Combinatorial Therapeutic Potential of Stem Cells and Benzimidazol Derivatives for the Reduction of Liver Fibrosis.

(1) Background: Liver fibrosis is currently one of the top ten causes of death worldwide. Stem cells transplantation using mesenchymal stem cells (MSCs) is an alternative therapy which is used in the place of organ transplant, due to the incapacity of stem cells to endure oxidative stress in the damage site, thus affecting the healing process. The present study aimed to enhance the therapeutic potential of MSCs using combined therapy, along with the novel synthetic compounds of benzimidazol derivatives. (2) Methods: Eighteen compound series (benzimidazol derivatives) were screened against liver fibrosis using an in vitro CCl4-induced injury model on cultured hepatocytes. IC50 values were calculated on the bases of LDH assay and cell viability assay. (3) Results: Among the eighteen compounds, compounds (10), (14) and (18) were selected on the basis of IC50 value, and compound (10) was the most potent and had the lowest IC50 value in the LDH assay (8.399 ± 0.23 uM) and cell viability assay (4.73 ± 0.37 uM). Next, these compounds were combined with MSCs using an in vitro hepatocytes injury culture and in vivo rat fibrotic model. The effect of the MSCs + compounds treatment on injured hepatocytes was evaluated using LDH assay, cell viability assay, GSH assay and real-time PCR analysis and immuno-staining for caspase-3. Significant reductions in LDH level, caspase-3 and apoptotic marker genes were noted in MSCs + compounds-treated injured hepatocytes. In vivo data also showed the increased homing of the MSCs, along with compounds after transplantation. Real-time PCR analysis and TUNEL assay results also support our study. (4) Conclusions: It was concluded that compounds (10), (14) and (18) can be used in combination with MSCs to reduce liver fibrosis.

Two novel homozygous variants of ATP6V0A2 and ALDH18A1 lead to autosomal recessive cutis laxa type 2 and 3 in two Pakistani families.

BACKGROUND: Autosomal recessive cutis laxa type 2A (ARCL2A; OMIM: 219200) is characterized by neurovegetative, developmental and progeroid elastic skin anomalies. It is caused by biallelic variation in ATPase, H+ transporting V0 subunit A2 (ATP6V0A2; OMIM: 611716) located on chromosome 12q24.31. Autosomal recessive cutis laxa type 3A (ARCL3A; OMIM: 219150) is another subclinical type characterized by short stature, ophthalmological abnormalities and a progeria-like appearance. The ARCL3A is caused by loss of function alterations in the aldehyde dehydrogenase 18 family member A1 (ALDH18A1; OMIM: 138250) gene located at chromosome 10q24.1. METHODS: Whole-exome sequencing (WES), and Sanger sequencing were performed for molecular diagnosis. 3D protein modeling was performed to investigate the deleterious effect of the variant on protein structure. RESULTS: In this study, clinical and molecular diagnosis were performed for two families, ED-01 and DWF-41, which displayed hallmark features of ARCL2A and ARCL3A, respectively. Three affected individuals in the ED-01 family (IV-4, IV-5 and V-3) displayed sagging loose skin, down-slanting palpebral fissures, excessive wrinkles on the abdomen, hands and feet, and prominent veins on the trunk. Meanwhile the affected individuals in the DWF-41 family (V-2 and V-3) had progeroid skin, short stature, dysmorphology, low muscle tone, epilepsy, lordosis, scoliosis, delayed puberty and internal genitalia. WES in the index patient (ED-01: IV-4) identified a novel homozygous deletion (NM_012463.3: c.1977_1980del; p.[Val660LeufsTer23]) in exon 16 of the ATP6V0A2 while in DWF-41 a novel homozygous missense variant (NM_001323413.1:c.1867G>A; p.[Asp623Asn]) in exon 15 of the ALDH18A1 was identified. Sanger validation in all available family members confirmed the autosomal recessive modes of inheritances in each family. Three dimensional in-silico protein modeling suggested deleterious impact of the identified variants. Furthermore, these variants were assigned class 1 or "pathogenic" as per guidelines of American College of Medical Genetics 2015. Screening of ethnically matched healthy controls (n = 200 chromosomes), excluded the presence of these variations in general population. CONCLUSIONS: To the best of our knowledge, this is the first report of ATP6V0A2 and ALDH18A1 variations in the Pakhtun ethnicity of Pakistani population. The study confirms that WES can be used as a first-line diagnostic test in patients with cutis laxa, and provides basis for population screening and premarital testing to reduce the diseases burden in future generations.

