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https://www.readbyqxmd.com/read/29161611/the-application-of-ion-mobility-mass-spectrometry-to-metabolomics
#1
REVIEW
Xing Zhang, Kevin Quinn, Charmion Cruickshank-Quinn, Richard Reisdorph, Nichole Reisdorph
Mass spectrometry-based metabolomics is being increasingly utilized in various research fields including investigating human diseases, nutrition, industrial applications, and plant/natural products studies. Although new analytical approaches have enhanced the performance of metabolomic analyses, significant challenges associated with throughput, metabolome coverage, and compound identification still exist. Ion mobility mass spectrometry offers great potential for improving throughput and depth of coverage in metabolomics experiments...
November 18, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29161569/denitrification-of-landfill-leachate-under-different-hydraulic-retention-time-in-a-two-stage-anoxic-oxic-combined-membrane-bioreactor-process-performances-and-bacterial-community
#2
Jianbo Liu, Panyue Zhang, Haibo Li, Yuan Tian, Siyu Wang, Yonghui Song, Guangming Zeng, Chen Sun, Zhiyong Tian
Two-stage anoxic/oxic combined membrane bioreactor (A/O-A/O-MBR) process was used to treat leachate generated from Shenyang Laohuchong landfill, and the effect of hydraulic retention time (HRT) was studied. A long HRT of 9 d and a short HRT of 5 d showed negative effect on the stability of process, resulting in a higher organic concentration of effluent than that with a HRT of 7 d, while the highest removal of chemical oxygen demand (COD), ammonia (NH4(+)-N) and total nitrogen (TN) were achieved with a HRT of 7 d, which was 82...
November 11, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29161511/a-customizable-flow-injection-system-for-automated-high-throughput-and-time-sensitive-ion-mobility-spectrometry-and-mass-spectrometry-measurements
#3
Daniel J Orton, Malak M Tfaily, Ronald J Moore, Brian L LaMarche, Xueyun Zheng, Thomas L Fillmore, Rosalie K Chu, Karl K Weitz, Matthew E Monroe, Ryan T Kelly, Richard D Smith, Erin Shammel Baker
To better understand disease conditions and environmental perturbations, multi-omic studies combining proteomic, lipidomic, and metabolomic analyses are vastly increasing in popularity. In a multi-omic study, a single sample is typically extracted in multiple ways and various analyses are performed using different instruments. Thus, one sample becomes many measurements, making high throughput and reproducible evaluations a necessity. One way to address the numerous samples and varying instrumental conditions is to utilize a flow injection analysis (FIA) system for rapid sample injection...
November 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29161508/design-and-fabrication-of-wettability-gradients-with-tunable-profiles-through-degrafting-organosilane-layers-from-silica-surfaces-by-tetrabutylammonium-fluoride
#4
Jason R Miles, Spencer L Schlenker, Yeongun Ko, Rohan R Patil, Balaji M Rao, Jan Genzer
Surface-bound wettability gradients allow for a high-throughput approach to evaluate surface interactions for many biological and chemical processes. Here we describe the fabrication of surface wettability gradients on flat surfaces by a simple, two-step procedure that permits precise tuning of the gradient profile. This process involves the deposition of homogeneous silane SAMs followed by the formation of a surface coverage gradient through the selective removal of silanes from the substrate. Removal of silanes from the surface is achieved by using tetrabutylammonium fluoride which cleaves selectively the Si-O bonds at the headgroup of the silane...
November 21, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29161304/proposal-for-a-common-nomenclature-for-fragment-ions-in-mass-spectra-of-lipids
#5
Josch K Pauling, Martin Hermansson, Jürgen Hartler, Klaus Christiansen, Sandra F Gallego, Bing Peng, Robert Ahrends, Christer S Ejsing
Advances in mass spectrometry-based lipidomics have in recent years prompted efforts to standardize the annotation of the vast number of lipid molecules that can be detected in biological systems. These efforts have focused on cataloguing, naming and drawing chemical structures of intact lipid molecules, but have provided no guidelines for annotation of lipid fragment ions detected using tandem and multi-stage mass spectrometry, albeit these fragment ions are mandatory for structural elucidation and high confidence lipid identification, especially in high throughput lipidomics workflows...
