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https://www.readbyqxmd.com/read/29232650/internal-validation-of-two-new-retrotransposons-based-kits-innoquant%C3%A2-hy-and-innotyper%C3%A2-21-at-a-forensic-lab
#1
Cátia Martins, Paulo Miguel Ferreira, Raquel Carvalho, Sandra Cristina Costa, Carlos Farinha, Luísa Azevedo, António Amorim, Manuela Oliveira
Obtaining a genetic profile from pieces of evidence collected at a crime scene is the primary objective of forensic laboratories. New procedures, methods, kits, software or equipment must be carefully evaluated and validated before its implementation. The constant development of new methodologies for DNA testing leads to a steady process of validation, which consists of demonstrating that the technology is robust, reproducible, and reliable throughout a defined range of conditions. The present work aims to internally validate two new retrotransposon-based kits (InnoQuant® HY and InnoTyper® 21), under the working conditions of the Laboratório de Polícia Científica da Polícia Judiciária (LPC-PJ)...
November 29, 2017: Forensic Science International
https://www.readbyqxmd.com/read/29232508/programmable-payload-release-from-transient-polymer-microcapsules-triggered-by-a-specific-ion-co-activation-effect
#2
Shijia Tang, Liuyan Tang, Xiaocun Lu, Huiying Liu, Jeffrey S Moore
Stimuli-responsive materials activated by a pair of molecular or ionic species are of interest in the design of chemical logic gates and signal amplification schemes. There are relatively few ma-terials whose co-activated response has been well-characterized. Here, we demonstrate a specific ion co-activation (SICA) effect at the interfaces of transient polymer solids and liquid solu-tions. We found that depolymerization of the transient poly-mer, cyclic poly(phthalaldehyde) (cPPA), exhibited a SICA effect when the cPPA core-shell microcapsules were suspended in ion-containing acidic methanol solutions...
December 12, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29232489/achieving-biocompatible-sabre-an-in-vitro-cytotoxicity-study
#3
Simon Duckett, Anand Manoharan, Peter J Rayner, Michael J Burns, Wissam Iali, V Hugh Perry
Production of a biocompatible hyperpolarized bolus by Signal Amplification By Reversible Exchange (SABRE) could open the door to simple clinical diagnosis via magnetic resonance imaging. Essential to successful progression to pre-clinical/clinical applications is the determination of the toxicology profile of the SABRE reaction mixture. Here we exemplify the cytotoxicity of the SABRE approach using in vitro cell assay. We conclude that the main cause of observed toxicity is due to the SABRE catalyst. Thus we develop two catalyst removal methods, one involving deactivation and ion-exchange chromatography and the second biphasic catalysis...
December 12, 2017: ChemMedChem
https://www.readbyqxmd.com/read/29232417/evaluation-of-the-suitability-of-mitochondrial-dna-for-species-identification-of-microtraces-and-forensic-traces
#4
Małgorzata Natonek-Wiśniewska, Piotr Krzyścin
The objective of the study was to demonstrate how mitochondrial DNA (mtDNA) can be used to determine the species origin of animal microtraces. The study included pieces of cat and dog hair without the root, a fragment of cooked chicken bone (0.1g), three goose down samples (0.028 g), a pork swab, a pork scratching (5×5×5 mm), and pork lard (0.22 g). DNA was isolated from all of these samples using the method appropriate for the particular source material. The extracts had DNA concentration exceeding 5.4 ng/µl with A260/280 purity range of 1...
December 13, 2017: Acta Biochimica Polonica
https://www.readbyqxmd.com/read/29232014/mutations-of-the-glycine-cleavage-system-genes-possibly-affect-the-negative-symptoms-of-schizophrenia-through-metabolomic-profile-changes
#5
Akane Yoshikawa, Fumichika Nishimura, Aya Inai, Yosuke Eriguchi, Masaki Nishioka, Atsuhiko Takaya, Mamoru Tochigi, Yoshiya Kawamura, Tadashi Umekage, Kayoko Kato, Tsukasa Sasaki, Yoshiaki Ohashi, Kazuya Iwamoto, Kiyoto Kasai, Chihiro Kakiuchi
AIM: Hypofunction of N-methyl-D-aspartate receptors (NMDARs) may contribute to the pathophysiology of schizophrenia (SCZ). Recently, the glycine cleavage system (GCS) was shown to affect NMDAR function in the brain. GCS functional defects cause nonketotic hyperglycinemia (NKH), the atypical phenotype of which presents psychiatric symptoms similar to SCZ. Here, we examined the involvement of GCS in SCZ. METHODS: First, to identify the rare variants and the exonic deletions, we re-sequenced all the coding exons and the splice sites of four GCS genes (GLDC, AMT, GCSH, DLD) in 474 patients with SCZ and 475 controls and performed multiplex ligation-dependent probe amplification (MLPA) analysis in SCZ...
