Read by QxMD icon Read


Saurabh Sudha Dhiman, Namita Shrestha, Aditi David, Neha Basotra, Glenn R Johnson, Bhupinder S Chadha, Venkataramana Gadhamshetty, Rajesh K Sani
Residual solid and liquid streams from the one-pot CRUDE (Conversion of Raw and Untreated Disposal into Ethanol) process were treated with two separate biochemical routes for renewable energy transformation. The solid residual stream was subjected to thermophilic anaerobic digestion (TAD), which produced 95 ± 7 L methane kg-1 volatile solid with an overall energy efficiency of 12.9 ± 1.7%. A methanotroph, Methyloferula sp., was deployed for oxidation of mixed TAD biogas into methanol. The residual liquid stream from CRUDE process was used in a Microbial Fuel Cell (MFC) to produce electricity...
March 12, 2018: Bioresource Technology
Paulo P Amaral, Tommaso Leonardi, Namshik Han, Emmanuelle Viré, Dennis K Gascoigne, Raúl Arias-Carrasco, Magdalena Büscher, Luca Pandolfini, Anda Zhang, Stefano Pluchino, Vinicius Maracaja-Coutinho, Helder I Nakaya, Martin Hemberg, Ramin Shiekhattar, Anton J Enright, Tony Kouzarides
BACKGROUND: The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and lack of identified shared properties. Here we consider promoter conservation and positional conservation as indicators of functional commonality. RESULTS: We identify 665 conserved lncRNA promoters in mouse and human that are preserved in genomic position relative to orthologous coding genes...
March 15, 2018: Genome Biology
Yan Yan, Yue Ding, Fenfei Leng, David Dunlap, Laura Finzi
Supercoiling can alter the form and base pairing of the double helix and directly impact protein binding. More indirectly, changes in protein binding and the stress of supercoiling also influence the thermodynamic stability of regulatory, protein-mediated loops and shift the equilibria of fundamental DNA/chromatin transactions. For example, supercoiling affects the hierarchical organization and function of chromatin in topologically associating domains (TADs) in both eukaryotes and bacteria. On the other hand, a protein-mediated loop in DNA can constrain supercoiling within a plectonemic structure...
March 10, 2018: Nucleic Acids Research
Marcin D Tomala, Katarzyna Magiera-Mularz, Katarzyna Kubica, Sylwia Krzanik, Bartosz Zieba, Bogdan Musielak, Marcin Pustula, Grzegorz M Popowicz, Michael Sattler, Grzegorz Dubin, Lukasz Skalniak, Tad A Holak
USP2a is a deubiquitinating protease that rescues its target proteins from destruction by the proteasome by reversing the process of protein ubiquitination. USP2a shows oncogenic properties in vivo and has been found to be a specific activator of cyclin D1. Many types of cancers are addicted to cyclin D1 expression. Targeting USP2a is a promising strategy for cancer therapy but little progress has been made in the field of inhibition of USP2a. Using NMR-based fragment screening and biophysical binding assays, we have discovered small molecules that bind to USP2a...
March 5, 2018: European Journal of Medicinal Chemistry
Ezequiel Nazer, Ryan K Dale, Madoka Chinen, Behram Radmanesh, Elissa P Lei
Drosophila Argonaute2 (AGO2) has been shown to regulate expression of certain loci in an RNA interference (RNAi)-independent manner, but its genome-wide function on chromatin remains unknown. Here, we identified the nuclear scaffolding protein LaminB as a novel interactor of AGO2. When either AGO2 or LaminB are depleted in Kc cells, similar transcription changes are observed genome-wide. In particular, changes in expression occur mainly in active or potentially active chromatin, both inside and outside LaminB-associated domains (LADs)...
March 12, 2018: PLoS Genetics
Laercio R Porto-Neto, Derek M Bickhart, Antonio J Landaeta-Hernandez, Yuri T Utsunomiya, Melvin Pagan, Esbal Jimenez, Peter J Hansen, Serdal Dikmen, Steven G Schroeder, Eui-Soo Kim, Jiajie Sun, Edward Crespo, Norman Amati, John B Cole, Daniel J Null, Jose F Garcia, Antonio Reverter, William Barendse, Tad S Sonstegard
Evolutionary adaptations are occasionally convergent solutions to the same problem. A mutation contributing to a heat tolerance adaptation in Senepol cattle, a New World breed of mostly European descent, results in the distinct phenotype known as slick, where an animal has shorter hair and lower follicle density across its coat than wild type animals. The causal variant, located in the 11th exon of prolactin receptor , produces a frameshift that results in a truncated protein. However, this mutation does not explain all cases of slick coats found in criollo breeds...
