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https://www.readbyqxmd.com/read/29029327/the-exonization-and-functionalization-of-an-alu-j-element-in-the-protein-coding-region-of-glycoprotein-hormone-alpha-gene-represent-a-novel-mechanism-to-the-evolution-of-hemochorial-placentation-in-primates
#1
Haidi Chen, Li Chen, Yune Wu, Hao Shen, Guang Yang, Cheng Deng
Alu elements contribute considerably to gene regulation and genome evolution in primates. The generation of new exons from Alu elements has been found in various human genes, and the regulatory function of the Alu exon has been investigated in many studies. However, the functionalization of Alu elements in protein coding regions remains unknown. Here, we reported that an Alu-J element exonized in the glycoprotein hormone alpha (GPHA) gene and encoded an additional N-terminal peptide (Alu-J encoding peptide) of the mature GPHA peptide, leading to a splicing variant of Alu-GPHA in anthropoid primates approximately 35 million years ago...
September 26, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29027161/considerations-on-experimental-design-and-data-analysis-of-chromatin-immunoprecipitation-experiments
#2
Antonio Jordán-Pla, Neus Visa
Arguably one of the most valuable techniques to study chromatin organization, ChIP is the method of choice to map the contacts established between proteins and genomic DNA. Ever since its inception, more than 30 years ago, ChIP has been constantly evolving, improving, and expanding its capabilities and reach. Despite its widespread use by many laboratories across a wide variety of disciplines, ChIP assays can be sometimes challenging to design, and are often sensitive to variations in practical implementation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29026649/unique-genome-organization-of-non-mammalian-papillomaviruses-provides-insights-into-the-evolution-of-viral-early-proteins
#3
Koenraad Van Doorslaer, Valeria Ruoppolo, Annie Schmidt, Amelie Lescroël, Dennis Jongsomjit, Megan Elrod, Simona Kraberger, Daisy Stainton, Katie M Dugger, Grant Ballard, David G Ainley, Arvind Varsani
The family Papillomaviridae contains more than 320 papillomavirus types, with most having been identified as infecting skin and mucosal epithelium in mammalian hosts. To date, only nine non-mammalian papillomaviruses have been described from birds (n = 5), a fish (n = 1), a snake (n = 1), and turtles (n = 2). The identification of papillomaviruses in sauropsids and a sparid fish suggests that early ancestors of papillomaviruses were already infecting the earliest Euteleostomi. The Euteleostomi clade includes more than 90 per cent of the living vertebrate species, and progeny virus could have been passed on to all members of this clade, inhabiting virtually every habitat on the planet...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/28994416/a-high-quality-genome-assembly-of-quinoa-provides-insights-into-the-molecular-basis-of-salt-bladder-based-salinity-tolerance-and-the-exceptional-nutritional-value
#4
Changsong Zou, Aojun Chen, Lihong Xiao, Heike M Muller, Peter Ache, Georg Haberer, Meiling Zhang, Wei Jia, Ping Deng, Ru Huang, Daniel Lang, Feng Li, Dongliang Zhan, Xiangyun Wu, Hui Zhang, Jennifer Bohm, Renyi Liu, Sergey Shabala, Rainer Hedrich, Jian-Kang Zhu, Heng Zhang
Chenopodium quinoa is a halophytic pseudocereal crop that is being cultivated in an ever-growing number of countries. Because quinoa is highly resistant to multiple abiotic stresses and its seed has a better nutritional value than any other major cereals, it is regarded as a future crop to ensure global food security. We generated a high-quality genome draft using an inbred line of the quinoa cultivar Real. The quinoa genome experienced one recent genome duplication about 4.3 million years ago, likely reflecting the genome fusion of two Chenopodium parents, in addition to the γ paleohexaploidization reported for most eudicots...
