PhageLeads: Rapid Assessment of Phage Therapeutic Suitability Using an Ensemble Machine Learning Approach.

The characterization of therapeutic phage genomes plays a crucial role in the success rate of phage therapies. There are three checkpoints that need to be examined for the selection of phage candidates, namely, the presence of temperate markers, antimicrobial resistance (AMR) genes, and virulence genes. However, currently, no single-step tools are available for this purpose. Hence, we have developed a tool capable of checking all three conditions required for the selection of suitable therapeutic phage candidates. This tool consists of an ensemble of machine-learning-based predictors for determining the presence of temperate markers (integrase, Cro/CI repressor, immunity repressor, DNA partitioning protein A, and antirepressor) along with the integration of the ABRicate tool to determine the presence of antibiotic resistance genes and virulence genes. Using the biological features of the temperate markers, we were able to predict the presence of the temperate markers with high MCC scores (>0.70), corresponding to the lifestyle of the phages with an accuracy of 96.5%. Additionally, the screening of 183 lytic phage genomes revealed that six phages were found to contain AMR or virulence genes, showing that not all lytic phages are suitable to be used for therapy. The suite of predictors, PhageLeads, along with the integrated ABRicate tool, can be accessed online for in silico selection of suitable therapeutic phage candidates from single genome or metagenomic contigs.

Identifying mineral decrement with bone injury by quantifying osteocalcin on current-volt sensor.

Osteoporosis, a bone disease is caused by the deterioration of bone and shows an enhanced risk of bone fracture and decreasing bone mineral density. Unfortunately, the available radiological techniques are expensive, and have disadvantages such as radiation intake, need a specialist to handle the instrument, and so forth. This research is focused to develop a point-of-care system to identify osteocalcin on current-volt sensor, which helps to diagnose the bone metabolism and prognostics. Antiosteocalcin antibody was attached on the electrode through the silane-modified iron material. The antibody-immobilized sensing surface was utilized to identify the level of osteocalcin and the detection limit of 100 pg/ml reached on linear concentrations of 0.01-3000 ng/ml. Calculations were made by triplicates (n = 3; 3δ) on the determination coefficient of y = 0.2637x-0.6012; R2 = 0.9319. Further, control proteins failed to bind with immobilized antibody, confirmed by the specific osteocalcin detection. This research is to identify the osteoporosis biomarker and to help determine the conditions with osteoporosis.

Nanosensing colon cancer biomarker on zeolite-modified gap-fingered dielectrodes.

Nanomaterial on the sensing area elevates the biomolecular immobilization by its right orientation with a proper alignment, and zeolite is one of the suitable materials. In this research, the zeolite nanoparticles were synthesized using rice hush ash as the basic source and the prepared zeolite by the addition of sodium silicate was utilized to attach antibody as a probe on a gap-fingered dielectrode surface to identify the colon cancer biomarker, "colon cancer-secreted protein-2" (CCSP-2). Field Emission Scanning Electron Microscopy and Field Emission Transmission Electron Microscopy images confirmed the size of the nanoparticle to be ∼15 nm and the occurrence of silica and alumina. Zeolite was modified on the electrode surface through the amine linker, and then anti-CCSP-2 was attached by an aldehyde linker. On this surface, CCSP-2 was detected and attained the detection limit to be 3 nM on the linear regression curve with 3-5 nM of CCSP-2. Estimated by the determination coefficient of y = 2.3952x - 4.4869 and R2 = 9041 with 3δ (n = 3). In addition, control proteins did not produce the notable current response representing the specific sensing of CCSP-2. This research is suitable to identify CCSP-2 at a lower level in the bloodstream under the physiological condition of a colon cancer patient.

Monitoring Bioaccumulation (in Gills and Muscle Tissues), Hematology, and Genotoxic Alteration in Ctenopharyngodon idella Exposed to Selected Heavy Metals.

