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https://www.readbyqxmd.com/read/28922802/succession-of-arbuscular-mycorrhizal-fungi-along-a-52-year-agricultural-recultivation-chronosequence
#1
Julien Roy, Rüdiger Reichel, Nicolas Brüggemann, Stefan Hempel, Matthias C Rillig
Arbuscular mycorrhizal (AM) fungi provide a range of functions in natural and managed ecosystems. However, the trajectory of AM fungal diversity after land degradation is poorly known. We studied the succession of AM fungi along an agricultural recultivation chronosequence after open-cast mining near Cologne, Germany. We used high-throughput sequencing of the large-subunit ribosomal RNA genes to characterize the soil AM fungal communities of 10 agricultural fields spanning 52 years of recultivation. During three years, soils are recultivated with a legume, and then converted to agriculture to be later returned to local farmers implementing conventional agriculture...
September 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28922630/effects-of-iron-and-calcium-carbonate-on-contaminant-removal-efficiencies-and-microbial-communities-in-integrated-wastewater-treatment-systems
#2
Zhimiao Zhao, Xinshan Song, Yinjiang Zhang, Yufeng Zhao, Bodi Wang, Yuhui Wang
In the paper, we explored the influences of different dosages of iron and calcium carbonate on contaminant removal efficiencies and microbial communities in algal ponds combined with constructed wetlands. After 1-year operation of treatment systems, based on the high-throughput pyrosequencing analysis of microbial communities, the optimal operating conditions were obtained as follows: the ACW10 system with Fe(3+) (5.6 mg L(-1)), iron powder (2.8 mg L(-1)), and CaCO3 powder (0.2 mg L(-1)) in influent as the adjusting agents, initial phosphorus source (PO4(3-)) in influent, the ratio of nitrogen to phosphorus (N/P) of 30 in influent, and hydraulic retention time (HRT) of 1 day...
September 8, 2017: Chemosphere
https://www.readbyqxmd.com/read/28922619/identification-of-angiogenesis-inhibitors-using-a-co-culture-cell-model-in-a-high-content-and-high-throughput-screening-platform
#3
Shuaizhang Li, Chia-Wen Hsu, Srilatha Sakamuru, Chaozhong Zou, Ruili Huang, Menghang Xia
Angiogenesis is an important hallmark of cancer, contributing to tumor formation and metastasis. In vitro angiogenesis models for analyzing tube formation serve as useful tools to study these processes. However, current in vitro co-culture models using primary cells have limitations in usefulness and consistency. Therefore, in the present study, an in vitro co-culture assay system was optimized in a 1536-well format for high-throughput screening using human telomerase reverse transcriptase (hTERT)-immortalized mesenchymal stem cells and aortic endothelial cells...
September 1, 2017: SLAS Technology
https://www.readbyqxmd.com/read/28922562/association-between-polymorphisms-in-microrna-target-sites-and-survival-in-early-stage-non-small-cell-lung-cancer
#4
Seung Soo Yoo, Mi Jeong Hong, Jang Hyuck Lee, Jin Eun Choi, Shin Yup Lee, Jaehee Lee, Seung Ick Cha, Chang Ho Kim, Yangki Seok, Eungbae Lee, Sukki Cho, Sanghoon Jheon, Jae Yong Park
A high-throughput mapping method of RNA-RNA interactions by crosslinking, ligation, and sequencing of hybrids (CLASH) can not only provide information about canonical but also non-canonical interactions. We evaluated the associations between variants in microRNA target sites using CLASH data and survival outcomes of 782 early-stage non-small cell lung cancer (NSCLC) patients who underwent curative surgical resection. Among the 100 variants studied, two variants showed significant association with survival outcomes...
September 18, 2017: Thoracic Cancer
https://www.readbyqxmd.com/read/28922139/3d-printed-multiplexed-electrospinning-sources-for-large-scale-production-of-aligned-nanofiber-mats-with-small-diameter-spread
#5
Erika García-López, Daniel Olvera-Trejo, Luis F Velásquez-García
We report the design, fabrication, and characterization of novel, low-cost, and modular miniaturized nanofiber electrospinning sources for the scalable production of non-woven aligned nanofiber mats with low diameter variation. The devices are monolithic arrays of electrospinning emitters made via stereolithography; the emitters are arranged so each element has an independent line of sight to a rotating collector surface. Linear and zigzag emitter packing were evaluated using a PEO solution with the aim of maximizing the throughput of nanofibers with the smallest diameter and narrowest distribution...
