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https://www.readbyqxmd.com/read/28611392/targeted-sequencing-of-both-dna-strands-barcoded-and-captured-individually-by-rna-probes-to-identify-genome-wide-ultra-rare-mutations
#1
Qing Wang, Xu Wang, Pheobe S Tang, Grace M O'leary, Ming Zhang
Next Generation Sequencing (NGS) has been widely implemented in biological research and has made a profound impact on patient care. One of the essential NGS applications is to identify disease-causing sequence variants, where high coverage and accuracy are needed. Here, we reported a novel NGS pipeline, termed a Sequencing System of Digitalized Barcode Encrypted Single-stranded Library from Extremely Low (quality and quantity) DNA Input with Probe-based DNA Enrichment by RNA probes targeting DNA duplex (DEEPER-Seq)...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28611213/spacer-capture-and-integration-by-a-type-i-f-cas1-cas2-3-crispr-adaptation-complex
#2
Robert D Fagerlund, Max E Wilkinson, Oleg Klykov, Arjan Barendregt, F Grant Pearce, Sebastian N Kieper, Howard W R Maxwell, Angela Capolupo, Albert J R Heck, Kurt L Krause, Mihnea Bostina, Richard A Scheltema, Raymond H J Staals, Peter C Fineran
CRISPR-Cas adaptive immune systems capture DNA fragments from invading bacteriophages and plasmids and integrate them as spacers into bacterial CRISPR arrays. In type I-E and II-A CRISPR-Cas systems, this adaptation process is driven by Cas1-Cas2 complexes. Type I-F systems, however, contain a unique fusion of Cas2, with the type I effector helicase and nuclease for invader destruction, Cas3. By using biochemical, structural, and biophysical methods, we present a structural model of the 400-kDa Cas14-Cas2-32 complex from Pectobacterium atrosepticum with bound protospacer substrate DNA...
June 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28611171/pitfalls-of-the-duplex-system-the-mystery-of-the-missing-stone
#3
Donald Kudakwashe Nyanhongo, Satpal Antil, Syed Nasir
A duplex ureter constitutes about 1% of the renal tract anomalies.A 39-year-old man presented with a 4-week history of left loin pain and microscopic haematuria. Investigation with a non-contrast CT KUB revealed a 6 mm non-obstructing calculus in the left distal ureter.Left ureteroscopy and lithotripsy was planned. However, ureteroscopy failed to identify the calculus. A double J ureteric stent was left in situ and the procedure abandoned in favour of further assessment with a CT urogram. Imaging surprisingly showed a left duplex ureter with the calculus in the non-stented ureter...
June 13, 2017: BMJ Case Reports
https://www.readbyqxmd.com/read/28608333/in-vitro-formation-of-plant-rna-induced-silencing-complexes-using-an-extract-of-evacuolated-tobacco-protoplasts
#4
Taichiro Iki, Masayuki Ishikawa, Manabu Yoshikawa
Small RNA-mediated gene silencing is involved in a variety of biological processes among many eukaryotic organisms. The silencing effector, generally referred to as RNA-induced silencing complex (RISC), comprises an ARGONAUTE (AGO) protein and a small single-stranded guide RNA in its core. RISCs recognize target genes containing sequences complementary to the guide RNA and repress their expression transcriptionally or posttranscriptionally. In vitro systems that recapitulate RISC assembly are useful not only to decipher the molecular mechanisms underlying the assembly process itself but also to dissect the downstream silencing pathways mediated by RISCs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28603040/a-real-time-control-system-of-gene-expression-using-ligand-bound-nucleic-acid-aptamer-for-metabolic-engineering
#5
Jing Wang, Xun Cui, Le Yang, Zhe Zhang, Liping Lv, Haoyuan Wang, Zhenmin Zhao, Ningzi Guan, Lichun Dong, Rachel Chen
Artificial control of bio-functions through regulating gene expression is one of the most important and attractive technologies to build novel living systems that are useful in the areas of chemical synthesis, nanotechnology, pharmacology, cell biology. Here, we present a novel real-time control system of gene regulation that includes an enhancement element by introducing duplex DNA aptamers upstream promoter and a repression element by introducing a RNA aptamer upstream ribosome binding site. With the presence of ligands corresponding to the DNA aptamers, the expression of the target gene can be potentially enhanced at the transcriptional level by strengthening the recognition capability of RNAP to the recognition region and speeding up the separation efficiency of the unwinding region due to the induced DNA bubble around the thrombin-bound aptamers; while with the presence of RNA aptamer ligand, the gene expression can be repressed at the translational level by weakening the recognition capability of ribosome to RBS due to the shielding of RBS by the formed aptamer-ligand complex upstream RBS...
