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https://www.readbyqxmd.com/read/29345218/mitochondrial-dna-suggests-cryptic-speciation-in-prodiplosis-longifila-gagn%C3%A3-diptera-cecidomyiidae-associated-with-geographic-distance-and-host-specialization
#1
D N Duque-Gamboa, M F Castillo-Cárdenas, L M Hernández, Y C Guzmán, M R Manzano, N Toro-Perea
Prodiplosis longifila is reported as a pest of a wide range of species cultivated in America, including citrus, solanaceous species and asparagus. This species has different behavioural traits that are primarily centred on the oviposition habit and the feeding of larvae, which can change depending on the host. However, scarce information is available on population studies and the natural history of this insect, and uncertainty exists about the taxonomic identity and the geographic distribution of this species...
January 18, 2018: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/29343578/a-new-quinoline-brd4-inhibitor-targets-a-distinct-latent-hiv-1-reservoir-for-re-activation-from-other-shock-drugs
#2
Erik Abner, Mateusz Stoszko, Lei Zeng, Heng-Chang Chen, Andrea Izquierdo-Bouldstridge, Tsuyoshi Konuma, Eduard Zorita, Elisa Fanunza, Qiang Zhang, Tokameh Mahmoudi, Ming-Ming Zhou, Guillaume J Filion, Albert Jordan
Upon HIV-1 infection, a reservoir of latently infected resting T cells prevents the eradication of the virus from patients. To achieve complete depletion, the existing virus-suppressing antiretroviral therapy must be combined with drugs that reactivate the dormant viruses. We previously described a novel chemical scaffold compound, MMQO (8-methoxy-6-methylquinolin-4-ol) that is able to reactivate viral transcription in several models of HIV latency including J-Lat cells through an unknown mechanism. MMQO potentiates the activity of known latency-reversing agents (LRAs) or 'shock' drugs such as PKC agonists or HDAC inhibitors...
January 17, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29342169/interactions-between-the-invasive-burmese-python-python-bivittatus-kuhl-and-the-local-mosquito-community-in-florida-usa
#3
Lawrence E Reeves, Kenneth L Krysko, Michael L Avery, Jennifer L Gillett-Kaufman, Akito Y Kawahara, C Roxanne Connelly, Phillip E Kaufman
The Burmese python, Python bivittatus Kuhl, is a well-established invasive species in the greater Everglades ecosystem of southern Florida, USA. Most research on its ecological impacts focuses on its role as a predator and its trophic interactions with native vertebrate species, particularly mammals. Beyond predation, there is little known about the ecological interactions between P. bivittatus and native faunal communities. It is likely that established populations of P. bivittatus in southern Florida serve as hosts for native mosquito communities...
2018: PloS One
https://www.readbyqxmd.com/read/29340236/dna-barcode-based-survey-of-trichoptera-in-the-crooked-river-reveals-three-new-species-records-for-british-columbia
#4
Daniel J Erasmus, Emily A Yurkowski, Dezene P W Huber
Anthropogenic pressures on aquatic systems have placed a renewed focus on biodiversity of aquatic macroinvertebrates. By combining classical taxonomy and DNA barcoding we identified 39 species of caddisflies from the Crooked River, a unique and sensitive system in the southernmost arctic watershed in British Columbia. Our records include three species never before recorded in British Columbia: Lepidostoma togatum (Lepidostomatidae), Ceraclea annulicornis (Leptoceridae), and possibly Cheumatopsyche harwoodi (Hydropsychidae)...
2018: PeerJ
https://www.readbyqxmd.com/read/29338807/genetic-diversity-of-blastocystis-in-non-primate-animals
#5
Emma L Betts, Eleni Gentekaki, Adele Thomasz, Vicki Breakell, Angus I Carpenter, Anastasios D Tsaousis
Blastocystis is an anaerobic protist, commonly inhabiting the intestinal tract of both humans and other animals. Blastocystis is extremely diverse comprising 17 genetically distinct subtypes in mammals and birds. Pathogenicity of this enteric microbe is currently disputed and knowledge regarding its distribution, diversity and zoonotic potential is fragmentary. Most research has focused on Blastocystis from primates, while sampling from other animals remains limited. Herein, we investigated the prevalence and distribution of Blastocystis in animals held within a conservation park in South East England...
