Genetic characterization, structural analysis, and detection of positive selection in small heat shock proteins of Cypriniformes and Clupeiformes.

In the current investigation, a total of 42 full-length, non-redundant small heat shock proteins (sHsp) were detected in Cyprinus carpio, Labeo rohita, Danio rerio, Salmo salar, Oncorhynchus mykiss, and Clupea harengus. The sHsp genes were classified into three groups based on phylogenetic analysis. All the sHsps were shown to have higher aliphatic index values, which is an indication that these proteins are more thermally stable. The hydrophilic nature of sHsps was deduced from the fact that all fish species had negative GRAVY scores. In all of the representative fish species, sHsp genes were assigned to distinct chromosomes in an inconsistent and unequal manner. Segmental duplications are the main events that have contributed to the expansion of the sHsp genes in all species. We were also able to determine the selective pressure that was placed on particular codons and discovered several significant coding sites within the coding region of sHsps. Eventually, diversifying positive selection was found to be connected with evolutionary changes in sHsp proteins, which showed that gene evolution controlled the fish adaption event in response to environmental conditions. Clarification of the links between sHsps and environmental stress in fish will be achieved through rigorous genomic comparison, which will also yield substantial new insights.

Comparative genomic studies on the TGF-ß superfamily in blue whale.

TGF-ß supergene family has a wide range of physiological functions including cell adhesion, motility, proliferation, apoptosis, and differentiation. We systematically analyzed and characterized the TGF-ß gene superfamily from the whole blue whale (Balaenoptera musculus) genome, using comparative genomic and evolutionary analysis. We identified 30 TGF-ß genes and were split into two subgroups, BMP-like and TGF-like. All TGF-ß proteins demonstrating a basic nature, with the exception of BMP1, BMP2, BMP10, GDF2, MSTN, and NODAL modulator, had acidic characteristics. All the blue whale (B. musculus) TGF-ß proteins, excluding BMP1, are thermostable based on aliphatic index. The instability index showed all proteins except the NODAL modulator was unstable. TGF-ß proteins showed a hydrophilic character, with the exception of GDF1 and INHBC. Moreover, all the detected TGF-ß genes showed evolutionary conserved nature. A segmental duplication was indicated by TGF-ß gene family, and the Ka/Ks ratio showed that the duplicated gene pairs were subjected to selection pressure, indicating both purifying and positive selection pressure. Two possible recombination breakpoints were also predicted. This study provides insights into the genetic characterization and evolutionary aspects of the TGF-ß superfamily in blue whales (B. musculus).

In silico molecular characterization of TGF-ß gene family in Bufo bufo: genome-wide analysis.

Bufo bufo is a living example of evolutionary processes due to its numerous physiological and ecological adaptations. This is the first study to genetically characterize the TGF-ß gene family in B. bufo at the genome-wide level, and a total of 28 TGF-ß gene family homologs are identified. Physicochemical characteristics of TGF-ß homologs exhibit a basic nature except for BMP1, BMP4, BMP10, BMP15, AMH, INHA, NODAL Modulator and TGFB1. Phylogenetic analysis divided the TGF-ß gene family homologs into 2 major clades along with other vertebrate species. In domain and motif composition analysis, the gene structure for all TGF-ß homologs exhibited homogeneity except BMP1. We have identified the TGF-ß propeptide domain together with the TGF-ß in all family homologs of TGF-ß superfamily. Gene structure comparisons indicated that the TGF-ß gene family have arisen by gene duplications. We also identified 10 duplicated gene pairs, all of which were detected to be segmental duplications. The Ka/Ks test ratio findings for every pair of genes revealed that none of the ratios surpassed 1 except for one gene pair (INHA/BMP1), indicating that these proteins are under positive selection. Circos analysis showed that TGF-ß gene family homologs are arranged in 11 dispersed clusters and all were segmentally arrayed in the genome. This study provides a molecular basis for TGF-ß ligand protein functional analysis and may serve as a reference for in-depth phylogenomics and may promote the development of novel strategies.Communicated by Ramaswamy H. Sarma.

