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Diversity and Phylogenetic Relationships of Full Genome Sequences of Cassava Brown Streak Viruses in Kenya
No full textCassava brown streak disease is caused by cassava brown streak virus (CBSV) and Uganda cassava brown streak virus (UCBSV). Many of the CBSV and UCBSV diversity studies utilize partial coat protein sequences due to the unavailability of representative full genome sequences. Hence, there is little information on the diversity of cassava brown streak viruses in the rest of the genomes of the two species that are present in the farmers’ fields. The aim of this study was to determine Kenyan full CBSV and UCBSV genomes, and their sequence diversity and phylogenetic relationships within various genome and genome segments. Twenty four CBSVs positive samples tested by RT PCR from major cassava producing regions in Kenya were sequenced using Illumina MiSeq. Quality assessment of the output reads was done using the CLC Genomics 5.5.1 software programs. Genome assembly was done by de novo and reference guided assembly. Nucleotide sequence similarity of CBSV and UCBSV was determined. Phylogenetic relationships between CBSV and UCBSV were determined by performing the neighbour-joining analysis using MEGA 6.0 software. Six CBSV and 9 UCBSV genomes were generated from this study. The coat protein of the CBSV sequences had nucleotide sequence similarity of 92-100% while P1 and P3 gene had 75-100% and 76-100%, respectively. The coat protein of the UCBSV sequences had nucleotide sequence similarity of 91-99%. P1 and P3 gene had 83-100% and 86-99%, respectively. The phylogenetic analysis of full genomes revealed two distinct clusters one for UCBSV and another cluster for CBSV. Individual gene segments phylogenetic tree resembled that of the whole genome by clustering the nucleotide sequences into two clusters, one belonging to UCBSV and the other CBSV. The study revealed an average genome nucleotide diversity of 21.5% and 15.8% in CBSV and UCBSV respectively. A vast genetic diversity observed in CBSV and UCBSV in this study portends a lot of challenges in developing molecular diagnostic techniques as well as control strategies against the viruses
Gene Clone and Bioinformatics Analysis of Subtilisin-Like Protease in Cucumis sativus
No full textBackground: Cucumber target leaf spot (TLS), caused by Corynespora cassiicola (C. Cassiicola), is a serious disease in cucumber (Cucumis sativus) production worldwide. Therefore, cultivating new varieties of TLS resistance of C. sativus is an important goal of cucumber breeding. Previous studies have shown that subtilisin-like protease (SUBP) plays an important role in response to C. Cassiicola infection in resistant plants.
Objective: In this study, the full-length cDNA of the CsSUBP gene was cloned, and the prokaryotic expression vector was successfully constructed in order to study the effects of subtilisin. Futhermore, vital clues regarding CsSUBP gene involved in TLS resistance of C. sativus are gained from the bioinformatics assay.
Method: The CsSUBP gene was identified by sequencing with the intermediate vector pMD18 by designing specific primers and PCR amplification techniques. The prokaryotic expression vector pET30a-CsSUBP was further constructed and identified by colony PCR and EcoR V and SalⅠ double digestion.
Result: The primary structure of CsSUBP was predicted and analyzed by bioinformatics analysis. The results showed that CsSUBP was weakly acidic protein, N-terminal signal peptide region, including a Inhibitor_I9 domain domain.
Conclusion: The pET30a-CsSUBP prokaryotic expression vector was constructed successfully. This study is convenient for the study of prokaryotic expression and its kinase activity
Effect of Two Kinds of Antistaling Agent on the Pigments of Cutting Branch for Cornus alba L.
No full textAims: The research was aimed to study the effects of antistaling agent on the fresh-keeping of cutting branches in order to provide the foundation on sticks-cutting preservation in production.
Study Design: In order to analyze the function and action mechanism of antistaling agent A(3% sucrose +50mg·L-1 aluminium sulfate + 200mg·L-1 citric acid + 100mg·L-1 GA) and B (3% sucrose + 0.5% benzene propionic acid sodium), we used the Cornus alba L., as materials, observed fresh-keeping life and morphological changes, measured the fresh weight, the contents of chlorophyll, soluble sugar, red pigment and anthocyanin in cutting branchs of Cornus alba L.
Place and Duration of Study: College of Biological Science and Technology, Shenyang Agricultural University, between February 2017 and March 2018.
