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https://www.readbyqxmd.com/read/28938720/deep-whole-genome-sequencing-of-90-han-chinese-genomes
#1
Tianming Lan, Haoxiang Lin, Wenjuan Zhu, Tellier Christian Asker Melchior Laurent, Mengcheng Yang, Xin Liu, Jun Wang, Jian Wang, Huanming Yang, Xun Xu, Xiaosen Guo
Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938616/identification-of-potential-cancer-related-pseudogenes-in-lung-adenocarcinoma-based-on-cerna-hypothesis
#2
Yunzhen Wei, Zhiqiang Chang, Cheng Wu, Yinling Zhu, Kun Li, Yan Xu
Pseudogenes are initially regarded as non-functional genomic fossils resulted from inactivating gene mutations during evolution. Far from being silent, pseudogenes are proved to regulate the expression of protein-coding genes through function as microRNA sponge in vivo. The aim of our study was to propose an integrative systems biology approach to identify disease pseudogenes base on competitive endogenous RNA (ceRNA) hypothesis. Here, we applied our method to lung adenocarcinoma (LUAD) RNASeq data from TCGA and identified 33 candidate pseudogenes...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938609/pegylated-arginine-deiminase-can-modulate-tumor-immune-microenvironment-by-affecting-immune-checkpoint-expression-decreasing-regulatory-t-cell-accumulation-and-inducing-tumor-t-cell-infiltration
#3
Elena Brin, Katherine Wu, Hsin-Tze Lu, Yudou He, Zhaoming Dai, Wei He
PEGylated arginine deiminase (ADI-PEG 20) is being investigated in clinical studies in arginine auxotrophic cancers and is well-tolerated. The anti-tumor properties of ADI-PEG 20 have been extensively investigated - ADI-PEG 20 inhibits the growth of auxotrophic cancers in vitro and in vivo - however, its impact on immune cells is largely unknown. Here we report the potential impact of ADI-PEG 20 on the tumor immune microenvironment. ADI-PEG 20 induced immunosuppressive programmed death-ligand 1 expression on some cancer cells in vitro, but the magnitude of the increase was cell line dependent and in most relatively small...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938577/mitochondria-chaperone-grp75-moonlighting-as-a-cell-cycle-controller-to-derail-endocytosis-provides-an-opportunity-for-nanomicrosphere-intracellular-delivery
#4
Zhihui Gao, Xiuran Niu, Qing Zhang, Hang Chen, Aiai Gao, Shanshan Qi, Rong Xiang, Mattias Belting, Sihe Zhang
Understanding how cancer cells regulate endocytosis during the cell cycle could lead us to capitalize this event pharmacologically. Although certain endocytosis pathways are attenuated during mitosis, the endocytosis shift and regulation during the cell cycle have not been well clarified. The conventional concept of glucose-regulated proteins (GRPs) as protein folding chaperones was updated by discoveries that translocated GRPs assume moonlighting functions that modify the immune response, regulate viral release, and control intracellular trafficking...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938576/computational-prediction-of-human-disease-related-micrornas-by-path-based-random-walk
#5
Israel Mugunga, Ying Ju, Xiangrong Liu, Xiaoyang Huang
MicroRNAs (miRNAs) are a class of small, endogenous RNAs that are 21-25 nucleotides in length. In animals and plants, miRNAs target specific genes for degradation or translation repression. Discovering disease-related miRNA is fundamental for understanding the pathogenesis of diseases. The association between miRNA and a disease is mainly determined via biological investigation, which is complicated by increased biological information due to big data from different databases. Researchers have utilized different computational methods to harmonize experimental approaches to discover miRNA that articulates restrictively in specific environmental situations...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938445/mini-review-discovery-of-gnih-and-its-role-in-hypothyroidism-induced-delayed-puberty
#6
Kazuyoshi Tsutsui, You Lee Son, Mika Kiyohara, Ichiro Miyata
It is known that hypothyroidism delays puberty in mammals. Interaction between the hypothalamo-pituitary-thyroid (HPT) and hypothalamo-pituitary-gonadal (HPG) axes may be important processes in delayed puberty. Gonadotropin-inhibitory hormone (GnIH) is a newly discovered hypothalamic neuropeptide inhibiting gonadotropin synthesis and release in quail. It now apperas that GnIH is conserved across various mammals and primates including humans and inhibits reproduction. We have further demonstrated that GnIH is involved in pubertal delay induced by thyroid dysfunction in female mice...
