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.

The virulence system of Porphyromonas gingivalis: Genes, mechanism and potential role of gingipains inhibitors

ABSTRACT@#The oral microbiome comprises several hundreds of bacterial species that contribute to periodontitis, the most complex polymicrobial inflammatory disorder. Porphyromonas gingivalis is a prominent periodontitis pathogen that produces gingipains as a major virulent factor. Gingipain facilitates P. gingivalis survival, pathogenicity, and growth. Several genes were identified to have a role in the regulating of P. gingivalis pathogenesis. Studies suggest that gingipains inhibition is key for the successful treatment of periodontitis. As of now, several gingipain inhibitors have been developed, some exhibit high inhibition activity against gingipains. However, most inhibitors offer unknown toxicity and undesirable side effects. Hence, the development of highly potent and safe gingipain inhibitor is a major concern for periodontitis treatment. The present review highlights the connectivity between P. gingivalis, virulent factors, and its gene, periodontitis, and gingipain inhibitors. Development of gingipains inhibitors would not only treat periodontitis but would also assist in the treatment of other associated systemic diseases, for example: rheumatoid arthritis, cardiovascular diseases, diabetes, and Alzheimer's disease.

Immunohistochemical, histological and ultrastructural evaluation of protection provided by cholera vaccine against V. cholerae O139.

In our previous study, complete protection was observed in rabbit immunized with 1 × 1010 CFU of live attenuated VCUSM21P vaccine against challenge with 1 × 109 CFU Vibrio cholerae O139. In the present study, we investigated whether the vaccines can effectively protect immunized animals from any pathologic changes using histological, immunohistochemical and ultrastructural techniques. Severe pathology is evident in wild type injected ileum in non-immunized, showing extensive villous destruction, edema, necrosis and inflammation with infiltration of large numbers of inflammatory cells, extensive damage to the villi and microvilli with pore formation. Histology of ileum injected with wild type in immunized rabbit shows no significant pathological changes except for a few inflammatory cells in lamina propria with mild edema in mucosa and submucosa. immunohistochemical staining revealed O139 antigens of wild type are seen in the lamina propria of edematous villi, muscularis mucosa and submucosa with weak presence in the muscle coat in non-immunized rabbit after challenged with wild type in non-immunized rabbits, but in immunized rabbit localisation of the O139 LPS antigen is seen at the tips of the intact villi, within lamina propria and muscularis mucosa only. These observations suggest that the vaccine can effectively protect animals from any pathologic changes and eliminate V. cholerae O139 from the immunized animals.

Effect of cellulosic filler loading on mechanical and thermal properties of date palm seed/vinyl ester composites.

There are numerous better applications of fibre reinforced polymer composites today, when compared with metals and alloys. Many studies have been conducted to further improve the inherent mechanical and thermal properties of the composite materials, especially with sustainable, environmental friendly, recyclable and biodegradable reinforcements. Consequently, in this current study, the composites were prepared by combining bio solid waste (date seed filler) and vinyl ester to enhance the properties of polymer composites. The date seed filler reinforced vinyl ester (DSF-VE) composites were prepared by using conventional compression moulding technique with varying fillers loadings from 5% to 50%. The mechanical (tensile, flexural, impact and hardness), water absorption and thermal (heat deflection temperature and thermo-gravimetric analysis) properties of the DSF-VE composites were experimentally evaluated. Scanning electron microscopic analysis was carried out to analyse the surface characteristics and fractured surface of the DSF-VE composites. It was evident from the results obtained that 30 wt% of the DSF-VE composites exhibited the highest mechanical properties: impact, tensile, hardness and flexural of 17.03 KJ/m2, 40.3 MPa, 51 and 149 MPa, respectively, among the fabricated composites. Similarly, the heat deflection temperatures of DSF-VE composites increased by 58.49%, when compared with the neat, pure vinyl ester resin. The thermo-gravimetric analysis showed that the natural filler-based (DSF-VE) composites possessed thermal stability up to 400.2 °C, which was within the polymerisation process temperature. Furthermore, the DSF-VE composites have been successfully utilized for various potential applications, such as fabrication of a table fan blade, an engine guard for two-wheelers and self-motor guard for four wheelers.

Complete genome sequence of Sphingomonas paucimobilis AIMST S2, a xenobiotic-degrading bacterium.