October 10, 2017: Cell Research
https://www.readbyqxmd.com/read/28989719/experimental-phase-determination-with-selenomethionine-or-mercury-derivatization-in-serial-femtosecond-crystallography
#5
Keitaro Yamashita, Naoyuki Kuwabara, Takanori Nakane, Tomohiro Murai, Eiichi Mizohata, Michihiro Sugahara, Dongqing Pan, Tetsuya Masuda, Mamoru Suzuki, Tomomi Sato, Atsushi Kodan, Tomohiro Yamaguchi, Eriko Nango, Tomoyuki Tanaka, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Hiroshi Manya, Tamao Endo, Ryuichi Kato, Toshiya Senda, Hiroaki Kato, So Iwata, Hideo Ago, Masaki Yamamoto, Fumiaki Yumoto, Toru Nakatsu
Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) holds enormous potential for the structure determination of proteins for which it is difficult to produce large and high-quality crystals. SFX has been applied to various systems, but rarely to proteins that have previously unknown structures. Consequently, the majority of previously obtained SFX structures have been solved by the molecular replacement method. To facilitate protein structure determination by SFX, it is essential to establish phasing methods that work efficiently for SFX...
September 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28989710/protein-microcrystallography-using-synchrotron-radiation
#6
REVIEW
Masaki Yamamoto, Kunio Hirata, Keitaro Yamashita, Kazuya Hasegawa, Go Ueno, Hideo Ago, Takashi Kumasaka
The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as small in meso crystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features...
September 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28987463/therapeutic-approaches-to-target-alpha-synuclein-pathology
#7
REVIEW
Patrik Brundin, Kuldip D Dave, Jeffrey H Kordower
Starting two decades ago with the discoveries of genetic links between alpha-synuclein and Parkinson's disease risk and the identification of aggregated alpha-synuclein as the main protein constituent of Lewy pathology, alpha-synuclein has emerged as the major therapeutic target in Parkinson's disease and related synucleinopathies. Following the suggestion that alpha-synuclein pathology gradually spreads through the nervous system following a stereotypic pattern and the discovery that aggregated forms of alpha-synuclein can propagate pathology from one cell to another, and thereby probably aggravate existing deficits as well as generate additional symptoms, the idea that alpha-synuclein is a viable therapeutic target gained further support...
October 4, 2017: Experimental Neurology
https://www.readbyqxmd.com/read/28987188/diseases-of-the-skeletal-muscle
#8
Edoardo Malfatti, Norma Beatriz Romero
After the advances created by the use of cryostat sections and histochemistry 60 years ago, muscle histopathology is now living a real renaissance. In the field of genetic neuromuscular disorders, muscle biopsy analysis is fundamental to address questions about pathogenicity and protein expression when new genes are discovered through next-generation sequencing approaches. Moreover, the identification of the same gene mutated in previously considered distinct histopathologic entities imposes a constant reassessment of morphologic boundaries in several groups of disorders...
2017: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/28984274/nonclassical-nucleation-pathways-in-protein-crystallization
#9
Fajun Zhang
Classical nucleation theory (CNT), which was established about 90 years ago, has been very successful in many research fields, and continues to be the most commonly used theory in describing the nucleation process. For a fluid-to-solid phase transition, CNT states that the solute molecules in a supersaturated solution reversibly form small clusters. Once the cluster size reaches a critical value, it becomes thermodynamically stable and favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously...
October 6, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28982935/the-evolution-of-interferon-tau
#10
REVIEW
Alan D Ealy, Lydia K Wooldridge
Thirty years ago, a novel type I interferon (IFN) was identified by molecular cloning of cDNA libraries constructed from RNA extracted from ovine and bovine pre-implantation embryos. This protein was eventually designated as IFN-tau (IFNT) to highlight its trophoblast-dependent expression. IFNT function is not immune related. Instead, it interacts with the maternal system to initiate the establishment and maintenance of pregnancy. This activity is indispensable for the continuation of pregnancy. Our review will describe how IFNT evolved from other type I IFNs to function in this new capacity...
