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https://www.readbyqxmd.com/read/29224189/acute-loss-of-adipose-tissue-derived-adiponectin-triggers-immediate-metabolic-deterioration-in-mice
#1
Jonathan Y Xia, Kai Sun, Chelsea Hepler, Alexandra L Ghaben, Rana K Gupta, Yu A An, William L Holland, Thomas S Morley, Andrew C Adams, Ruth Gordillo, Christine M Kusminski, Philipp E Scherer
AIM/HYPOTHESIS: Adiponectin (APN), a circulating hormone secreted by mature adipocytes, has been extensively studied because it has beneficial metabolic effects. While many studies have focused on the congenital loss of APN and its effects on systemic body glucose and lipid metabolism, little is known about the effects triggered by acute loss of APN in the adult mouse. We anticipated that genetically induced acute depletion of APN in adult mice would have a more profound effect on systemic metabolic health than congenital deletion of Adipoq, the gene encoding APN, with its associated potential for adaptive responses that may mask the phenotypes...
December 9, 2017: Diabetologia
https://www.readbyqxmd.com/read/29224169/multiplexing-for-oxidative-bisulfite-sequencing-oxbs-seq
#2
Kristina Kirschner, Felix Krueger, Anthony R Green, Tamir Chandra
DNA modifications, especially methylation, are known to play a crucial part in many regulatory processes in the cell. Recently, 5-hydroxymethylcytosine (5hmC) was discovered, a DNA modification derived as an intermediate of 5-methylcytosine (5mC) oxidation. Efforts to gain insights into function of this DNA modification are underway and several methods were recently described to assess 5hmC levels using sequencing approaches. Here we integrate adaptation based multiplexing and high-efficiency library prep into the oxidative Bisulfite Sequencing (oxBS-seq) workflow reducing the starting amount and cost per sample to identify 5hmC levels genome-wide...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224167/dna-methylation-analysis-of-free-circulating-dna-in-body-fluids
#3
Maria Jung, Glen Kristiansen, Dimo Dietrich
Circulating cell-free DNA in body fluids is an analyte of great interest in basic and clinical research. The analyses of DNA methylation and hydroxymethylation patterns in body fluids might allow one to determine the certain state of a disease, in particular of cancer. DNA methylation biomarkers in liquid biopsies, i.e. blood plasma samples, may help optimizing personalized therapy for individual patients. DNA methylation analyses of specific loci usually require a bisulfite conversion of the DNA, which requires a sufficiently high amount of DNA at the appropriate concentration...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224148/digital-restriction-enzyme-analysis-of-methylation-dream
#4
Jaroslav Jelinek, Justin T Lee, Matteo Cesaroni, Jozef Madzo, Shoudan Liang, Yue Lu, Jean-Pierre J Issa
Digital Restriction Enzyme Analysis of Methylation (DREAM) is a method for quantitative mapping of DNA methylation across genomes using next-generation sequencing (NGS) technology. The method is based on sequential cuts of genomic DNA with a pair of restriction enzymes (SmaI and XmaI) at CCCGGG target sites. Unmethylated sites are first digested with SmaI. This enzyme cuts the sites in the middle at CCC^GGG, leaving behind blunt ended fragments. CpG methylation completely blocks SmaI; therefore, only unmethylated sites are cleaved...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224146/the-help-based-dna-methylation-assays
#5
John M Greally
Restriction enzymes have been valuable tools for representing the genome for DNA methylation assays, whether by using methylation-dependent enzymes or by sampling a reduced representation of the genome using a methylation-insensitive enzyme. These survey assays have remained mainstays of genome-wide approaches even with the development of more comprehensive shotgun genome-wide bisulphite sequencing-based assays, as they are significantly more affordable. DNA methylation survey assays are numerous and include reduced representation bisulphite sequencing (RRBS), the Illumina HumanMethylation450K and EPIC microarray system, and our evolving series of HELP-based assays...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224144/low-input-whole-genome-bisulfite-sequencing-using-a-post-bisulfite-adapter-tagging-approach
#6
Julian R Peat, Sébastien A Smallwood
