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https://www.readbyqxmd.com/read/28728057/integrating-the-microbiome-as-a-resource-in-the-forensics-toolkit
#1
Thomas H Clarke, Andres Gomez, Harinder Singh, Karen E Nelson, Lauren M Brinkac
The introduction of DNA fingerprinting to forensic science rapidly expanded the available evidence that could be garnered from a crime scene and used in court cases. Next generation sequencing technologies increased available genetic data that could be used as evidence by orders of magnitude, and as such, significant additional genetic information is now available for use in forensic science. This includes DNA from the bacteria that live in and on humans, known as the human microbiome. Next generation sequencing of the human microbiome demonstrates that its bacterial DNA can be used to uniquely identify an individual, provide information about their life and behavioral patterns, determine the body site where a sample came from, and estimate postmortem intervals...
June 27, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28728049/application-of-forensic-image-analysis-in-accident-investigations
#2
REVIEW
Ellen Verolme, Arjan Mieremet
Forensic investigations are primarily meant to obtain objective answers that can be used for criminal prosecution. Accident analyses are usually performed to learn from incidents and to prevent similar events from occurring in the future. Although the primary goal may be different, the steps in which information is gathered, interpreted and weighed are similar in both types of investigations, implying that forensic techniques can be of use in accident investigations as well. The use in accident investigations usually means that more information can be obtained from the available information than when used in criminal investigations, since the latter require a higher evidence level...
July 8, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28727806/genocore-a-simple-and-fast-algorithm-for-core-subset-selection-from-large-genotype-datasets
#3
Seongmun Jeong, Jae-Yoon Kim, Soon-Chun Jeong, Sung-Taeg Kang, Jung-Kyung Moon, Namshin Kim
Selecting core subsets from plant genotype datasets is important for enhancing cost-effectiveness and to shorten the time required for analyses of genome-wide association studies (GWAS), and genomics-assisted breeding of crop species, etc. Recently, a large number of genetic markers (>100,000 single nucleotide polymorphisms) have been identified from high-density single nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS) data. However, there is no software available for picking out the efficient and consistent core subset from such a huge dataset...
2017: PloS One
https://www.readbyqxmd.com/read/28727723/analytical-sensitivity-and-specificity-of-a-loop-mediated-isothermal-amplification-lamp-kit-prototype-for-detection-of-trypanosoma-cruzi-dna-in-human-blood-samples
#4
Susana A Besuschio, Mónica Llano Murcia, Alejandro F Benatar, Severine Monnerat, Israel Cruz Mata, Albert Picado de Puig, María de Los Ángeles Curto, Yutaka Kubota, Diana P Wehrendt, Paula Pavia, Yasuyoshi Mori, Concepción Puerta, Joseph M Ndung'u, Alejandro G Schijman
This study aimed to assess analytical parameters of a prototype LAMP kit that was designed for detection of Trypanosoma cruzi DNA in human blood. The prototype is based on the amplification of the highly repetitive satellite sequence of T.cruzi in microtubes containing dried reagents on the inside of the caps. The reaction is carried out at 65°C during 40 minutes. Calcein allows direct detection of amplified products with the naked eye. Inclusivity and selectivity were tested in purified DNA from Trypanosoma cruzi stocks belonging to the six discrete typing units (DTUs), in DNA from other protozoan parasites and in human DNA...
July 20, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28727054/rapid-communication-mir-92a-as-a-housekeeping-gene-for-analysis-of-bovine-mastitis-related-microrna-in-milk
#5
Y C Lai, T Fujikawa, T Ando, G Kitahara, M Koiwa, C Kubota, N Miura
Our aim was to identify a suitable microRNA housekeeping gene for real-time PCR analysis of bovine mastitis-related microRNA in milk. We identified , , and as housekeeping gene candidates on the basis of previous Solexa sequencing results. Threshold cycle (CT) values for , , and did not differ between milk from control cows and milk from mastitis-affected cows. NormFinder software identified as the most stable single housekeeping gene. We evaluated the suitability of the housekeeping gene candidates by using them to assess expression levels of the inflammation-related gene ...
