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https://www.readbyqxmd.com/read/28542210/drosophila-dna-polymerase-theta-utilizes-both-helicase-like-and-polymerase-domains-during-microhomology-mediated-end-joining-and-interstrand-crosslink-repair
#1
Kelly Beagan, Robin L Armstrong, Alice Witsell, Upasana Roy, Nikolai Renedo, Amy E Baker, Orlando Scharer, Mitch McVey
Double strand breaks (DSBs) and interstrand crosslinks (ICLs) are toxic DNA lesions that can be repaired through multiple pathways, some of which involve shared proteins. One of these proteins, DNA Polymerase θ (Pol θ), coordinates a mutagenic DSB repair pathway named microhomology-mediated end joining (MMEJ) and is also a critical component for bypass or repair of ICLs in several organisms. Pol θ contains both polymerase and helicase-like domains that are tethered by an unstructured central region. While the role of the polymerase domain in promoting MMEJ has been studied extensively both in vitro and in vivo, a function for the helicase-like domain, which possesses DNA-dependent ATPase activity, remains unclear...
May 25, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28535560/nomogram-for-predicting-intradiscal-cement-leakage-following-percutaneous-vertebroplasty-in-patients-with-osteoporotic-related-vertebral-compression-fractures
#2
Bin-Yan Zhong, Shi-Cheng He, Hai-Dong Zhu, Tao Pan, Wen Fang, Li Chen, Jin-He Guo, Gang Deng, Guang-Yu Zhu, Gao-Jun Teng
BACKGROUND: Intradiscal cement leakage (ICL) is a common complication following percutaneous vertebroplasty (PVP). However, the risk factors for such a complication are under debate and there is no accurate predictive nomogram to predict ICL. OBJECTIVES: To establish an effective and novel nomogram for ICL following PVP in patients with osteoporotic-related vertebral compression fractures (OVCFs). STUDY DESIGN: This was a retrospective study approved by the Institutional Review Board of our institution...
May 2017: Pain Physician
https://www.readbyqxmd.com/read/28535027/arsenite-binds-to-the-ring-finger-domain-of-fancl-e3-ubiquitin-ligase-and-inhibits-dna-interstrand-cross-link-repair
#3
Ji Jiang, Marina Bellani, Lin Li, Pengcheng Wang, Michael M Seidman, Yinsheng Wang
Human exposure to arsenic in drinking water is known to be associated with the development of bladder, lung, kidney, and skin cancers. The molecular mechanisms underlying the carcinogenic effects of arsenic species remain incompletely understood. DNA interstrand cross-links (ICLs) are among the most cytotoxic type of DNA lesions that block DNA replication and transcription, and these lesions can be induced by endogenous metabolism and by exposure to exogenous agents. Fanconi anemia (FA) is a congenital disorder manifested with elevated sensitivity toward DNA interstrand cross-linking agents...
May 23, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28530598/understanding-the-fine-structure-of-intermediate-materials-of-maize-starches
#4
Wenfang Han, Binjia Zhang, Jiangtao Li, Siming Zhao, Meng Niu, Caihua Jia, Shanbai Xiong
Here we concern the molecular fine structure of intermediate material (IM) fraction in regular maize starch (RMS) and Starpro 40 maize starch (S40). IM had a branching degree and a molar mass (Mw) somewhere between amylopectin (AP) and amylose (AM). Compared with AP, IM had more extra-long (Fr I) and long (Fr II) chains and fb3-chains (degree of polymerization (DP)>36), with a higher average chain length (CL). Also, IM contained less A-chains but more B-chains (both BS-chains with DP 3-25 and BL-chains with DP≥26), accompanied by longer B- and BL-chains, total internal chains (TICL) and average internal chains (ICL), and a similar average external chain length (ECL)...
October 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28524769/machine-learning-for-epigenetics-and-future-medical-applications
#5
Lawrence B Holder, M Muksitul Haque, Michael K Skinner
Understanding epigenetic processes holds immense promise for medical applications. Advances in Machine Learning (ML) are critical to realize this promise. Previous studies used epigenetic data sets associated with the germline transmission of epigenetic transgenerational inheritance of disease and novel ML approaches to predict genome-wide locations of critical epimutations. A combination of Active Learning (ACL) and Imbalanced Class Learning (ICL) was used to address past problems with ML to develop a more efficient feature selection process and address the imbalance problem in all genomic data sets...
