Evidence for heightened genetic instability in precancerous spasmolytic polypeptide expressing gastric glands

BackgroundSpasmolytic polypeptide-expressing metaplasia (SPEM) is present in more than 90% of resected gastric cancer tissues. However, although widely regarded as a pre-cancerous tissue, its genetic characteristics have not been well studied.MethodsImmunohistochemistry using Trefoil factor 2 (TFF2) antibodies was used to identify TFF2-positive SPEM cells within SPEM glands in the stomach of Helicobacter felis (H. felis) -infected mice and human clinical samples. Laser microdissection was used to isolate specific cells from both the infected mice and the human samples. The genetic instability in these cells was examined by measuring the lengths of microsatellite (MS) markers using capillary electrophoresis. Also, genome-wide genetic variations in the SPEM cells from the clinical sample was examined using deep whole-exome sequencing.ResultsSPEM cells indeed exhibit not only heightened MS instability (MSI), but also genetic instabilities that extend genome-wide. Furthermore, surprisingly, we found that morphologically normal, TFF2-negative cells also contain a comparable degree of genomic instabilities as the co-resident SPEM cells within the SPEM glands.ConclusionThese results, for the first time, clearly establish elevated genetic instability as a critical property of SPEM glands, which may provide a greater possibility for malignant clone selection. More importantly, these results indicate that SPEM cells may not be the sole origin of carcinogenesis in the stomach and strongly suggest the common progenitor of these cells, the stem cells, as the source of these genetic instabilities, and thus, potential key players in carcinogenesis.

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Are Three Items Sufficient to Measure Sense of Coherence?

European Journal of Psychological Assessment ◽

10.1027/1015-5759/a000337 ◽

2018 ◽

Vol 34 (4) ◽

pp. 229-237 ◽

Cited By ~ 2

Author(s):

Francesca Chiesi ◽

Andrea Bonacchi ◽

Caterina Primi ◽

Alessandro Toccafondi ◽

Guido Miccinesi

Keyword(s):

Sense Of Coherence ◽

Convergent Validity ◽

Clinical Sample ◽

Clinical Samples ◽

Depression Symptoms ◽

Time Saving ◽

Positive Role ◽

Patients With Cancer ◽

Measure Sense

Abstract. The present study aimed at evaluating if the three-item sense of coherence (SOC) scale developed by Lundberg and Nystrom Peck (1995) can be effectively used for research purpose in both nonclinical and clinical samples. To provide evidence that it represents adequately the measured construct we tested its validity in a nonclinical (N = 658) and clinical sample (N = 764 patients with cancer). Results obtained in the nonclinical sample attested a positive relation of SOC – as measured by the three-item SOC scale – with Antonovsky’s 13-item and 29-item SOC scales (convergent validity), and with dispositional optimism, sense of mastery, anxiety, and depression symptoms (concurrent validity). Results obtained in the clinical sample confirmed the criterion validity of the scale attesting the positive role of SOC – as measured by the three-item SOC scale – on the person’s capacity to respond to illness and treatment. The current study provides evidence that the three-item SOC scale is a valid, low-loading, and time-saving instrument for research purposes on large sample.

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Investigation of duck plague virus in hoar areas of Bangladesh

Bangladesh Journal of Livestock Research ◽

10.3329/bjlr.v26i1-2.49939 ◽

2020 ◽

Vol 26 (1-2) ◽

pp. 73-78

Author(s):

A Hossen ◽

MH Rahman ◽

MZ Ali ◽

MA Yousuf ◽

MZ Hassan ◽

...

Keyword(s):