The epigenetic mark 5-methylcytosine confers heritable regulation of gene expression that can be dynamically modulated during transitions in cell fate. With the development of high-throughput sequencing technologies, it is now possible to obtain comprehensive genome-wide maps of the mammalian DNA methylation landscape, but the application of these techniques to limited material remains challenging. Here, we present an optimized protocol to perform whole-genome bisulfite sequencing on low inputs (100-5000 somatic cells) using a post-bisulfite adapter tagging approach...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224143/multiplexed-reduced-representation-bisulfite-sequencing-with-magnetic-bead-fragment-size-selection
#7
William P Accomando, Karin B Michels
Reduced representation bisulfite sequencing (RRBS) is a technique for assessing genome-wide DNA methylation in an organism whose genome has been fully sequenced. It allows researchers to target gene regions with particular CpG densities, thereby selecting the desired genomic contexts. Here, we describe an approach that uses magnetic beads to accomplish this selection. In addition, the use of indexed, methylated adapters enables up to 12 samples to be pooled, and subjected to multiplexed RRBS in a single-sequencing lane...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224141/tagmentation-based-library-preparation-for-low-dna-input-whole-genome-bisulfite-sequencing
#8
Dieter Weichenhan, Qi Wang, Andrew Adey, Stephan Wolf, Jay Shendure, Roland Eils, Christoph Plass
Aberrations of the DNA methylome contribute to onset and progression of diseases. Whole genome bisulfite sequencing (WGBS) is the only analytical method covering the complete methylome. Alternative methods requiring less DNA than WGBS analyze only a minor portion of the methylome and do not cover important regulatory features like enhancers and noncoding RNAs. In tagmentation-based WGBS (TWGBS), several DNA and time-consuming steps of the conventional WGBS library preparation are circumvented by the use of a hyperactive transposase, which simultaneously fragments DNA and appends sequencing adapters...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224079/primer-extension-capture-and-on-bead-cdna-ligation-an-efficient-rnaseq-library-prep-method-for-determining-reverse-transcription-termination-sites
#9
Phillip Ordoukhanian, Jessica Nichols, Steven R Head
In this chapter, we describe a method for making Illumina-compatible sequencing libraries from RNA. This protocol can be used for standard RNAseq analysis for detecting differentially expressed genes. In addition, this protocol is ideally suited for adapting to RIPseq, 5'-RACE, RNA structural probing, nascent RNA sequencing, and other protocols where polymerase termination sites need to be profiled. The utilization of solid-phase bead chemistries facilitates simple workflow and efficient library yields.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224073/cleantag-adapters-improve-small-rna-next-generation-sequencing-library-preparation-by-reducing-adapter-dimers
#10
Sabrina Shore, Jordana M Henderson, Anton P McCaffrey
Next-generation small RNA sequencing is a valuable tool which is increasing our knowledge regarding small noncoding RNAs and their function in regulating genetic information. Library preparation protocols for small RNA have thus far been restricted due to higher RNA input requirements (>10 ng), long workflows, and tedious manual gel purifications. Small RNA library preparation methods focus largely on the prevention or depletion of a side product known as adapter dimer that tends to dominate the reaction...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224070/genome-wide-analysis-of-dna-methylation-in-single-cells-using-a-post-bisulfite-adapter-tagging-approach
#11
Heather J Lee, Sébastien A Smallwood
DNA methylation is an epigenetic mark implicated in the regulation of key biological processes. Using high-throughput sequencing technologies and bisulfite-based approaches, it is possible to obtain comprehensive genome-wide maps of the mammalian DNA methylation landscape with a single-nucleotide resolution and absolute quantification. However, these methods were only applicable to bulk populations of cells. Here, we present a protocol to perform whole-genome bisulfite sequencing on single cells (scBS-Seq) using a post-bisulfite adapter tagging approach...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224067/multiplexed-targeted-sequencing-for-oxford-nanopore-minion-a-detailed-library-preparation-procedure