September 18, 2017: Endocrinology
https://www.readbyqxmd.com/read/28938432/mitochondrial-function-regulated-by-mitoguardin-1-2-is-crucial-for-ovarian-endocrine-functions-and-ovulation
#7
Xiao-Man Liu, Yin-Li Zhang, Shu-Yan Ji, Long-Wen Zhao, Wei-Na Shang, Dali Li, Zijiang Chen, Chao Tong, Heng-Yu Fan
The balances of mitochondrial dynamic changes, mitochondrial morphology, and mitochondrial number are critical in cell metabolism. Once disturbed, disorders in these processes generally cause diseases or even death in animals. We performed large-scale genetic screenings in fruit flies and discovered the new gene mitoguardin (miga) that encodes for a mitochondrial outer membrane protein. In order to examine the physiological functions of its mammalian homologs Miga1 and 2, we generated Miga1 and Miga2 single- and double-knockout mouse strains and found that the knockout mice were viable, but the females were subfertile...
August 23, 2017: Endocrinology
https://www.readbyqxmd.com/read/28938404/the-transcriptome-of-estrogen-independent-mammary-growth-in-female-mice-reveals-that-not-all-mammary-glands-are-created-equally
#8
Grace E Berryhill, Danielle G Lemay, Josephine F Trott, Lucila Aimo, Adam L Lock, Russell C Hovey
Allometric growth of ducts in the mammary glands (MG) is widely-held to be estrogen (E)-dependent. We previously discovered that the dietary fatty acid trans-10, cis-12 conjugated linoleic acid (CLA) stimulates E-independent allometric growth and TEB formation in ovariectomized mice. Given the similar phenotype induced by E and CLA, we investigated the shared and/or divergent mechanisms underlying these changes. We confirmed MG growth induced by CLA is temporally distinct from that elicited by E, then used RNA-Sequencing to compare the transcriptome of the MG during similar proliferative and morphological states...
July 27, 2017: Endocrinology
https://www.readbyqxmd.com/read/28938317/postoperative-changes-in-isolated-medial-orbital-wall-fractures-based-on-computed-tomography
#9
Soyeon Jung, Jang Won Lee, Chung Hun Kim, Euna Hwang, Hyoseob Lim, Sung Won Jung, Sung Hoon Koh
The treatment has been improved on the accurate reduction of blow-out fracture for many decades. But still, it has been limited to reduce completely when surgeons are approaching by conventional technique. The authors analyzed the postoperative results using computed tomography (CT) scans after conventional open reduction of isolated medial wall fracture. Thirty-seven patients with isolated medial wall fracture were reviewed. All patients underwent preoperative, immediate, and postoperative CT scans. Two surgeons have performed the surgery by conventional open reduction with transcaruncular approach and absorbable mesh insertion...
September 21, 2017: Journal of Craniofacial Surgery
https://www.readbyqxmd.com/read/28938162/characterization-of-wedge-waves-propagating-along-wedge-tips-with-defects
#10
Ming-I Chen, Seng-Po Tesng, Pei-Yuan Lo, Che-Hua Yang
Wedge waves are guided acoustic waves propagating along the tip of a wedge with the energy tightly confined near the wedge. Anti-symmetric flexural (ASF) modes are wedge waves with their particle motion anti-symmetric with the apex mid-plane. This study investigates the behaviors of ASF modes propagation along wedge tips with perfect and imperfect rectangular defects. Numerical finite element simulations and experimental measurements using a laser ultrasound technique are employed to explore the behaviors of ASF modes interacting with defects...