Health and environmental problems arising from metals present in the aquatic ecosystem are very well known. The present study investigated toxicological effects of LC15 of metals such as copper, chromium, and lead for 24, 48, 72, and 96 h on hematological indices, RBC nucleus and cell morphology, and gill and muscle tissues of grass carp (Ctenopharyngodon idella). Experimental dose concentrations of copper were 1.5, 1.4, 1.2, and 1 mgL-1. Similarly, dose concentrations of chromium were 25.5, 22.5, 20, and 18 mgL-1 while those of lead were 250, 235, 225, and 216 mgL-1, respectively. Maximum decrease in the concentration of Hb, RBCs, and monocytes was observed against chromium, while maximum increase in the concentration of lymphocytes was reported against lead. Abnormalities such as single and double micronuclei, deformed nucleus, nuclear shift, irregular nucleus, deformed cells, microcyte cells, and vacuolated and swollen cells were observed. Gill tissues absorbed maximum concentration of lead followed by chromium and copper. Muscle tissues also absorbed maximum concentration of lead followed by chromium and copper, respectively. Histological alterations such as epithelial lifting, interlamellar spaces, club gill filaments, gill bridging, curling filaments, swelling and fusion of cells, irregular cells, destruction of epithelial cells, cellular necrosis, and inflammatory cells were observed in gill tissues while inflammation and necrosis of muscle fibers, degeneration of muscle fibers, edema of muscle bundles, zig-zag of muscle fibers, and lesions were observed in muscle tissues of fish exposed with different doses of these heavy metals, indicating the toxicity of metals to aquatic fauna as well as to human being via food chain.

Deciduous DPSCs Ameliorate MPTP-Mediated Neurotoxicity, Sensorimotor Coordination and Olfactory Function in Parkinsonian Mice.

Parkinson's disease (PD) is a neurodegenerative disorder defined by progressive deterioration of dopaminergic neurons in the substantia nigra pars compacta (SNpc). Dental pulp stem cells (DPSCs) have been proposed to replace the degenerated dopaminergic neurons due to its inherent neurogenic and regenerative potential. However, the effective delivery and homing of DPSCs within the lesioned brain has been one of the many obstacles faced in cell-based therapy of neurodegenerative disorders. We hypothesized that DPSCs, delivered intranasally, could circumvent these challenges. In the present study, we investigated the therapeutic efficacy of intranasally administered DPSCs in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced mouse model of PD. Human deciduous DPSCs were cultured, pre-labelled with PKH 26, and intranasally delivered into PD mice following MPTP treatment. Behavioural analyses were performed to measure olfactory function and sensorimotor coordination, while tyrosine hydroxylase (TH) immunofluorescence was used to evaluate MPTP neurotoxicity in SNpc neurons. Upon intranasal delivery, degenerated TH-positive neurons were ameliorated, while deterioration in behavioural performances was significantly enhanced. Thus, the intranasal approach enriched cell delivery to the brain, optimizing its therapeutic potential through its efficacious delivery and protection against dopaminergic neuron degeneration.

Highly deleterious variations in COX1, CYTB, SCG5, FK2, PRL and PGF genes are the potential adaptation of the immigrated African ostrich population.

Because of variable inconvenient living conditions in some places around the world, it is difficult to collect reliable physiological data for ostriches. Therefore, this study aims to provide a comprehensive in silico insight for the nature of polymorphism of important genetic loci that are related to physiological and reproductive traits. Sixty-nine mature ostriches ranging over half of Iraq were screened. Six exonic genetic loci, including cytochrome c oxidase I (COX1), cytochrome b (CYTB), secretogranin V (SCG5), feather keratin 2-like (FK2), prolactin (PRL) and placenta growth factor (PGF) were genotyped by PCR-single stranded conformation polymorphism (SSCP). Thirty-six novel SNPs, including seventeen nonsynonymous (ns) SNPs, were observed. Several computational software programs were utilized to assess the extent of the nsSNPs on their corresponding proteins structure, function and stability. The results showed several deleterious functional and stability changes in almost all the proteins studied. The total severity of each missense mutation was evaluated and compared with other nsSNPs accumulatively. It is evident from the extensive cumulative in silico computation that both p.E34D and p.E60K in PGF have the highest deleterious effect. The cumulative predictions from the present study are an impressive guide for the genotypes of African ostriches, which bypassed the expensive protocols for wet laboratory screening, to identify the effects of variants. To the best of our knowledge, this is the first investigation of its kind on the analyses and prediction outcome of missense mutations in African ostrich populations. The highly deleterious nsSNPs in the placenta growth factor are possible adaptive mutations which might be associated with adaptation in extreme and new environments. The flow and protocol of the computational predictions can be extended for various wild animals to identify the molecular nature of adaptations.

