Decoding the molecular phylogenetics of ornamental catfishes (siluriformes) of North East India using DNA barcoding approach

BACKGROUND

Catfishes (order Siluriformes) are among the most diverse and widely distributed fish groups in the world. They are not only used for human consumption but are also a major part of the ornamental fish trade. Being a Biodiversity Hotspot, the North Eastern Region of India is home to a diverse population of ornamental fishes. Catfishes contain a humongous number of species; in this study, the authors have tried to elucidate the phylogenetic relationship of some important ornamental catfishes found in North East India using DNA barcodes.

METHODS AND RESULTS

In this study, we have tried to explore the phylogenetic history of 13 species (41 specimens) of ornamental catfishes spanning 12 genera and 9 families of Siluriformes using DNA barcoding. Pairwise genetic distances using Kimura 2-Parameter (K2P) were calculated at intra-specific and inter-specific levels. A Neighbor-Joining tree was constructed to understand the phylogenetic relationship among the nine different catfish families. All the specimens under this study clustered with their respective species under the same family and formed three sub-clades. However, Olyra longicaudata, belonging to the Bagridae family, did not cluster with other species from the same family. In this study, the authors have suggested a revision of the classification of O. longicaudata back to its original family, Olyridae.

CONCLUSIONS

In this study, the maximum intraspecific genetic distance of 0.03 and the minimum interspecific genetic distance of 0.14 were observed among the species. Therefore, it is evident that there is a barcoding gap among the species, which helped in the correct identification of the species. Thus, DNA barcoding helped complement the phenetic approach and also revealed a different phylogenetic relationship among the catfishes belonging to the Bagridae family.

Proteomics analysis of differentially abundant proteins in the rohu kidney infected with Edwardsiella tarda

Edwardsiella tarda (Et) is a zoonotic gram-negative pathogen with a diverse host range, including fish. However, the in-depth molecular mechanisms underlying the response of Labeo rohita (rohu) kidney to Et are poorly understood. A proteomic and histopathological analysis was performed for the rohu kidney after Et infection. The histopathology of the infected rohu kidney showed vacuolation and necrosis. After LC-MS/MS analysis, ~1240 proteins were identified with ≥2 unique peptides. A total of 96 differentially abundant proteins (DAPs) were observed between the control and Et infected group (ET). Metascape and STRING analysis were used for the gene ontology (GO), and protein-protein interaction network (PPI) for the significant pathways of DAPs. In PPI, low-abundant proteins were mapped to metabolic pathways and oxidative phosphorylation (cox5ab, uqcrfs1). High-abundance proteins were mapped to ribosomes (rplp2), protein process in the ER (hspa8), and immune system (ptgdsb.1, muc2). Our label-free proteomic approach in the rohu kidney revealed abundant enriched proteins involved in vesicle coat (ehd4), complement activation (c3a.1, c9, c7a), phagosome (thbs4, mapk1), metabolic reprogramming (hao1, glud1a), wound healing (vim, alox5), and the immune system (psap) after Et infection. A targeted proteomics approach of multiple reaction monitoring (MRM) validated the DAPs (nprl3, ambp, vmo1a, hspg2, muc2, hao1 and glud1a) between control and ET. Overall, the current analysis of histology and proteome in the rohu kidney provides comprehensive data on pathogenicity and the potential immune proteins against Et.

Development and characterization of a new muscle cell culture system from Clarias magur (Hamilton, 1822)

The cell line has been used as a novel in vitro tool for executing several studies in life sciences. The current study aimed to develop and characterize a muscle cell culture system derived from Clarias magur. The primary muscle cell cultures derived from the caudal peduncle muscle have been successfully sub cultured up to 13 passages to establish a new muscle cell culture system known as CMM. At a temperature of 28 °C, L-15 medium supplemented with 20% FBS produced the maximum growth of muscle cells. However, muscle cells were optimized to grow at 10% FBS. To enhance the proliferation capacity of the CMM cells, a growth-promoting factor bFGF (10 ng/ml) was added, thereby reducing the time interval of passages for the subsequent cultures. DNA barcoding of the CMM cell culture system authenticated the species of origin. The cell culture system was successfully cryopreserved by a slow freezing procedure at - 80 °C with a revival efficiency of 60%.