January 17, 2018: Parasitology
https://www.readbyqxmd.com/read/29337374/pooled-lentiviral-delivery-genetic-screens
#6
Federica Piccioni, Scott T Younger, David E Root
Pooled cell-based screens of mammalian genetic perturbations enable systematic large-scale, even genome-scale, evaluation of gene function. Pooled screens introduce genetic perturbations into a cell population through viral transduction such that each cell integrates into its DNA a single or small number of library perturbations with barcodes identifying the perturbations. One then selects and physically isolates the subset of cells that exhibit the phenotype of interest. Sequencing the barcodes in the hit cells reveals which genes favored or inhibited the hit phenotype...
January 16, 2018: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/29337274/species-delimitation-of-the-north-american-orchard-spider-leucauge-venusta-walckenaer-1841-araneae-tetragnathidae
#7
Jesús A Ballesteros, Gustavo Hormiga
The orchard spider, Leucauge venusta (Walckenaer, 1841) is one of the most common and abundant orb-weavers in North America. This species has a broad geographic distribution extending across tropical and temperate regions of the Americas from Canada to Brazil. Guided by a preliminary observation of the barcode gap between sequences from specimens of L. venusta collected in Florida and other North American localities, we collected across a transect through southeastern states of the USA to investigate the observed genetic divide...
January 11, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29336682/preliminary-phylogeny-of-coemansia-kickxellales-with-descriptions-of-four-new-species-from-taiwan
#8
Shu-Cheng Chuang, Hsiao-Man Ho, Nicole Reynolds, Matthew E Smith, Gerald L Benny, Chiu-Yuan Chien, Ju-Lin Tsai
Four new species of Coemansia from Taiwan are described. Three produce spirally twisted sporangiophores, and these new taxa increase the number of species in the Coemansia spiralis complex from three to six. Each new taxon is morphologically unique. Coemansia biformis, sp. nov., has two different asexual reproductive types on the same thallus; one is straight and the other has a spiral fertile region. Coemansia helicoidea, sp. nov., has stoloniferous sporangiophores with a helicoid fertile region. Coemansia pennisetoides, sp...
November 13, 2017: Mycologia
https://www.readbyqxmd.com/read/29336049/a-distinct-group-of-north-european-aedes-vexans-as-determined-by-mitochondrial-and-nuclear-markers
#9
T Lilja, K Troell, H Kirik, A Lindström
The floodwater mosquito Aedes (Aedimorphus) vexans (Meigen, 1830) (Diptera: Culicidae) is common in several areas of Sweden and is predicted to become more abundant in the wake of expected changes in precipitation and temperature caused by climate change. As well as being a nuisance, Ae. vexans can act as a vector of over 30 viruses. In the event of an outbreak of disease caused by a vector-borne virus, knowledge of the distribution, population structure and intermixing of populations from different locations will help direct resources to target locations to prevent spread of the pathogen...
January 16, 2018: Medical and Veterinary Entomology
https://www.readbyqxmd.com/read/29335281/high-throughput-identification-of-rna-nuclear-enrichment-sequences
#10
Chinmay J Shukla, Alexandra L McCorkindale, Chiara Gerhardinger, Keegan D Korthauer, Moran N Cabili, David M Shechner, Rafael A Irizarry, Philipp G Maass, John L Rinn
In the post-genomic era, thousands of putative noncoding regulatory regions have been identified, such as enhancers, promoters, long noncoding RNAs (lncRNAs), and a cadre of small peptides. These ever-growing catalogs require high-throughput assays to test their functionality at scale. Massively parallel reporter assays have greatly enhanced the understanding of noncoding DNA elements en masse Here, we present a massively parallel RNA assay (MPRNA) that can assay 10,000 or more RNA segments for RNA-based functionality...