A novel antimicrobial peptide derived from fish goose type lysozyme disrupts the membrane of Salmonella enterica.

In aquaculture, accumulation of antibiotics resulted in development of resistance among bacterial pathogens. Consequently, it became mandatory to find alternative to synthetic antibiotics. Antimicrobial peptides (AMPs) which are described as evolutionary ancient weapons have been considered as promising alternates in recent years. In this study, a novel antimicrobial peptide had been derived from goose type lysozyme (LyzG) which was identified from the cDNA library of freshwater fish Channa striatus (Cs). The identified lysozyme cDNA contains 585 nucleotides which encodes a protein of 194 amino acids. CsLyzG was closely related to Siniperca chuatsi with 92.8% homology. The depicted protein sequence contained a GEWL domain with conserved GLMQ motif, 7 active residues and 2 catalytic residues. Gene expression analysis revealed that CsLyzG was distributed in major immune organs with highest expression in head kidney. Results of temporal expression analysis after bacterial (Aeromonas hydrophila) and fungal (Aphanomyces invadans) challenges indicated a stimulant-dependent expression pattern of CsLyzG. Two antimicrobial peptides IK12 and TS10 were identified from CsLyzG and synthesized. Antibiogram showed that IK12 was active against Salmonella enterica, a major multi-drug resistant (MDR) bacterial pathogen which produces beta lactamase. The IK12 induced loss of cell viability in the bacterial pathogen. Flow cytometry assay revealed that IK12 disrupt the membrane of S. enterica which is confirmed by scanning electron microscope (SEM) analysis that reveals blebs around the bacterial cell membrane. Conclusively, CsLyzG is a potential innate immune component and the identified antimicrobial peptide has great caliber to be used as an ecofriendly antibacterial substance in aquaculture.

Molecular characterization of a novel proto-type antimicrobial protein galectin-1 from striped murrel.

In this study, we reported a molecular characterization of a novel proto-type galectin-1 from the striped murrel Channa striatus (named as CsGal-1). The full length CsGal-1 was identified from an established striped murrel cDNA library and further we confirmed the sequence by cloning. The complete cDNA sequence of CsGal-1 is 590 base pairs (bp) in length and its coding region encoded a poly peptide of 135 amino acids. The polypeptide contains a galactoside binding lectin domain at 4-135. The domain carries a sugar binding site at 45-74 along with its signatures (H(45)-X-Asn(47)-X-Arg(49) and Trp(69)-X-X-Glu(72)-X-Arg(74)). CsGal-1 shares a highly conserved carbohydrate recognition domain (CRD) with galectin-1 from other proto-type galectin of teleosts. The mRNA expressions of CsGal-1 in healthy and various immune stimulants including Aphanomyces invadans, Aeromonas hydrophila, Escherchia coli lipopolysaccharide and poly I:C injected tissues of C. striatus were examined using qRT-PCR. CsGal-1 mRNA is highly expressed in kidney and is up-regulated with different immune stimulants at various time points. To understand its biological activity, the coding region of CsGal-1 gene was expressed in an E. coli BL21 (DE3) cloning system and its recombinant protein was purified. The recombinant CsGal-1 protein was agglutinated with mouse erythrocytes at a concentration of 4µg/mL in a calcium independent manner. CsGal-1 activity was inhibited by d-galactose at 25mM(-1) and d-glucose and d-fructose at 100mM(-1). The results of microbial binding assay showed that the recombinant CsGal-1 protein agglutinated only with the Gram-negative bacteria. Interestingly, we observed no agglutination against Gram-positive bacteria. Overall, the study showed that CsGal-1 is an important immune gene involved in the recognition and elimination of pathogens in C. striatus.

Gold-nanoparticle based electrochemical DNA sensor for the detection of fish pathogen Aphanomyces invadans.