June 8, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28602637/inhibition-mechanism-of-an-anti-crispr-suppressor-acriia4-targeting-spycas9
#6
Hui Yang, Dinshaw J Patel
Prokaryotic CRISPR-Cas adaptive immune systems utilize sequence-specific RNA-guided endonucleases to defend against infection by viruses, bacteriophages, and mobile elements, while these foreign genetic elements evolve diverse anti-CRISPR proteins to overcome the CRISPR-Cas-mediated defense of the host. Recently, AcrIIA2 and AcrIIA4, encoded by Listeria monocytogene prophages, were shown to block the endonuclease activity of type II-A Streptococcus pyogene Cas9 (SpyCas9). We now report the crystal structure of AcrIIA4 in complex with single-guide RNA-bound SpyCas9, thereby establishing that AcrIIA4 preferentially targets critical residues essential for PAM duplex recognition, as well as blocks target DNA access to key catalytic residues lining the RuvC pocket...
June 2, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28602578/femoral-arterial-haemostasis-using-an-anchored-collagen-plug-after-percutaneous-evar-with-an-ultra-low-profile-device-prospective-audit-of-an-evolving-post-close-technique
#7
A Chaudhuri
OBJECTIVE: To present an audit of a successful "post-close" haemostatic technique using the Angio-Seal VIP vascular closure device (VCD) after percutaneous endovascular aneurysm repair (p-EVAR) using an ultra-low profile (ULP) device. METHODS: Thirty patients underwent EVAR using the Ovation device, of which 26 procedures were totally percutaneous. Data including patient habitus, procedural details, number of VCDs deployed including use of the double wire approach, and technical success/complications were prospectively recorded...
June 8, 2017: European Journal of Vascular and Endovascular Surgery
https://www.readbyqxmd.com/read/28599801/relation-of-ideal-cardiovascular-health-metrics-to-asymptomatic-polyvascular-disease-in-a-chinese-population
#8
Qian Zhang, Ruixuan Jiang, Yizheng Wang, Shufeng Zhang, Shengyun Chen, Yaqing Zhang, Xiuhua Guo, Shouling Wu, Xingquan Zhao
Atherosclerosis is a systemic disease with manifestations in multiple vascular beds. Ideal cardiovascular health (CVH) metrics relate to cardiovascular and cerebrovascular disease. However, the relation between ideal CVH metrics and asymptomatic polyvascular disease (polyVD) is unknown. We collected information on the 7 CVH metrics among 5,224 participants aged ≥40 years from 2010 to 2011. Intracranial artery stenosis, extracranial artery stenosis, and lower extremity artery disease were detected by transcranial Doppler, duplex sonography, and by calculating ankle-brachial index...
May 10, 2017: American Journal of Cardiology
https://www.readbyqxmd.com/read/28599199/the-haemodynamic-effects-of-bolus-versus-slower-infusion-of-intravenous-crystalloid-in-healthy-volunteers
#9
Ida F Ukor, Andrew K Hilton, Michael J Bailey, Rinaldo Bellomo
PURPOSE: This pilot study aimed to characterise the haemodynamic effect of 1L of IV normal saline (NS) administered as a rapid versus slow infusion on cardiac output (CO), heart rate (HR), systemic blood pressures, and carotid blood flow in six healthy volunteers. MATERIALS AND METHODS: Six healthy male volunteers aged 18-65years were randomized to receive 1L NS given over 30min or 120min. On a subsequent study session the alternate fluid regimen was administered...