#12
Timokratis Karamitros, Gkikas Magiorkinis
MinION is a small form factor sequencer recently retailed by Oxford Nanopore technologies. This lighter-sized USB3.0-interfaced device uses innovative nanotechnology to generate extra-long reads from libraries prepared using only standard molecular biology lab equipment. The flexibility and the portability of the platform makes it ideal for point-of-interest and real-time surveillance applications. However, MinION's limited capacity is not enough for the study of specific targets within larger genomes. Apart from just PCR-amplifying regions of interest, the capture of long reads spanning the edges of known-unknown genomic regions is of great importance for structural studies, such as the identification of mobile elements' integrations sites, bridging over low complexity repetitive regions etc...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223936/-relationship-between-crowding-and-community-acquired-skin-and-soft-tissues-infections
#13
Marcelo A Beltrán, Horacio J García Del Corro, Mónica Couso, María D Gallo, Antonio Lettieri, Patricia V Barna
The association of the spread of community infections with poverty and overcrowding is well known. In our hospital, located in José C. Paz, we assist sporadic cases of post-cesarean infections caused by community acquired methicillin-resistant Staphylococcus aureus (CaMRSA). In a prospective study of families treated at our hospital, we investigated the relationship between a history of skin and soft tissue infections (SSTI) and extreme overcrowding defined as households with unsatisfied basic needs type 3 (NBI 3)...
2017: Medicina
https://www.readbyqxmd.com/read/29223926/an-update-on-factor-xi-structure-and-function
#14
REVIEW
Bassem M Mohammed, Anton Matafonov, Ivan Ivanov, Mao-Fu Sun, Qiufang Cheng, S Kent Dickeson, Chan Li, David Sun, Ingrid M Verhamme, Jonas Emsley, David Gailani
Factor XI (FXI) is the zymogen of a plasma protease, factor XIa (FXIa), that contributes to thrombin generation during blood coagulation by proteolytic activation of several coagulation factors, most notably factor IX (FIX). FXI is a homolog of prekallikrein (PK), a component of the plasma kallikrein-kinin system. While sharing structural and functional features with PK, FXI has undergone adaptive changes that allow it to contribute to blood coagulation. Here we review current understanding of the biology and enzymology of FXI, with an emphasis on structural features of the protein as they relate to protease function...
October 10, 2017: Thrombosis Research
https://www.readbyqxmd.com/read/29223875/snakes-exhibit-tissue-specific-variation-in-cardiotonic-steroid-sensitivity-of-na-k-atpase
#15
Shabnam Mohammadi, Georg Petschenka, Susannah S French, Akira Mori, Alan H Savitzky
Toads are among several groups of organisms chemically defended with lethal concentrations of cardiotonic steroids. As a result, most predators that prey on amphibians avoid toads. However, several species of snakes have gained resistance-conferring mutations of Na+/K+-ATPase, the molecular target of cardiotonic steroids, and can feed on toads readily. Despite recent advances in our understanding of this adaptation at the genetic level, we have lacked functional evidence for how mutations of Na+/K+-ATPase account for cardiotonic steroid resistance in snake tissues...
December 6, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/29223857/when-it-is-apt-to-adapt-flexible-reasoning-guides-children-s-use-of-talker-identity-and-disfluency-cues
#16
Justine M Thacker, Craig G Chambers, Susan A Graham
An eye-tracking methodology was used to examine whether children flexibly engage two voice-based cues, talker identity and disfluency, during language processing. Across two experiments, 5-year-olds (N = 58) were introduced to two characters with distinct color preferences. These characters then used fluent or disfluent instructions to refer to an object in a display containing items bearing either talker-preferred or talker-dispreferred colors. As the utterance began to unfold, the 5-year-olds anticipated that talkers would refer to talker-preferred objects...