2018: Frontiers in Genetics
Junya Zhang, Qianwen Sui, Hui Zhong, Xiaoshan Meng, Ziyue Wang, Yawei Wang, Yuansong Wei
This study investigated the fate of antibiotic resistance genes (ARGs) during mesophilic (mAD) and thermophilic digestion (tAD) of swine manure through zero valent iron (ZVI), natural zeolite and Dnase addition. Changes of microbial community, intI1, heavy metal resistance genes (MRGs) and virulence factors (VFs) were followed to clarify the influencing factors to ARGs reduction. Results showed that AD could realize ARGs reduction with tAD superior to mAD, and ZVI and natural zeolite could further enhance the reduction, especially for natural zeolite addition at mAD...
March 2, 2018: Bioresource Technology
Ibai Irastorza-Azcarate, Rafael D Acemel, Juan J Tena, Ignacio Maeso, José Luis Gómez-Skarmeta, Damien P Devos
The use of 3C-based methods has revealed the importance of the 3D organization of the chromatin for key aspects of genome biology. However, the different caveats of the variants of 3C techniques have limited their scope and the range of scientific fields that could benefit from these approaches. To address these limitations, we present 4Cin, a method to generate 3D models and derive virtual Hi-C (vHi-C) heat maps of genomic loci based on 4C-seq or any kind of 4C-seq-like data, such as those derived from NG Capture-C...
March 9, 2018: PLoS Computational Biology
Shehab A Aly, Doha Alyan, Mona S Fayed, Maged S Alhammadi, Yehya A Mostafa
AIM: The objective of the present study was to investigate success rates and associated factors affecting temporary anchorage device (TAD) failure in different biomechanical applications. METHODS: A total of 180 TADs were used as a part of 82 patients' treatment plan (24 males and 58 females); their mean age was 21.41 years. Three types of TADs were used: 50 (3M ESPE, Neuss, Germany), 56 (Bone screw; Jeil Medical, Seoul, Korea), and 74 (Morelli, Sorocaba, Brazil)...
March 6, 2018: Journal of Investigative and Clinical Dentistry
Quentin Szabo, Daniel Jost, Jia-Ming Chang, Diego I Cattoni, Giorgio L Papadopoulos, Boyan Bonev, Tom Sexton, Julian Gurgo, Caroline Jacquier, Marcelo Nollmann, Frédéric Bantignies, Giacomo Cavalli
Deciphering the rules of genome folding in the cell nucleus is essential to understand its functions. Recent chromosome conformation capture (Hi-C) studies have revealed that the genome is partitioned into topologically associating domains (TADs), which demarcate functional epigenetic domains defined by combinations of specific chromatin marks. However, whether TADs are true physical units in each cell nucleus or whether they reflect statistical frequencies of measured interactions within cell populations is unclear...
February 2018: Science Advances
Nicholas J K Breitborde, Letitia Labrecque, Aubrey Moe, Tad Gary, Mike Meyer
Growing evidence suggests that specialized, multicomponent intervention provided early in the course of a psychotic disorder may have a positive effect in ameliorating the morbidity and mortality associated with these disorders. This column describes the development of the Institute for Mental Health Research Early Psychosis Intervention Center, which leverages the unique strengths of a community and academic partnership to provide such specialty care in a youth-friendly, stigma-free environment. Since it opened in 2016, the program has had numerous successes, including securing increased reimbursements rates and performance-based incentives for the treatment of first-episode psychosis...
March 1, 2018: Psychiatric Services: a Journal of the American Psychiatric Association
I G Marchenko, I I Marchenko, A V Zhiglo
We present a study of the diffusion enhancement of underdamped Brownian particles in a one-dimensional symmetric space-periodic potential due to external symmetric time-periodic driving with zero mean. We show that the diffusivity can be enhanced by many orders of magnitude at an appropriate choice of the driving amplitude and frequency. The diffusivity demonstrates abnormal (decreasing) temperature dependence at the driving amplitudes exceeding a certain value. At any fixed driving frequency Ω normal temperature dependence of the diffusivity is restored at low enough temperatures, T<T_{TAD}(Ω)-in contrast with the problem with constant external driving...
January 2018: Physical Review. E
Upneet K Sokhi, Mark P Liber, Laura Frye, Sungho Park, Kyuho Kang, Tania Pannellini, Baohong Zhao, Rada Norinsky, Lionel B Ivashkiv, Shiaoching Gong
Enhancers regulate gene expression and have been linked with disease pathogenesis. Little is known about enhancers that regulate human disease-associated genes in primary cells relevant for pathogenesis. Here we use BAC transgenics and genome editing to dissect, in vivo and in primary immune cells, enhancers that regulate human TNFAIP3, which encodes A20 and is linked with autoimmune diseases. A20 expression is dependent on a topologically associating subdomain (sub-TAD) that harbors four enhancers, while another >20 enhancers in the A20 locus are redundant...
February 13, 2018: Nature Communications
Sasha D Hafner, Johan T Madsen, Johanna M Pedersen, Charlotte Rennuit
Combining aerobic and anaerobic digestion in a two-stage system can improve the degradation of wastewater sludge over the use of either technology alone. But use of aerobic digestion as a pre-treatment before anaerobic digestion generally reduces methane production due to loss of substrate through oxidation. An inter-stage configuration may avoid this reduction in methane production. Here, we evaluated the use of thermophilic aerobic digestion (TAD) as an inter-stage treatment for wastewater sludge using laboratory-scale semi-continuous reactors...