September 18, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28921968/automated-solid-phase-click-synthesis-of-oligonucleotide-conjugates-from-small-molecules-to-diverse-n-acetylgalactosamine-clusters
#6
Valentina M Farzan, Egor A Ulashchik, Yury V Martynenko-Makaev, Maksim V Kvach, Ilya Olegovich Aparin, Vladimir A Brylev, Tatiana A Prikazchikova, Svetlana Yu Maklakova, Alexander G Majouga, Alexey V Ustinov, German A Shipulin, Vadim V Shmanai, Vladimir A Korshun, Timofei S Zatsepin
We developed a novel technique for efficient conjugation of oligonucleotides with various alkyl azides (fluorescent dyes, biotin, cholesterol, GalNAc, etc.) using CuAAC on solid phase and CuI·P(OEt)3 as a catalyst. Conjugation is carried out in an oligonucleotide synthesizer in fully automated mode and is coupled to oligonucleotide synthesis and on-column deprotection. We also suggest a set of reagents for the construction of diverse conjugates. The sequential double click procedure using a pentaerythritol-derived tetraazide followed by the addition of a GalNAc or tris-GalNAc alkyne gives oligonucleotide-GalNAc dendrimer conjugates in good yields with minimal excess of sophisticated alkyne reagents...
September 18, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28921802/environmental-dna-metabarcoding-transforming-how-we-survey-animal-and-plant-communities
#7
Kristy Deiner, Holly M Bik, Elvira Mächler, Mathew Seymour, Anaïs Lacoursière-Roussel, Florian Altermatt, Simon Creer, Iliana Bista, David M Lodge, Natasha de Vere, Michael E Pfrender, Louis Bernatchez
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ('HTS') platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed 'environmental DNA' or 'eDNA'). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called 'eDNA metabarcoding' and offers a powerful molecular tool capable of non-invasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance...
September 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28921475/legacy-effects-of-continuous-chloropicrin-fumigation-for-3-years-on-soil-microbial-community-composition-and-metabolic-activity
#8
Shuting Zhang, Xiaojiao Liu, Qipeng Jiang, Guihua Shen, Wei Ding
Chloropicrin is widely used to control ginger wilt in China, which have an enormous impact on soil microbial diversity. However, little is known on the possible legacy effects on soil microbial community composition with continuous fumigation over different years. In this report, we used high throughput Illumina sequencing and Biolog ECO microplates to determine the bacterial community and microbial metabolic activity in ginger harvest fields of non-fumigation (NF), chloropicrin-fumigation for 1 year (F_1) and continuous chloropicrin-fumigation for 3 years (F_3)...
September 18, 2017: AMB Express
https://www.readbyqxmd.com/read/28921440/microplate-based-method-for-high-throughput-screening-hts-of-chromatographic-conditions-studies-for-recombinant-protein-purification
#9
Rimenys J Carvalho, Thayana A Cruz
High-throughput screening (HTS) systems have emerged as important tools to provide fast and low cost evaluation of several conditions at once since it requires small quantities of material and sample volumes. These characteristics are extremely valuable for experiments with large number of variables enabling the application of design of experiments (DoE) strategies or simple experimental planning approaches. Once, the capacity of HTS systems to mimic chromatographic purification steps was established, several studies were performed successfully including scale down purification...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28921426/production-of-full-length-antibody-by-pichia-pastoris
#10
Adam Nylen, Ming-Tang Chen
The methylotrophic yeast Pichia pastoris has become an increasingly popular host for recombinant protein expression in recent times. MRL pioneered a glycoengineered humanized P. pastoris expression system that could produce glycoproteins with glycosylation profiles similar to mammalian systems. Therapeutic glycoproteins produced by the humanized P. pastoris platform have shown comparable folding, stability, and in vitro and in vivo efficacies in preclinical models to their counterparts produced from the CHO cells...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28921387/analysis-of-24-genes-reveals-a-monogenic-cause-in-11-1-of-cases-with-steroid-resistant-nephrotic-syndrome-at-a-single-center
#11
Weizhen Tan, Svjetlana Lovric, Shazia Ashraf, Jia Rao, David Schapiro, Merlin Airik, Shirlee Shril, Heon Yung Gee, Michelle Baum, Ghaleb Daouk, Michael A Ferguson, Nancy Rodig, Michael J G Somers, Deborah R Stein, Asaf Vivante, Jillian K Warejko, Eugen Widmeier, Friedhelm Hildebrandt
BACKGROUND: Steroid-resistant nephrotic syndrome (SRNS) is the second most frequent cause of end-stage renal disease (ESRD) among patients manifesting at under 25 years of age. We performed mutation analysis using a high-throughput PCR-based microfluidic technology in 24 single-gene causes of SRNS in a cohort of 72 families, who presented with SRNS before the age of 25 years. METHODS: Within an 18-month interval, we obtained DNA samples, pedigree information, and clinical information from 77 consecutive children with SRNS from 72 different families seen at Boston Children's Hospital (BCH)...