December 12, 2017: Psychiatry and Clinical Neurosciences
https://www.readbyqxmd.com/read/29231168/multiple-sources-of-slow-activity-fluctuations-in-a-bacterial-chemosensory-network
#6
Remy Colin, Christelle Rosazza, Ady Vaknin, Victor Sourjik
Cellular networks are intrinsically subject to stochastic fluctuations, but analysis of the resulting noise remained largely limited to gene expression. The pathway controlling chemotaxis of Escherichia coli provides one example where posttranslational signaling noise has been deduced from cellular behavior. This noise was proposed to result from stochasticity in chemoreceptor methylation, and it is believed to enhance environment exploration by bacteria. Here we combined single-cell FRET measurements with analysis based on the fluctuation-dissipation theorem (FDT) to characterize origins of activity fluctuations within the chemotaxis pathway...
December 12, 2017: ELife
https://www.readbyqxmd.com/read/29231025/-comparison-of-mpure-12-automatic-nucleic-acid-purification-and-chelex-100-method
#7
X Shen, M Li, Y L Wang, Y L Chen, Y Lin, Z M Zhao, T Z Que
OBJECTIVES: To explore the forensic application value of MPure-12 automatic nucleic acid purification (MPure-12 Method) for DNA extraction by extracting and typing DNA from bloodstains and various kinds of biological samples with different DNA contents. METHODS: Nine types of biological samples, such as bloodstains, semen stains, and saliva were collected. DNA were extracted using MPure-12 method and Chelex-100 method, followed by PCR amplification and electrophoresis for obtaining STR-profiles...
April 2017: Fa Yi Xue za Zhi
https://www.readbyqxmd.com/read/29230995/-individual-identification-of-cartilage-by-direct-amplification-in-mass-disasters
#8
C H Wang, C Xu, X Q Li, Y Wu, Z Du
OBJECTIVES: To explore the effectiveness of direct amplification for the STR analysis of cartilage, and to accelerate the effectiveness of disaster victim identification. METHODS: Eighty-eight cartilage samples were directly amplified by PowerPle® 21 kit, and the results of genotyping were compared with that obtained by the magnetic beads method. RESULTS: In 88 cartilage samples, the STR genotypes were successfully detected from 84 samples by direct amplification and magnetic beads method, and both the results of genotyping by two method were consistent...
June 2017: Fa Yi Xue za Zhi
https://www.readbyqxmd.com/read/29230864/complete-magnetic-field-dependence-of-sabre-derived-polarization
#9
Alexey S Kiryutin, Alexandra V Yurkovskaya, Herbert Zimmermann, Hans-Martin Vieth, Konstantin L Ivanov
SABRE (Signal Amplification By Reversible Exchange) is a promising hyperpolarization technique, which makes use of spin order transfer from parahydrogen (the H2 molecule in its singlet spin state) to a to-be-polarized substrate in a transient organometallic complex, termed the SABRE complex. In this work we present an experimental method for measuring the magnetic field dependence of the SABRE effect over an ultra-wide field range, namely, from 10 nT to 10 T. This approach gives a way to determine the complete magnetic field dependence of SABRE-derived polarization...
December 12, 2017: Magnetic Resonance in Chemistry: MRC
https://www.readbyqxmd.com/read/29230579/prevalence-of-cysticercosis-in-estonian-pigs-and-cattle
#10
Elisabeth Dorbek-Kolin, Tuuli Åhlberg, Lea Tummeleht, Dennis Tappe, Maria Vang Johansen, Brian Lassen
Taenia solium has been ranked as the most important foodborne parasite and Taenia saginata as the most commonly found human Taenia tapeworm worldwide. The last official reports of taeniosis from Estonia were in 2003 for T. solium and 2012 for T. saginata. By law, all animal cases of cysticercosis must be registered and reported when found. Our aim was to estimate the prevalence of cysticercosis in Estonia caused by T. solium in pigs and T. saginata in cattle. The four slaughterhouses participating in the study slaughter between them approximately 80% of pigs and cattle in Estonia annually...