Methodology: The contents of soluble sugar, chlorophyll, anthocyanin and red pigment in stem bark were determined at 3d, 6d, 9d, 12d and 15d after treatment, respectively. The contents of chlorophyll, red pigment and anthocyanin in cutting branchs of Cornus alba L. were measured by method of spectrophotometer. The content of soluble sugar was determined by anthrone colorimetry.
Results: The effects of antistaling agent A (3% sucrose +50mg·L-1 aluminium sulfate + 200mg·L-1 citric acid + 100mg·L-1 GA) and antistaling agent B (3% sucrose + 0.5% benzene propionic acid sodium) were tested in this paper in order to investigate their effects on contents of chlorophyll, soluble sugar, red pigment and anthocyanin in cutting branchs of Cornus alba L., which provided foundation on sticks-cutting preservation in production. Early spring sticks of Cornus alba L. were used as materials by antistaling agent A and B treatment, respectively, and sterilized water as control. Results showed that contents of chlorophyll and soluable sugar in the antistaling agent A group were higher than those in B group. And the contents of anthocyanin and red pigments in the antistaling agent B group were higher than those in A group. Above all, the antistaling agent B had better preservation effect than the antistaling agent A.
Conclusion: The contents of chlorophyll and soluable sugar in the antistaling agent A group were higher than those in the antistaling agent B group. And the contents of anthocyanin and red pigments in the antistaling agent B group were higher than those in A group. Above all, the antistaling agent B had better preservation effect than the antistaling agent A
Molecular Variability of Ocimum gratissimum L. Accessions Using RAPD Marker
No full textAim: This study investigated the molecular variability among accessions of Ocimum gratissimum from selected states in Nigeria and Mali using RAPD marker.
Study Design: The experimental design was complete randomized design (CRD) with three replicates.
Materials and Methods: Twenty accessions of Ocimum gratissimum were collected from nineteen selected Local Governments in four South-western States of Nigeria (Ogun, Oyo, Osun and Lagos) and Mali, to assess their genetic diversity and phylogenetic relationship. Molecular statistics of binary data generated from Random Amplified Polymorphic DNA (RAPD) marker was conducted using numerical taxonomic and multivariate analysis (NTSYS-PC) package, while dendrogram was constructed by Jaccard’s similarity coefficient using unweighted paired group method of arithmetic mean (UPGMA).
Results: Accession Y3 from Ona-Ara yielded the highest total volume of DNA concentration (736.9 µ/l), while the highest genomic DNA concentration of 2.44 ng/ was recorded in accession L-04 from Agege.
Out of total number of 52 bands from three primers of RAPD, 48 produced polymorphic amplified products. OPO-08 primer was highly polymorphic with 94.73%, and had the highest allele numbers, gene diversity and polymorphic information contents of 16.0, 0.914 and 0.909 respectively, while OPO-06 produced the highest number of 20 polymorphic bands. Cluster II was the highest group in the dendogram, and comprised of two states (Oyo and Lagos) and Mali which constituted seven accessions; Y-03 (Ona-Ara), Y-04 (Egbeda), Y-05 (Ido), L-01 (Surulere), L-03 (Ifako-Ijaye), L-04 (Agege) and M (Mali).
Accession S-03 from Ife-North was the most distant with highest similarity index of 1.188.
Conclusion: The RAPD is highly polymorphic, and could be useful in characterizing and revealing wide range of genomic variation and phylogenetic relationship among different accessions of O. gratissimum with broad genetic base
Feasibilitiy Study of Bioethanol Production: A Case of Spent Mushroom and Waste Paper as Potential Substrate
No full textAims: The aim of the present study is to produce ethanol from waste paper and spent mushroom using Saccharomyces cerevisiae as enzymes for the fermentation process.
Study Design: Waste paper and spent mushroom samples were subjected to fermentation and hydrolysis by Aspergilus niger and Saccharomyces cerevisiae to produce bioethanol.
Place and Duration of Study: This study was carried out in the Environmental Microbiology Laboratory, University of Port Harcourt, Nigeria, between May and October 2017.
Methodology: Waste paper and spent mushrooms samples were hydrolyzed by Aspergillus niger, and the hydrolysate from each set up subjected to fermentation by Saccharomyces cerevisiae. Ethanol was extracted by fractional distillation, and qualitatively determined by Gas Chromatography with Mass Spectrometry.