Development of a cell line from skeletal trunk muscle of the fish Labeo rohita

Labeo rohita is a widely cultivated tropical freshwater carp and found in rivers of South Asian region. A new cell line, designated LRM, has been developed from the muscle tissue of L. rohita. Muscle cells were subcultured up to 38 passages in a Leibovitz's-15 (L-15) supplemented with 10% FBS (Fetal Bovine Serum) and 10 ng/ml bFGF. The LRM cells exhibited fibroblastic morphology with a doubling time of 28 h, and a plating efficiency of 17%. A maximum growth rate was observed for LRM cells at 28 °C, 10% FBS and 10 ng/ml bFGF. A cytochrome C oxidase subunit I (COI) gene sequence was used to authenticate the developed cell line. Chromosome analysis revealed 50 diploid chromosomes. The fibroblastic characteristics of the of the LRM cells was confirmed by immunocytochemistry. The expression of MyoD gene in LRM cells was analyzed by quantitative PCR in comparison with passages 3, 18 and 32. The expression of MyoD was higher at passage 18 compared to the passages 3 and 32. The LRM cells attached properly onto the 2D scaffold and the expression of the F-actin filament protein was confirmed by phalloidin staining followed by counter staining with DAPI to observe the distribution of the muscle cell nuclei and the cytoskeleton protein. A revival rate of 70-80% was achieved when the LRM cells were cryopreserved at - 196 °C using liquid nitrogen. This study would further contribute to understanding the in vitro myogenesis and progress toward cultivated fish meat production.

Functional characterization of Labeo rohita muscle cell line for in vitro research

BACKGROUND

Labeo rohita represents the most dominant fish species in Indian aquaculture and the fish cell lines have been used as an excellent in vitro platform for performing various biological research.

METHODS AND RESULTS

The LRM cell culture developed from the muscle tissue of L. rohita was used to study the in vitro applications. The developed muscle cells were maintained in a Leibovitz's-15 (L-15) supplemented with 10% FBS (Fetal Bovine Serum) and 10 ng/ml bFGF at 28 ^oC temperature. The LRM cells showed fibroblastic-like morphology and was authenticated by sequencing mitochondrial gene 16S rRNA. The expression of myogenic regulatory factors (MRFs) was studied in different stages of LRM cells; however, the expression patterns varied at different passages. The MEF2A, Mrf-4, and Myogenin expressions were higher in passage 25, while the expression of MyoD was maximum in passage 15, and the expression of Myf-5 was highest in passage 1. The transfection efficiency of LRM cells revealed 14 % of the GFP expression with a pmaxGFP vector DNA. The LRM cells were susceptible to the extracellular products prepared from Aeromonas hydrophilla and Edwardsiella tarda. The acute cytotoxicity of six heavy metals (Hg, Cd, Zn, Cu, Pb, Ni) was assessed in LRM cells by a dose-dependent manner in comparison to IC₅₀ values obtained from MTT and NR assays. A revival rate of 70-75% was achieved when the LRM cells were cryopreserved at - 196 °C using liquid nitrogen.

CONCLUSION

The developed muscle cells serve as an functional in vitro tool for toxicological and biotechnological studies.

Proteomic analysis of liver tissue reveals Aeromonas hydrophila infection mediated modulation of host metabolic pathways in Labeo rohita

