Microhomology-mediated end joining induces hypermutagenesis at breakpoint junctions

Microhomology (MH) flanking a DNA double-strand break (DSB) drives chromosomal rearrangements but its role in mutagenesis has not yet been analyzed. Here we determined the mutation frequency of a URA3 reporter gene placed at multiple locations distal to a DSB, which is flanked by different sizes (15-, 18-, or 203-bp) of direct repeat sequences for efficient repair in budding yeast. Induction of a DSB accumulates mutations in the reporter gene situated up to 14-kb distal to the 15-bp MH, but more modestly to those carrying 18- and 203-bp or no homology. Increased mutagenesis in MH-mediated end joining (MMEJ) appears coupled to its slower repair kinetics and the extensive resection occurring at flanking DNA. Chromosomal translocations via MMEJ also elevate mutagenesis of the flanking DNA sequences 7.1 kb distal to the breakpoint junction as compared to those without MH. The results suggest that MMEJ could destabilize genomes by triggering structural alterations and increasing mutation burden

ChimerDB 2.0—a knowledgebase for fusion genes updated

Chromosome translocations and gene fusions are frequent events in the human genome and have been found to cause diverse types of tumor. ChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and the Mitelman’s database. In this updated version, we significantly modified the algorithm of identifying fusion transcripts. Specifically, the new algorithm is more sensitive and has detected 2699 fusion transcripts with high confidence. Furthermore, it can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments. Importantly, results from the analysis of next-generation sequencing data in the short read archives are incorporated as well. We updated and integrated all contents (GenBank, Sanger CGP, OMIM, PubMed publications and the Mitelman’s database), and the user-interface has been improved to support diverse types of searches and to enhance the user convenience especially in browsing PubMed articles. We also developed a new alignment viewer that should facilitate examining reliability of fusion transcripts and inferring functional significance. We expect ChimerDB 2.0, available at http://ercsb.ewha.ac.kr/fusiongene, to be a valuable tool in identifying biomarkers and drug targets

Risk factors for and clinical outcomes of carbapenem non-susceptible gram negative bacilli bacteremia in patients with acute myelogenous leukemia

Background Carbapenem is frequently used when gram negative bacilli (GNB) bacteremia is detected especially in neutropenic patients. Consequently, appropriate treatment could be delayed in GNB bacteremia cases involving organisms which are not susceptible to carbapenem (carba-NS), resulting in a poor clinical outcomes. Here, we explored risk factors for carba-NS GNB bacteremia and its clinical outcomes in patients with acute myelogenous leukemia (AML) that underwent chemotherapy. Methods We reviewed all GNB bacteremia cases that occurred during induction or consolidation chemotherapy, over a 15-year period, in a tertiary-care hospital. Results Among 489 GNB bacteremia cases from 324 patients, 45 (9.2%) were carba-NS and 444 (90.8%) were carbapenem susceptible GNB. Independent risk factors for carba-NS GNB bacteremia were: carbapenem use at bacteremia onset (adjusted odds ratio [aOR]: 91.2; 95% confidence interval [95%CI]: 29.3–284.1; P < 0.001); isolation of carbapenem-resistant Acinetobacter baumannii (aOR: 19.4, 95%CI: 3.4–112.5; P = 0.001) in the prior year; and days from chemotherapy to GNB bacteremia (aOR: 1.1 per day, 95%CI: 1.1–1.2; P < 0.001). Carba-NS bacteremia was independently associated with in-hospital mortality (aOR: 6.6, 95%CI: 3.0–14.8; P < 0.001). Conslusion Carba-NS organisms should be considered for antibiotic selection in AML patients having these risk factors

Laboratory information management system for COVID-19 non-clinical efficacy trial data