Cytopathic Effect ◽

Clinical Sample ◽

Chorioallantoic Membrane ◽

Clinical Samples ◽

Isolation And Identification ◽

Duck Plague Virus ◽

Pcr Method ◽

Polymerase Chain ◽

The Individual ◽

Free Ranging

Duck plague (DP) is the most important infectious disease of geese, ducks and free-ranging water birds. The present study was conducted to determine the prevalence of duck plague virus followed by isolation and identification. For these purposes, a total of 155 cloacal swabs samples were collected randomly from duck of different haor areas of Bangladesh including 45 (41 surveillance and 4 clinical) samples from Netrokona; 42 (40 surveillance and 2 clinical) samples from Kishoregonj; 30 samples from Brahmanbaria and 38 samples from Sunamganj. The samples were processed and pooled (1:5 ratio) for initial screening of target polymerase gene of duck plague virus by polymerase chain reaction (PCR) method. All the samples of a positive pool were then tested individually for identifying the individual positive samples. The result showed that out of 155 samples, 41 (26.45%) were found positive in which 17 were from Netrokona, where 15 (36.58%) were from surveillance samples and 2 (50%) were from clinical sample; 16 were from Kishoregonj, where 14 (35%) were from surveillance samples and 2 (100%) were from clinical sample; 2 (6.6%) were from Brahmanbaria and 5 (13.15%) were from Sunamganj. These positive samples were inoculated into 9-10 days embryonated duck eggs (EDE) through chorioallantoic membrane (CAM) route for the isolation of virus. The EDE died earlier was also chilled, and in a similar way, the CAMs were collected and again performed PCR for id entification of virus. Out of 41 PCR positive samples, 26 samples were isolated and reconfirmed by PCR. Subsequently, DPV was isolated in primary duck embryo fibroblasts cell culture and confirmed by observing cytopathic effect (CPE). Bang. J. Livs. Res. Vol. 26 (1&2), 2019: P. 73-78

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The Prevalence of Symptoms of Depression in An Australian General Population

Australian & New Zealand Journal of Psychiatry ◽

10.3109/00048678009159356 ◽

1980 ◽

Vol 14 (1) ◽

pp. 65-71 ◽

Cited By ~ 17

Author(s):

D. G. Byrne

Keyword(s):

Depressive Symptoms ◽

General Population ◽

Random Sample ◽

Clinical Sample ◽

Depression Scale ◽

Clinical Samples ◽

Demographic Differences ◽

Symptoms Of Depression ◽

The Subject ◽

Depressive States

The prevalence of depressive symptoms was estimated in a random sample of an Australian general population by administration of the Zung Self-Rating Depression Scale (S.D.S.). Rates, calculated according to criteria derived from a previously studied clinical sample, were somewhat higher in this population than had been reported in similar studies elsewhere. It was reasoned that this finding related to the relative laxity of criteria employed in the present study. Socio-demographic influences on the reporting of depressive symptoms were evident, the most prominent of these being the sex of the subject. It was suggested that these influences may underlie socio-demographic differences in rates of recognized depressive states occurring within clinical samples.

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Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation

mBio ◽

10.1128/mbio.00898-18 ◽

2018 ◽

Vol 9 (4) ◽

Cited By ~ 9

Author(s):

Sho Iketani ◽

Ryan C. Shean ◽

Marion Ferren ◽

Negar Makhsous ◽

Dolly B. Aquino ◽

...

Keyword(s):

Primary Culture ◽

Parainfluenza Virus ◽

Clinical Samples ◽

Genomic Change ◽

Viral Isolation ◽

Dimer Interface ◽

Genome Wide ◽

A Genome ◽

Immortalized Cells ◽

Human Parainfluenza Virus

ABSTRACTHuman parainfluenza viruses cause a large burden of human respiratory illness. While much research relies upon viruses grown in cultured immortalized cells, human parainfluenza virus 3 (HPIV-3) evolves in culture. Cultured viruses differ in their properties compared to clinical strains. We present a genome-wide survey of HPIV-3 adaptations to culture using metagenomic next-generation sequencing of matched pairs of clinical samples and primary culture isolates (zero passage virus). Nonsynonymous changes arose during primary viral isolation, almost entirely in the genes encoding the two surface glycoproteins—the receptor binding protein hemagglutinin-neuraminidase (HN) or the fusion protein (F). We recovered genomes from 95 HPIV-3 primary culture isolates and 23 HPIV-3 strains directly from clinical samples. HN mutations arising during primary viral isolation resulted in substitutions at HN’s dimerization/F-interaction site, a site critical for activation of viral fusion. Alterations in HN dimer interface residues known to favor infection in culture occurred within 4 days (H552 and N556). A novel cluster of residues at a different face of the HN dimer interface emerged (P241 and R242) and imply a role in HPIV-3-mediated fusion. Functional characterization of these culture-associated HN mutations in a clinical isolate background revealed acquisition of the fusogenic phenotype associated with cultured HPIV-3; the HN-F complex showed enhanced fusion and decreased receptor-cleaving activity. These results utilize a method for identifying genome-wide changes associated with brief adaptation to culture to highlight the notion that even brief exposure to immortalized cells may affect key viral properties and underscore the balance of features of the HN-F complex required for fitness by circulating viruses.IMPORTANCEHuman parainfluenza virus 3 is an important cause of morbidity and mortality among infants, the immunocompromised, and the elderly. Using deep genomic sequencing of HPIV-3-positive clinical material and its subsequent viral isolate, we discover a number of known and novel coding mutations in the main HPIV-3 attachment protein HN during brief exposure to immortalized cells. These mutations significantly alter function of the fusion complex, increasing fusion promotion by HN as well as generally decreasing neuraminidase activity and increasing HN-receptor engagement. These results show that viruses may evolve rapidly in culture even during primary isolation of the virus and before the first passage and reveal features of fitness for humans that are obscured by rapid adaptation to laboratory conditions.