Aeromonas hydrophila (Ah) is a Gram-negative bacterium and a serious global pathogen causing Motile Aeromonas Septicaemia (MAS) in fish leading to global loss in aquaculture. Investigation of the molecular alterations of host tissues such as liver could be a powerful approach to identify mechanistic and diagnostic immune signatures of disease pathogenesis. We performed a proteomic analysis of Labeo rohita liver tissue to examine the protein dynamics in the host cells during Ah infection. The proteomic data was acquired using two strategies; discovery and targeted proteomics. Label-free quantification was performed between Control and challenged group (AH) to identify the differentially expressed proteins (DEPs). A total of 2525 proteins were identified and 157 were DEPs. DEPs include metabolic enzymes (CS, SUCLG2), antioxidative proteins, cytoskeletal proteins and immune related proteins (TLR3, CLEC4E). Pathways like lysosome pathway, apoptosis, metabolism of xenobiotics by cytochrome P450 were enriched by downregulated proteins. However, upregulated proteins majorly mapped to innate immune system, signaling of B cell receptor, proteosome pathway, ribosome, carbon metabolism and protein processing in ER. Our study would help in exploring the role of Toll-like receptors, C-type lectins and, metabolic intermediates like citrate and succinate in Ah pathogenesis to understand the Ah infection in fish. SIGNIFICANCE: Bacterial diseases such as motile aeromonas septicaemia (MAS) are among the most serious problems in aquaculture industry. Small molecules that target the metabolism of the host have recently emerged as potential treatment possibilities in infectious diseases. However, the ability to develop new therapies is hampered due to lack of knowledge about pathogenesis mechanisms and host-pathogen interactions. We examined alterations in the host proteome during MAS caused by Aeromonas hydrophila (Ah) infection, in Labeo rohita liver tissue to find cellular proteins and processes affected by Ah infection. Upregulated proteins belong to innate immune system, signaling of B cell receptor, proteosome pathway, ribosome, carbon metabolism and protein processing. Our work is an important step towards leveraging host metabolism in targeting the disease by providing a bigger picture on proteome pathology correlation during Ah infection.

Establishment and characterization of a new fibroblast-like cell line from the skin of a vertebrate model, zebrafish (Danio rerio)

BACKGROUND

The available fully sequenced genome and genetic similarities compared to humans make zebrafish a prominent in vitro vertebrate model for drug discovery & screening, toxicology, and radiation biology. Zebrafish also possess well developed immune systems which is ideal for studying infectious diseases. Fish skin confers immunity by serving as a physical barrier against the invading pathogens in the aquatic habitat. Therefore in vitro models from the skin tissue of zebrafish help to study the physiology, functional genes in vitro, wound healing, and pathogenicity of microbes. Hence the study aimed to develop and characterize a skin cell line from the wild-type zebrafish Danio rerio.

METHODS AND RESULTS

A novel cell line designated as DRS (D. rerio skin) was established and characterized from the skin tissue of wild-type zebrafish, D. rerio, by the explant technique. The cells thrived well in the Leibovitz's -15 medium supplemented with 15% FBS and routinely passaged at regular intervals. The DRS cells mainly feature fibroblast-like morphology. The culture conditions of the cells were determined by incubating the cells at varying concentrations of FBS and temperature; the optimum was 15% FBS and 28 °C, respectively. Cells were cryopreserved and revived with 70-75% viability at different passage levels. Two extracellular products from bacterial species Aeromonas hydrophila and Edwardsiella tarda were tested and found toxic to the DRS cells. Mitochondrial genes, namely COI and 16S rRNA PCR amplification and partial sequencing authenticated the species of origin of cells. The modal diploid (2n) chromosome number of the cells was 50. The cell line DRS was found to be free from mycoplasma. The cells were transfected with pMaxGFP plasmid and tested positive for green fluorescence at 24-48 h post-transfection.

CONCLUSION

The findings from this study thus confirm the usefulness of the developed cell line in bacterial susceptibility and transgene expression studies.

Ecological Monitoring and Omics: A Comprehensive Comparison of Workflows for Mass Spectrometry-Based Quantitative Proteomics of Fish (Labeo rohita) Liver Tissue