January 15, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29334378/supermultiplexed-optical-imaging-and-barcoding-with-engineered-polyynes
#11
Fanghao Hu, Chen Zeng, Rong Long, Yupeng Miao, Lu Wei, Qizhi Xu, Wei Min
Optical multiplexing has a large impact in photonics, the life sciences and biomedicine. However, current technology is limited by a 'multiplexing ceiling' from existing optical materials. Here we engineered a class of polyyne-based materials for optical supermultiplexing. We achieved 20 distinct Raman frequencies, as 'Carbon rainbow', through rational engineering of conjugation length, bond-selective isotope doping and end-capping substitution of polyynes. With further probe functionalization, we demonstrated ten-color organelle imaging in individual living cells with high specificity, sensitivity and photostability...
January 15, 2018: Nature Methods
https://www.readbyqxmd.com/read/29334293/dna-barcoding-for-species-identification-in-deep-sea-clams-mollusca-bivalvia-vesicomyidae
#12
Jun Liu, Haibin Zhang
Deep-sea clams (Bivalvia: Vesicomyidae) have been found in reduced environments over the world oceans, but taxonomy of this group remains confusing at species and supraspecific levels due to their high-morphological similarity and plasticity. In the present study, we collected mitochondrial COI sequences to evaluate the utility of DNA barcoding on identifying vesicomyid species. COI dataset identified 56 well-supported putative species/operational taxonomic units (OTUs), approximately covering half of the extant vesicomyid species...
January 15, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29333345/ontogeny-reversal-and-phylogenetic-analysis-of-turritopsis-sp-5-cnidaria-hydrozoa-oceaniidae-a-possible-new-species-endemic-to-xiamen-china
#13
Jun-Yuan Li, Dong-Hui Guo, Peng-Cheng Wu, Li-Sheng He
Ontogeny reversal, as seen in some cnidarians, is an unprecedented phenomenon in the animal kingdom involving reversal of the ordinary life cycle. Three species of Turritopsis have been shown to be capable of inverted metamorphosis, a process in which the pelagic medusa transforms back into a juvenile benthic polyp stage when faced with adverse conditions. Turritopsis sp.5 is a species of Turritopsis collected from Xiamen, China which presents a similar ability, being able to reverse its life cycle if injured by mechanical stress...
2018: PeerJ
https://www.readbyqxmd.com/read/29332696/a-comparison-of-plastic-cable-ties-based-on-physical-chemical-and-stable-isotopic-measurements
#14
Lisa M Nienaber, Sarah L Cresswell, James F Carter, Tony Peter
Plastic cable ties can be utilised in a range of serious criminal activities and a comparison of cable ties, or fragments, may form part of the physical evidence presented to a Court of law. This research assessed the potential value of evidence based on the analysis of plastic cable ties. Twenty packets of black coloured plastic cable ties (nominally 200mm×4.8mm) were purchased in pack sizes ranging from 25 to 100 individual cable ties (Brisbane, Australia, March 2015). Representative samples from each packet were visually examined, compared and tested to determine their physical dimensions, chemical compositions and stable isotopic compositions (δ2H, δ13C and δ15N)...
January 2018: Science & Justice: Journal of the Forensic Science Society
https://www.readbyqxmd.com/read/29330936/give-me-a-sample-of-air-and-i-will-tell-which-species-are-found-from-your-region-molecular-identification-of-fungi-from-airborne-spore-samples
#15
Nerea Abrego, Veera Norros, Panu Halme, Panu Somervuo, Heini Ali-Kovero, Otso Ovaskainen
Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning, and are important for human health, food production, and nature conservation. Our knowledge on fungal diversity and fungal ecology is however still very limited, in part because surveying and identifying fungi is time demanding and requires expert knowledge. We present a method that allows anyone to generate a list of fungal species likely to occur in a region of interest, with minimal effort and without requiring taxonomical expertise...