Dengue hemorrhagic fever: a growing global menace.

Dengue virus is an arthropod-borne virus, transmitted by Aedes aegypti among humans. In this review, we discussed the epidemiology of dengue hemorrhagic fever (DHF) as well as the disease's natural history, cycles of transmission, clinical diagnosis, aetiology, prevention, therapy, and management. A systematic literature search was done by databases such as PubMed and Google Scholar using search terms, 'dengue fever', 'symptoms and causes of dengue fever', 'dengue virus transmission', and 'strategies to control dengue'. We reviewed relevant literature to identify hazards related to DHF and the most recent recommendations for its management and prevention. Clinical signs and symptoms of dengue infection range from mild dengue fever (DF) to potentially lethal conditions like DHF or dengue shock syndrome (DSS). Acute-onset high fever, muscle and joint pain, myalgia, a rash on the skin, hemorrhagic episodes, and circulatory shock are among the most common symptoms. An early diagnosis is vital to lower mortality. As dengue virus infections are self-limiting, but in tropical and subtropical areas, dengue infection has become a public health concern. Hence, developing and executing long-term control policies that can reduce the global burden of DHF is a major issue for public health specialists everywhere.

In Silico Analysis: Genome-Wide Identification, Characterization and Evolutionary Adaptations of Bone Morphogenetic Protein (BMP) Gene Family in Homo sapiens.

We systematically analyzed BMP gene family in H. sapiens to elucidate genetic structure, phylogenetic relationships, adaptive evolution and tissue-specific expression pattern. Total of 13 BMPs genes were identified in the H. sapiens genome. Bone morphogenetic proteins (BMPs) are composed of a variable number of exons ranging from 2 to 21. They exhibit a molecular weight ranging from 31,081.81 to 82,899.61 Da. These proteins possess hydrophilic characteristics, display thermostability, and exhibit a pH range from acidic to basic. We identified four segmental and two tandem duplication events in BMP gene family of H. sapiens. All of the vertebrate species that were studied show the presence of BMPs 1, 2, 3, 4, 5, 6, 7, 8A, and 15, however only Homo sapiens demonstrated the presence of BMP9 and BMP11. The pathway and process enrichment analysis of BMPs genes showed that these were considerably enriched in positive regulation of pathway-restricted SMAD protein phosphorylation (92%) and cartilage development (77%) biological processes. These genes exhibited positive selection signals that were shown to be conserved across vertebrate lineages. The results showed that BMP2/3/5/6/8a/15 proteins underwent adaptive selection at many amino acid locations and increased positive selection was detected in TGF-ß propeptide and TGF-ß super family domains which were involved in dorso-ventral patterning, limb bud development. More over the expression pattern of BMP genes revealed that BMP1 and BMP5; BMP4 and BMP6 exhibited substantially identical expression patterns in all tissues while BMP10, BMP15, and BMP3 showed tissue-specific expression.

Molecular Characterization and Phylogenetic Analysis of Casein Gene Family in Camelus ferus.

Camel milk is known for its exceptional medical uses. It has been used since ancient times to treat infant diarrhea, hepatitis, insulin-dependent diabetes (IDDM), lactose intolerance, alcohol-induced liver damage, allergies, and autism. It has the power to treat several diseases, with cancer being the most significant. This study investigated the evolutionary relationship, physiochemical characteristics, and comparative genomic analysis of the casein gene family (CSN1S1, CSN2, CSN1S2, and CSN3) in Camelus ferus. Molecular phylogenetics showing the camelid species clustered casein nucleotide sequences into four groups: CSN1S1, CSN2, CSN1S2, and CSN3. The casein proteins from camels were evaluated and found to be unstable, thermostable, and hydrophilic. CSN1S2, CSN2, and CSN3 were acidic, but CSN1S1 was basic. CSN1S1 showed positive selection for one amino acid (Q), CSN1S2 and CSN2 for three (T, K, Q), and CSN3 showed no positive selection. We also compared high-milk-output species such as cattle (Bos Tarus) and low-milk-yield species such as sheep (Ovies Aries) with camels (Camel ferus) and discovered that YY1 sites are more frequent in sheep than in camels and very low in cattle. We concluded that the ratio of YY1 sites in these species may affect milk production.