December 11, 2017: Parasitology Research
https://www.readbyqxmd.com/read/29230288/embryonal-tumor-with-multilayered-rosettes-c19mc-altered-report-of-an-extremely-rare-malignant-pediatric-central-nervous-system-neoplasm
#11
Muhammad Usman Tariq, Zubair Ahmad, Muhammad Khurram Minhas, Aisha Memon, Noreen Mushtaq, Cynthia Hawkins
The 2016 update of the WHO Classification of Tumours of the Central Nervous System has redefined a number of tumors. Embryonal tumor with multilayered rosettes, C19MC-altered is one such tumor entity which has been newly defined on the basis of a characteristic molecular alteration. We report, to our knowledge, the first case of this rare pediatric brain neoplasm in the Pakistani population. An 8-month-old girl was presented with vomiting and left-sided ptosis, and magnetic resonance imaging scan showed a cerebellar tumor...
2017: SAGE Open Medical Case Reports
https://www.readbyqxmd.com/read/29229980/molecular-cloning-of-novel-transcripts-of-human-kallikrein-related-peptidases-5-6-7-8-and-9-klk5-klk9-using-next-generation-sequencing
#12
Panagiotis G Adamopoulos, Christos K Kontos, Andreas Scorilas
Alternative splicing of cancer-related genes is a common cellular mechanism accounting for cancer cell transcriptome complexity and affecting cell cycle control, proliferation, apoptosis, angiogenesis, invasion, and metastasis. In this study, we describe the discovery and molecular cloning of thirty novel transcripts of the human KLK5, KLK6, KLK7, KLK8 and KLK9 genes, using 3' rapid amplification of cDNA ends (3' RACE) and NGS technology, as well as their expression analysis in many established cell lines, originating from several distinct cancerous and normal tissues...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229373/paper-based-detection-of-hiv-1-drug-resistance-using-isothermal-amplification-and-an-oligonucleotide-ligation-assay
#13
Mary E Natoli, Brittany A Rohrman, Carolina de Santiago, Gert U van Zyl, Rebecca R Richards-Kortum
Regular HIV-1 viral load monitoring is the standard of care to assess antiretroviral therapy effectiveness in resource-rich settings. Persistently elevated viral loads indicate virologic failure (VF), which warrants HIV drug resistance testing (HIVDRT) to allow individualized regimen switches. However, in settings lacking access to HIVDRT, clinical decisions are often made based on symptoms, leading to unnecessary therapy switches and increased costs of care. This work presents a proof-of-concept assay to detect M184V, the most common drug resistance mutation after first-line antiretroviral therapy failure, in a paper format...
December 8, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/29228984/note-on-the-pcr-threshold-standard-curve
#14
Benedict G Archer
OBJECTIVE: The PCR threshold standard curve is based on an exponential model of the initial phase of a PCR run where template replication efficiency is constant cycle to cycle. As such it requires that a threshold is at a level of amplified template not higher than where replication efficiency falls from its initial value. A second requirement is that all amplification profiles, both calibration and test, have the same initial efficiency. However, whether these requirements are met may not be checked, and there seems an apparent awareness that thresholds can be set higher than where efficiency has dropped from the initial value without compromising result validity...
December 11, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29228836/complete-mtdna-sequencing-reveals-mutations-m-9185t-c-and-m-13513g-a-in-three-patients-with-leigh-syndrome
#15
Dita Pelnena, Birute Burnyte, Eriks Jankevics, Baiba Lace, Evelina Dagyte, Kristina Grigalioniene, Algirdas Utkus, Zita Krumina, Jolanta Rozentale, Irina Adomaitiene, Janis Stavusis, Liana Pliss, Inna Inashkina
The most common mitochondrial disorder in children is Leigh syndrome, which is a progressive and genetically heterogeneous neurodegenerative disorder caused by mutations in nuclear genes or mitochondrial DNA (mtDNA). In the present study, a novel and robust method of complete mtDNA sequencing, which allows amplification of the whole mitochondrial genome, was tested. Complete mtDNA sequencing was performed in a cohort of patients with suspected mitochondrial mutations. Patients from Latvia and Lithuania (n = 92 and n = 57, respectively) referred by clinical geneticists were included...