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ANTIBACTERIAL RESISTANCE PATTERN OF PSEUDOMONAS AERUGINOSA ISOLATED FROM CLINICAL SAMPLES AT A GENERAL HOSPITAL IN PADANG, WEST SUMATRA, INDONESIA

Asian Journal of Pharmaceutical and Clinical Research ◽

10.22159/ajpcr.2017.v10i8.18539 ◽

2017 ◽

Vol 10 (8) ◽

pp. 158

Author(s):

Rustini Rustini ◽

Jamsari Jamsari ◽

Marlina Marlina ◽

Nasrul Zubir ◽

Yori Yuliandra

Keyword(s):

Pseudomonas Aeruginosa ◽

Bacterial Resistance ◽

Clinical Sample ◽

Opportunistic Pathogen ◽

Positive Control ◽

Diffusion Method ◽

Clinical Samples ◽

Resistance Pattern ◽

Tract Infections ◽

Almost All

Objectives: Pseudomonas aeruginosa is an opportunistic pathogen that has an innate resistance to some antibiotics. This bacterium is one of the mostcommon causes of nosocomial infections that include surgical wound infections, burns, and urinary tract infections. The bacteria have been reportedlyresistant to many antibiotics and have developed multidrug resistance (MDR). The objective of the study was to determine the resistance pattern ofP. aeruginosa isolated from clinical samples of patients against some major antibiotics.Methods: Isolates of P. aeruginosa were obtained from clinical sample of urine, sputum, swabs, pus, feces, and blood and cultured in cetrimide agar. P.aeruginosa ATCC 27853 was used as a positive control. The antibacterial susceptibility testing was conducted against 13 antibiotics: Ceftazidime, cefotaxime,ceftriaxone, cefoperazone, ciprofloxacin, levofloxacin, ofloxacin, gentamicin, amikacin, piperacillin, ticarcillin, meropenem, and imipenem. The examinationwas carried out using agar diffusion method of Kirby-Bauer and following the standards from Clinical and Laboratory Standards Institute (CLSI).Results: The results showed that bacterial resistance was established against all tested antibiotics. The highest number of resistance was shownagainst ceftriaxone (44.21%), whereas the most susceptibility was exhibited against amikacin (only 9.47% of resistance). MDR P. aeruginosa (MDRPA)was detected on almost all clinical samples tested, except the feces. The sample with the highest percentage of MDRPA was the pus.Conclusion: The study concludes that the most effective antibiotic against P. aeruginosa is amikacin (91.51%), whereas the most resistance is exhibited to ceftriaxone (43.16%).

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From raw reads to trees: Whole genome SNP phylogenetics across the tree of life

10.1101/032250 ◽

2015 ◽

Cited By ~ 10

Author(s):

Sanaa Afroz Ahmed ◽

Chien-Chi Lo ◽

Po-E Li ◽

Karen W Davenport ◽

Patrick S.G. Chain

Keyword(s):

Ad Hoc ◽

Phylogenetic Reconstruction ◽

Clinical Samples ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Complex Samples ◽