September 18, 2017: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
https://www.readbyqxmd.com/read/28920441/new-insight-of-common-regulatory-pathways-in-human-trabecular-meshwork-cells-in-response-to-dexamethasone-and-prednisolone-using-an-integrated-quantitative-proteomics-swath-and-mrm-hr-mass-spectrometry
#12
Sze Wan Shan, Chi Wai Do, Thomas Chuen Lam, Ricky Pak Wing Kong, King Kit Li, Ka Man Chun, William Daniel Stamer, Chi Ho To
The molecular pathophysiology of corticosteroid-induced ocular hypertension (CIH) is not well understood. To determine the biological mechanisms of CIH, this study investigated protein expression profiles of human trabecular meshwork (hTM) cells in response to dexamethasone and prednisolone treatment. Both discovery-based Sequential Windowed data independent Acquisition of the Total High-resolution mass spectra (SWATH(TM)-MS) and targeted based high resolution multiple reaction monitoring (MRM-HR) confirmation were applied using a hybrid quadrupole-time-of-flight mass spectrometer...
September 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28920431/isolation-and-characterization-of-a-novel-highly-selective-astaxanthin-producing-marine-bacterium
#13
Dalal Asker
A high throughput screening approach for astaxanthin-producing bacteria led to the discovery of a novel highly selective astaxanthin-producing marine bacterium (strain N-5). Phylogenetic analysis based on partial 16S rRNA gene and phenotypic metabolic testing indicated it belongs to the genus Brevundimonas. Therefore, it was designated as Brevundimonas sp. strain N-5. To identify and quantify carotenoids produced by strain N-5, HPLC-DAD and HPLC-MS methods were used. The culture conditions including media, shaking and time had significant effects on cell growth and carotenoids production including astaxanthin...
September 18, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28919931/improving-hierarchical-models-using-historical-data-with-applications-in-high-throughput-genomics-data-analysis
#14
Ben Li, Yunxiao Li, Zhaohui S Qin
Modern high-throughput biotechnologies such as microarray and next generation sequencing produce a massive amount of information for each sample assayed. However, in a typical high-throughput experiment, only limited amount of data are observed for each individual feature, thus the classical 'large p, small n' problem. Bayesian hierarchical model, capable of borrowing strength across features within the same dataset, has been recognized as an effective tool in analyzing such data. However, the shrinkage effect, the most prominent feature of hierarchical features, can lead to undesirable over-correction for some features...
