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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
https://www.readbyqxmd.com/read/29322255/-electronic-vision-aids-new-options-for-rehabilitation-of-the-visually-impaired
#7
REVIEW
N Celik, K Rohrschneider
Due to technical advances, there has been an enormous improvement of electronic vision aids in recent years. New developments are especially small portable devices which can be easily carried. The majority of electronic vision aids serve as a reading aid. Electronic magnifiers are a portable alternative to conventional screen readers. In addition, there are mobile reading devices and special computer tools. Color recognition devices and barcode scanners are helpful in everyday life. Ultrasonic orientation systems enable the recognition of obstacles also at head height...
January 10, 2018: Der Ophthalmologe: Zeitschrift der Deutschen Ophthalmologischen Gesellschaft
https://www.readbyqxmd.com/read/29320544/diversity-patterns-leishmania-dna-detection-and-bloodmeal-identification-of-phlebotominae-sand-flies-in-villages-in-northern-colombia
#8
Camila González, Cielo León, Andrea Paz, Marla López, Gisell Molina, Diana Toro, Mario Ortiz, Juan Manuel Cordovez, María Claudia Atencia, Germán Aguilera, Catalina Tovar
Leishmaniases are neglected tropical diseases exhibiting complex transmission cycles due to the number of parasite species circulating, sand fly species acting as vectors and infected mammals, including humans, which are defined in the New World as accidental hosts. However, current transmission scenarios are changing, and the disease is no longer exclusively related to forested areas but urban transmission foci occur, involving some species of domestic animals as suspected reservoirs. The aim of this study was to determine the transmission cycles in urban environments by evaluating sand fly diversity, detection of Leishmania DNA, and bloodmeal sources through intra and peridomestic collections...
2018: PloS One
https://www.readbyqxmd.com/read/29319504/automated-cell-type-classification-in-intact-tissues-by-single-cell-molecular-profiling
#9
Monica Nagendran, Daniel P Riordan, Pehr B Harbury, Tushar J Desai
A major challenge in biology is identifying distinct cell classes and mapping their interactions in vivo. Tissue-dissociative technologies enable deep single cell molecular profiling but do not provide spatial information. We developed a proximity ligation- in situ hybridization technology (PLISH) with exceptional signal strength, specificity, and sensitivity in tissue. Multiplexed data sets can be acquired using barcoded probes and rapid label-image-erase cycles, with automated calculation of single cell profiles, enabling clustering and anatomical re-mapping of cells...
January 10, 2018: ELife
https://www.readbyqxmd.com/read/29317789/aspergillus-subgenus-polypaecilum-from-the-built-environment
#10
J B Tanney, C M Visagie, N Yilmaz, K A Seifert
Xerophilic fungi, especially Aspergillus species, are prevalent in the built environment. In this study, we employed a combined culture-independent (454-pyrosequencing) and culture-dependent (dilution-to-extinction) approach to investigate the mycobiota of indoor dust collected from 93 buildings in 12 countries worldwide. High and low water activity (aw) media were used to capture mesophile and xerophile biodiversity, resulting in the isolation of approximately 9 000 strains. Among these, 340 strains representing seven putative species in Aspergillus subgenus Polypaecilum were isolated, mostly from lowered aw media, and tentatively identified based on colony morphology and internal transcribed spacer rDNA region (ITS) barcodes...
September 2017: Studies in Mycology
https://www.readbyqxmd.com/read/29316123/from-designing-the-molecules-of-life-to-designing-life-future-applications-derived-from-advances-in-dna-technologies
#11
Richie E Kohman, Aditya M Kunjapur, Eriona Hysolli, Yu Wang, George M Church
Since the elucidation of its structure, DNA has been at the forefront of biological research. In the past half century, an explosion of DNA-based technology development has occurred with the most rapid advances being made for DNA sequencing. In parallel, dramatic improvements have also been made in the synthesis and editing of DNA from the oligonucleotide to the genome scale. In this Review, we will summarize four different subfields relating to DNA technologies following this trajectory of smaller to larger scale...
January 9, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29314756/sorting-specimen-rich-invertebrate-samples-with-cost-effective-ngs-barcodes-validating-a-reverse-workflow-for-specimen-processing
#12
Wendy Y Wang, Amrita Srivathsan, Maosheng Foo, Seiki Yamane, Rudolf Meier
Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an NGS barcoding pipeline that allows for cost-effective high throughput generation of short specimen-specific barcodes (313 bp of COI; lab cost <$0...
January 5, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29312567/b-can-a-resource-sharing-platform-to-improve-the-operation-visualization-and-integrated-analysis-of-tcga-breast-cancer-data
#13
Can-Hong Wen, Shao-Min Ou, Xiao-Bo Guo, Chen-Feng Liu, Yan-Bo Shen, Na You, Wei-Hong Cai, Wen-Jun Shen, Xue-Qin Wang, Hai-Zhu Tan
Breast cancer is a high-risk heterogeneous disease with myriad subtypes and complicated biological features. The Cancer Genome Atlas (TCGA) breast cancer database provides researchers with the large-scale genome and clinical data via web portals and FTP services. Researchers are able to gain new insights into their related fields, and evaluate experimental discoveries with TCGA. However, it is difficult for researchers who have little experience with database and bioinformatics to access and operate on because of TCGA's complex data format and diverse files...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29310715/fast-and-accurate-identification-of-cryptic-and-sympatric-mayfly-species-of-the-baetis-rhodani-group
#14
Roberta Bisconti, Roberta Tenchini, Carlo Belfiore, Giuseppe Nascetti, Daniele Canestrelli
OBJECTIVE: Species of the Baetis rhodani group are among the most widespread mayflies of the Palearctic region. However, frequent occurrence of morphologically cryptic species complicates the identification of sympatric species. Here, we proposed and tested a method for the fast, accurate, and cost-effective assignment of a large number of individuals to their putative species, based on high resolution melting profiles of a standard mitochondrial gene fragment. We tested this method using a system of three recently identified cryptic species inhabiting the Tyrrhenian Islands (western Mediterranean basin)...