Resistance Patterns of Frequently Applied Antimicrobials and Occurrence of Antibiotic Resistance Genes in Edwardsiella tarda Detected in Edwardsiellosis-Infected Tilapia Species of Fish Farms of Punjab in Pakistan.

Edwardsiella tarda is one of the most significant fish pathogens, causes edwardsiellosis in a variety of freshwater fish species, and its antibiotic resistance against multiple drugs has made it a health risk worldwide. In this study, we aimed to investigate the antibiotic resistance (ABR) genes of E. tarda and establish its antibiotic susceptibility. Thus, 540 fish (299 Oreochromis niloticus, 138 O.mossambicus, and 103 O. aureus) were collected randomly from twelve fish farms in three districts of Punjab in Pakistan. E. tarda was recovered from 147 fish showing symptoms of exophthalmia, hemorrhages, skin depigmentation, ascites, and bacteria-filled nodules in enlarged liver and kidney. Antimicrobial susceptibility testing proved chloramphenicol, ciprofloxacin, and streptomycin effective, but amoxicillin, erythromycin, and flumequine ineffective in controlling edwardsiellosis. Maximum occurrence of qnrA, blaTEM, and sul3 genes of E. tarda was detected in 45% in the liver, 58%, and 42% respectively in the intestine; 46.5%, 67.2%, and 55.9% respectively in O. niloticus; 24%, 36%, and 23% respectively in summer with respect to fish organs, species, and season, respectively. Motility, H2S, indole, methyl red, and glucose tests gave positive results. Overall, E. tarda infected 27.2% of fish, which ultimately caused 7.69% mortality. The Chi-squared test of independence showed a significant difference in the occurrence of ABR genes of E. tarda with respect to sampling sites. In conclusion, the misuse of antibacterial agents has led to the emergence of ABR genes in E. tarda, which in association with high temperatures cause multiple abnormalities in infected fish and ultimately resulting in massive mortality.

Effect of hemoglobin on Nile tilapia (Oreochromis niloticus) kidney (NTK) cell line damage.

Bacteria or viral outbreaks can cause tilapia hemorrhage, ensuring considerable volume of hemoglobin (Hb) into the tissue. However, the hemoglobin toxicity on tissue and high doses also effect on tissue this phenomena is still under consideration. Therefore, current study exploited Nile tilapia kidney (NTK) cells to deeply expose the toxic effect of Hb on NTK cells. Toxicity of Hb on NTK cells was determined in terms of cells growth, expression of iron metabolism and inflammation-related genes, consequently examined antioxidant-related enzymes genes expression, intracellular iron and reactive oxygen species (ROS) contents, and apoptosis-related genes expression. The results showed that Hb and heme significantly inhibited NTK cells growth and up-regulated iron metabolism-related genes expression in different degrees. The Hb and heme activated the expression of pro-inflammatory cytokines (TNF-α, tumor necrosis factor-α; IL-1ß, interleukin 1ß; IL-6, interleukin 6), the anti-inflammatory factor (IL-10, interleukin 10) and the chemotactic factors (IL-4, interleukin 4; IL-8, interleukin 8) through NF-κB pathway, meanwhile activated the expression of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px). Moreover, the Hb significantly increased intracellular iron and ROS contents while the expression of apoptosis-related genes was significantly activated by both Hb and heme. Current investigation suggested that high oxidative activity of Hb could activate iron metabolism- and inflammation-related genes expression, and increase intracellular iron and ROS levels, lead to up-regulated the expression of apoptosis genes in NTK cells.