February 2018: Water Science and Technology: a Journal of the International Association on Water Pollution Research
Mary Ann Sanders, Jane E Brock, Beth T Harrison, Tad J Wieczorek, Xuefei Hong, Anthony J Guidi, Deborah A Dillon, Leslie Max, Susan C Lester
CONTEXT: - Patients choosing to retain the nipple when undergoing therapeutic or prophylactic mastectomy are at risk for cancers arising at that site. OBJECTIVE: - To identify cases of invasive carcinoma arising within the nipple and to investigate their clinical, imaging, biologic, and staging features. DESIGN: - Carcinomas were identified by prospective review of surgical and consult cases at 4 hospitals. RESULTS: - The 24 patients identified presented with symptoms related to the nipple...
February 12, 2018: Archives of Pathology & Laboratory Medicine
Federico Comoglio, Hyun Jung Park, Stefan Schoenfelder, Iros Barozzi, Daniel Bode, Peter Fraser, Anthony R Green
Thrombopoietin (TPO) is a critical cytokine regulating hematopoietic stem cell maintenance and differentiation into the megakaryocytic lineage. However, the transcriptional and chromatin dynamics elicited by TPO signaling are poorly understood. Here, we study the immediate early transcriptional and cis-regulatory responses to TPO in hematopoietic stem/progenitor cells (HSPCs) and use this paradigm of cytokine signaling to chromatin to dissect the relation between cis- regulatory activity and chromatin architecture...
February 2, 2018: Genome Research
Riccardo Maria Lanzetti, Auro Caraffa, Domenico Lupariello, Paolo Ceccarini, Giulio Gambaracci, Luigi Meccariello, Francesco Manfreda, Daniele Maiettini, Cristina Ibáñez Vicente, Michele Scialpi, Olga Bisaccia, Giuseppe Rinonapoli, Michele Bisaccia
BACKGROUND: Intertrochanteric fractures are of great interest worldwide and are the most frequently operated fractures. Intramedullary nailing is commonly used in the treatment of intertrochanteric fractures. The purpose of this study is to assess the necessity of using the distal blocking screw in 31-A1 and 31-A2 fractures, classified according to the Orthopaedic Trauma Association classification system (AO/OTA). METHODS: This is a prospective study of 143 consecutive patients (mean age 85...
February 9, 2018: European Journal of Orthopaedic Surgery & Traumatology: Orthopédie Traumatologie
Yanjian Li, Yi He, Zhengyu Liang, Yang Wang, Fengling Chen, Mohamed Nadhir Djekidel, Guipeng Li, Xu Zhang, Shuqin Xiang, Zejun Wang, Juntao Gao, Michael Q Zhang, Yang Chen
Chromatin conformation plays a key role in regulating gene expression and controlling cell differentiation. However, the whole-genome chromatin conformation changes that occur during leukemia cell differentiation are poorly understood. Here, we characterized the changes in chromatin conformation, histone states, chromatin accessibility, and gene expression using an all-trans retinoic acid (ATRA)-induced HL-60 cell differentiation model. The results showed that the boundaries of topological associated domains (TADs) were stable during differentiation; however, the chromatin conformations within several specific TADs were obviously changed...
February 8, 2018: Cell Death & Disease
Petros Kolovos, Rutger W W Brouwer, Christel E M Kockx, Michael Lesnussa, Nick Kepper, Jessica Zuin, A M Ali Imam, Harmen J G van de Werken, Kerstin S Wendt, Tobias A Knoch, Wilfred F J van IJcken, Frank Grosveld
Chromosome conformation capture (3C) and its derivatives (e.g., 4C, 5C and Hi-C) are used to analyze the 3D organization of genomes. We recently developed targeted chromatin capture (T2C), an inexpensive method for studying the 3D organization of genomes, interactomes and structural changes associated with gene regulation, the cell cycle, and cell survival and development. Here, we present the protocol for T2C based on capture, describing all experimental steps and bio-informatic tools in full detail. T2C offers high resolution, a large dynamic interaction frequency range and a high signal-to-noise ratio...
March 2018: Nature Protocols
Yixiao Gong, Charalampos Lazaris, Theodore Sakellaropoulos, Aurelie Lozano, Prabhanjan Kambadur, Panagiotis Ntziachristos, Iannis Aifantis, Aristotelis Tsirigos
The metazoan genome is compartmentalized in areas of highly interacting chromatin known as topologically associating domains (TADs). TADs are demarcated by boundaries mostly conserved across cell types and even across species. However, a genome-wide characterization of TAD boundary strength in mammals is still lacking. In this study, we first use fused two-dimensional lasso as a machine learning method to improve Hi-C contact matrix reproducibility, and, subsequently, we categorize TAD boundaries based on their insulation score...
February 7, 2018: Nature Communications
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"