January 13, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29329703/highly-sensitive-microrna-detection-based-on-bio-bar-code-assay-and-catalytic-hairpin-assembly-two-stage-amplification
#16
Songsong Tang, Yuan Gu, Huiting Lu, Haifeng Dong, Kai Zhang, Wenhao Dai, Xiangdan Meng, Fan Yang, Xueji Zhang
Herein, a highly-sensitive microRNA (miRNA) detection strategy was developed by combining bio-bar-code assay (BBA) with catalytic hairpin assembly (CHA). In the proposed system, two nanoprobes of magnetic nanoparticles functionalized with DNA probes (MNPs-DNA) and gold nanoparticles with numerous barcode DNA (AuNPs-DNA) were designed. In the presence of target miRNA, the MNP-DNA and AuNP-DNA hybridized with target miRNA to form a "sandwich" structure. After "sandwich" structures were separated from the solution by the magnetic field and dehybridized by high temperature, the barcode DNA sequences were released by dissolving AuNPs...
April 3, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29328081/is-qr-code-an-optimal-data-container-in-optical-encryption-systems-from-an-error-correction-coding-perspective
#17
Shuming Jiao, Zhi Jin, Changyuan Zhou, Wenbin Zou, Xia Li
Quick response (QR) code has been employed as a data carrier for optical cryptosystems in many recent research works, and the error-correction coding mechanism allows the decrypted result to be noise free. However, in this paper, we point out for the first time that the Reed-Solomon coding algorithm in QR code is not a very suitable option for the nonlocally distributed speckle noise in optical cryptosystems from an information coding perspective. The average channel capacity is proposed to measure the data storage capacity and noise-resistant capability of different encoding schemes...
January 1, 2018: Journal of the Optical Society of America. A, Optics, Image Science, and Vision
https://www.readbyqxmd.com/read/29326217/draft-genome-sequences-of-bifidobacterium-strains-n4g05-and-n5g01-isolated-from-the-human-vaginal-microbiome
#18
Aline C Freitas, Janet E Hill
We report here the draft genome sequences of Bifidobacterium strains N4G05 and N5G01, isolated from the human vaginal microbiome. Genome sequences were obtained by de novo assembly from high-quality reads. Both strains were closely related to Bifidobacterium kashiwanohense based on barcode marker sequences and average nucleotide identity analysis.
January 11, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29325146/dramatic-changes-in-malaria-population-genetic-complexity-in-dielmo-and-ndiop-senegal-revealed-using-genomic-surveillance
#19
Amy K Bei, Makhtar Niang, Awa B Deme, Rachel F Daniels, Fatoumata D Sarr, Cheikh Sokhna, Cheikh Talla, Joseph Faye, Nafissatou Diagne, Souleymane Doucoure, Souleymane Mboup, Dyann F Wirth, Adama Tall, Daouda Ndiaye, Daniel L Hartl, Sarah K Volkman, Aissatou Toure-Balde
Dramatic changes in transmission intensity can impact Plasmodium population diversity. Using samples from 2 distant time-points in the Dielmo/Ndiop longitudinal cohorts from Senegal, we applied a molecular barcode tool to detect changes in parasite genotypes and complexity of infection that corresponded to changes in transmission intensity. We observed a striking statistically significant difference in genetic diversity between the 2 parasite populations. Furthermore, we identified a genotype in Dielmo and Ndiop previously observed in Thiès, potentially implicating imported malaria...
January 9, 2018: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29325009/efficient-generation-of-complete-sequences-of-mdr-encoding-plasmids-by-rapid-assembly-of-minion-barcoding-sequencing-data
#20
Ruichao Li, Miaomiao Xie, Ning Dong, Dachuan Lin, Xuemei Yang, Marcus Ho Yin Wong, Edward Wai-Chi Chan, Sheng Chen
Background: Multidrug resistance (MDR)-encoding plasmids are considered major molecular vehicles responsible for transmission of antibiotic resistance genes among bacteria of the same or different species. Delineating the complete sequences of such plasmids could provide valuable insight into the evolution and transmission mechanisms underlying bacterial antibiotic resistance development. However, due to the presence of multiple repeats of mobile elements, complete sequencing of MDR plasmids remains technically complicated, expensive and time-consuming...
January 9, 2018: GigaScience
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