September 14, 2017: Ultrasonics
https://www.readbyqxmd.com/read/28938159/lunatic-fringe-and-p53-cooperatively-suppress-mesenchymal-stem-like-breast-cancer
#11
Wen-Cheng Chung, Shubing Zhang, Lavanya Challagundla, Yunyun Zhou, Keli Xu
Claudin-low breast cancer (CLBC) is a poor prognosis molecular subtype showing stemness and mesenchymal features. We previously discovered that deletion of a Notch signaling modulator, Lunatic Fringe (Lfng), in the mouse mammary gland induced a subset of tumors resembling CLBC. Here we report that deletion of one copy of p53 on this background not only accelerated mammary tumor development but also led to a complete penetrance of the mesenchymal stem-like phenotype. All mammary tumors examined in the Lfng/p53 compound mutant mice displayed a mesenchymal/spindloid pathology...
September 19, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28938083/how-many-species-of-insects-and-other-terrestrial-arthropods-are-there-on-earth
#12
Nigel E Stork
In the last decade, new methods of estimating global species richness have been developed and existing ones improved through the use of more appropriate statistical tools and new data. Taking the mean of most of these new estimates indicates that globally there are approximately 1.5 million, 5.5 million, and 7 million species of beetles, insects, and terrestrial arthropods, respectively. Previous estimates of 30 million species or more based on the host specificity of insects to plants now seem extremely unlikely...
September 22, 2017: Annual Review of Entomology
https://www.readbyqxmd.com/read/28938065/in-vitro-selection-of-diversely-functionalized-aptamers
#13
Dehui Kong, Wayland Yeung, Ryan Hili
We describe the application of T4 DNA ligase-catalyzed DNA templated oligonucleotide polymerization toward the evolution of a diversely functionalized nucleic acid aptamer for human α-thrombin. Using a 256-membered ANNNN co-monomer library comprising 16 sub-libraries modi-fied with different functional groups, a highly-functionalized aptamer for thrombin was raised with a dissociation constant of 1.6 nM. The aptamer was found to be selective for thrombin, and re-quired the modifications for binding affinity...
September 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28937982/protein-complex-prediction-via-dense-subgraphs-and-false-positive-analysis
#14
Cecilia Hernandez, Carlos Mella, Gonzalo Navarro, Alvaro Olivera-Nappa, Jaime Araya
Many proteins work together with others in groups called complexes in order to achieve a specific function. Discovering protein complexes is important for understanding biological processes and predict protein functions in living organisms. Large-scale and throughput techniques have made possible to compile protein-protein interaction networks (PPI networks), which have been used in several computational approaches for detecting protein complexes. Those predictions might guide future biologic experimental research...
2017: PloS One
https://www.readbyqxmd.com/read/28937618/novel-fxa-inhibitor-identification-through-integration-of-ligand-and-structure-based-approaches
#15
Carlos F Lagos, Gerardine F Segovia, Nicolás Nuñez-Navarro, Mario A Faúndez, Flavia C Zacconi
Factor Xa (FXa), a vitamin K-dependent serine protease plays a pivotal role in the coagulation cascade, one of the most interesting targets for the development of new anticoagulants. In the present work, we performed a virtual screening campaign based on ligand-based shape and electrostatic similarity search and protein-ligand docking to discover novel FXa-targeted scaffolds for further development of inhibitors. From an initial set of 260,000 compounds from the NCI Open database, 30 potential FXa inhibitors were identified and selected for in vitro biological evaluation...
