) sequences. A 758bp portion of the control region in 287 individuals and a 576bp portion of the COI gene in 291individuals from 10 locations along the distribution range were amplified resulting in 236 and 84 haplotypes, respectively. The high haplotype and low nucleotide diversity values (0.99 and 0.19 for control region and 0.85 and 0.004 for COI, respectively) are characteristic of populations having undergone a demographic expansion. Genetic differentiation, ΦST, was low and insignificant between populations using both control region and COI gene markers. Mismatch analysis showed a recent demographic and spatial expansion coinciding with the late Pleistocene epoch. Mantel tests revealed the lack of isolation by distance which is attributable either to high levels of migration overriding the effect of genetic drift or to insufficient time for accomplishing a balance between migration and drift after a recent range expansion.
•Genetic stock structure of Indian oil sardine studied using mtDNA markers.•High haplotype diversity values associated with low nucleotide diversity values.•Genetic differentiation (Φst) was low and insignificant between populations.•Molecular evidence for demographic expansion coinciding with Pleistocene epoch.•Values of present-day effective population sizes are quite high.
We present the effect of noise on the hysteresis characteristics of a prototypical thermoacoustic system, a horizontal Rijke tube. As we increase the noise intensity, we find that the width of the ...hysteresis zone decreases. However, we find that the rate of decrease in hysteresis width is constant for all the mass flow rates considered in the present study. We also show that the subcritical transition observed in the absence of noise is no longer discernible once the intensity of noise is above a threshold value and the transition appears to be continuous. We compare our experimental observations with the results obtained from a numerical model perturbed with additive Gaussian white noise and we find a qualitative agreement between the experimental and the numerical results.
Clupeoid fish can be considered excellent candidates to understand the role of mitochondrial DNA in adaptive evolution, as they have colonized different habitats (marine, brackish, freshwater, ...tropical and temperate regions) over millions of years. Here, we investigate patterns of tRNA location, codon usage bias, and lineage-specific diversifying selection signals to provide novel insights into how evolutionary improvements of mitochondrial metabolic efficiency have allowed clupeids to adapt to different habitats. Based on whole mitogenome data of 70 Clupeoids with a global distribution we find that purifying selection was the dominant force acting and that the mutational deamination pressure in mtDNA was stronger than the codon/amino acid constraints. The codon usage pattern appears evolved to achieve high translational efficiency (codon/amino acid-related constraints), as indicated by the complementarity of most codons to the GT-saturated tRNA anticodon sites (retained by deamination-induced pressure) and usage of the codons of the tRNA genes situated near to the control region (fixed by deamination pressure) where transcription efficiency was high. The observed shift in codon preference patterns between marine and euryhaline/freshwater Clupeoids indicates possible selection for improved translational efficiency in mitochondrial genes while adapting to low-salinity habitats. This mitogenomic plasticity and enhanced efficiency of the metabolic machinery may have contributed to the evolutionary success and abundance of Clupeoid fish.
Role of calcium ion (Ca2+) in the functioning of neurons from their naïve state to mature state is of vital importance. It controls functions such as neuronal functioning, neuronal ATP production, ...central nervous system migration and many others. Failure in Ca2+ homeostasis mechanisms and the resulting cellular Ca2+ ion load initiates a cascade of reactions involving various cytosolic enzymes and proteins. This total mechanism leads to the neuronal death. The ability of neurons to resist such death mechanisms fails as a result of extensive cell death signaling cascade reactions and later brings brain damage. The role of neuronal endoplasmic reticulum and protein channels like CaVs, TRP channels, and NMDAR as the mediators of cell damage and death has been evaluated in the studies related to cerebral ischemia. Here, we portray Ca2+ ion as one of the role players in neuronal death and cerebral damage following ischemia. The role of Ca2+ in neuronal functioning, its regulatory mechanisms and the failure of homeostatic mechanisms are discussed in detail.
This study was undertaken to study the efficiency of Adsflt-1 engineered human eutopic mesenchymal stem cells (MSCs) secreting anti-angiogenic sFlt-1 as a targeted cell-based therapy for ...endometriosis (EM). Eutopic MSCs were transduced with Adsflt-1/AdV0 viral vectors and were evaluated for expression and secretion of sFlt-1. EM was created in NOD/SCID mice using subcutaneous implantation techniques. Four doses of 10(6) MSC-Adsflt-1/MSC-AdV0 were administered to the model and therapeutic anti-angiogenic ability was analyzed by lesion size measurement, microvessel density, immunohistochemistry and real-time reverse transcriptase-PCR analysis. Approximately 86% of transduced MSCs expressed and secreted sFlt-1. MSC-Adsflt-1-treated animals exhibited significant reduction (52.8±1.8%) in size of endometriotic lesions. We observed a 2.3-fold decrease in the number and a 10-fold decrease in the size of endometrial glands in MSC-Adsflt-1-treated animals. A two-fold decrease in stromal cell densities was also observed in MSC-Adsflt-1-treated animals compared with the MSC-AdV0 group. Specific positive immunostaining for MSC marker, CD146 and sFlt-1 in the lesion sites of the MSC-Adsflt-1 group suggests possible homing of transduced MSCs, their survival and secretion of sFlt-1 at the target sites. A marked reduction in size of microvessels and microvessel density within endometriotic lesions and surrounding host subcutaneous layers was observed in MSC-Adsflt-1 group along with significantly downregulated expression of transcripts for vascular endothelial growth factor, fetal liver kinase 1 and matrix metalloproteinases (2 and 9). Our findings indicate the efficacy of a novel eutopic MSC-Adsflt-1 therapy in EM study models. Evaluating long-term effects of genetically modified MSCs in vivo is essential in translating MSC-Adsflt-1 therapy to the clinics.
Despite its excellent properties, the inherent unstable nature of black phosphorus (BP) in ambient atmosphere has severely restricted its use in electrochemical sensing applications. In this work, ...polyaniline (PANI) sheathed BP was prepared via the electrochemical polymerisation of aniline on BP coated screen printed carbon electrode (i. e., SPCE/BP) which resulted in an efficient, stable electrochemical platform (i. e., SPCE/BP@PANI) with improved properties which was evaluated for electrochemical detection of two model bioanalytes namely, ascorbic acid (AA) and Hydrazine (Hy). The formation of PANI on the SPCE/BP exhibited a pair of stable and well‐defined redox peaks indicating the better adsorption energy and fast electron transfer nature of BP as compared to other 2D materials like graphene and transitional metal dichalcogenides. FESEM and XPS studies revealed the formation and uniform growth of PANI on BP surface without any aggregation. Electrochemical impedance spectroscopy analyses revealed that SPCE/BP@PANI can act as a suitable electrocatalyst material for the sensing of AA and Hy. Thus, SPCE/BP@PANI electrode exhibited low limit of detection (DL; 1.69 μM), excellent reproducibility and better selectivity towards AA oxidation over glucose, sucrose, urea, citric acid, sodium, nitrate, nitrite and magnesium with a sensitivity of 3.38 A M−1 cm−2 (R2=0.98) in the dynamic range of 10–1100 μM. The excellent analytical performance of the BP@PANI is plausible due to better adsorption energy and fast electron transfer of BP. Further, SPCE/BP@PANI was also used for successful detection of AA in processed fruit juice with good recovery. Under the optimal DPV conditions, the modified electrode was extended for detection of Hy in a linear range of 100–1500 μM with sensitivity of 0.09 A M−1 cm−2 (R2=0.99) and DL=89 μM validating the potential of BP based composites in wide range of electrochemical applications.
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