Complete genomes of xenobiotic-degrading microorganisms provide valuable resources for researchers to understand molecular mechanisms involved in bioremediation. Despite the well-known ability of Sphingomonas paucimobilis to degrade persistent xenobiotic compounds, a complete genome sequencing is lacking for this organism. In line with this, we report the first complete genome sequence of Sphingomonas paucimobilis (strain AIMST S2), an organophosphate and hydrocarbon-degrading bacterium isolated from oil-polluted soil at Kedah, Malaysia. The genome was derived from a hybrid assembly of short and long reads generated by Illumina HiSeq and MinION, respectively. The assembly resulted in a single contig of 4,005,505 bases which consisted of 3,612 CDS and 56 tRNAs. An array of genes involved in xenobiotic degradation and plant-growth promoters were identified, suggesting its' potential role as an effective microorganism in bioremediation and agriculture. Having reported the first complete genome of the species, this study will serve as a stepping stone for comparative genome analysis of Sphingomonas strains and other xenobiotic-degrading microorganisms as well as gene expression studies in organophosphate biodegradation.

Evaluation of intestinal damage caused by V. cholerae O139, an in vivo study.

Cholera, a severe form of gastroenteritis, is one of the most widespread diseases in developing countries. The mechanism of intestinal infection caused by V. cholerae O139 remains unclear. In order to explore some morphological aspects of its infection in the intestine including Peyer's patches, we investigated the V. cholerae O139 infection at intestinal site of the rabbit gut-loop model. The electron microscopic analysis revealed denuded mucosal surface with loss of microvilli and integrity of the surface epithelium. Infection of the intestine with V. cholerae O139 induces destruction of villi, microvilli and lining epithelium with exposure of crypts of Lieberkuhn.

Electrochemical genosensor assay using lyophilized gold nanoparticles/latex microsphere label for detection of Vibrio cholerae.

Vibrio cholerae is a Gram-negative bacterium that causes cholera, a diarrheal disease. Cholera is widespread in poor, under-developed or disaster-hit countries that have poor water sanitation. Hence, a rapid detection method for V. cholerae in the field under these resource-limited settings is required. In this paper, we describe the development of an electrochemical genosensor assay using lyophilized gold nanoparticles/latex microsphere (AuNPs-PSA) reporter label. The reporter label mixture was prepared by lyophilization of AuNPs-PSA-avidin conjugate with different types of stabilizers. The best stabilizer was 5% sorbitol, which was able to preserve the dried conjugate for up to 30 days. Three methods of DNA hybridization were compared and the one-step sandwich hybridization method was chosen as it was fastest and highly specific. The performance of the assay using the lyophilized reagents was comparable to the wet form for detection of 1aM to 1fM of linear target DNA. The assay was highly specific for V. cholerae, with a detection limit of 1fM of PCR products. The ability of the sensor is to detect LAMP products as low as 50ngµl(-1). The novel lyophilized AuNPs-PSA-avidin reporter label with electrochemical genosensor detection could facilitate the rapid on-site detection of V. cholerae.

Construction and evaluation of V. cholerae O139 mutant, VCUSM21P, as a safe live attenuated cholera vaccine.

Cholera is a major infectious disease, affecting millions of lives annually. In endemic areas, implementation of vaccination strategy against cholera is vital. As the use of safer live vaccine that can induce protective immunity against Vibrio cholerae O139 infection is a promising approach for immunization, we have designed VCUSM21P, an oral cholera vaccine candidate, which has ctxA that encodes A subunit of ctx and mutated rtxA/C, ace and zot mutations. VCUSM21P was found not to disassemble the actin of HEp2 cells. It colonized the mice intestine approximately 1 log lower than that of the Wild Type (WT) strain obtained from Hospital Universiti Sains Malaysia. In the ileal loop assay, unlike WT challenge, 1×106 and 1×108 colony forming unit (CFU) of VCUSM21P was not reactogenic in non-immunized rabbits. Whereas, the reactogenicity caused by the WT in rabbits immunized with 1×10¹° CFU of VCUSM21P was found to be reduced as evidenced by absence of fluid in loops administered with 1×10²-1×107 CFU of WT. Oral immunization using 1×10¹° CFU of VCUSM21P induced both IgA and IgG against Cholera Toxin (CT) and O139 lipopolysaccharides (LPS). The serum vibriocidal antibody titer had a peak rise of 2560 fold on week 4. Following Removable Intestinal Tie Adult Rabbit Diarrhoea (RITARD) experiment, the non-immunized rabbits were found not to be protected against lethal challenge with 1×109 CFU WT, but 100% of immunized rabbits survived the challenge. In the past eleven years, V. cholerae O139 induced cholera has not been observed. However, attenuated VCUSM21P vaccine could be used for vaccination program against potentially fatal endemic or emerging cholera caused by V. cholerae O139.