Results: After 8 days of fermentation, there was decrease in glucose content in waste paper hydrolysate ranging from (0.51-0.1 mg/l), and spent mushroom substrate (0.3-0.07 mg/l). Upon extraction of the bioethanol, the highest yield was recorded for waste paper hydrolysate which after characterization with GC-MS ethanol concentration was 28.01 mg/l, followed by spent mushroom hydrolysate 26.8 mg/l.
Conclusion: This study revealed that bioethanol can be obtained from fermentation of waste paper using Saccharomyces cerevisiae and ethanol can be obtained after the paper has been used in growing edible mushroom; if adopted, this could be a way to achieving environmental sustainability
Viability of Hydrocarbon-degrading Bacterial Consortium Immobilized on Different Carriers
No full textAim: Viability of hydrocarbon-degrading bacterial consortium immobilized on different carriers was studied.
Methodology: Hydrocarbon-degrading bacteria were isolated from crude oil contaminated sites in Gio and K-Dera, Rivers State, Nigeria using enrichment method. Proximate analyses were carried out on the best carrier materials. Immobilization was by direct adsorption of the isolates onto the carrier materials and viability was determined by plate count method. The carrier materials tested included soya bran, sugarcane bagasse, corn cob, brown saw dust, white saw dust, cassava peel and red mud (bentonite).
Results: The bacterial isolates demonstrated varied degradation capacity. The best carrier material was saw dust (103.6% survival) and corn cob (103.6% survival) followed by soya bran (94.4% survival rate) and cassava peel (94.4% survival rate). The saw dust had moisture content, 5.92%; ash content, 7.49%; crude protein, 2.2%; volatile matter, 74.28; and fixed carbon, 12.34%; whereas, the percentage chemical composition observed for soya bran were 10.11, 4.08, 5.22, 42.61, 18.37 and 8.89 for moisture content, ash content, crude fibre, crude protein, crude fat and carbohydrate, respectively. There was significant difference (p=0.05) between viability rate observed with the different carrier materials.
Conclusion: This study showed that the agro-wastes used in this study can effectively enhance the viability of hydrocarbon-utilizing bacterial. The result is significant as it shows the possibility of using these carrier materials for bioremediation of hydrocarbon contaminated media
Pathogenicity of a Strain of Streptococcus suis Type 2 to Mice and Swine Isolated from Jingzhou City
No full textAims: The objective of this study is to identify S. suis type 2 and evaluate the virulence of ZHJ01 strain isolation, and verity the clinical and pathological outcome of a systemic infection caused by one serotype 2 when simultaneously inoculated with ZHJ01 strain. We also want to clarify the epidemiologic, clinical, microbiologic characteristics and the pathogenesis mechanism of S. suis type 2 in Hubei province, China.
Study Design: Pigs suspected of being infected with S. suis in Jingzhou regions of Hubei province, China were studied. S. suis type 2 isolation was obtained from the suspicion of diseased pig. The case of S. suis type 2 was detected by the virulence factor amplification based on PCR detection and bacterial isolation, identification in the laboratory. According to the experimental infections of mice and piglets, pathogenicity of this S. suis type 2 isolation to mice and swine was monitored. This study was conducted in the key laboratory of pathogenic microbiology, College of Animal Science of Yangtze University, and Institute of Black Pigs Research, Yangtze University.
Methodology: Proper serological typing can be performed using a co-agglutination test. The typical colonies purificated and cultured were inoculated with Glucose, Lactose, Raffinos, Sorbitol, D (+)-sucrose, Trehalose, 6.5%NaCl, D (-)-Salicin, Hippurate, Esculin hydrate, V-p, etc., then the test results were recorded. Detection of virulence factors were performed using PCR amplification and DNA sequencing. S.suis type 2 isolation was inoculated to mice and piglets for the virulence test, and the observation of the clinical signs and pathological changes.
Results: The virulence factor of extracellular protein factor (EF) was determined from ZHJ01 strain based on PCR detection. Sequence analysis indicated that the isolate was very similar to nucleotide homology with others SS2 strains from different county or contries, and there was not much variation. LD50 of S. suis type 2 for mice was 2.5 x 107cfu. LD50 of S. suis type 2 for piglets was 3.92 x 109cfu.