Epizootic ulcerative syndrome (EUS) is a devastating fish disease caused by the fungus, Aphanomyces invadans. Rapid diagnosis of EUS is needed to control and treat this highly invasive disease. The current diagnostic methods for EUS are labor intensive. We have developed a highly sensitive and specific electrochemical genosensor towards the 18S rRNA and internal transcribed spacer regions of A. invadans. Multiple layers of latex were synthesized with the help of polyelectrolytes, and labeled with gold nanoparticles to enhance sensitivity. The gold-latex spheres were functionalized with specific DNA probes. We describe here the novel application of this improved platform for detection of PCR product from real sample of A. invadans using a premix sandwich hybridization assay. The premix assay was easier, more specific and gave higher sensitivity of one log unit when compared to the conventional method of step-by-step hybridization. The limit of detection was 0.5 fM (4.99 zmol) of linear target DNA and 1 fM (10 amol) of PCR product. The binding positions of the probes to the PCR amplicons were optimized for efficient hybridization. Probes that hybridized close to the 5' or 3' terminus of the PCR amplicons gave the highest signal due to minimal steric hindrance for hybridization. The genosensor is highly suitable as a surveillance and diagnostic tool for EUS in the aquaculture industry.

Toxicity of buprofezin on the survival of embryo and larvae of African catfish, Clarias gariepinus (Bloch).

Buprofezin is an insect growth regulator and widely used insecticide in Malaysia. The present study evaluated the toxic effects of buprofezin on the embryo and larvae of African catfish (Clarias gariepinus) as a model organism. The embryos and larvae were exposed to 7 different concentrations (0, 0.05, 0.5, 5, 25, 50 and 100 mg/L) of buprofezin. Each concentration was assessed in five replicates. Eggs were artificially fertilized and 200 eggs and larvae were subjected to a static bath treatment for all the concentrations. The mortality of embryos was significantly increased with increasing buprofezin concentrations from 5 to 100 mg/L (p< 0.05). However, the mortality was not significantly different (p<0.05) among the following concentrations: 0 (control), 0.05, 0.5 and 5 mg/L. Data obtained from the buprofezin acute toxicity tests were evaluated using probit analysis. The 24 h LC50 value (with 95% confidence limits) of buprofezin for embryos was estimated to be 6.725 (3.167-15.017) mg/L. The hatching of fish embryos was recorded as 68.8, 68.9, 66.9, 66.4, 26.9, 25.1 and 0.12% in response to 7 different concentrations of buprofezin, respectively. The mortality rate of larvae significantly (p<0.05) increased with increasing buprofezin concentrations exposed to 24-48 h. The 24 and 48 h LC50 values (with 95% confidence limits) of buprofezin for the larvae was estimated to be 5.702 (3.198-8.898) and 4.642 (3.264-6.287) mg/L respectively. There were no significant differences (p>0.05) in the LC50 values obtained at 24 and 48 h exposure times. Malformations were observed when the embryos and larvae exposed to more than 5 mg/L. The results emerged from the study suggest that even the low concentration (5 mg/L) of buprofezin in the aquatic environment may have adverse effect on the early embryonic and larval development of African catfish.

Fish lily type lectin-1 contains ß-prism architecture: immunological characterization.

In this study we report a full-length lily type lectin-1 (CsLTL-1) identified from striped murrel, Channa striatus. CsLTL-1 was identified from the established C. striatus cDNA library using GS-FLX™ genome sequencing technology and was found to contain 354 nucleotide base pairs and its open reading frame (ORF) encodes a 118 amino acid residue. CsLTL-1 mRNA is predominately expressed in the gills and is up-regulated upon infection with fungus (Aphanomyces invadans) and bacteria (Aeromonas hydrophila). Hemagglutination studies with recombinant CsLTL-1 show that, at 4µg/ml agglutinates occurs in a calcium independent manner and is inhibited in the presence of d-mannose (50mM) and d-glucose (100mM). The CsLTL-1 sequence was completely characterized using various bioinformatics tools. CsLTL-1 peptide contains a mannose binding site at 30-99 along with its specific motif of ß-prism architecture. The phylogenetic analysis showed that CsLTL-1 clustered together with LTL-1 from Oplegnathus fasciatus. CsLTL-1 protein 3D structure was predicted by I-Tasser program and the model was evaluated using Ramachanran plot analysis. The secondary structure analysis of CsLTL-1 reveals that the protein contains 23% ß-sheets and 77% coils. The overall results showed that CsLTL-1 is an important immune gene involved in the recognition and elimination of pathogens in murrels.