May 19, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28524082/cellular-repair-of-dna-dna-cross-links-induced-by-1-2-3-4-diepoxybutane
#6
Lisa N Chesner, Amanda Degner, Dewakar Sangaraju, Shira Yomtoubian, Susith Wickramaratne, Bhaskar Malayappan, Natalia Tretyakova, Colin Campbell
Xenobiotic-induced interstrand DNA-DNA cross-links (ICL) interfere with transcription and replication and can be converted to toxic DNA double strand breaks. In this work, we investigated cellular responses to 1,4-bis-(guan-7-yl)-2,3-butanediol (bis-N7G-BD) cross-links induced by 1,2,3,4-diepoxybutane (DEB). High pressure liquid chromatography electrospray ionization tandem mass spectrometry (HPLC-ESI⁺-MS/MS) assays were used to quantify the formation and repair of bis-N7G-BD cross-links in wild-type Chinese hamster lung fibroblasts (V79) and the corresponding isogenic clones V-H1 and V-H4, deficient in the XPD and FANCA genes, respectively...
May 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28522139/in-vivo-confocal-raman-microscopic-determination-of-depth-profiles-of-the-stratum-corneum-lipid-organization-influenced-by-application-of-various-oils
#7
ChunSik Choe, Johannes Schleusener, Jürgen Lademann, Maxim E Darvin
BACKGROUND: The intercellular lipids (ICL) of stratum corneum (SC) play an important role in maintaining the skin barrier function. The lateral and lamellar packing order of ICL in SC is not homogenous, but rather depth-dependent. OBJECTIVE: This study aimed to analyze the influence of the topically applied mineral-derived (paraffin and petrolatum) and plant-derived (almond oil and jojoba oil) oils on the depth-dependent ICL profile ordering of the SC in vivo. METHOD: Confocal Raman microscopy (CRM), a unique tool to analyze the depth profile of the ICL structure non-invasively, is employed to investigate the interaction between oils and human SC in vivo...
May 6, 2017: Journal of Dermatological Science
https://www.readbyqxmd.com/read/28516845/activity-and-functional-properties-of-the-isocitrate-lyase-in-the-cyanobacterium-cyanothece-sp-pcc-7424
#8
Marianne Gründel, Henning Knoop, Ralf Steuer
Cyanobacteria are ubiquitous photoautotrophs that assimilate atmospheric CO2 as their main source of carbon. Several cyanobacteria are known to be facultative heterotrophs that are able to grow on diverse carbon sources. For selected strains, assimilation of organic acids and mixotrophic growth on acetate has been reported for decades. However, evidence for the existence of a functional glyoxylate shunt in cyanobacteria has long been contradictory and unclear. Genes coding for isocitrate lyase (ICL) and malate synthase were recently identified in two strains of the genus Cyanothece, and the existence of the complete glyoxylate shunt was verified in a strain of Chlorogloeopsis fritschii...
May 18, 2017: Microbiology
https://www.readbyqxmd.com/read/28503437/comparison-of-postoperative-optical-quality-according-to-the-degree-of-decentering-of-v4c-implantable-collamer-lens
#9
Min Ji Park, Hye Min Jeon, Kyoung Heon Lee, Sang Youp Han
AIM: To evaluate the clinical outcomes of V4c implantable collamer lens (Hole ICL) implantation with regard to the optical quality assessed according to different degrees of decentering. METHODS: This included 49 eyes that received conventional ICL and 94 eyes that received Hole ICL. The eyes that received Hole ICL were divided into three groups according to the degree of decentering: group 1, central hole within 1 hole diameter (HD) from the pupil center; group 2, central hole within 1 HD to 2 HD; and group 3, central hole within 2 HD to 3 HD...
2017: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/28497960/using-dynamic-covalent-chemistry-to-drive-morphological-transitions-controlled-release-of-encapsulated-nanoparticles-from-block-copolymer-vesicles
#10
Renhua Deng, Matthew J Derry, Charlotte J Mable, Yin Ning, Steven P Armes
Dynamic covalent chemistry is exploited to drive morphological order-order transitions to achieve the controlled release of a model payload (e.g., silica nanoparticles) encapsulated within block copolymer vesicles. More specifically, poly(glycerol monomethacrylate)-poly(2-hydroxypropyl methacrylate) (PGMA-PHPMA) diblock copolymer vesicles were prepared via aqueous polymerization-induced self-assembly in either the presence or absence of silica nanoparticles. Addition of 3-aminophenylboronic acid (APBA) to such vesicles results in specific binding of this reagent to some of the pendent cis-diol groups on the hydrophilic PGMA chains to form phenylboronate ester bonds in mildly alkaline aqueous solution (pH ∼ 10)...