2017: PloS One
https://www.readbyqxmd.com/read/29161291/declust-a-statistical-approach-for-obtaining-differential-expression-profiles-of-multiple-conditions
#6
Yoshimasa Aoto, Tsuyoshi Hachiya, Kazuhiro Okumura, Sumitaka Hase, Kengo Sato, Yuichi Wakabayashi, Yasubumi Sakakibara
High-throughput RNA sequencing technology is widely used to comprehensively detect and quantify cellular gene expression. Thus, numerous analytical methods have been proposed for identifying differentially expressed genes (DEGs) between paired samples such as tumor and control specimens, but few studies have reported methods for analyzing differential expression under multiple conditions. We propose a novel method, DEclust, for differential expression analysis among more than two matched samples from distinct tissues or conditions...
2017: PloS One
https://www.readbyqxmd.com/read/29161272/global-transcriptome-profile-reveals-abundance-of-dna-damage-response-and-repair-genes-in-individuals-from-high-level-natural-radiation-areas-of-kerala-coast
#7
Vinay Jain, Birajalaxmi Das
The high level natural radiation areas (HLNRA) of Kerala coast in south west India is unique for its wide variation in the background radiation dose (<1.0mGy to 45mGy/year) and vast population size. Several biological studies conducted in this area did not reveal any adverse effects of chronic low dose and low dose rate radiation on human population. In the present study, global transcriptome analysis was carried out in peripheral blood mono-nuclear cells of 36 individuals belonging to different background dose groups [NLNRA, (Group I, ≤1...
2017: PloS One
https://www.readbyqxmd.com/read/29161047/mapping-extracellular-matrix-proteins-in-formalin-fixed-paraffin-embedded-tissues-by-maldi-imaging-mass-spectrometry
#8
Peggi M Angel, Susana Comte-Walters, Lauren E Ball, Kacey Talbot, Anand Mehta, Kelvin G M Brockbank, Richard R Drake
Collagens and elastin form the fundamental framework of all tissues and organs and their expression and post-translational processing are tightly regulated in disease and health. Due to their unique structural composition and properties, it is a recognized challenge to access these protein structures within the complex tissue microenvironment to understand how localized changes modulate tissue health. We describe a new workflow using a combination of matrix-assisted laser desorption /ionization imaging mass spectrometry (MALDI IMS) with collagenase and matrix metalloproteinase (MMP) enzymes to access and report on spatial localization of collagen and elastin sequences in formalin-fixed, paraffin-embedded (FFPE) tissues...
November 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29161008/mapping-the-functional-tortuosity-and-spatio-temporal-heterogeneity-of-porous-polymer-membranes-with-super-resolution-nanoparticle-tracking
#9
Yu Cai, Daniel K Schwartz
As particles flow through porous media, they follow complex pathways and experience heterogeneous environments that are challenging to characterize. Tortuosity is often used as a parameter to characterize the complexity of pathways in porous materials and is useful in understanding hindered mass transport in industrial filtration and mass separation processes. However, conventional calculations of tortuosity provide only average values under static conditions; they are insensitive to the intrinsic heterogeneity of porous media and do not account for potential effects of operating conditions...
November 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29161005/esi-ms-for-microsized-bioparticles
#10
Abdil Ozdemir, Jung-Lee Lin, Mustafa Gulfen, Szu-Hsueh Lai, Chun-Jen Hsiao, Nelson Gee-Con Chen, Chung-Hsuan Chen
An ESI ion trap mass spectrometer was designed for high throughput and rapid mass analysis of large bio-particles. Mass calibration of the instrument was performed using commercially available polystyrene micro-particles, and the selected sizes of the polystyrene (PS) particles were approximately 3 to 15 µm, which is consistent with the size of the cancer cells selected for this work. It provides the analysis of micro-sized inorganic and bioparticles. Different sizes of MCF-7 breast cancer cells (8 to 15 µm) were used in this study...