November 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28977639/biochemical-and-single-molecule-analyses-of-the-rna-silencing-suppressing-activity-of-crpv-1a
#11
Mariko Watanabe, Hiro-Oki Iwakawa, Hisashi Tadakuma, Yukihide Tomari
Viruses often encode viral silencing suppressors (VSSs) to counteract the hosts' RNA silencing activity. The cricket paralysis virus 1A protein (CrPV-1A) is a unique VSS that binds to a specific Argonaute protein (Ago)-the core of the RNA-induced silencing complex (RISC)-in insects to suppress its target cleavage reaction. However, the precise molecular mechanism of CrPV-1A action remains unclear. Here we utilized biochemical and single-molecule imaging approaches to analyze the effect of CrPV-1A during target recognition and cleavage by Drosophila Ago2-RISC...
August 24, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28975734/a-jack-of-all-trades-the-rna-binding-protein-vigilin
#12
REVIEW
Matthew Hk Cheng, Ralf-Peter Jansen
The vigilin family of proteins is evolutionarily conserved from yeast to humans and characterized by the proteins' 14 or 15 hnRNP K homology (KH) domains, typically associated with RNA-binding. Vigilin is the largest RNA-binding protein (RBP) in the KH domain-containing family and one of the largest RBP known to date. Since its identification 30 years ago, vigilin has been shown to bind over 700 mRNAs and has been associated with cancer progression and cardiovascular disease. We provide a brief historic overview of vigilin research and outline the proteins' different functions, focusing on maintenance of genome ploidy, heterochromatin formation, RNA export, as well as regulation of translation, mRNA transport, and mRNA stability...
October 4, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28973902/drk-mediated-signaling-to-rho-kinase-is-required-for-anesthesia-resistant-memory-in-drosophila
#13
Vasileia Kotoula, Anastasios Moressis, Ourania Semelidou, Efthimios M C Skoulakis
Anesthesia-resistant memory (ARM) was described decades ago, but the mechanisms that underlie this protein synthesis-independent form of consolidated memory in Drosophila remain poorly understood. Whether the several signaling molecules, receptors, and synaptic proteins currently implicated in ARM operate in one or more pathways and how they function in the process remain unclear. We present evidence that Drk, the Drosophila ortholog of the adaptor protein Grb2, is essential for ARM within adult mushroom body neurons...
September 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28972150/building-the-cua-site-of-cytochrome-c-oxidase-a-complicated-redox-dependent-process-driven-by-a-surprisingly-large-complement-of-accessory-proteins
#14
Kimberly A Jett, Scot C Leary
Cytochrome c oxidase (COX) was initially purified more than 70 years ago. A tremendous amount of insight into its structure and function has since been gleaned from biochemical, biophysical, genetic and molecular studies. As a result, we now appreciate that COX relies on its redox-active metal centers (heme a and a3 , CuA and CuB) to reduce oxygen and pump protons in a reaction essential for most eukaryotic life. Questions persist, however, about how individual structural subunits are assembled into a functional holoenzyme...
September 29, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28971854/in-vitro-reconstitution-of-chaperone-mediated-human-risc-assembly
#15
Ken Naruse, Eriko Matsuura-Suzuki, Mariko Watanabe, Shintaro Iwasaki, Yukihide Tomari
To silence target mRNAs, small RNAs and Argonaute (Ago) proteins need to be assembled into RNA-induced silencing complexes (RISCs). Although the assembly of Drosophila melanogaster RISC was recently reconstituted by Ago2, the Dicer-2/R2D2 heterodimer, and 5 chaperone proteins, the absence of a reconstitution system for mammalian RISC assembly has posed analytical challenges. Here we describe reconstitution of human RISC assembly using Ago2 and 5 recombinant chaperone proteins: Hsp90β, Hsc70, Hop, Dnaja2, and p23...