Detection of genetic alterations in gastric cancer patients from Saudi Arabia using comparative genomic hybridization (CGH).

BACKGROUND: The present study was conducted to discover genetic imbalances such as DNA copy number variations (CNVs) associated with gastric cancer (GC) and to examine their association with different genes involved in the process of gastric carcinogenesis in Saudi population. METHODS: Formalin-fixed paraffin-embedded (FFPE) tissues samples from 33 gastric cancer patients and 15 normal gastric samples were collected. Early and late stages GC samples were genotyped and CNVs were assessed by using Illumina HumanOmni1-Quad v.1.0 BeadChip. RESULTS: Copy number gains were more frequent than losses throughout all GC samples compared to normal tissue samples. The mean number of the altered chromosome per case was 64 for gains and 40 for losses, and the median aberration length was 679115bp for gains and 375889bp for losses. We identified 7 high copy gain, 52 gains, 14 losses, 32 homozygous losses, and 10 copy neutral LOHs (loss of heterozygosities). Copy number gains were frequently detected at 1p36.32, 1q12, 1q22, 2p11.1, 4q23-q25, 5p12-p11, 6p21.33, 9q12-q21.11, 12q11-q12, 14q32.33, 16p13.3, 17p13.1, 17q25.3, 19q13.32, and losses at 1p36.23, 1p36.32, 1p32.1, 1q44, 3q25.2, 6p22.1, 6p21.33, 8p11.22, 10q22.1, 12p11.22, 14q32.12 and 16q24.2. We also identified 2 monosomy at chromosome 14 and 22, 52 partially trisomy and 22 whole chromosome 4 neutral loss of heterozygosities at 13q14.2-q21.33, 5p15.2-p15.1, 5q11.2-q13.2, 5q33.1-q34 and 3p14.2-q13.12. Furthermore, 11 gains and 2 losses at 1p36.32 were detected for 11 different GC samples and this region has not been reported before in other populations. Statistical analysis confirms significant association of H. pylori infection with T4 stage of GC as compare to control and other stages. CONCLUSIONS: We found that high frequency of copy number gains and losses at 1p36.23, 1p32.1, 1p36.32, 3q25.2, 6p21.33 and 16q24.2 may be common events in gastric cancer. While novel CNVs at 1p36.32 harbouring PRDM16, TP73 and TP73-AS1 genes showed 11 gains and 2 losses for 11 different GC cases and this region is not reported yet in Database of Genomic Variants may be specific to Saudi population.

Chromosomal Micro-aberration in a Saudi Family with Juvenile Myoclonic Epilepsy.

BACKGROUND AND OBJECTIVE: Epilepsy is etiologically and genetically complex neurological disorder affecting millions of people worldwide. Juvenile myoclonic epilepsy (JME) is the most common epilepsy syndrome that starts in the teen age group commonly between ages 12, 18, and lasts till adulthood. One out of fourteen people with epilepsy suffers with JME. Myoclonic seizures and muscle twitching or uncontrolled jerking are the most common type of seizures in the people suffering with JME. METHOD: To observe the novel CNVs involved in JME, we investigated a Saudi family with nine siblings including one male and one female affected members. In this study we used high density whole genome Agilent sure print G3 Hmn CGH 2x 400K array-CGH chips. Our results showed CNVs including the amplifications and deletions in different chromosomal regions in the patients as compared to the normal members of the family. Amplifications were observed in the chromosome 22 cytoband 22q11.23 with LDL receptor related protein 5 like (LRP5L), Immunoglobulin Lambda-Like Polypeptide 3 (IGLL3) and crystallin beta B2 pseudogene (CRYBB2P) genes respectively whereas the deletions were observed in the chromosomal regions 4q22.2 with Glutamate receptor, ionotropic, delta 2 (GRID2) as potential gene cytoband 1p31.1 with potential Neuronal Growth Regulator 1 gene (NEGR1) gene in this region and NME/NM23 family member (NME7) gene cytoband 1q24. Moreover, the array CGH resulting in deletions and duplication were also validated by using primer for simple PCR or also by using quantitative real time PCR analysis. We found deletions and duplication in JME patients in our study for the first time in Saudi population. RESULTS & CONCLUSION: The findings in this study suggest that the array-CGH may be considered as a first line of genetic testing for diagnosis of epilepsy unless strong evidence is presented for a monogenic syndrome. The use of high throughput technique in this study will help to identify novel mechanisms underlying epileptic disorder in order to lower the burden of epilepsy in Saudi Arabia.

