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Molecular diagnostic methods

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https://www.readbyqxmd.com/read/28731923/human-bocavirus-can-it-trigger-hemophagocytic-lymphohistiocytosis
#1
Sevgen Tanir Basaranoglu, Kubra Aykac, Yasemin Ozsurekci, Inci Bajin, Betul Tavil, Fatma Gumruk, Mehmet Ceyhan
With improvements in molecular diagnostic methods, report of Human bocavirus (HBoV) as an etiologic agent in many studies on viral respiratory and gastrointestinal infections has been increasing. Two pediatric patients who presented with secondary hemophagocytic lymphohistiocytosis were examined for etiologic causes, including viruses. Whole bacterial and fungal cultures and viral serological studies were negative. Viral polymerase chain reaction of nasopharyngeal secretions showed HBoV. One was successfully treated with intravenous immunoglobulins, whereas the other died with multiorgan failure...
July 20, 2017: Journal of Pediatric Hematology/oncology
https://www.readbyqxmd.com/read/28731080/a-tumor-targeted-polymer-theranostics-platform-for-positron-emission-tomography-and-fluorescence-imaging
#2
Eva Koziolová, Shreya Goel, Petr Chytil, Olga Janoušková, Todd E Barnhart, Weibo Cai, Tomáš Etrych
Here, we describe a novel polymer platform suitable for efficient diagnostics and potential theranostics based on (89)Zr-labeled N-(2-hydroxypropyl)methacrylamide (HPMA)-based copolymer conjugates. A set of polymers differing in molecular weight with either low dispersity or high dispersity were designed and synthesized and their biodistribution in vivo was successfully and precisely observed over 72 h. Moreover, the feasibility of two imaging techniques, fluorescence imaging (FI) and positron emission tomography (PET), was compared using labeled polymer conjugates...
July 21, 2017: Nanoscale
https://www.readbyqxmd.com/read/28730438/x-aptamer-selection-and-validation
#3
Ganesh L Lokesh, Hongyu Wang, Curtis H Lam, Varatharasa Thiviyanathan, Nancy Ward, David G Gorenstein, David E Volk
Aptamers and second generation analogs, such as X-Aptamers (XAs), SOMAmers, locked nucleic acids (LNAs), and others are increasingly being used for molecular pathway targeting, biomarker discovery, or disease diagnosis by interacting with protein targets on the surface of cells or in solution. Such targeting is being used for imaging, diagnostic evaluation, interference of protein function, or delivery of therapeutic agents. Selection of aptamers using the original SELEX method is cumbersome and time-consuming, often requiring 10-15 rounds of selection, and provides aptamers with a limited number of functional groups, namely four bases of DNA or RNA, although newer SELEX methods have increased this diversity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28728997/sepsis-reconsidered-identifying-novel-metrics-for-behavioral-landscape-characterization-with-a-high-performance-computing-implementation-of-an-agent-based-model
#4
Chase Cockrell, Gary An
OBJECTIVES: Sepsis affects nearly 1 million people in the United States per year, has a mortality rate of 28-50% and requires more than $20 billion a year in hospital costs. Over a quarter century of research has not yielded a single reliable diagnostic test or a directed therapeutic agent for sepsis. Central to this insufficiency is the fact that sepsis remains a clinical/physiological diagnosis representing a multitude of molecularly heterogeneous pathological trajectories. Advances in computational capabilities offered by High Performance Computing (HPC) platforms call for an evolution in the investigation of sepsis to attempt to define the boundaries of traditional research (bench, clinical and computational) through the use of computational proxy models...
July 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28727229/volatile-organic-compound-detection-as-a-potential-means-of-diagnosing-cutaneous-wound-infections
#5
Mohammed Ashrafi, Matt Bates, Mohamed Baguneid, Teresa Alonso-Rasgado, Riina Rautemaa-Richardson, Ardeshir Bayat
Chronic cutaneous wound infections and surgical site infections (SSIs) present a huge burden on the healthcare system and can lead to increased morbidity and mortality. Current diagnostic methods of identifying and confirming infection involve culture-based and molecular methods. Both techniques are time consuming and delays commonly lead to un-targeted empirical treatment. An ideal diagnostic method would be non-invasive and highly sensitive and detect pathogenic organisms with a high degree of accuracy in order to allow targeted treatment...