Background : As the number of large-scale studies involving multiple organizations producing data has steadily increased, an integrated system for a common interoperable format is needed. In response to the coronavirus disease 2019 (COVID-19) pandemic, a number of global efforts are underway to develop vaccines and therapeutics. We are therefore observing an explosion in the proliferation of COVID-19 data, and interoperability is highly requested in multiple institutions participating simultaneously in COVID-19 pandemic research. Results : In this study, a laboratory information management system (LIMS) approach has been adopted to systemically manage various COVID-19 non-clinical trial data, including mortality, clinical signs, body weight, body temperature, organ weights, viral titer (viral replication and viral RNA), and multiorgan histopathology, from multiple institutions based on a web interface. The main aim of the implemented system is to integrate, standardize, and organize data collected from laboratories in multiple institutes for COVID-19 non-clinical efficacy testings. Six animal biosafety level 3 institutions proved the feasibility of our system. Substantial benefits were shown by maximizing collaborative high-quality non-clinical research. Conclusions : This LIMS platform can be used for future outbreaks, leading to accelerated medical product development through the systematic management of extensive data from non-clinical animal studies.This research was supported by the National research foundation of Korea(NRF) grant funded by the Korea government(MSIT) (2020M3A9I2109027 and 2021M3H9A1030260)

Design of a CMOS Image Sensor with Bi-Directional Gamma-Corrected Digital-Correlated Double Sampling

We present a 640 × 480 CMOS image sensor (CIS) with in-circuit bi-directional gamma correction with a proposed digital-correlated double sampling (CDS) structure. To operate the gamma correction in the CIS, the transfer function of the analog-to-digital converter can be changed by controlling the clock frequency of the counter using analog CDS. However, the analog CDS is vulnerable to capacitor mismatch, clock feedthrough, etc. Therefore, we propose a digital-CDS method with a hold-and-go counter structure to operate the bi-directional gamma correction in the CIS. The proposed CIS achieves a 10-bit resolution using a global log-exponential counter and configurable column reset counter with a resolution of 8/9 bits. The sensor was fabricated in a 0.11 μm CIS process, and the full chip area was 5.9 mm × 5.24 mm. The measurement results showed a maximum SNR improvement of 10.41% with the proposed bi-directional gamma-corrected digital-CDS with the hold-and-go counter. The total power consumption was 6.3 mW at a rate of 16.6 frames per second with analog, pixel, and digital supply voltages of 3.3 V, 3.3 V, and 1.5 V, respectively

Ahnak Protein Activates Protein Kinase C (PKC) through Dissociation of the PKC-Protein Phosphatase 2A Complex

We have previously reported that central repeated units (CRUs) of Ahnak act as a scaffolding protein networking phospholipase C and protein kinase C (PKC). Here, we demonstrate that an Ahnak derivative consisting of four central repeated units binds and activates PKC- in a phosphatidylserine/1,2-dioleoyl-sn-glycerol-independent manner. Moreover, NIH3T3 cells expressing the 4 CRUs of Ahnak showed enhanced c-Raf, MEK, and Erk phosphorylation in response to phorbol 12-myristate 13-acetate (PMA) compared with parental cells. To evaluate the effect of loss-of-function of Ahnak in cell signaling, we investigated PKC activation and Raf phosphorylation in embryonic fibroblast cells (MEFs) of the Ahnak knock-out (Ahnak-/-) mouse. Membrane translocation of PKC- and phosphorylation of Raf in response to PMA or platelet-derived growth factor were decreased in Ahnak null MEF cells compared with wild type MEFs. Several lines of evidence suggest that PKC- activity is regulated through association with protein phosphatase 2A (PP2A). A co-immunoprecipitation assay indicated that the association of PKC- with PP2A was disrupted in NIH3T3 cells expressing 4 CRUs of Ahnak in response to PMA. Consistently, Ahnak null MEF cells stimulated by PMA showed enhanced PKC-PP2A complex formation, and add-back expression of Ahnak into Ahnak null MEF cells abolished the PKC-PP2A complex formation in response to PMA. These data indicate that Ahnak potentiates PKC activation through inhibiting the interaction of PKC with PP2A.This work was supported in part by the National Core Research Center program of the Ministry of Science and Technology/Korea Science and Engineering Foundation (Grant R15-2006-020-00000-0) through the Center for Cell Signaling and Drug Discovery Research at Ewha Womans University, Basic Research Program of the Korea Science and Engineering Foundation Grant RO1-2005-000-10480-0 (to Y. S. B.), and 21C Frontier Functional Proteomics Projects Grant FPR0502-470 (to S. G. R.)