Detection and Genotyping of Helicobacter pylori among Gastric ulcer and Cancer Patients from Saudi Arabia.

BACKGROUND AND OBJECTIVES: Helicobacter pylori (H. pylori) infection is cause of several gastrointestinal diseases in humans. Virulence genes of H. pylori are associated with severity of disease and vary geographically. The aim of present study was to detect H. pylori in formalin-fixed paraffin-embedded (FFPE) tissues and further investigate prevalence of babA2, cagA, iceA1, iceA2, vacA s1/s2 and vacA m1/m2 genotypes in H. pylori from gastric cancer (GC) and gastric ulcer (GU) patients' biopsy samples. METHODS: We used FFPE tissues of 35 GC and 10 GU patients' biopsy samples. Using Polymerase Chain Reaction (PCR), detection of H. pylori strain was performed by using specific primers targeting 16S rRNA and ureC encodes for phosphoglucosamine mutase genes. We have identified different virulence genes of H. pylori by PCR. RESULTS: Of all the 45 samples tested, 20 GC and all 10 GU samples were positive for identification of H. pylori using specific genes (16S rRNA and ureC). The prevalence of babA2 (100%) was significantly higher in GC as compared to GU (40%) samples. The rate of virulence genes vacAs1 was higher in both GU 8 (80%) and GC (100%). CONCLUSIONS: Our study finds that vacAs1am1 and babA2 are most prominent genotypes and may play role in development of Gastric cancer.

Bacteria From Marine Sponges: A Source of New Drugs.

BACKGROUND: Sponges are rich source of bioactive natural products synthesized by the symbiotic bacteria belonging to different phyla. Due to a competition for space and nutrients the marine bacteria associated with sponges could produce more antibiotic substances. To explore the proactive potential of marine microbes extensive research has been done. These bioactive metabolites have some unique properties that are pharmaceutically important. METHODS: For this review, we have performed a non-systematic search of the available literature though various online search engines. This review provides an insight that how majority of active metabolites have been identified from marine invertebrates of which sponges predominate. RESULTS: Sponges harbor abundant and diverse microorganisms, which are the sources of a range of marine bioactive metabolites. From sponges and their associated microorganisms, approximately 5,300 different natural compounds are known. Current research on sponge-microbe interaction and their active metabolites has become a focal point for many researchers. Various active metabolites derived from sponges are now known to be produced by their symbiotic microflora. CONCLUSION: In this review, we attempt to report the latest studies regarding capability of bacteria from sponges as producers of bioactive metabolite. Moreover, these sponge associated bacteria are an important source of different enzymes of industrial significance. In present review, we will address some novel approaches for discovering marine metabolites from bacteria that have the greatest potential to be used in clinical treatments.

microRNA analysis of gastric cancer patients from Saudi Arabian population.

BACKGROUND: The role of small non-coding microRNAs (miRNAs) in several types of cancer has been evident. However, its expression studies have never been performed in gastric cancer (GC) patients from Saudi population. First time this study was conducted to identify miRNAs that are differentially expressed in GC patients compared with normal controls. METHODS: We investigated the role of miRNAs in GC patients using formalin-fixed paraffin-embedded (FFPE) tissues of 34 samples from GC patients (early stage = 7 and late-stage = 26) and 15 from normal control. We have used miRNA microarray analysis and validated the results by Real-time quantitative PCR (RT-qPCR). RESULTS: We obtained data of 1082 expressed genes, from cancer tissues and noncancerous tissues (49 samples in total). Where 129 genes were up-regulated (P > 0.05) and 953 genes (P > 0.05) were down-regulated in 49 FFPE tissue samples. Only 33 miRNAs had significant expression in early and late-stage cancer tissues. After candidate miRNAs were selected, RT-qPCR further confirmed that four miRNAs (hsa-miR-200c-3p, hsa-miR-3613, hsa-miR-27b-3p, hsa-miR-4668-5p) were significantly aberrant in GC tissues compared to the normal gastric tissues. CONCLUSIONS: In this study we provide miRNAs profile of GC where many miRNAs showed aberrant expression from normal tissues, suggesting their involvement in the development and progression of gastric cancer. In early and late-stage miR-200c-3p showed significant down regulation as compare to control samples. Many of miRNAs reported in our study showing up-regulation are new and not reported before may be due to population difference. In conclusion, our results suggest that miR-200c-3p had potential to use as diagnostic biomarker for distinguishing GC patients from normal individuals and can be used for diagnosis of cancer at early stage.

Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov.

Strain JCE(T) was isolated from the fecal sample of a 24-year-old obese man living in Jeddah, Saudi Arabia. It is an aerobic, Gram-positive, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.5 % with Bacillus niacini, the phylogenetically closest species with standing nomenclature. Moreover, the strain JCE(T) presents many phenotypic differences, when it is compared to other Bacillus species, and shows a low MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely that this strain represents a new species. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,762,944 bp long genome (1 chromosome but no plasmid) contains 4,654 protein-coding and 98 RNAs genes, including 92 tRNA genes. The strain JCE(T) differs from most of the other closely Bacillus species by more than 1 % in G + C content. In addition, digital DNA-DNA hybridization values for the genome of the strain JCE(T) against the closest Bacillus genomes range between 19.5 to 28.1, that confirming again its new species status. On the basis of these polyphasic data made of phenotypic and genomic analyses, we propose the creation of Bacillus jeddahensis sp. nov. that contains the strain JCE(T).

Recent Developments in Nanomedicines for Management of Various Health Issues Via Metabolism and Physico-Chemical Properties.

During the last decade the nanotechnologists began research on applications of nanomaterials for medicine and therapeutics. Various nanoparticles (nanomedicines) are being used worldwide for the diagnosis and management in a number of disorders including cancer and neurodegenerative disorders. The successful non-viral gene therapy is now possible with the advancements in nanotechnology. Mostly nanoparticles are divided into two main classes: organic and inorganic nanoparticles. Diverse features of nanomedicines with surface modification help to make them biocompatible with addition of varying polymer that facilitates targeted delivery of drug and its controlled release into the cells, tissues and organs. Liposomes, quantum dots, silver and gold nanoparticles are the most common examples of nanomedicines.

Implication of gut microbiota in human health.

Gut-microbiota (GM) is considered a hidden metabolic organ of the human body, providing biochemical pathways which are absent in the host. Balanced diet with calorie restriction (CR) promotes growth of healthy microbiota, leading to longevity by down-regulating inflammatory responses. While, dysbiosis leads to body dysfunction, inducing metabolic disorders, causing poor epithelial architecture, and impeding the development of mucosal-associated lymphoid tissue, resulting in with reduced T and B cell populations, rendering the body prone to infections, cancer and allergy. The GM enzymes activity is a new risk factor for cancer while gut-derived interleukin-6 is associated with hepatocellular carcinoma development. GM can also influence the brain biochemistry and emotional behavior. The altered GM affects the genes involved in second messenger pathway and long-term potentiation, leading to their differential expression in the hippocampus, cortex, striatum and cerebellum. In addition, the dysbiotic GM is associated with autistic disorder. Living with dysbiotic GM is possible with consequences of serious impairments.

Chitinophaga eiseniae sp. nov., isolated from vermicompost.

A Gram-negative, rod-shaped bacterial strain, YC6729(T), was isolated from vermicompost collected at Masan, Korea, and its taxonomic position was investigated by a polyphasic taxonomic approach. Strain YC6729(T) grew optimally at 30 °C and at pH 6.5-8.5. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC6729(T) belongs to the genus Chitinophaga in the family Chitinophagaceae. It was related most closely to Chitinophaga terrae KP01(T) (96.4 % 16S rRNA gene sequence similarity), Chitinophaga ginsengisegetis Gsoil 040(T) (96.1 %), Chitinophaga arvensicola IAM 12650(T) (96.1 %) and Chitinophaga pinensis DSM 2588(T) (93.3 %). Strain YC6729(T) contained MK-7 as the major menaquinone and homospermidine as the major polyamine. The fatty acids of strain YC6729(T) were iso-C(15 : 0), C(16 : 1)ω5c, iso-C(17 : 0) 3-OH, C(16 : 0), anteiso-C(18 : 0) and/or C(18 : 2)ω6,9c, iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c, C(14 : 0), iso-C(15 : 0) 3-OH, iso-C(15 : 1) G, C(18 : 1)ω5c, iso-C(15 : 1) I and/or C(13 : 0) 3-OH, C(13 : 0) 2-OH, C(16 : 0) 3-OH and unknown fatty acid ECL 13.565. The polar lipid profile contained phosphatidylethanolamine, unknown aminolipids and unknown lipids. The total DNA G+C content of strain YC6729(T) was 48.9 mol%. The phenotypic, chemotaxonomic and phylogenetic data showed that strain YC6729(T) represents a novel species of the genus Chitinophaga, for which the name Chitinophaga eiseniae sp. nov. is proposed. The type strain is YC6729(T) ( = KACC 13774(T)  = DSM 22224(T)).