November 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29160895/differential-expression-of-micrornas-contributed-to-the-health-efficacy-of-egcg-in-in-vitro-subarachnoid-hemorrhage-model
#11
Ying Chen, Liyong Huang, Lei Wang, Lingyun Chen, Wenhua Ren, Wenke Zhou
(-)-Epigallocatechin-3-gallate (EGCG) exhibits a broader spectrum health efficacy in subarachnoid hemorrhage (SAH) therapy; the mechanisms, however, are largely unknown. Given that miRNAs play important roles in regulation of thousands of gene expressions, the effect of EGCG on the expression of miRNAs was investigated to explore the multi-targeting actions of EGCG by using an in vitro SAH model. MTT and western blot assays were used to assess the health effects of EGCG in SAH progression; the results showed that oxyhemoglobin (OxyHb)-induced cell proliferation and excessive autophagic activation were significantly inhibited by 50 μM EGCG, but not by 1 μM EGCG...
November 21, 2017: Food & Function
https://www.readbyqxmd.com/read/29160815/assessment-of-bifidobacterium-species-using-groel-gene-on-the-basis-of-illumina-miseq-high-throughput-sequencing
#12
Lujun Hu, Wenwei Lu, Linlin Wang, Mingluo Pan, Hao Zhang, Jianxin Zhao, Wei Chen
The next-generation high-throughput sequencing techniques have introduced a new way to assess the gut's microbial diversity on the basis of 16S rRNA gene-based microbiota analysis. However, the precise appraisal of the biodiversity of Bifidobacterium species within the gut remains a challenging task because of the limited resolving power of the 16S rRNA gene in different species. The groEL gene, a protein-coding gene, evolves quickly and thus is useful for differentiating bifidobacteria. Here, we designed a Bifidobacterium-specific primer pair which targets a hypervariable sequence region within the groEL gene that is suitable for precise taxonomic identification and detection of all recognized species of the genus Bifidobacterium so far...
November 21, 2017: Genes
https://www.readbyqxmd.com/read/29160623/saddlebags-a-software-interface-for-submitting-full-length-hla-allele-sequences-to-the-embl-ena-nucleotide-database
#13
B M Matern, M Groeneweg, C E M Voorter, M G J Tilanus
Submission of full-length HLA allele sequences presents a unique challenge, both for high-throughput sequencing laboratories, and smaller diagnostic laboratories. HLA's extensive polymorphism means that accurate representation and annotation of allele sequence is of critical importance, and curators of nucleotide databases must establish submission formats to ensure high-quality data, and prevent ambiguities. The IPD-IMGT/HLA database is established as the standard repository for HLA sequences, and it is a major goal of the 17th International HLA and Immunogenetics Workshop to fill the IPD-IMGT/HLA database with full-length HLA sequences...
November 21, 2017: HLA
https://www.readbyqxmd.com/read/29160556/digest-room-for-geckos-of-all-shapes-and-sizes
#14
H Christoph Liedtke
Closely related lineages co-existing geographically are expected to show morphological divergence via character displacement. Moritz et al. (2017) use high-throughput sequencing to uncover cryptic diversity in a complex of Australian geckos and, with the resulting phylogeny, discern patterns of morphological evolution in relation to patterns of geographic overlap. They found that divergence in body size is greater in species pairs occurring in sympatry than in parapatry, which is consistent with the idea that body size divergence facilitates sympatry...
November 21, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29160067/molecular-tension-probes-for-imaging-forces-at-the-cell-surface
#15
Yang Liu, Kornelia Galior, Victor Pui-Yan Ma, Khalid Salaita
Mechanical forces are essential for a variety of biological processes ranging from transcription and translation to cell adhesion, migration, and differentiation. Through the activation of mechanosensitive signaling pathways, cells sense and respond to physical stimuli from the surrounding environment, a process widely known as mechanotransduction. At the cell membrane, many signaling receptors, such as integrins, cadherins and T- or B-cell receptors, bind to their ligands on the surface of adjacent cells or the extracellular matrix (ECM) to mediate mechanotransduction...
November 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29159928/the-immunogenetics-of-neurological-disease
#16
REVIEW
Maneesh K Misra, Vincent Damotte, Jill A Hollenbach
Genes encoding antigen-presenting molecules within the human major histocompatibility complex (MHC) account for the highest component of genetic risk for many neurological diseases, such as multiple sclerosis, neuromyelitis optica, Parkinson's disease, Alzheimer's disease, schizophrenia, myasthenia gravis and amyotrophic lateral sclerosis. Myriad genetic, immunological and environmental factors may contribute to an individual's susceptibility to neurological disease. Here, we review and discuss the decades long research on the influence of genetic variation at the MHC locus and the role of immunogenetic killer cell immunoglobulin-like receptor (KIR) loci in neurological diseases, including multiple sclerosis, neuromyelitis optica, Parkinson's disease, Alzheimer's disease, schizophrenia, myasthenia gravis and amyotrophic lateral sclerosis...