July 20, 2017: Wound Repair and Regeneration
https://www.readbyqxmd.com/read/28725280/single-molecule-quantification-of-5-hydroxymethylcytosine-for-diagnosis-of-blood-and-colon-cancers
#6
Noa Gilat, Tzlil Tabachnik, Amit Shwartz, Tamar Shahal, Dmitry Torchinsky, Yael Michaeli, Gil Nifker, Shahar Zirkin, Yuval Ebenstein
BACKGROUND: The DNA modification 5-hydroxymethylcytosine (5hmC) is now referred to as the sixth base of DNA with evidence of tissue-specific patterns and correlation with gene regulation and expression. This epigenetic mark was recently reported as a potential biomarker for multiple types of cancer, but its application in the clinic is limited by the utility of recent 5hmC quantification assays. We use a recently developed, ultra-sensitive, fluorescence-based single-molecule method for global quantification of 5hmC in genomic DNA...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28724556/performance-assessment-of-a-trypanosoma-cruzi-chimeric-antigen-in-multiplex-liquid-microarray-assays
#7
Fred Luciano Neves Santos, Paola Alejandra Fiorani Celedon, Nilson Ivo Tonin Zanchin, Amanda Leitolis, Sandra Crestani, Leonardo Foti, Wayner Vieira de Souza, Yara de Miranda Gomes, Marco Aurélio Krieger
Diagnosing chronic Chagas disease (CD) requires antibody--antigen detection methods, traditionally based on enzymatic assay techniques whose performance depend on the type and quality of antigen used. Previously, 4 recombinant chimeric proteins from Instituto de Biologia Molecular do Paraná (IBMP-8.1 to -8.4) comprising immuno-dominant regions of diverse Trypanosoma cruzi antigens showed excellent diagnostic performance in enzyme-linked immunosorbent assays. Considering that next-generation platforms offer improved CD diagnostic accuracy with different T...
July 19, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28721409/single-antibody-antigen-interactions-monitored-via-transient-ionic-current-recording-using-nanopore-sensors
#8
Yi-Lun Ying, Ru-Jia Yu, Yong-Xu Hu, Rui Gao, Yi-Tao Long
Understanding the single molecular protein-protein interaction has great significance in evaluating the affinity of a specific antibody. Herein, the interaction between single α-fetal protein (AFP) and its antibody was monitored via transient ionic current recording by using the antibody functionalized nanopore sensors. More importantly, the kinetic evaluation was performed at the single molecule level to determine the dissociation constant of this interaction. This method enables the monitoring of the kinetic antigen-antibody interaction in their heterogenetic state without any labelling...
July 19, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28720110/molecular-characterisation-of-protist-parasites-in-human-habituated-mountain-gorillas-gorilla-beringei-beringei-humans-and-livestock-from-bwindi-impenetrable-national-park-uganda
#9
Matthew J Nolan, Melisa Unger, Yuen-Ting Yeap, Emma Rogers, Ilary Millet, Kimberley Harman, Mark Fox, Gladys Kalema-Zikusoka, Damer P Blake
BACKGROUND: Over 60 % of human emerging infectious diseases are zoonotic, and there is growing evidence of the zooanthroponotic transmission of diseases from humans to livestock and wildlife species, with major implications for public health, economics, and conservation. Zooanthroponoses are of relevance to critically endangered species; amongst these is the mountain gorilla (Gorilla beringei beringei) of Uganda. Here, we assess the occurrence of Cryptosporidium, Cyclospora, Giardia, and Entamoeba infecting mountain gorillas in the Bwindi Impenetrable National Park (BINP), Uganda, using molecular methods...
July 18, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28717669/pitfalls-in-genetic-testing-a-case-of-a-snp-in-primer-annealing-region-leading-to-allele-dropout-in-brca1
#10
Felipe Carneiro Silva, Giovana Tardin Torrezan, Rafael Canfield Brianese, Raquel Stabellini, Dirce Maria Carraro
BACKGROUND: Hereditary breast and ovarian cancer is characterized by mutations in BRCA1 or BRCA2 genes and PCR-based screening techniques, such as capillary sequencing and next-generation sequencing (NGS), are considered gold standard methods for detection of pathogenic mutations in these genes. Single-nucleotide polymorphisms (SNPs) constitute a vast source of variation in the human genome and represent a risk for misdiagnosis in genetic testing, since the presence of a SNP in primer-annealing sites may cause false negative results due to allele dropout...