Introduction: The liver is highly sensitive to the environmental factors. Liver tissue, particularly from fish, is often used as a biological target in ecological monitoring, disease research, and stress response studies. Labeo rohita (rohu) is a fish with a significant role in the global aquaculture economy. Methods: Bottom-up proteomics relies on efficient sample preparation for performing mass spectrometric analysis of the liver tissue. Optimization of protein solubilization and digestion strategies is the key step to obtain reliable data for a successful proteomics experiment. Because the goal of extraction is to acquire the optimum protein quality and yield, the first step should be to choose an appropriate extraction method based on the type of sample. Solubilization buffers containing sodium dodecyl sulfate (SDS) or urea, and digestion methods such as filter-aided sample preparation (FASP), suspension trap (S-Trap) and in-solution are often used in proteomics but are in need of comparative evaluation with an eye to protocol optimization. Experiment: We applied two different solubilization buffers (one containing SDS, and other containing urea) and three digestion methods (FASP, S-Trap, and in-solution) to the proteomic analysis of the fish (L. rohita) liver tissue. Label-free quantification analysis was performed to analyze the similarities and differences in the results with each method. Gene ontology-based functional analysis was performed for the identified proteome across the experimental conditions to overview their protein classes, molecular functions, and biological processes. Results: SDS lysis followed by S-Trap digestion outperformed the other combinations of lysis and digestion in terms of higher protein coverage, consistency in the results and repeatability. Filter-based methods provided comparatively better results than in-solution digestion. Discussion: This protocol presents new insights on ways to optimize discovery and targeted proteomic analyses of liver tissue using the fish L. rohita as a case study. Other tissues can also be evaluated in the future drawing from the results in this study. This would help the scientific community with hypothesis-driven studies on topics ranging from basic biology to applied aquaculture research and ecological monitoring. This is particularly relevant in the current era of ecological crises and environmental pollution, where advances and optimization in research protocols can contribute to in-depth studies of ecosystems and planetary health.

Current intraoperative storage and handling practices of autologous bypass conduit: A survey of the royal australasian college of surgeons

During bypass surgery for peripheral arterial occlusive disease and ischaemic heart disease, autologous graft conduit including great saphenous veins and radial arteries are frequently stored in solution. Endothelial damage adversely affects the performance and patency of autologous bypass grafts, and intraoperative graft storage solutions have been shown to influence this process. The distribution of storage solutions currently used amongst Cardiothoracic and Vascular Surgeons from Australia and New Zealand is not well defined in the literature. The aim of this study was to determine current practices regarding autologous graft storage and handling amongst this cohort of surgeons, and discuss their potential relevance in the context of early graft failure. From this survey, the most frequently used storage solutions were heparinized saline for great saphenous veins, and pH-buffered solutions for radial arteries. Duration of storage was 30–45 min for almost half of respondents, although responses to this question were limited. Further research is required to investigate whether ischaemic endothelial injury generates a prothrombotic state, whether different storage media can alter this state, and whether this is directly associated with clinical outcomes of interest such as early graft failure.

The PeptideAtlas of a widely cultivated fish Labeo rohita: A resource for the Aquaculture Community

Labeo rohita (Rohu) is one of the most important fish species produced in world aquaculture. Integrative omics research provides a strong platform to understand the basic biology and translate this knowledge into sustainable solutions in tackling disease outbreak, increasing productivity and ensuring food security. Mass spectrometry-based proteomics has provided insights to understand the biology in a new direction. Very little proteomics work has been done on 'Rohu' limiting such resources for the aquaculture community. Here, we utilised an extensive mass spectrometry based proteomic profiling data of 17 histologically normal tissues, plasma and embryo of Rohu to develop an open source PeptideAtlas. The current build of "Rohu PeptideAtlas" has mass-spectrometric evidence for 6015 high confidence canonical proteins at 1% false discovery rate, 2.9 million PSMs and ~150 thousand peptides. This is the first open-source proteomics repository for an aquaculture species. The 'Rohu PeptideAtlas' would promote basic and applied aquaculture research to address the most critical challenge of ensuring nutritional security for a growing population.

Organ-Based Proteome and Post-Translational Modification Profiling of a Widely Cultivated Tropical Water Fish, Labeo rohita

Proteomics has enormous applications in human and animal research. However, proteomic studies in fisheries science are quite scanty particularly for economically important species. Few proteomic studies have been carried out in model fish species, but comprehensive proteomics of aquaculture species are still scarce. This study aimed to perform a comprehensive organ-based protein profiling of important tissue samples for one of the most important aquaculture species,Labeo rohita.Deep proteomic profiling of 17 histologically normal tissues, blood plasma, and embryo provided mass-spectrometric evidence for 8498 proteins at 1% false discovery rate that make up about 26% of the total annotated protein-coding sequences in Rohu. Tissue-wise expression analysis was performed, and the presence of several biologically important proteins was also verified using a targeted proteomic approach. We identified the global post-translational modifications (PTMs) in terms of acetylation (N-terminus and lysine), methylation (N-terminus, lysine, and arginine), and phosphorylation (serine, threonine, and tyrosine) to present a comprehensive proteome resource. An interactive web-based portal has been developed for an overall landscape of protein expression across the studied tissues of Labeo rohita (www.fishprot.org). This draft proteome map of Labeo rohita would advance basic and applied research in aquaculture to meet the most critical challenge of providing food and nutritional security to an increasing world population.