June 2017: Statistics in Biosciences
https://www.readbyqxmd.com/read/28919906/screening-for-natural-inhibitors-of-topoisomerases-i-from-rhamnus-davurica-by-affinity-ultrafiltration-and-high-performance-liquid-chromatography-mass-spectrometry
#15
Guilin Chen, Mingquan Guo
Topoisomerase I (Topo I) catalyzes topological interconversion of duplex DNA during DNA replication and transcription, and has been deemed as important antineoplastic targets. In this study, the fraction R.d-60 from ethyl acetate extracts of Rhamnus davurica showed higher inhibitory rates against SGC-7901 and HT-29 compared with the R.d-30 fraction in vitro. However, the specific active components of R.d-60 fraction remain elusive. To this end, a method based on bio-affinity ultrafiltration and high performance liquid chromatography/electrospray mass spectrometry (HPLC- ESI-MS/MS) was developed to rapidly screen and identify the Topo I inhibitors in this fraction...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28919550/improving-the-genotyping-resolution-of-cryptosporidium-hominis-subtype-iba10g2-using-one-step-pcr-based-amplicon-sequencing
#16
Jessica Beser, Björn M Hallström, Abdolreza Advani, Sofia Andersson, Gabriel Östlund, Jadwiga Winiecka-Krusnell, Marianne Lebbad, Erik Alm, Karin Troell, Romanico B G Arrighi
Cryptosporidium hominis gp60 subtype IbA10G2 is a common cause of cryptosporidiosis. This subtype is responsible for many waterborne outbreaks as well as sporadic cases and is considered virulent and highly important in the epidemiology of cryptosporidiosis. Due to low heterogeneity within the genome of C. hominis it has been difficult to identify epidemiological markers with higher resolution than gp60. However, new markers are required in order to improve outbreak investigations and studies of the transmission dynamics of this clinically important subtype...
September 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28919018/de-novo-transcriptome-assembly-of-the-calanoid-copepod-neocalanus-flemingeri-a-new-resource-for-emergence-from-diapause
#17
Vittoria Roncalli, Matthew C Cieslak, Stephanie A Sommer, Russell R Hopcroft, Petra H Lenz
Copepods, small planktonic crustaceans, are key links between primary producers and upper trophic levels, including many economically important fishes. In the subarctic North Pacific, the life cycle of copepods like Neocalanus flemingeri includes an ontogenetic migration to depth followed by a period of diapause (a type of dormancy) characterized by arrested development and low metabolic activity. The end of diapause is marked by the production of the first brood of eggs. Recent temperature anomalies in the North Pacific have raised concerns about potential negative effects on N...
September 14, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28918708/removal-of-sulfadiazine-and-tetracycline-in-membrane-bioreactors-mbrs-linking-pathway-to-microbial-community-shift
#18
Ronghua Xu, Zhiyong Wu, Zhongbo Zhou, Fangang Meng
In this study, the removal pathway of sulfadiazine (SDZ) and tetracycline (TC) and their roles in shaping microbial community were separately explored in two lab-scale membrane bioreactors (MBRs) operating in parallel with one control MBR. Results show that the MBR system eliminated more than 90% of TC in the feed, whereas removal efficiency of SDZ decreased from 100% to 40% with increasing SDZ concentrations (1-1000 μg/L). Based on batch tests, biodegradation and adsorption was the main removal route for SDZ and TC, respectively...
September 18, 2017: Environmental Technology
https://www.readbyqxmd.com/read/28918538/genetic-manipulation-of-borrelia-spp
#19
Dan Drecktrah, D Scott Samuels
The spirochetes Borrelia (Borreliella) burgdorferi and Borrelia hermsii, the etiologic agents of Lyme disease and relapsing fever, respectively, cycle in nature between an arthropod vector and a vertebrate host. They have extraordinarily unusual genomes that are highly segmented and predominantly linear. The genetic analyses of Lyme disease spirochetes have become increasingly more sophisticated, while the age of genetic investigation in the relapsing fever spirochetes is just dawning. Molecular tools available for B...
September 17, 2017: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28918473/complete-genome-sequences-of-two-insect-specific-flaviviruses
#20
Jermilia Charles, Chandra S Tangudu, Andrew E Firth, Bradley J Blitvich
We determined the complete genomic sequences of two previously discovered insect-specific flaviviruses, Marisma mosquito virus (MMV) and Nanay virus (NANV), using a combination of high-throughput sequencing, reverse transcription-polymerase chain reaction, 5' and 3' rapid amplification of cDNA ends and Sanger sequencing. Complete polyprotein amino acid sequence alignments revealed that the closest known relatives of MMV and NANV are Donggang virus (89% identity, 95% similarity) and Nounané virus (53% identity, 70% similarity), respectively...
September 16, 2017: Archives of Virology
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