Conclusion: The results show that Swine S. suis type 2 has a relatively strong pathogenicity to pigs in Hubei province, China. This study can be, in part, sufficient to explain the pathogenicity for ZHJ01 strain in area of Zhijing, Jingzhou city, China, which may provide insights into the pathogenesis SS2 and more valid data to support the development of S. suis vaccine as well as the epidemiological investigation, further monitoring and effective prevention to S. suis
Screening and Identification of Lactic Acid Bacteria with D-tagatose Production Capability
No full textAims: D-tagatose is a natural ketohexose which can be used as a functional sweetener in foods, diary and beverages products. Isolation of new bacterial strains having the ability to produce D-tagatose is a continuously trending topic of research.
Study Design: Screening of strains with D-tagatose production by identification and determination of its ability to produce D-tagatose content.
Place and Duration of Study: School of Food and Biological Engineering, Jiangsu University between May 2018 and April 2019.
Methodology: We initially screened and identified the strains capable of producing D-tagatose through kimchi liquid, and determined the species and genetic characteristics of the strain by physiological, biochemical and molecular biological identification, and then determined the content of D-tagatose by high performance liquid chromatography. Finally calculate the ability of the strain to produce D-tagatose.
Results: In this study, 4 strains of lactic acid bacteria (LAB) were isolated from kimchi sample. The isolates were identified as Lactobacillus spp. (Lactobacillus plantarum, Lactobacillus fermentum and Lactobacillus salivarius) on the basis of morphological, physicochemical characteristics and analysis of 16S rDNA gene sequence. Because of the novelty, strain designated as L. salivarius UJS 003 was considered for D-tagatose yield. Fermentation of D-tagatose was carried out using galactose as substrate for 48 hr at 37 °C, and HPLC method was used to determine the yield. The experimental results exhibited a D-tagatose yield of 3.134 g/L by L. salivarius UJS 003.
Conclusion: The strain UJS 003 represented as a potent D-tagatose producer and could be useful in a variety of biotechnological and industrial processes, particularly food and beverage industries
Exploration on the Effectiveness of Radio Frequency Treatment and Flash Pasteurisation on Enzyme and Microbial Activity for Coconut Water Preservation
No full textThe aim of this research work is to explore the effect of flash pasteurisation (FP) and radio frequency (RF) treatment on enzyme activity, microbial activity and physicochemical properties of matured coconut water (MCW). The process conditions for FP were treatment temperature and time in combinations. The process conditions for RF treatment were different electrode position with constant current load 0.8 A. The results obtained from these treatments reveal that FP conditions had significant effect on inactivation of natural microbial flora, polyphenoloxidase (PPO) and peroxidase (POD) activity. From the results it is observed that FP at 90°C for 10 minutes is better for complete enzyme and microbial inactivation than RF treated MCW. The result is also evident that PPO has higher thermal stability than POD. From observed results the study also concludes that, FP is a better option for enzyme and microbial inactivation but RF treatment was found superior for retaining physicochemical attributes
Potentials of Sugarcane Bagasse and Poultry Manure in the Remediation of Spent Motor Oil Contaminated Soil
No full textThis study sought to investigate the potential of sugarcane bagasse, poultry manure and their combination in the remediation of spent motor oil contaminated soil. About 1.5 L of spent motor oil was sprinkled on plots measuring 0.5 m x 0.5 m dimension in 12 replicate plots to simulate a major spill. Poultry dung (PD), Sugarcane bagasse (SB) and hybrid of bagasse and Poultry dung (SB - PD) were applied as organic amendments and bulking agents. The amendments were randomly administered twice within two weeks to treatment plots except the control at rate of 24tons/ha. The soil was tilled to enhance aeration and watered twice a week for 56 days. A significant decrease in Total Petroleum Hydrocarbon, TPH of 61, 53, 46 and 23% for PD, SB - PD, SB and Control plots respectively was observed. TOC and TN decreased in all the plots except the control. Soil moisture contents between 21 and 24% while soil pH within the range of 6.9 to 7.5 enhanced biodegradation process. The Total Heterotrophic Bacterial Counts (THBC) varied in all the plots while heavy metals content remained unchanged during the study. The application of these biostimulants gave promising results on hydrocarbons removal from contaminated soil