December 12, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29228723/an-ngs-based-approach-for-the-identification-of-sex-specific-markers-in-snakehead-channa-argus
#16
Mi Ou, Cheng Yang, Qing Luo, Rong Huang, Ai-Di Zhang, Lan-Jie Liao, Yong-Ming Li, Li-Bo He, Zuo-Yan Zhu, Kun-Ci Chen, Ya-Ping Wang
We described a next generation sequencing (NGS)-based approach to identify sex-specific markers and subsequently determine whether a species has male or female heterogamety. To test the accuracy of this technique, we examined the snakehead (Channa argus), which is economically important freshwater fish in China. Males grow faster than females, and there is significant interest in developing methods to skew breeding towards all-males to increase biomass yields. NGS was conducted on DNAs of individual female and male, the male reads were spitted into 60 bp K-mers and aligned to the female reference genome assembled by female reads, unaligned male K-mers-60 were kept in next filter process...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228452/establishment-and-analysis-of-the-prediction-model-for-cervical-squamous-cell-carcinoma
#17
Y-H Zhou, W-F Fan, J Deng, H-L Xi
OBJECTIVE: This study aimed to construct a prediction model for cervical squamous cell carcinoma and evaluate its accuracy in diagnosing cervical squamous cell carcinoma. PATIENTS AND METHODS: Fifty patients with initially histopathologically confirmed cervical squamous cell carcinoma and 150 patients with initially histopathologically confirmed cervical intraepithelial neoplasia (CIN) were enrolled. The high-risk human papillomavirus (HR-HPV) infection, human telomerase mRNA component (hTERC) gene and cell-myc (c-myc) gene amplification, and minichromosome maintenance protein 5 (MCM5) protein expression were detected...
November 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29228377/genotyping-of-pneumocystis-jirovecii-in-colonized-patients-with-various-pulmonary-diseases
#18
Magdalena Sokulska, Marta Kicia, Maria Wesolowska, Pawel Piesiak, Aneta Kowal, Maria Luísa Lobo, Zaneta Kopacz, Andrzej B Hendrich, Olga Matos
Pneumocystis jirovecii is an opportunistic fungus causing Pneumocystis pneumonia primarily in immunosuppressed patients. However, immunocompetent individuals may become colonized and, as asymptomatic carriers, serve as reservoirs of the pathogen. Moreover, these asymptomatic carriers are at higher risk of developing pneumonia if favorable conditions occur. This study aimed to determine the prevalence of P. jirovecii in patients with various pulmonary diseases and to characterize the genetic diversity of organisms circulating in the studied population...
December 8, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29228273/direct-detection-of-exophiala-and-scedosporium-species-in-sputa-of-patients-with-cystic-fibrosis
#19
Min Chen, Nahid Kondori, Shuwen Deng, A H G Gerrits van den Ende, M Lackner, Wanqing Liao, G S de Hoog
Detection of species of Exophiala and Scedosporium in the respiratory tracts of cystic fibrosis (CF) patients remains controversial because of highly variable results. The results of our study suggested a significantly higher prevalence and more complex colonization than previously estimated. Approximately 17% (27/162) of clinical sputum samples were found to be positive for Exophiala dermatitidis and 30% (49/162) were positive for Scedosporium apiospermum / S. boydii species complex determined by reverse line blot (RLB) hybridization...
December 8, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29228024/detection-of-duo-schistosome-infection-from-filtered-urine-samples-from-school-children-in-zambia-after-mda
#20
Megan J Hessler, Austin Cyrs, Steven C Krenzke, El Shaimaa Mahmoud, Chummy Sikasunge, James Mwansa, Nilanjan Lodh
Schistosomiasis is one of the major Neglected Tropical Diseases (NTDs) in sub-Saharan Africa. In sub-Saharan Africa, two major human schistosome species namely Schistosoma mansoni and S. haematobium often occur sympatrically largely affecting children. Recognizing the public health impact of Schistosomiasis, the World Health Organization (WHO) is urging member states to regularly treat at least 75% and up to 100%, of all school-aged children at risk of morbidity. For control strategies based on targeted mass drug administration (MDA) to succeed it is essential to have a simple and sensitive test for monitoring the success of these interventions...
2017: PloS One
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