October 2, 2017: RNA
https://www.readbyqxmd.com/read/28970560/endogenous-mirna-in-the-green-alga-chlamydomonas-regulates-gene-expression-through-cds-targeting
#16
Betty Y-W Chung, Michael J Deery, Arnoud J Groen, Julie Howard, David C Baulcombe
MicroRNAs (miRNAs) are 21-24-nucleotide RNAs present in many eukaryotes that regulate gene expression as part of the RNA-induced silencing complex. The sequence identity of the miRNA provides the specificity to guide the silencing effector Argonaute (AGO) protein to target mRNAs via a base-pairing process (1) . The AGO complex promotes translation repression and/or accelerated decay of this target mRNA (2) . There is overwhelming evidence both in vivo and in vitro that translation repression plays a major role (3-7) ...
October 2, 2017: Nature Plants
https://www.readbyqxmd.com/read/28964625/regulation-of-the-hippo-pathway-transcription-factor-tead
#17
REVIEW
Kimberly C Lin, Hyun Woo Park, Kun-Liang Guan
The TEAD transcription factor family is best known for transcriptional output of the Hippo signaling pathway and has been implicated in processes such as development, cell growth and proliferation, tissue homeostasis, and regeneration. Our understanding of the functional importance of TEADs has increased dramatically since its initial discovery three decades ago. The majority of our knowledge of TEADs is in the context of Hippo signaling as nuclear DNA-binding proteins passively activated by Yes-associated protein (YAP) and transcriptional activator with PDZ-binding domain (TAZ), transcription coactivators downstream of the Hippo pathway...
September 27, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28964526/pirna-biogenesis-in-drosophila-melanogaster
#18
REVIEW
Xiawei Huang, Katalin Fejes Tóth, Alexei A Aravin
The PIWI-interacting RNA (piRNA) pathway is a conserved defense system that protects the genome integrity of the animal germline from deleterious transposable elements. Targets of silencing are recognized by small noncoding piRNAs that are processed from long precursor molecules. Although piRNAs and other classes of small noncoding RNAs, such as miRNAs and small interfering (si)RNAs, interact with members of the same family of Argonaute (Ago) proteins and their function in target repression is similar, the biogenesis of piRNAs differs from those of the other two small RNAs...
September 27, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28962157/pien-tze-huang-alleviates-5-fluorouracil-induced-intestinal-mucositis-in-ct-26-tumor-bearing-mice
#19
Caixuan Fu, Jianfeng Chu, Aling Shen, Liya Liu, Hongwei Chen, Jiumao Lin, Thomas J Sferra, Youqin Chen, Jun Peng
Chemotherapeutic agents, including 5-fluorouracil (5-FU), frequently cause intestinal mucositis as a side effect, leading to life quality reduction in colorectal cancer (CRC) patients and interruption of CRC treatment. Traditional Chinese medicines (TCMs) have recently received attention due to their relatively few adverse effects. Pien Tze Huang (PZH), a well-known TCM formulation first documented to have been prescribed >450 years ago, has been demonstrated to be clinically effective in treating various types of cancer including CRC...
September 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28962129/microrna-186-affects-the-proliferation-of-tumor-cells-via-yes-associated-protein-1-in-the-occurrence-and-development-of-pancreatic-cancer
#20
Qinghui Niu, Xiaoyu Li, Di Xia, Yueping Jiang, Zibin Tian, Cheng Bian, Cuiping Zhang, Pei Liu, Fengjuan Zhang, Yuling Yang, Guanglan Wang
The present study aimed to determine the expression of microRNA (miRNA or miR)-186 in tumor tissues and peripheral blood of patients with pancreatic cancer (PC), as well as its mechanism of regulation. A total of 65 patients with PC who underwent surgery between June 2013 and October 2015 were included. In addition, 59 healthy subjects were recruited as controls. Reverse transcription-quantitative polymerase chain reaction was used to measure the expression of mRNA and miRNA. Western blotting and enzyme-linked immunosorbent assay were used to determine protein expression...
September 2017: Experimental and Therapeutic Medicine
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