Photoluminescence Path Bifurcations by Spin Flip in Two-Dimensional CrPS4

Ultrathin layered crystals of coordinated chromium-(III) are promising not only as two-dimensional (2D) magnets but also as 2D near-infrared (NIR) emitters due to long-range spin correlation and efficient transition between high-and low-spin excited states of Cr3+ ions. In this study, we report on the dual-band NIR photoluminescence (PL) of CrPS4 and show that its excitonic emission bifurcates into fluorescence and phosphorescence depending on thickness, temperature, and defect density. In addition to the spectral branching, the biexponential decay of PL transients, also affected by the three factors, could be well described within a three-level kinetic model for Cr(III). In essence, the PL bifurcations are governed by activated reverse intersystem crossing from the low- to high-spin states, and the transition barrier becomes lower for thinner 2D samples because of surface-localized defects. Our findings can be generalized to 2D solids of coordinated metals and will be valuable in realizing groundbreaking magneto-optic functions and devices.11Nsciescopu

A fully automated immunoassay from whole blood on a disc

A portable, disc-based, and fully automated enzyme-linked immuno-sorbent assay (ELISA) system is developed to test infectious diseases from whole blood. The innovative laser irradiated ferrowax microvalves and centrifugal microfluidics were utilized for the full integration of microbead-based suspension ELISA assays on a disc starting from whole blood. The concentrations of the antigen and the antibody of Hepatitis B virus (HBV), HBsAg and Anti-HBs respectively, were measured using the lab-on-a-disc (LOD). All the necessary reagents are preloaded on the disc and the total process of the plasma separation, incubation with target specific antigen or antibody coated microbeads, multiple steps of washing, enzyme reaction with substrates, and the absorbance detection could be finished within 30 minutes. Compared to the conventional ELISA, the operation time was dramatically reduced from over 2 hours to less than 30 minutes while the limit of detection was kept similar; e. g. the limit of detection of Anti-HBs tests were 8.6 mIU mL(-1) and 10 mIU mL(-1) for the disc-based and the conventional ELISA respectively.close11011

Surface Engineering Strategies of Layered LiCoO2 Cathode Material to Realize High-Energy and High-Voltage Li-Ion Cells

Battery industries and research groups are further investigating LiCoO2 to unravel the capacity at high-voltages (&gt;4.3 vs Li). The research trends are towards the surface modification of the LiCoO2 and stabilize it structurally and chemically. In this report, the recent progress in the surface-coating materials i.e., single-element, binary, and ternary hybrid-materials etc. and their coating methods are illustrated. Further, the importance of evaluating the surface-coated LiCoO2 in the Li-ion full-cell is highlighted with our recent results. Mg, P-coated LiCoO2 full-cells exhibit excellent thermal stability, high-temperature cycle and room-temperature rate capabilities with high energydensity of approximate to 1.4 W h cc(-1) at 10 C and 4.35 V. Besides, pouch-type full-cells with high-loading (18 mg cm(-2)) electrodes of layered-Li(Ni,Mn)O-2 -coated LiCoO2 not only deliver prolonged cycle-life at room and elevated-temperatures but also high energy-density of approximate to 2 W h cc(-1) after 100 cycles at 25 degrees C and 4.47 V (vs natural graphite). The post-mortem analyses and experimental results suggest enhanced electrochemical performances are attributed to the mechanistic behaviour of hybrid surface-coating layers that can mitigate undesirable side reactions and micro-crack formations on the surface of LiCoO2 at the adverse conditions. Hence, the surface-engineering of electrode materials could be a viable path to achieve the high-energy Li-ion cells for future applications.clos