May 23, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28497691/fine-tuned-photoactive-and-interconnection-layers-for-achieving-over-13-efficiency-in-a-fullerene-free-tandem-organic-solar-cell
#11
Yong Cui, Huifeng Yao, Bowei Gao, Yunpeng Qin, Shaoqing Zhang, Bei Yang, Chang He, Bowei Xu, Jianhui Hou
Fabricating organic solar cells (OSCs) with a tandem structure has been considered an effective method to overcome the limited light absorption spectra of organic photovoltaic materials. Currently, the most efficient tandem OSCs are fabricated by adopting fullerene-derivatives as acceptors. Here, we design a new NF-acceptor with an E(opt)g of 1.68 eV for the front sub-cells and optimize the phase separation morphology of a fullerene-free active layer with an E(opt)g of 1.36 eV to fabricate the rear sub-cell...
May 12, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28485930/reactivity-and-cross-linking-of-5-terminal-abasic-sites-within-dna
#12
Suzanne J Admiraal, Patrick J O'Brien
Nicking of the DNA strand immediately upstream of an internal abasic (AP) site produces 5'-terminal abasic (dRp) DNA. Both the intact and the nicked abasic species are reactive intermediates along the DNA base excision repair (BER) pathway and can be derailed by side reactions. Aberrant accumulation of the 5'-terminal abasic intermediate has been proposed to lead to cell death, so we explored its reactivity and compared it to the reactivity of the better-characterized internal abasic intermediate. We find that the 5'-terminal abasic group cross-links with the exocyclic amine of a nucleotide on the opposing strand to form an interstrand DNA-DNA cross-link (ICL)...
May 9, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28482825/effect-of-limbal-relaxing-incisions-during-implantable-collamer-lens-surgery
#13
Zhen Li, Yu Han, Budan Hu, Huibin Du, Gengsheng Hao, Xiaoxi Chen
BACKGROUND: The limbal relaxing incisions (LRIs) technique is a safe and an inexpensive procedure, which is simple for experts to perform. It can effectively reduce astigmatism and result in a rapid visual rehabilitation. But there are few reports about reducing pre-existing corneal astigmatism by LRI in ICL surgery. Our research was aimed to study the effect of limbal relaxing inci sions during implantable collamer lens (ICL) surgery. METHODS: A prospective analysis reviewing consecutive cases of corneal astigmatism that had either independent ICL surgery (control group) or combined with LRIs (LRIs group)...
May 8, 2017: BMC Ophthalmology
https://www.readbyqxmd.com/read/28474969/hla-drb1-04-05-allele-is-associated-with-intracortical-lesions-on-three-dimensional-double-inversion-recovery-images-in-japanese-patients-with-multiple-sclerosis
#14
Koji Shinoda, Takuya Matsushita, Yuri Nakamura, Katsuhisa Masaki, Ryo Yamasaki, Hiroo Yamaguchi, Osamu Togao, Akio Hiwatashi, Jun-Ichi Kira
BACKGROUND: Cortical lesions (CLs) frequently observed in Caucasian patients with multiple sclerosis (MS) contribute to disability. However, it remains unclear whether CLs are associated with clinical features and genetic risk factors, such as HLA-DRB1*15:01 and -DRB1*04:05 in Asian MS patients. OBJECTIVE: To elucidate the frequency of CLs and their association with HLA-DRB1 and DPB1 alleles in Japanese MS patients. METHODS: Three-dimensional double inversion recovery imaging and clinical information were retrospectively obtained from 92 Japanese MS patients...
May 1, 2017: Multiple Sclerosis: Clinical and Laboratory Research
https://www.readbyqxmd.com/read/28471211/arithmetical-calculation-and-related-neuropsychological-skills-in-subjects-with-isolated-oral-clefts
#15
Jon W Goodwin, Amy L Conrad, Timothy Ansley, Peg Nopoulos
OBJECTIVE: The current study examined whether the arithmetical calculation skills of children, adolescents, and young adults with isolated cleft of the lip and/or palate (iCL/P) differ significantly from unaffected control participants. Comparisons of potential neuropsychological predictors of arithmetical calculation were also conducted to determine whether these variables differ significantly for participants with iCL/P. METHOD: Participants (N = 176; 93 iCL/P and 83 Control) ranged in age from 7 to 26 years old...