Bacillus graminis sp. nov., an endophyte isolated from a coastal dune plant.

A Gram-stain-positive endophytic bacterium, designated strain YC6957(T), was isolated from surface-sterilized roots of a halophyte (Elymus mollis Trin.) inhabiting coastal tidal flats of Namhae Island, located on the southern coast of Korea, and was subjected to a polyphasic taxonomic study. Cells were facultatively anaerobic, endospore-forming rods to coccoid rods, motile by a single flagellum. Strain YC6957(T) was catalase-positive, oxidase-negative and able to grow in the presence of 0-8 % (w/v) NaCl, with optimum growth at 4-5 % (w/v) NaCl. Growth occurred at 15-45 °C (optimal growth at 30-35 °C) and pH 6.0-8.5 (optimal growth at pH 7.0-8.0). The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major cellular fatty acids were C(16 : 0) (11.3 %), iso-C(15 : 0) (19.2 %) and anteiso-C(15 : 0) (36.4 %). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 41.6 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate belonged to the genus Bacillus. Strain YC6957(T) exhibited high 16S rRNA gene sequence similarity to its closest neighbours, Bacillus ruris LMG 22866(T) (96.14 %), Bacillus lentus NCIMB 8773(T) (95.97 %) and Bacillus galactosidilyticus LMG 17892(T) (95.91 %), and less than 95.84 % similarity to all other type strains in the genus Bacillus. On the basis of the phylogenetic, physiological and biochemical data, it is suggested that strain YC6957(T) represents a novel species of the genus Bacillus, for which the name Bacillus graminis sp. nov. is proposed. The type strain is YC6957(T) ( = KACC 13779(T)  = DSM 22162(T)).

Nocardioides caricicola sp. nov., an endophytic bacterium isolated from a halophyte, Carex scabrifolia Steud.

A Gram-staining-positive, coccoid to rod-shaped bacterium, designated strain YC6903(T), was isolated from a halophytic plant (Carex scabrifolia Steud.) collected from sand dunes at Namhae Island, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain YC6903(T) grew optimally at 30 °C and at pH 8.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC6903(T) belongs to the genus Nocardioides in the family Nocardioidaceae. Strain YC6903(T) was related most closely to Nocardioides pyridinolyticus OS4(T) (97.0 % 16S rRNA gene sequence similarity), Nocardioides dokdonensis FR1436(T) (96.6 %), Nocardioides aquiterrae GW-9(T) (96.6 %) and Nocardioides hankookensis DS-30(T) (96.6 %). The cell-wall peptidoglycan contained LL-diaminopimelic acid and MK-8(H(4)) was the major respiratory quinone. The mean (±SD) level of DNA-DNA relatedness between strain YC6903(T) and N. pyridinolyticus OS4(T) was 53.5±5.5 %. The predominant cellular fatty acid of strain YC6903(T) was iso-C(16 : 0) (28.9 %). The DNA G+C content was 71.7 mol%. Phenotypic, phylogenetic and chemotaxonomic data indicated that strain YC6903(T) represents a novel species of the genus Nocardioides, for which the name Nocardioides caricicola sp. nov. is proposed. The type strain is YC6903(T) (=KACC 13778(T) =DSM 22177(T)).

Chitinophaga vermicomposti sp. nov., with antifungal activity, isolated from vermicompost.

A Gram-negative, rod-shaped bacterial strain, YC6729T, was isolated from the vermicompost (VC) collected at Masan, Korea and its taxonomic position was investigated by a polyphasic taxonomic approach. Strain YC6729T grew optimally at 30 degrees C and at pH 6.5-8.5. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC6729T belongs to the genus Chitinophaga in the family Chitinophagaceae. Most closely related species are Chitinophaga terra KP01T (96.4 %), Chitinophaga ginsengisegetis Gsoil 040T (96.1 %) and Chitinophaga arvensicola IAM 12650T (96.1 %). Strain YC6729T contained MK-7 as the major menaquinone and homospermidine as the major polyamine. The major fatty acids of strain YC6729T C15:0 iso, C16:1omega5c and C17:0 iso 3-OH. The total DNA G+C content was 48.9 mol%. The phenotypic, chemotaxonomic and phylogenetic data showed that strain YC6729T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga vermicomposti sp. nov. is proposed. The type strain is YC6729T (= KACC 13774T = DSM 22224T).