September 22, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28937220/a-fluorescence-polarization-activity-based-protein-profiling-assay-in-the-discovery-of-potent-selective-inhibitors-for-human-non-lysosomal-glucosylceramidase
#16
Daniel Lahav, Bing Liu, Richard J B H N van den Berg, Adrianus M C H van den Nieuwendijk, Tom Wennekes, Amar T Ghisaidoobe, Imogen Breen, Maria J Ferraz, Chi-Lin Kuo, Liang Wu, Paul P Geurink, Huib Ovaa, Gijsbert A van der Marel, Mario van der Stelt, Rolf G Boot, Gideon J Davies, Johannes M F G Aerts, Herman S Overkleeft
Human non-lysosomal glucosylceramidase (GBA2) is one of several enzymes that controls levels of glycolipids and whose activity is linked to several human disease states. There is a major need to design or discover selective GBA2 inhibitors both as chemical tools and as potential therapeutic agents. Here, we describe the development of a fluorescence polarization activity-based protein profiling (FluoPol-ABPP) assay for the rapid identification, from a 350+ library of iminosugars, of GBA2 inhibitors. A focused library is generated based on leads from the FluoPol-ABPP screen and assessed on GBA2 selectivity offset against the other glucosylceramide metabolizing enzymes, glucosylceramide synthase (GCS), lysosomal glucosylceramidase (GBA) and the cytosolic retaining β-glucosidase, GBA3...
September 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28936966/-progress-of-mechanical-ventilation-during-cardiopulmonary-resuscitation
#17
Cai Wen, Tao Yu, Lixiang Wang
Mechanical ventilation is regarded as an effective means of replacing artificial ventilation during cardiopulmonary resuscitation (CPR), and has been widely used in the treatment of cardiac arrest (CA) patients. However, there are still some controversial issues remaining to be settled, such as the assessment of the effectiveness of mechanical ventilation, the selection of the optimal oxygen concentration (FiO2), tidal volume (VT), respiratory frequency, and mode of ventilation during the CPR process. The pros and cons of positive pressure ventilation are also inconclusive...
September 2017: Zhonghua Wei Zhong Bing Ji Jiu Yi Xue
https://www.readbyqxmd.com/read/28936739/cardioprotective-effects-of-exosomes-and-their-potential-therapeutic-use
#18
Shengguang Ding, Jingying Zhang, Qiying Dai, Mengfei Zhao, Haitao Huang, Yiming Xu, Chongjun Zhong
Exosomes are membrane-contained vesicles released by various types of cells both in animals and human. They contain microRNAs and proteins and can travel to target cells, affecting their functions. There are specific factors on the surface of every exosomes, making sure that they will be taken up by certain type of cells. With these features, exosomes have been recognized to be one of the fundamental "messengers" for cell-cell communication. Recently, increased interest has been raised in exosomes since they were discovered to play an unneglectable role in preserving cardiac function and cardiomyocyte repair during stress...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28936526/modeling-the-impedance-spectra-of-mixed-conducting-thin-films-with-exposed-and-embedded-current-collectors
#19
Jiapeng Liu, Francesco Ciucci
In this article, we develop a new finite-element-based model for the simulation of the electrochemical impedance spectroscopy (EIS) response of mixed ionic electronic conducting (MIEC) thin films. We first validated the model against experimental data for Sm-doped CeO2 (SDC) symmetrical films deposited on an yittria-stabilized ZrO2 (YSZ) substrate, a pure ionic conductor. We first studied the configuration where the patterned electrodes are placed on top of the MIEC ("exposed" configuration). Our model is capable of correctly reproducing the EIS response and the total capacitance, together with their dependence on the oxygen partial pressure...
September 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28936489/landmark-based-alzheimer-s-disease-diagnosis-using-longitudinal-structural-mr-images
#20
Jun Zhang, Mingxia Liu, Le An, Yaozong Gao, Dinggang Shen
In this paper, we propose a landmark-based feature extraction method for AD diagnosis using longitudinal structural MR images, which requires no nonlinear registration or tissue segmentation in the application stage and is robust to the inconsistency among longitudinal scans. Specifically, (1) the discriminative landmarks are first automatically discovered from the whole brain, which can be efficiently localized using a fast landmark detection method for the testing images; (2) High-level statistical spatial features and contextual longitudinal features are then extracted based on those detected landmarks...
October 2016: Bayesian and Graphical Models for Biomedical Imaging: BAMBI 2014
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