Impact of g force and timing on the characteristics of platelet-rich fibrin matrices

Recently, new centrifugation protocols for the preparation of platelet-rich fibrin (PRF) have been introduced in an attempt to further improve the beneficial impact of these 2nd generation platelet concentrate membranes. This in-vitro study aimed to compare the biological and physical characteristics of three types of PRF membranes using two different centrifuges with adapted relative centrifugal forces (RCF): leucocyte- and platelet-rich fibrin, advanced platelet-rich fibrin, and advanced platelet-rich fibrin⁺. Release of growth factors, macroscopic dimensions, cellular content and mechanical properties of the respective membranes, prepared from blood of the same individual were explored. Furthermore, the impact of timing (blood draw-centrifugation and centrifugation-membrane preparation) was assessed morphologically as well as by electron microscopy scanning. No statistically significant differences amongst the three PRF modifications could be observed, neither in their release of growth factors or the cellular content, nor in clot/membrane dimensions. The difference between both centrifuges were negligible when the same g-force was used. A lower g-force, however, reduced membrane tensile strength. Timing in the preparation process had a significant impact. Adaptation of RCF only had a minimal impact on the final characteristics of PRF membranes.

Cross-cultural validation of the Portuguese from Portugal version of the test for respiratory and asthma control in kids questionnaire

Summary

Objective. The Test for Respiratory and Asthma Control in Kids (TRACK) is a tool to assess asthma control in preschool children. This study aims to validate the Portuguese from Portugal version of the TRACK questionnaire. Methods. A prospective cohort study was carried out to assess their psychometric characteristics. Caregivers of 141 children under age 5 with asthma symptoms were enrolled. Results. Internal reliability was close to 0.70 (Cronbach's α). The test-retest reliability was 0.87. TRACK scores were different between well, partially, and non-controlled asthma groups (p less than 0.001). Patients rated as having better control showed an increase in TRACK scores. Conclusions. The Portuguese version of the TRACK questionnaire is accurate and reliable for monitoring asthma control. Its use may help to overcome challenges with the management of this age group.

Short and extended provocation tests have similar negative predictive value in non-immediate hypersensitivity to beta-lactams in children

INTRODUCTION AND OBJECTIVES

Drug provocation tests (DPTs) are the gold-standard method to diagnose non-immediate hypersensitivity reactions (NIHSR) to beta-lactam antibiotics (BL) in children. Our aim was to compare the negative predictive value (NPV) of one-day (short) DPT versus 3-7 days (extended) DPT for the diagnosis of NIHSR to BL in paediatric age. A secondary aim was to compare confidence on drug re-exposure after short and extended negative DPTs.

METHODS

The occurrence of HSR on drug re-exposure and drug refusal after negative diagnostic DPTs were evaluated in children/adolescents with a history of NIHSR to BL using a questionnaire performed six months to ten years after DPT. Patients were divided into two groups according to the protocol performed: short DPT vs. extended DPT.

RESULTS

We enrolled 212 children and adolescents (86 females, 126 males, mean age at DPT 5.52 years, p25=3 years, p75=7.25 years): 69 tested with short DPT, and 143 with extended DPT. The NPV of both types of DPT together was 95.2%. The NPV of short DPT was 97.5% and the NPV of extended DPT was 93.8% (p=0.419). After negative DPT, beta-lactams were refused by carers in 14.75% of the children requiring subsequent treatment, 6.98% in the short DPT group and 18.99% in the extended DPT group (p=0.074).