June 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28727005/rapid-communication-generation-of-fgf5-knockout-sheep-via-the-crispr-cas9-system
#6
R Hu, Z Y Fan, B Y Wang, S L Deng, X S Zhang, J L Zhang, H B Han, Z X Lian
Sheep are an important source of fiber production. Fibroblast growth factor 5 (FGF5) is a dominant inhibitor of length of the anagen phase of the hair cycle. Knockout or silencing of the gene results in a wooly coat in mice, donkeys, dogs, and rabbits. In sheep breeding, wool length is one of the most important wool quality traits. However, traditional breeding cannot accurately and efficiently mediate an advanced genotype into the sheep genome. In this study, we generated 3 knockout sheep via the 1-step clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system...
May 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28726635/as-cath1-6-novel-cathelicidins-with-potent-antimicrobial-and-immunomodulatory-properties-from-alligator-sinensis-play-pivotal-roles-in-host-anti-microbial-immune-responses
#7
Yan Chen, Shasha Cai, Xue Qiao, Mali Wu, Zhilai Guo, Renping Wang, Yi-Qun Kuang, Haining Yu, Yipeng Wang
Crocodilians are regarded as possessing a powerful immune system. However, the composition and action of crocodilian immune system has remained unclear until now. Cathelicidins, the principal family of host defense peptides, play pivotal roles in vertebrate immune defense against microbial invasions. However, cathelicidins from crocodilians have not been extensively studied to date. In the present study, six novel cathelicidins (As-CATH1~6) were identified and characterized from the endangered Chinese Alligator ( Alligator sinensis )...
July 18, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28725274/news-in-al-amyloidosis-ash-2016-a%C3%A2-rapidly-evolving-field-of-investigation
#8
REVIEW
Hermine Agis
Amyloidosis is a rare but life-threatening protein misfolding disease. The early diagnosis and enrollment of patients into multicentre trials is of great importance, as is the need for intensive collaboration between multiple medical departments and experienced specialists. In the following review, the most interesting abstracts from the annual American Society of Hematology (ASH) meeting in 2016 are presented. The topics include the limitations of established biomarkers in risk assessment and response evaluation, the introduction of a new biomarker, the comparison of different treatment sequences and the efficacy of a multiple drug regimen in light-chain (AL) amyloidosis...
2017: Memo
https://www.readbyqxmd.com/read/28725237/a-novel-soybean-dirigent-gene-gmdir22-contributes-to-promotion-of-lignan-biosynthesis-and-enhances-resistance-to-phytophthora-sojae
#9
Ninghui Li, Ming Zhao, Tengfei Liu, Lidong Dong, Qun Cheng, Junjiang Wu, Le Wang, Xi Chen, Chuanzhong Zhang, Wencheng Lu, Pengfei Xu, Shuzhen Zhang
Phytophthora root and stem rot caused by the oomycete pathogen Phytophthora sojae is a destructive disease of soybean worldwide. Plant dirigent proteins (DIR) are proposed to have roles in biosynthesis of either lignan or lignin-like molecules, and are important for defense responses, secondary metabolism, and pathogen resistance. In the present work, a novel DIR gene expressed sequence tag is identified as up-regulated in the highly resistant soybean cultivar 'Suinong 10' inoculated with P. sojae. The full length cDNA is isolated using rapid amplification of cDNA ends, and designated GmDIR22 (GenBank accession no...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28725235/gateway-compatible-crispr-cas9-vectors-and-a-rapid-detection-by-high-resolution-melting-curve-analysis
#10
Cynthia J Denbow, Samantha Lapins, Nick Dietz, Raelynn Scherer, Zachary L Nimchuk, Sakiko Okumoto
CRISPR-Cas9 system rapidly became an indispensable tool in plant biology to perform targeted mutagenesis. A CRISPR-Cas9-mediated double strand break followed by non-homologous end joining (NHEJ) repair most frequently results in a single base pair deletion or insertions (indels), which is hard to detect using methods based on enzymes that detect heteroduplex DNA. In addition, somatic tissues of the T1 generation inevitably contain a mosaic population, in which the portion of cells carrying the mutation can be too small to be detected by the enzyme-based methods...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28724971/computational-design-of-a-symmetrical-%C3%AE-trefoil-lectin-with-cancer-cell-binding-activity
#11
Daiki Terada, Arnout R D Voet, Hiroki Noguchi, Kenichi Kamata, Mio Ohki, Christine Addy, Yuki Fujii, Daiki Yamamoto, Yasuhiro Ozeki, Jeremy R H Tame, Kam Y J Zhang
Computational protein design has advanced very rapidly over the last decade, but there remain few examples of artificial proteins with direct medical applications. This study describes a new artificial β-trefoil lectin that recognises Burkitt's lymphoma cells, and which was designed with the intention of finding a basis for novel cancer treatments or diagnostics. The new protein, called "Mitsuba", is based on the structure of the natural shellfish lectin MytiLec-1, a member of a small lectin family that uses unique sequence motifs to bind α-D-galactose...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724722/effect-of-directional-pulling-on-mechanical-protein-degradation-by-atp-dependent-proteolytic-machines
#12
Adrian O Olivares, Hema Chandra Kotamarthi, Benjamin J Stein, Robert T Sauer, Tania A Baker
AAA+ proteases and remodeling machines couple hydrolysis of ATP to mechanical unfolding and translocation of proteins following recognition of sequence tags called degrons. Here, we use single-molecule optical trapping to determine the mechanochemistry of two AAA+ proteases, Escherichia coli ClpXP and ClpAP, as they unfold and translocate substrates containing multiple copies of the titin(I27) domain during degradation initiated from the N terminus. Previous studies characterized degradation of related substrates with C-terminal degrons...