May 30, 2017: Journal of Critical Care
https://www.readbyqxmd.com/read/28594167/toward-an-expanded-genome-structural-and-computational-characterization-of-an-artificially-expanded-genetic-information-system
#10
Nigel G J Richards, Millie M Georgiadis
Although the fundamental properties of DNA as first proposed by Watson and Crick in 1953 provided a basic understanding of how duplex DNA was organized and might be replicated, it was not until the first crystal structures of DNA (Z-DNA in 1979, B-DNA in 1980, and A-DNA in 1982) that the true complexity of the molecule began to be appreciated. Many crystal structures of oligonucleotides have since shed light on the helical forms that "Watson-Crick" DNA can adopt, their associated groove widths, and the properties of the nucleobase pairs and their interactions in all three helical forms...
June 8, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28593133/the-hfq-regulon-of-neisseria%C3%A2-meningitidis
#11
Robert A G Huis In 't Veld, Gertjan Kramer, Arie van der Ende, Dave Speijer, Yvonne Pannekoek
The conserved RNA-binding protein, Hfq, has multiple regulatory roles within the prokaryotic cell, including promoting stable duplex formation between small RNAs and mRNAs, and thus hfq deletion mutants have pleiotropic phenotypes. Previous proteome and transcriptome studies of Neisseria meningitidis have generated limited insight into differential gene expression due to Hfq loss. In this study, reversed-phase liquid chromatography combined with data-independent alternate scanning mass spectrometry (LC-MS(E)) was utilized for rapid high-resolution quantitative proteomic analysis to further elucidate the differentially expressed proteome of a meningococcal hfq deletion mutant...
June 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28591517/an-atp-responsive-co-delivery-system-of-doxorubicin-and-mir-34a-to-synergistically-inhibit-the-cell-proliferation-and-migration
#12
Yudi Wang, Jiawen Chen, Xiao Liang, Haobo Han, Hao Wang, Yan Yang, Quanshun Li
Establishing stimuli-responsive nanosystems for the co-delivery of anticancer drug and oligonucleotide is a promising strategy in cancer treatment owing to the combination of chemotherapy and gene therapy in a synergistic manner. Herein, an ATP aptamer and its cDNA sequence were first hybridized to produce the duplex, into which chemotherapeutic agent doxorubicin (DOX) interacted through the GC-rich motif of duplex, and PEI25K was then employed as a carrier to condense the DOX-loading duplex and miR-34a to construct the ternary nanocomplex PEI/DOX-Duplex/miR-34a...
June 7, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28581122/the-application-of-wireless-near-infrared-spectroscopy-on-detecting-peripheral-circulation-in-patients-with-diabetes-foot-ulcer-when-doing-buerger-s-exercise
#13
Min-Ling Chen, Bor-Shyh Lin, Cheng-Wei Su, Yen-Bin Lin, Mei-Yen Chen, Jen-Hsiang Shen, Chang-Cheng Chang
BACKGROUND AND OBJECTIVES: The majority of patients with diabetes foot ulcer have peripheral arterial disease. The technique of near infrared spectroscopy (NIRS) used to monitor the dorsal foot blood circulation condition is by measuring the absorption differences between oxy-hemoglobin and deoxy-hemoglobin. STUDY DESIGNS/MATERIALS AND METHODS: Patients with diabetic foot ulcer (DFU) treated in our wound care center were divided into two sub-groups based on the Duplex ultrasound or angiography...
June 5, 2017: Lasers in Surgery and Medicine
https://www.readbyqxmd.com/read/28580123/temporal-control-of-i-motif-switch-lifetimes-for-autonomous-operation-of-transient-dna-nanostructures
#14
L Heinen, A Walther
Functional DNA nanotechnology creates increasingly complex behaviors useful for sensing, actuation or computation, as enabled via the integration of dynamic and responsive structural DNA motifs. However, temporally controlled and dynamic DNA structures with programmable lifetimes, that are able to operate autonomously and self-revert to the starting state are challenging to achieve due to tedious and very system-specific sequence design. Here, we present a straightforward concept to program transient lifetimes into DNA duplexes based on the pH-sensitive DNA i-motif switch...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28576484/signs-of-subclinical-atherosclerosis-in-asymptomatic-patients-at-increased-risk-of-type-2-diabetes-mellitus
#15
Loretta Zsuzsa Kiss, Zsolt Bagyura, Réka Vadas, Lívia Polgár, Árpád Lux, Eszter Édes, Orsolya Szenczi, Pál Soós, Zsolt Szelid, Dávid Becker, György Jermendy, Béla Merkely
AIMS: We aimed to study carotid intima media thickness (CIMT) in asymptomatic patients with an increased risk of type 2 diabetes mellitus (T2DM) and in a pre-diabetic state. METHODS: Diabetes risk assessment was performed in 2420 participants in a voluntary screening program between 2011 and 2013. The risk of T2DM was estimated by the Findrisc scoring system (FR). A FR≥12 was considered as increased risk. HbA1c% between 5.7 and 6.4% signified a pre-diabetic state...