CONCLUSIONS

In our paediatric sample, prolonging drug administration did not increase the NPV of diagnostic DPT for NIHSR to BL or reduce drug refusal. Altogether, the data here reported suggest that, however intuitive, prolonging DPT is not beneficial in the parameters analysed.

Effect of carrier tunneling on the structure of Si nanowires fabricated by metal assisted etching

The metal assisted etching mechanism for Si nanowire fabrication, triggered by doping type and level and coupled with choice of metal catalyst, is still very poorly understood. We explain the different etching rates and porosities of wires we observe based on extensive experimental data, using a new empirical model we have developed. We establish as a key parameter, the tunneling through the space charge region (SCR) which is the result of the reduction of the SCR width by level of the Si wafer doping in the presence of the opposite biases of the p- and n-type wafers. This improved understanding should permit the fabrication of high quality wires with predesigned structural characteristics, which hitherto has not been possible.

Diffusion induced effects on geometry of Ge nanowires

We report diffusion induced germanium nanowire growth and its dependence on the Ge evaporation flux. The wires show a growth rate (dL/dt) in agreement with the previously reported models, but detection of anomalies in the grown wires may indicate the prevalence of the direct Ge impinging effect on large diameter wires. Additionally, we demonstrate that change in deposition flux could directly affect the diffusion length of the Ge adatoms on the wire sidewalls. This in turn modifies the geometry of the grown wires by introducing a lateral growth starting from the base of the wire. A detailed understanding of the deposition flux effect on the growth and geometry of wires will result in improved knowledge of physical properties of wires.

A randomized clinical trial of adjuvant chemotherapy with doxorubicin, ifosfamide, and cisplatin followed by radiotherapy versus radiotherapy alone in patients with localized uterine sarcomas (SARCGYN study). A study of the French Sarcoma Group

BACKGROUND

There is no proven benefit of adjuvant treatment of uterine sarcoma (US). SARCGYN phase III study compared adjuvant polychemotherapy followed by pelvic radiotherapy (RT) (arm A) versus RT alone (arm B) conducted to detect an increase ≥ 20% of 3-year PFS.

METHODS

Patients with FIGO stage ≤ III US, physiological age ≤ 65 years; chemotherapy: four cycles of doxorubicin 50 mg/m² d1, ifosfamide 3 g/m²/day d1-2, cisplatin 75 mg/m² d3, (API) + G-CSF q 3 weeks. Study was stopped because of lack of recruitment.

RESULTS

Eighty-one patients were included: 39 in arm A and 42 in arm B; 52 stage I, 16 stage II, 13 stage III; 53 leiomyosarcomas, 9 undifferenciated sarcomas, 19 carcinosarcomas. Gr 3-4 toxicity during API (/37 patients): thrombopenia (76%), febrile neutropenia (22%) with two toxic deaths; renal gr 3 (1 patient). After a median follow-up of 4.3 years, 41/81 patients recurred, 15 in arm A, 26 in arm B. The 3 years DFS is 55% in arm A, 41% in arm B (P = 0.048). The 3-year overall survival (OS) is 81% in arm A and 69% in arm B (P = 0.41).

CONCLUSION

API adjuvant CT statistically increases the 3 year-DFS of patients with US.

A rare case of occipital stroke as a consequence of nonbacterial thrombotic endocarditis in ovarian clear cell carcinoma: a case report

Hypercoagulability occurs in 15% of patients with malignancy and represents a clinical spectrum ranging from abnormal coagulation tests but no clinically evident thromboembolic disease, to arterial and venous thrombosis, migratory thrombophlebitis, nonbacterial thrombotic endocarditis (NBTE) and disseminated intravascular coagulation. The combination of increased procoagulant activity and decreased fibrinolytic activity accelerates the prothrombotic potential of endothelial cells in malignancy. NBTE is a rare manifestation of cancer-induced hypercoagulability and is commonly seen with mucin-producing adenocarcinomas, but rarely seen with ovarian clear cell carcinoma (OCCC). Cerebrovascular embolization ranges from 14–91% in NBTE. We report a rare case of a 62-year-old female presenting with occipital stroke as a consequence of NBTE in OCCC. Association of NBTE in OCCC has only been reported in 2 cases so far, but presentation with stroke has never been reported in the literature.