December 7, 2017: Journal of Experimental Child Psychology
https://www.readbyqxmd.com/read/29223828/rationale-for-combination-of-therapeutic-antibodies-targeting-tumor-cells-and-immune-checkpoint-receptors-harnessing-innate-and-adaptive-immunity-through-igg1-isotype-immune-effector-stimulation
#17
REVIEW
Robert L Ferris, Heinz-Josef Lenz, Anna Maria Trotta, Jesús García-Foncillas, Jeltje Schulten, François Audhuy, Marco Merlano, Gerard Milano
Immunoglobulin (Ig) G1 antibodies stimulate antibody-dependent cell-mediated cytotoxicity (ADCC). Cetuximab, an IgG1 isotype monoclonal antibody, is a standard-of-care treatment for locally advanced and recurrent and/or metastatic squamous cell carcinoma of the head and neck (SCCHN) and metastatic colorectal cancer (CRC). Here we review evidence regarding the clinical relevance of cetuximab-mediated ADCC and other immune functions and provide a biological rationale concerning why this property positions cetuximab as an ideal partner for immune checkpoint inhibitors (ICIs) and other emerging immunotherapies...
December 2, 2017: Cancer Treatment Reviews
https://www.readbyqxmd.com/read/29223710/behavioral-responses-of-cd-1-mice-to-conspecific-and-heterospecific-blood-odors-and-to-a-blood-odor-component
#18
Christian Lahger, Matthias Laska
The odor of blood may have both aversive and attractive properties for mammals, depending on the species of the odor donor and the species perceiving the odor. To better understand the informational content of blood odor for a prey species we assessed behavioral responses of male CD-1 mice (n=60) to the odor of blood of same-sex and opposite-sex conspecifics, of a natural predator of mice (cat), and of a herbivore (horse) and an omnivore (human) non-predator of mice. Further, we assessed their behavior towards the mammalian blood odor component trans-4,5-epoxy-(E)-2-decenal which recent studies have shown to be as attractive to mammalian predators as the odor of real blood...
December 6, 2017: Physiology & Behavior
https://www.readbyqxmd.com/read/29223686/nourishing-networks-a-social-ecological-analysis-of-a-network-intervention-for-improving-household-nutrition-in-western-kenya
#19
Autumn L DeLorme, Erika R Gavenus, Charles R Salmen, Gor Ouma Benard, Brian Mattah, Elizabeth Bukusi, Kathryn J Fiorella
RATIONALE: A growing body of research emphasizes the need to engage social networks in maternal and child nutrition interventions. However, an understanding of how interventions functionally engage not only mothers but fathers, grandparents, friends, and other social network members remains limited. OBJECTIVE: This study uses an adaptation of a social-ecological model to analyze the multiple levels at which the Kanyakla Nutrition Program operates to change behavior...
November 20, 2017: Social Science & Medicine
https://www.readbyqxmd.com/read/29223682/neocortical-origin-and-progression-of-gray-matter-atrophy-in-nonamnestic-alzheimer-s-disease
#20
Jeffrey S Phillips, Fulvio Da Re, Laynie Dratch, Sharon X Xie, David J Irwin, Corey T McMillan, Sanjeev N Vaishnavi, Carlo Ferrarese, Edward B Lee, Leslie M Shaw, John Q Trojanowski, David A Wolk, Murray Grossman
Amnestic Alzheimer's disease (AD) is characterized by early atrophy of the hippocampus and medial temporal lobes before spreading to the neocortex. In contrast, nonamnestic Alzheimer's patients have relative sparing of the hippocampus, but the pattern in which the disease spreads is unclear. We examined spreading disease in nonamnestic AD using a novel magnetic resonance imaging-based analysis adapted from pathologic staging studies, applied here to cross-sectional imaging data. We selected 240 T1-weighted scans from 129 patients with pathology confirmed by autopsy or cerebrospinal fluid, and atrophy maps were computed relative to 238 scans from 115 elderly controls...
November 21, 2017: Neurobiology of Aging
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