July 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28724084/comparison-of-models-and-whole-genome-profiling-approaches-for-genomic-enabled-prediction-of-septoria-tritici-blotch-stagonospora-nodorum-blotch-and-tan-spot-resistance-in-wheat
#13
Philomin Juliana, Ravi P Singh, Pawan K Singh, Jose Crossa, Jessica E Rutkoski, Jesse A Poland, Gary C Bergstrom, Mark E Sorrells
The leaf spotting diseases in wheat that include Septoria tritici blotch (STB) caused by , Stagonospora nodorum blotch (SNB) caused by , and tan spot (TS) caused by pose challenges to breeding programs in selecting for resistance. A promising approach that could enable selection prior to phenotyping is genomic selection that uses genome-wide markers to estimate breeding values (BVs) for quantitative traits. To evaluate this approach for seedling and/or adult plant resistance (APR) to STB, SNB, and TS, we compared the predictive ability of least-squares (LS) approach with genomic-enabled prediction models including genomic best linear unbiased predictor (GBLUP), Bayesian ridge regression (BRR), Bayes A (BA), Bayes B (BB), Bayes Cπ (BC), Bayesian least absolute shrinkage and selection operator (BL), and reproducing kernel Hilbert spaces markers (RKHS-M), a pedigree-based model (RKHS-P) and RKHS markers and pedigree (RKHS-MP)...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723149/cyclewise-operation-of-printed-mos2-transistor-biosensors-for-rapid-biomolecule-quantification-at-femtomolar-levels
#14
Byunghoon Ryu, Hongsuk Nam, Bo-Ram Oh, Yujing Song, Pengyu Chen, Younggeun Park, Wenjie Wan, Katsuo Kurabayashi, Xiaogan Liang
Field-effect transistors made from MoS2 and other emerging layered semiconductors have been demonstrated to be able to serve as ultrasensitive biosensors. However, such nanoelectronic sensors still suffer seriously from a series of challenges associated with the poor compatibility between electronic structures and liquid analytes. These challenges hinder the practical biosensing applications that demand rapid, low-noise, highly specific biomolecule quantification at femtomolar levels. To address such challenges, we study a cyclewise process for operating MoS2 transistor biosensors, in which a series of reagent fluids are delivered to the sensor in a time-sequenced manner and periodically set the sensor into four assay-cycle stages, including incubation, flushing, drying, and electrical measurement...
February 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28722603/molecular-characterization-of-mycobacterium-tuberculosis-strains-with-tb-sprint
#15
Barbara Molina-Moya, Michel Kiréopori Gomgnimbou, Carmen Lafoz, Alicia Lacoma, Cristina Prat, Guislaine Refrégier, Sofia Samper, Jose Dominguez, Christophe Sola
We evaluated Tuberculosis-Spoligo-Rifampicin-Isoniazid Typing (TB-SPRINT), a microbead-based method for spoligotyping and detection of rifampicin and isoniazid resistance in Mycobacterium tuberculosis. For that, 67 M. tuberculosis complex strains were retrospectively selected. Membrane-based spoligotyping, restriction fragment length polymorphism, DNA sequencing/pyrosequencing of rpoB, katG, and inhA promoter, TB-SPRINT, and SNP typing were performed. Concordance between spoligotyping methods was 99.6% (2,785/2,795 spoligotype data points)...