Epidemiology of Helicobacter pylori among multiracial community in Northern Peninsular, Malaysia: effect of age across race and gender

OBJECTIVE@#To study the epidemiology of Helicobacter pylori (H. pylori) infection according to age group.@*METHODS@#H. pylori infection data among 1 965 consecutive patients referred to the Endoscopy Unit collected at Sungai Petani Hospital for oesophagogastro-duodenoscopy (OGD). The patients were divided into 9 age groups (10-19, 20-29, 30-39, 40-49, 50-59, 60-69, 70-79, 80-89 and 90-99 years). In addition these groups were further divided into three minor group namely young adults (10-39), older adults (40-69) and geriatric groups (70-99).@*RESULTS@#Overall prevalence of infection of H. pylori was analyzed and found that the prevalence increase with age (P<0.05). When the patients divided by ethnic and gender group with age, prevalence rate among young adults and older adults significantly higher (P<0.05) compared to geriatric groups across all races and gender (P<0.05). Furthermore, significantly higher number of males were infected compared to female (P<0.05) but such trend was only observed among older adult groups. In addition, there is a significant differences in H. pylori infection prevalence rates among ethnic groups (highest in Indians adults, followed Chinese and low in Malays, P<0.05).@*CONCLUSIONS@#The overall prevalence of H. pylori did increase with age group across ethnicity and gender, in Northern Peninsular Malaysia.

A global view of the nonprotein-coding transcriptome in Plasmodium falciparum.

Nonprotein-coding RNAs (npcRNAs) represent an important class of regulatory molecules that act in many cellular pathways. Here, we describe the experimental identification and validation of the small npcRNA transcriptome of the human malaria parasite Plasmodium falciparum. We identified 630 novel npcRNA candidates. Based on sequence and structural motifs, 43 of them belong to the C/D and H/ACA-box subclasses of small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs). We further observed the exonization of a functional H/ACA snoRNA gene, which might contribute to the regulation of ribosomal protein L7a gene expression. Some of the small npcRNA candidates are from telomeric and subtelomeric repetitive regions, suggesting their potential involvement in maintaining telomeric integrity and subtelomeric gene silencing. We also detected 328 cis-encoded antisense npcRNAs (asRNAs) complementary to P. falciparum protein-coding genes of a wide range of biochemical pathways, including determinants of virulence and pathology. All cis-encoded asRNA genes tested exhibit lifecycle-specific expression profiles. For all but one of the respective sense-antisense pairs, we deduced concordant patterns of expression. Our findings have important implications for a better understanding of gene regulatory mechanisms in P. falciparum, revealing an extended and sophisticated npcRNA network that may control the expression of housekeeping genes and virulence factors.

Fusarium sp in severe contact lens related fungal keratitis / 国际眼科杂志(Guoji Yanke Zazhi)

AIM: To report a rare case of severe contact lens related fungal keratitis due to fusarium sp, which not only was successfully treated with therapeutic penetrating keratoplasty but also aided in the confirmation of diagnosis. METHODS:Case report.RESULTS: A 39-year-old private clerk Malay lady who wore extended wear soft contact lens for the past 18 years, presented with acute right eye pain and redness for 10 days duration. Ocular examination showed multiple round feathery paracentral corneal ulcers with presence of minimal hypopyon. Clinical diagnosis of presumed fungal keratitis was made. She was treated with broad spectrum topical antibiotics and antifungal agents after repeated corneal scrapping was negative either for fungi or for the bacteria. However, she developed deterioration of the right eye keratitis. Other topical and systemic antifungal agents were instituted. Unfortunately the right corneal ulcer became further deteriorating. Finally a therapeutic penetrating keratoplasty has done in order to preserve the globe and limit the infection after one and a half months of presentation. The diagnosis and the etiology agent were only confirmed based on histopathological examina-tion and polymerase chain reaction (PCR) from corneal button revealed fusarium sp.CONCLUSION:This case highlights the rare case of fusarium sp as an etiology of severe contact lens related fungal keratitis. This case also illustrates the challenge in managing fungal keratitis. Therapeutic penetrating keratoplasty is the ultimate choice in controlling further infection and perserving the globe.