July 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28717661/a-strategy-for-molecular-diagnostics-of-fanconi-anemia-in-brazilian-patients
#11
Daniela V Pilonetto, Noemi F Pereira, Carmem M S Bonfim, Lisandro L Ribeiro, Marco A Bitencourt, Lianne Kerkhoven, Karijn Floor, Najim Ameziane, Hans Joenje, Johan J P Gille, Ricardo Pasquini
BACKGROUND: Fanconi anemia (FA) is a predominantly autosomal recessive disease with wide genetic heterogeneity resulting from mutations in several DNA repair pathway genes. To date, 21 genetic subtypes have been identified. We aimed to identify the FA genetic subtypes in the Brazilian population and to develop a strategy for molecular diagnosis applicable to routine clinical use. METHODS: We screened 255 patients from Hospital de Clínicas, Universidade Federal do Paraná for 11 common FA gene mutations...
July 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28717322/th1-th2-balance-and-humoral-immune-response-to-potential-antigens-as-early-diagnostic-method-of-equine-strongylus-nematode-infection
#12
Faten A M Abo-Aziza, Seham H M Hendawy, Amira H El Namaky, Heba M Ashry
AIM: The aim of this study was to investigate the early diagnosis of strongyle infection based on early changes in Th1 and Th2 cytokines beside the diagnostic accuracy values and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and western blotting profiles using prepared strongyles antigens. MATERIALS AND METHODS: A total of 73 donkeys had a mean age of 4-32 years old were parasitologically examined for strongyle infection. The early changes in Th1 and Th2 cytokines were determined, and the diagnostic accuracy values and SDS-PAGE and western blotting profiles were performed using prepared strongyles antigens; crude somatic Strongylusvulgaris (CSS), excretory-secretory S...
June 2017: Veterinary World
https://www.readbyqxmd.com/read/28716658/stool-antigen-immunodetection-for-diagnosis-of-giardia-duodenalis-infection-in-human-subjects-with-hiv-and-cancer
#13
Maryam Nooshadokht, Behjat Kalantari-Khandani, Iraj Sharifi, Hossein Kamyabi, Namal P M Liyanage, Laurel A Lagenaur, Martin F Kagnoff, Steven M Singer, Zahra Babaei, Shahram Solaymani-Mohammadi
Human infection with the protozoan parasite Giardia duodenalis is one the most common parasitic diseases worldwide. Higher incidence rates of giardiasis have been reported from human subjects with multiple debilitating chronic conditions, including hypogammaglobulinemia and common variable immunodeficiency (CVID). In the current study, stool specimens were collected from 199 individuals diagnosed with HIV or cancer and immunocompetent subjects. The sensitivity of microscopy-based detection on fresh stool preparations, trichrome staining and stool antigen immunodetection for the diagnosis of G...
July 14, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28716373/loop-mediated-isothermal-amplification-in-disposable-polyester-toner-microdevices
#14
Kezia Gomes de Oliveira, Juliane Cristina Borba, Alexandre Melo Bailão, Célia Maria de Almeida Soares, Emanuel Carrilho, Gabriela Rodrigues Mendes Duarte
In recent years, isothermal DNA amplification methods have emerged as an alternative in molecular diagnostics due to its ease of operation. The purpose of using isothermal amplification is to simplify the diagnostics work by i) eliminating heating cycles, ii) reducing equipment costs, and iii) providing rapid and accurate results in laboratories with limited resources. Here we show a simple and fast method for E. coli detection in disposable polyester-toner (PeT) microdevice. The amplification by LAMP of the malB gene from E...
July 14, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28715460/early-infant-diagnosis-of-hiv-1-infection-in-luanda-angola-using-a-new-dna-pcr-assay-and-dried-blood-spots
#15
Francisco Martin, Claudia Palladino, Rita Mateus, Anna Bolzan, Perpétua Gomes, José Brito, Ana Patrícia Carvalho, Yolanda Cardoso, Cristovão Domingos, Vanda Sofia Lôa Clemente, Nuno Taveira
BACKGROUND: Early diagnosis and treatment reduces HIV-1-related mortality, morbidity and size of viral reservoirs in infants infected perinatally. Commercial molecular tests enable the early diagnosis of infection in infants but the high cost and low sensitivity with dried blood spots (DBS) limit their use in sub-Saharan Africa. OBJECTIVES: To develop and validate a sensitive and cheap qualitative proviral DNA PCR-based assay for early infant diagnosis (EID) in HIV-1-exposed infants using DBS samples...