July 10, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28721829/ngs-technologies-as-a-turning-point-in-rare-disease-research-diagnosis-and-treatment
#16
Ana Fernández-Marmiesse, Sofía Gouveia, María L Couce
Approximately 25-50 million Americans, 30 million Europeans, and 8% of the Australian population have a rare disease. Rare diseases are thus a common problem for clinicians and account for enormous healthcare costs worldwide due to the difficulty of establishing a specific diagnosis. In this article we review the milestones achieved in our understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies and analyze how these advances have influenced research and diagnosis...
July 18, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28720895/rapid-response-of-eastern-mediterranean-deep-sea-microbial-communities-to-oil
#17
Jiang Liu, Stephen M Techtmann, Hannah L Woo, Daliang Ning, Julian L Fortney, Terry C Hazen
Deep marine oil spills like the Deepwater Horizon (DWH) in the Gulf of Mexico have the potential to drastically impact marine systems. Crude oil contamination in marine systems remains a concern, especially for countries around the Mediterranean Sea with off shore oil production. The goal of this study was to investigate the response of indigenous microbial communities to crude oil in the deep Eastern Mediterranean Sea (E. Med.) water column and to minimize potential bias associated with storage and shifts in microbial community structure from sample storage...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720805/a-portable-system-for-rapid-bacterial-composition-analysis-using-a-nanopore-based-sequencer-and-laptop-computer
#18
Satomi Mitsuhashi, Kirill Kryukov, So Nakagawa, Junko S Takeuchi, Yoshiki Shiraishi, Koichiro Asano, Tadashi Imanishi
We developed a portable system for 16S rDNA analyses consisting of a nanopore technology-based sequencer, the MinION, and laptop computers, and assessed its potential ability to determine bacterial compositions rapidly. We tested our protocols using a mock bacterial community that contained equimolar 16S rDNA and a pleural effusion from a patient with empyema, for time effectiveness and accuracy. MinION sequencing targeting 16S rDNA detected all 20 of the bacterial species present in the mock bacterial community...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720323/rapid-divergence-of-histones-in-hydrozoa-cnidaria-and-evolution-of-a-novel-histone-involved-in-dna-damage-response-in-hydra
#19
Puli Chandramouli Reddy, Suyog Ubhe, Neha Sirwani, Rasika Lohokare, Sanjeev Galande
Histones are fundamental components of chromatin in all eukaryotes. Hydra, an emerging model system belonging to the basal metazoan phylum Cnidaria, provides an ideal platform to understand the evolution of core histone components at the base of eumetazoan phyla. Hydra exhibits peculiar properties such as tremendous regenerative capacity, lack of organismal senescence and rarity of malignancy. In light of the role of histone modifications and histone variants in these processes it is important to understand the nature of histones themselves and their variants in hydra...
June 15, 2017: Zoology: Analysis of Complex Systems, ZACS
https://www.readbyqxmd.com/read/28719894/karyotype-evolution-and-phylogenetic-relationships-of-cricetulus-sokolovi-orlov-et-malygin-1988-cricetidae-rodentia-inferred-from-chromosomal-painting-and-molecular-data
#20
Natalia S Poplavskaya, Svetlana A Romanenko, Natalia A Serdyukova, Vladimir A Trifonov, Fengtang Yang, Wenhui Nie, Jinghuan Wang, Anna A Bannikova, Alexey V Surov, Vladimir S Lebedev
Sokolov's dwarf hamster (Cricetulus sokolovi) is the least studied representative of the striped hamsters (Cricetulus barabensis species group), the taxonomy of which remains controversial. The species was described based on chromosome morphology, but neither the details of the karyotype nor the phylogenetic relationships with other Cricetulus are known. In the present study, the karyotype of C. sokolovi was examined using cross-species chromosome painting. Molecular and cytogenetic data were employed to determine the phylogenetic position of Sokolov's hamster and to analyze the potential pathways of chromosome evolution in Cricetulus...
July 19, 2017: Cytogenetic and Genome Research
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