January 8, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29306434/focused-glycomic-profiling-with-an-integrated-microfluidic-lectin-barcode-system
#15
Yuqin Shang, Yong Zeng
Protein glycosylation is one of the key processes that play essential roles in biological functions and dysfunctions. However, progress in glycomics has considerably lagged behind genomics and proteomics, due in part to the enormous challenges associated with the analysis of glycans. Here we present a new integrated and automated microfluidic lectin barcode platform to substantially improve the performance of lectin array for focused glycomic profiling. The chip design and flow control were optimized to promote the lectin-glycan binding kinetics and the speed of lectin microarrays...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29304878/bionomic-aspects-of-lutzomyia-evansi-and-lutzomyia-longipalpis-proven-vectors-of-leishmania-infantum-in-an-endemic-area-of-non-ulcerative-cutaneous-leishmaniasis-in-honduras
#16
Ángel Mejía, Gabriela Matamoros, Gustavo Fontecha, Wilfredo Sosa-Ochoa
BACKGROUND: Some Lutzomyia species are the vectors of human leishmaniasis in the Americas. Visceral and cutaneous leishmaniasis are both endemic in the Pacific region of Honduras, but the non-ulcerative form is the more frequent clinical manifestation in this region, where Lutzomyia longipalpis is the most abundant and the only incriminated vector. Taxonomic identification and distribution studies of sand flies are important to understand the epidemiology and to control these neglected tropical diseases...
January 5, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29302302/neutral-molecular-markers-support-common-origin-of-aluminium-tolerance-in-three-congeneric-grass-species-growing-in-acidic-soils
#17
Roberto Contreras, Ana M Figueiras, F Javier Gallego, Elena Benavente, Antonio J Manzaneda, César Benito
Aluminium (Al) toxicity is the main abiotic stress limiting plant productivity in acidic soils that are widely distributed among arable lands. Plant species differ in the level of Al resistance showing intraspecific and interspecific variation in many crop species. However, the origin of Al-tolerance is not well known. Three annual species, difficult to distinguish phenotypically and that were until recently misinterpreted as a single complex species under Brachypodium distachyon, have been recently separated into three distinct species: the diploids B...
November 2017: AoB Plants
https://www.readbyqxmd.com/read/29301959/multiplexed-gene-synthesis-in-emulsions-for-exploring-protein-functional-landscapes
#18
Calin Plesa, Angus M Sidore, Nathan B Lubock, Di Zhang, Sriram Kosuri
Improving our ability to construct and functionally characterize DNA sequences would broadly accelerate progress in biology. Here, we introduce DropSynth, a scalable, low-cost method to build thousands of defined gene-length constructs in a pooled (multiplexed) manner. DropSynth uses a library of barcoded beads that pull down the oligonucleotides necessary for a gene's assembly, which are then processed and assembled in water-in-oil emulsions. We use DropSynth to successfully build >7000 synthetic genes that encode phylogenetically-diverse homologs of two essential genes in E...
January 4, 2018: Science
https://www.readbyqxmd.com/read/29299394/using-herbarium-derived-dnas-to-assemble-a-large-scale-dna-barcode-library-for-the-vascular-plants-of-canada
#19
Maria L Kuzmina, Thomas W A Braukmann, Aron J Fazekas, Sean W Graham, Stephanie L Dewaard, Anuar Rodrigues, Bruce A Bennett, Timothy A Dickinson, Jeffery M Saarela, Paul M Catling, Steven G Newmaster, Diana M Percy, Erin Fenneman, Aurélien Lauron-Moreau, Bruce Ford, Lynn Gillespie, Ragupathy Subramanyam, Jeannette Whitton, Linda Jennings, Deborah Metsger, Connor P Warne, Allison Brown, Elizabeth Sears, Jeremy R Dewaard, Evgeny V Zakharov, Paul D N Hebert
Premise of the study: Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada. Methods: Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci rbcL and matK and from the nuclear ITS2 region...
December 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29299292/dna-barcoding-of-reef-brittle-stars-ophiuroidea-echinodermata-from-the-southwestern-indian-ocean-evolutionary-hot-spot-of-biodiversity
#20
Emilie Boissin, Thierry Bernard Hoareau, Gustav Paulay, J Henrich Bruggemann
In anticipation of the current biodiversity crisis, it has become critical to rapidly and accurately assess biodiversity. DNA barcoding has proved efficient in facilitating the discovery and description of thousands of species and also provides insight into the dynamics of biodiversity. Here, we sequenced a portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene from all morphospecies of reef brittle stars collected during a large-scale biodiversity survey in the southwestern Indian Ocean (SWIO)...
December 2017: Ecology and Evolution
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