November 21, 2017: Immunology
https://www.readbyqxmd.com/read/29159726/liquid-chromatography-mass-spectrometry-lc-ms-based-analysis-of-molecular-lipids-in-algae-samples
#17
Heli Nygren, Tuulikki Seppänen-Laakso, Heiko Rischer
In this paper, an analytical method for the analysis of molecular lipids in algae samples is reported. The sample preparation is based on a modified Folch extraction, and the analysis is carried out with ultrahigh performance liquid chromatography combined with mass spectrometry (UPLC-MS). For further characterization of lipids, MS/MS analyses are carried out utilizing either a separate instrument (e.g., LTQ-Orbitrap mass spectrometer) or simultaneous fragmentation with the same instrument. Throughput of the method is over 100 samples/d...
November 21, 2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29159447/transcriptome-sequencing-of-the-long-nosed-bandicoot-perameles-nasuta-reveals-conservation-and-innovation-of-immune-genes-in-the-marsupial-order-peramelemorphia
#18
Katrina M Morris, Haylee J Weaver, Denis O'Meally, Marion Desclozeaux, Amber Gillett, Adam Polkinghorne
Bandicoots are omnivorous marsupials of the order Peramelemorphia. Conservation concerns and their unique biological characteristics suggest peramelomorphs are worthy research subjects, but knowledge of their genetics and immunology has lagged behind that of other high-profile marsupials. Here, we characterise the transcriptome of the long-nose bandicoot (Perameles nasuta), the first high-throughput data set from any peramelomorph. We investigate the immune gene repertoire of the bandicoot, with a focus on key immune gene families, and compare to previously characterised marsupial and mammalian species...
November 20, 2017: Immunogenetics
https://www.readbyqxmd.com/read/29158776/genomics-and-prevalence-of-bacterial-and-archaeal-isolates-from-biogas-producing-microbiomes
#19
Irena Maus, Andreas Bremges, Yvonne Stolze, Sarah Hahnke, Katharina G Cibis, Daniela E Koeck, Yong S Kim, Jana Kreubel, Julia Hassa, Daniel Wibberg, Aaron Weimann, Sandra Off, Robbin Stantscheff, Vladimir V Zverlov, Wolfgang H Schwarz, Helmut König, Wolfgang Liebl, Paul Scherer, Alice C McHardy, Alexander Sczyrba, Michael Klocke, Alfred Pühler, Andreas Schlüter
Background: To elucidate biogas microbial communities and processes, the application of high-throughput DNA analysis approaches is becoming increasingly important. Unfortunately, generated data can only partialy be interpreted rudimentary since databases lack reference sequences. Results: Novel cellulolytic, hydrolytic, and acidogenic/acetogenic Bacteria as well as methanogenic Archaea originating from different anaerobic digestion communities were analyzed on the genomic level to assess their role in biomass decomposition and biogas production...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29158606/detecting-macroecological-patterns-in-bacterial-communities-across-independent-studies-of-global-soils
#20
Kelly S Ramirez, Christopher G Knight, Mattias de Hollander, Francis Q Brearley, Bede Constantinides, Anne Cotton, Si Creer, Thomas W Crowther, John Davison, Manuel Delgado-Baquerizo, Ellen Dorrepaal, David R Elliott, Graeme Fox, Robert I Griffiths, Chris Hale, Kyle Hartman, Ashley Houlden, David L Jones, Eveline J Krab, Fernando T Maestre, Krista L McGuire, Sylvain Monteux, Caroline H Orr, Wim H van der Putten, Ian S Roberts, David A Robinson, Jennifer D Rocca, Jennifer Rowntree, Klaus Schlaeppi, Matthew Shepherd, Brajesh K Singh, Angela L Straathof, Jennifer M Bhatnagar, Cécile Thion, Marcel G A van der Heijden, Franciska T de Vries
The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries...
November 20, 2017: Nature Microbiology
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