Phylogenetic Characterization ◽

Genome Wide ◽

Genome Assemblies

Next-generation sequencing is increasingly being used to examine closely related organisms. However, while genome-wide single nucleotide polymorphisms (SNPs) provide an excellent resource for phylogenetic reconstruction, to date evolutionary analyses have been performed using different ad hoc methods that are not often widely applicable across different projects. To facilitate the construction of robust phylogenies, we have developed a method for genome-wide identification/characterization of SNPs from sequencing reads and genome assemblies. Our phylogenetic and molecular evolutionary (PhaME) analysis software is unique in its ability to take reads and draft/complete genome(s) as input, derive core genome alignments, identify SNPs, construct phylogenies and perform evolutionary analyses. Several examples using genomes and read datasets for bacterial, eukaryotic and viral linages demonstrate the broad and robust functionality of PhaME. Furthermore, the ability to incorporate raw metagenomic reads from clinical samples with suspected infectious agents shows promise for the rapid phylogenetic characterization of pathogens within complex samples.

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Pan-Cancer Analysis of Prognostic and Immune Infiltrates for CXCs

Cancers ◽

10.3390/cancers13164153 ◽

2021 ◽

Vol 13 (16) ◽

pp. 4153

Author(s):

Long Li ◽

Wenchao Yao ◽

Sen Yan ◽

Xianghui Dong ◽

Zhenyi Lv ◽

...

Keyword(s):

Animal Experiments ◽

Intestinal Flora ◽

Clinical Samples ◽

Mrna Levels ◽

Immune Infiltration ◽

Pancreatic Cancers ◽

Multiple Datasets ◽

Geo Dataset ◽

Cancer Tissues ◽

Pan Cancer

Background: CXCs are important genes that regulate inflammation and tumor metastasis. However, the expression level, prognosis value, and immune infiltration of CXCs in cancers are not clear. Methods: Multiple online datasets were used to analyze the expression, prognosis, and immune regulation of CXCs in this study. Network analysis of the Amadis database and GEO dataset was used to analyze the regulation of intestinal flora on the expression of CXCs. A mouse model was used to verify the fact that intestinal bacterial dysregulation can affect the expression of CXCs. Results: In the three cancers, multiple datasets verified the fact that the mRNA expression of this family was significantly different; the mRNA levels of CXCL3, 8, 9, 10, 14, and 17 were significantly correlated with the prognosis of three cancers. CXCs were correlated with six types of immuno-infiltrating cells in three cancers. Immunohistochemistry of clinical samples confirmed that the expression of CXCL8 and 10 was higher in three cancer tissues. Animal experiments have shown that intestinal flora dysregulation can affect CXCL8 and 10 expressions. Conclusion: Our results further elucidate the function of CXCs in cancers and provide new insights into the prognosis and immune infiltration of breast, colon, and pancreatic cancers, and they suggest that intestinal flora may influence disease progression through CXCs.

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Associations between Trauma, Dissociation, Adult Attachment and Proneness to Hallucinations

Behavioural and Cognitive Psychotherapy ◽

10.1017/s1352465817000716 ◽

2017 ◽

Vol 46 (3) ◽

pp. 292-301 ◽

Cited By ~ 4

Author(s):

Katherine Berry ◽

Paul Fleming ◽

Samantha Wong ◽

Sandra Bucci

Keyword(s):

Negative Affect ◽

Adult Attachment ◽

Clinical Symptoms ◽

Clinical Sample ◽

Childhood Adversity ◽

Self Report ◽

Clinical Population ◽

Clinical Samples ◽

Childhood Trauma Questionnaire ◽

Relative Contribution

Background: Childhood adversity, dissociation and adult attachment have all been implicated in the development of hallucinations or ‘voice-hearing’. Testing psychological models in relation to subclinical phenomena, such as proneness to hallucinations in non-clinical samples, provides a convenient methodology to develop understanding of the processes and mechanisms underlying clinical symptoms. Aims: This paper investigates the relative contribution of childhood adversity, dissociation and adult attachment in explaining hallucination proneness in a non-clinical sample. Methods: Students and staff with no previous contact with secondary care at the University of Manchester were recruited. Participants completed a series of self-report measures: the Launay‒Slade Hallucination Scale (LSHS), the Relationship Scale Questionnaire (RSQ), the Childhood Trauma Questionnaire (CTQ), the Dissociative Experiences Schedule (DES II) and the Positive and Negative Affect Schedule (PANAS). Results: As hypothesized, insecure attachment, childhood adversity and dissociative symptoms were correlated with hallucination proneness. Multiple regression analysis, controlling for confounds of age and negative affect, indicated that the RSQ, CTQ and DES II predicted hallucination proneness. Only DES II and RSQ avoidant attachment were significant independent predictors in the final model. Conclusions: This study provides further evidence to support the idea that attachment and dissociation are important psychological mechanisms involved in voice-hearing proneness. Further testing is required with a clinical population.