May 25, 2017: Journal of Diabetes and its Complications
https://www.readbyqxmd.com/read/28572901/allosteric-dna-nanoswitches-for-controlled-release-of-a-molecular-cargo-triggered-by-biological-inputs
#16
Marianna Rossetti, Simona Ranallo, Andrea Idili, Giuseppe Palleschi, Alessandro Porchetta, Francesco Ricci
Here we demonstrate the rational design of a new class of DNA-based nanoswitches which are allosterically regulated by specific biological targets, antibodies and transcription factors, and are able to load and release a molecular cargo (i.e. doxorubicin) in a controlled fashion. In our first model system we rationally designed a stem-loop DNA-nanoswitch that adopts two mutually exclusive conformations: a "Load" conformation containing a doxorubicin-intercalating domain and a "Release" conformation containing a duplex portion recognized by a specific transcription-factor (here Tata Binding Protein)...
February 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28558211/coumarin-appended-stable-fluorescent-self-complementary-quadruple-hydrogen-bonded-molecular-duplexes
#17
Sanjeev Kheria, Suresh Rayavarapu, Amol S Kotmale, Dinesh R Shinde, Rajesh G Gonnade, Gangadhar J Sanjayan
In this paper we report a coumarin-conjugated self-assembling system adorned with valuable features such as high duplex stability and a built-in fluorophore, which would augment its application potential. This system forms a highly stable molecular duplex in a nonpolar solvent (Kdim > 1.9 × 10(7) M(-1) in CDCl3). Due to the fluorescent property of coumarin, these new structural motifs may find potential application in material chemistry and supramolecular chemistry.
June 6, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28546042/occluded-superficial-femoral-artery-used-for-emergency-reconstruction-a-consecutive-case-series-about-the-proper-conduit-technique
#18
M S Marsman, A Kh Jahrome, F L Moll, G G Koning
INTRODUCTION: Deep wound infections in the groin region can result in an acute or life threatening condition. Especially when there is no suitable vein available because of many reasons (e.g. previous surgery, small vessel diameter). Synthetic prosthesis sometimes are not 'first-choice-technique' because of contamination or infection. It was ad hoc hypothesized in an acute setting that a segment of an occluded Superficial Femoral Artery (SFA) could be used as a conduit in combination with eversion technique, known from carotid surgery...
May 22, 2017: Annals of Vascular Surgery
https://www.readbyqxmd.com/read/28544846/genomic-dna-interactions-mechanize-peptidotoxin-mediated-anticancer-nanotherapy
#19
Santosh K Misra, Aaron S Schwartz-Duval, Dipanjan Pan
Host defense peptides (HDPs) are a class of evolutionarily conserved substances of the innate immune response that have been identified as major players in the defense system in many living organisms. Some of the HDPs are also referred to as peptidotoxins, which offer immense potential for anticancer therapy. However, their therapeutic potential is yet to be fully translated mainly due to their off-target toxicity. Here we show that their nanoenabled delivery may become beneficial in controlling their delivery in intracellular space...
June 7, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28544699/renal-anomalies-and-lymphedema-distichiasis-syndrome-a-rare-association
#20
Gabriela E Jones, Anna K Richmond, Osric Navti, Hatem A Mousa, Stephen Abbs, Edward Thompson, Sahar Mansour, Pradeep C Vasudevan
Lymphedema distichiasis syndrome (LDS) is a rare, autosomal dominant genetic condition, characterized by lower limb lymphedema and distichiasis. Other associated features that have been reported include varicose veins, cleft palate, congenital heart defects, and ptosis. We update a previously reported family with a pathogenic variant in FOXC2 (c.412-413insT) where five affected individuals from the youngest generation had congenital renal anomalies detected on prenatal ultrasound scan. These included four fetuses with hydronephrosis and one with bilateral renal agenesis...
May 23, 2017: American Journal of Medical Genetics. Part A
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