2017: PloS One
https://www.readbyqxmd.com/read/28715206/high-throughput-screening-and-quantitation-of-target-compounds-in-biofluids-by-coated-blade-spray-mass-spectrometry
#16
Marcos Tascon, German Augusto Gómez-Ríos, Nathaly Reyes-Garcés, Justen J Poole, Ezel Boyaci, Janusz Pawliszyn
Most contemporary methods of screening and quantitating controlled substances and therapeutic drugs in biofluids typically require laborious, time-consuming, and expensive analytical workflows. In recent years, our group has worked towards developing microextraction (µe)-mass spectrometry (MS) technologies that merge all of the tedious steps of the classical methods into a simple, efficient, and low-cost methodology. Unquestionably, the automation of these technologies allows for faster sample throughput, greater reproducibility, and radically reduced analysis times...
July 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28715041/diagnostic-single-gene-analyses-beyond-sanger-economic-high-throughput-sequencing-of-small-genes-involved-in-congenital-coagulation-and-platelet-disorders
#17
Juliane Najm, Matthias Rath, Winnie Schröder, Ute Felbor
Molecular testing of congenital coagulation and platelet disorders offers confirmation of clinical diagnoses, supports genetic counselling, and enables predictive and prenatal diagnosis. In some cases, genotype-phenotype correlations are important for predicting the clinical course of the disease and adaptation of individualized therapy. Until recently, genotyping has been mainly performed by Sanger sequencing. While next generation sequencing (NGS) enables the parallel analysis of multiple genes, the cost-value ratio of custom-made panels can be unfavorable for analyses of specific small genes...
July 17, 2017: Hämostaseologie
https://www.readbyqxmd.com/read/28713579/ring-trial-2016-for-bluetongue-virus-detection-by-real-time-rt-pcr-in-france
#18
Corinne Sailleau, Cyril Viarouge, Emmanuel Breard, Damien Vitour, Stephan Zientara
Since the unexpected emergence of BTV-8 in Northern Europe and the incursion of BTV-8 and 1 in France in 2006-2007, molecular diagnosis has considerably evolved. Several real-time RT-PCR (rtRT-PCR) methods have been developed and published, and are currently being used in many countries across Europe for BTV detection and typing. In France, the national reference laboratory (NRL) for orbiviruses develops and validates 'ready-to-use' kits with private companies for viral RNA detection. The regional laboratories network that was set up to deal with a heavy demand for analyses has used these available kits...
May 2017: Veterinary Medicine and Science
https://www.readbyqxmd.com/read/28711944/analysis-of-long-non-coding-rna-expression-profiles-identifies-novel-lncrna-biomarkers-in-the-tumorigenesis-and-malignant-progression-of-gliomas
#19
Gang Chen, Yanfei Cao, Lina Zhang, Hongxing Ma, Chao Shen, Jiang Zhao
Long non-coding RNAs have been shown to be associated with cancer development and progression, demonstrating potential applications as novel diagnostic or prognostic molecular markers in clinical management and treatment. However, the functional significance of lncRNAs in the development and malignant progression of gliomas is still unclear and needed to be further explored. we first obtained genome-wide lncRNA expression profiles in a large cohort of patients with gliomas from the Gene Expression Omnibus database using microarray probes repurposing method and investigated the lncRNA expression patterns during the tumorigenesis and malignant progression of gliomas...
June 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28711408/biochemical-characteristics-of-newborns-with-carnitine-transporter-defect-identified-by-newborn-screening-in-california
#20
N M Gallant, K Leydiker, Y Wilnai, C Lee, F Lorey, L Feuchtbaum, H Tang, J Carter, G M Enns, S Packman, H J Lin, W R Wilcox, S D Cederbaum, J E Abdenur
Carnitine transporter defect (CTD; also known as systemic primary carnitine deficiency; MIM 212140) is due to mutations in the SLC22A5 gene and leads to extremely low carnitine levels in blood and tissues. Affected individuals may develop early onset cardiomyopathy, weakness, or encephalopathy, which may be serious or even fatal. The disorder can be suggested by newborn screening. However, markedly low newborn carnitine levels can also be caused by conditions unrelated to CTD, such as the low carnitine levels often associated with normal pregnancies and some metabolic disorders occurring in the mother...
July 8, 2017: Molecular Genetics and Metabolism
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