May 4, 2017: Neuropsychology
https://www.readbyqxmd.com/read/28458043/targeting-isocitrate-lyase-for-the-treatment-of-latent-tuberculosis
#16
REVIEW
Ram Prasad Bhusal, Ghader Bashiri, Brooke X C Kwai, Jonathan Sperry, Ivanhoe K H Leung
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis that can remain dormant for many years before becoming active. One way to control and eliminate TB is the identification and treatment of latent TB, preventing infected individuals from developing active TB and thus eliminating the subsequent spread of the disease. Isocitrate lyase (ICL) is involved in the mycobacterial glyoxylate and methylisocitrate cycles. ICL is important for the growth and survival of M. tuberculosis. ICL is not present in humans and is therefore a potential therapeutic target for the development of anti-TB agents...
April 27, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/28457282/outcomes-after-implantable-collamer-lens-surgery-in-a-canadian-cohort
#17
Aaron T Chan, Noa A Zauberman, Clara C Chan, David S Rootman
OBJECTIVE: To describe refractive outcomes and complications after implantable collamer lens (ICL) implantation. DESIGN: Retrospective, interventional case series. METHODS: A database search of ICL surgeries over a 5-year period (2009-2013) was conducted, and 83 eyes of 44 patients were included. The Visian ICL (STAAR Surgical, Monrovia, Calif.) was used in all eyes. The primary outcome measure was postoperative uncorrected distance acuity (UCDA)...
April 2017: Canadian Journal of Ophthalmology. Journal Canadien D'ophtalmologie
https://www.readbyqxmd.com/read/28453336/the-relationship-between-the-intercrease-line-and-the-a1-digital-pulley-a-cadaveric-study
#18
Colyn J Watkins, Nikola Zivaljevic, Kyle R Eberlin, Michael Rivlin, Chaitanya S Mudgal
BACKGROUND: Accurate identification of surface anatomy is critical to identify the location of the A1 pulley. The intercrease line (ICL) describes a transverse line between the radial edge of the proximal palmar crease and the ulnar edge of the distal palmar crease. We hypothesize that this easily identifiable surface landmark approximates the location of the A1 pulley. METHODS: The ICL was marked on 7 cadaver hands. We marked a point proximal to the proximal digital crease (PDC) equal to the distance between each digit's proximal interphalangeal crease (PIC) and PDC (the PIC/PDC point)...
May 2017: Hand: Official Journal of the American Association for Hand Surgery
https://www.readbyqxmd.com/read/28448050/single-molecule-analysis-of-laser-localized-psoralen-adducts
#19
Jing Huang, Himabindu Gali, Julia Gichimu, Marina A Bellani, Durga Pokharel, Manikandan Paramasivam, Michael M Seidman
The DNA Damage Response (DDR) has been extensively characterized in studies of double strand breaks (DSBs) induced by laser micro beam irradiation in live cells. The DDR to helix distorting covalent DNA modifications, including interstrand DNA crosslinks (ICLs), is not as well defined. We have studied the DDR stimulated by ICLs, localized by laser photoactivation of immunotagged psoralens, in the nuclei of live cells. In order to address fundamental questions about adduct distribution and replication fork encounters, we combined laser localization with two other technologies...
April 20, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28432345/distant-phe345-mutation-compromises-the-stability-and-activity-of-mycobacterium-tuberculosis-isocitrate-lyase-by-modulating-its-structural-flexibility
#20
Harish Shukla, Rohit Shukla, Amit Sonkar, Tripti Pandey, Timir Tripathi
Isocitrate lyase (ICL), a potential anti-tubercular drug target, catalyzes the first step of the glyoxylate shunt. In the present investigation, we studied the conformational flexibility of MtbICL to better understand its stability and catalytic activity. Our biochemical results showed that a point mutation at Phe345, which is topologically distant (>10 Å) to the active site signature sequence ((189)KKCGH(193)), completely abolishes the activity of the enzyme. In depth computational analyses were carried out for understanding the structural alterations using molecular dynamics, time-dependent secondary structure and principal component analysis...
April 21, 2017: Scientific Reports
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