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Genome-wide profiling in colorectal cancer identifies PHF19 and TBC1D16 as oncogenic super enhancers

Nature Communications ◽

10.1038/s41467-021-26600-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Qing-Lan Li ◽

Xiang Lin ◽

Ya-Li Yu ◽

Lin Chen ◽

Qi-Xin Hu ◽

...

Keyword(s):

Colorectal Cancer ◽

Colorectal Cancer Patient ◽

Nucleotide Polymorphisms ◽

Rna Seq ◽

Motif Analysis ◽

Single Nucleotide ◽

Super Enhancer ◽

Genome Wide ◽

Functional Factors ◽

Cancer Tissues

AbstractColorectal cancer is one of the most common cancers in the world. Although genomic mutations and single nucleotide polymorphisms have been extensively studied, the epigenomic status in colorectal cancer patient tissues remains elusive. Here, together with genomic and transcriptomic analysis, we use ChIP-Seq to profile active enhancers at the genome wide level in colorectal cancer paired patient tissues (tumor and adjacent tissues from the same patients). In total, we sequence 73 pairs of colorectal cancer tissues and generate 147 H3K27ac ChIP-Seq, 144 RNA-Seq, 147 whole genome sequencing and 86 H3K4me3 ChIP-Seq samples. Our analysis identifies 5590 gain and 1100 lost variant enhancer loci in colorectal cancer, and 334 gain and 121 lost variant super enhancer loci. Multiple key transcription factors in colorectal cancer are predicted with motif analysis and core regulatory circuitry analysis. Further experiments verify the function of the super enhancers governing PHF19 and TBC1D16 in regulating colorectal cancer tumorigenesis, and KLF3 is identified as an oncogenic transcription factor in colorectal cancer. Taken together, our work provides an important epigenomic resource and functional factors for epigenetic studies in colorectal cancer.

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Genome Analysis of the Enterococcus faecium Entfac.YE Prophage

Avicenna Journal of Medical Biotechnology ◽

10.18502/ajmb.v14i1.8170 ◽

2022 ◽

Author(s):

Yara Elahi ◽

Ramin Mazaheri Nezhad Fard ◽

Arash Seifi ◽

Saeideh Mahfouzi ◽

Ali Akbar Saboor Yaraghi

Keyword(s):

Genome Analysis ◽

Enterococcus Faecium ◽

Clinical Sample ◽

Bacterial Species ◽

Bacterial Genome ◽

Rapid Evolution ◽

Housekeeping Genes ◽

Water Sources ◽

Clinical Samples ◽

Transfer Resistance

Background: Bacteriophages are viruses that infect bacteria. Bacteriophages are widely distributed in various environments. The prevalence of bacteriophages in water sources, especially wastewaters, is naturally high. These viruses affect evolution of most bacterial species. Bacteriophages are able to integrate their genomes into the chromosomes of their hosts as prophages and hence transfer resistance genes to the bacterial genomes. Enterococci are commensal bacteria that show high resistance to common antibiotics. For example, prevalence of vancomycin-resistant enterococci has increased within the last decades. Methods: Enterococcal isolates were isolated from clinical samples and morphological, phenotypical, biochemical, and molecular methods were used to identify and confirm their identity. Bacteriophages extracted from water sources were then applied to isolated Enterococcus faecium (E. faecium). In the next step, the bacterial genome was completely sequenced and the existing prophage genome in the bacterial genome was analyzed. Results: In this study, E. faecium EntfacYE was isolated from a clinical sample. The EntfacYE genome was analyzed and 88 prophage genes were identified. The prophage content included four housekeeping genes, 29 genes in the group of genes related to replication and regulation, 25 genes in the group of genes related to structure and packaging, and four genes belonging to the group of genes associated with lysis. Moreover, 26 genes were identified with unknown functions. Conclusion: In conclusion, genome analysis of prophages can lead to a better understanding of their roles in the rapid evolution of bacteria.

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