Single Breaks Research Articles

Rapid antigen diversification through mitotic recombination in the human malaria parasite Plasmodium falciparum

Malaria parasites possess the remarkable ability to maintain chronic infections that fail to elicit a protective immune response, characteristics that have stymied vaccine development and cause people living in endemic regions to remain at risk of malaria despite previous exposure to the disease. These traits stem from the tremendous antigenic diversity displayed by parasites circulating in the field. For Plasmodium falciparum, the most virulent of the human malaria parasites, this diversity is exemplified by the variant gene family called var, which encodes the major surface antigen displayed on infected red blood cells (RBCs). This gene family exhibits virtually limitless diversity when var gene repertoires from different parasite isolates are compared. Previous studies indicated that this remarkable genome plasticity results from extensive ectopic recombination between var genes during mitotic replication; however, the molecular mechanisms that direct this process to antigen-encoding loci while the rest of the genome remains relatively stable were not determined. Using targeted DNA double-strand breaks (DSBs) and long-read whole-genome sequencing, we show that a single break within an antigen-encoding region of the genome can result in a cascade of recombination events leading to the generation of multiple chimeric var genes, a process that can greatly accelerate the generation of diversity within this family. We also found that recombinations did not occur randomly, but rather high-probability, specific recombination products were observed repeatedly. These results provide a molecular basis for previously described structured rearrangements that drive diversification of this highly polymorphic gene family.

Effects of electronic waste on cytogenetic and physiological changes in snakehead fish (Channa striata).

The objectives of this study were to investigate cadmium (Cd), chromium (Cr), and lead (Pb) concentrations in water and sediment as well as the muscle, gill, and liver of snakehead fish (Channa striata) and to reveal chromosomal aberrations, changes in serum biochemical parameters, and histopathological alterations of fish from a reservoir near an electronic waste dumping area. Cd, Cr, and Pb concentrations were determined using inductively coupled plasma optical emission spectrometry. Chromosomal aberrations were studied in kidney cells using a conventional technique. The biochemical parameters were measured using an automated analyzer, and histopathological photographs were obtained using a transmission electron microscope. The results showed that heavy-metal concentrations in water and sediment did not exceed the standards, whereas Cd and Pb concentrations in the gill and liver exceeded the standards. The accumulation pattern of heavy metals in organ tissues was exhibited according to the following order: gill > liver > muscle. Five types of chromosomal aberrations were a centromere gap, single chromatid break, deletion, single chromatid gap, and fragmentation. The average percentages of chromosomal aberrations in polluted and reference C. striata were 4.60% and 1.00%, respectively. The statistical analyses of chromosomal aberration and biochemical parameters indicated that total protein, aspartate aminotransferase, and alanine aminotransferase significantly differed between the polluted and reference C. striata (p < 0.05). The liver histopathological alterations revealed atypical cellular structures, such as vacuolar appearance, nucleus degeneration, rough endoplasmic reticulum disintegration, abnormal cytoplasmic mitochondria, and deposition of heavy metals. Heavy-metal contaminations from electronic waste dumping areas affect fish in terms of chromosomal aberration, serum biochemistry, and histopathology.

Testing for structural changes in linear regressions with time-varying variance

This article proposes a nonparametric test for structural changes in linear regression models that allows for serial correlation, autoregressive conditional heteroskedasticity and time-varying variance in error terms. The test requires no trimming of the boundary region near the end points of the sample period, and requires no prior information on the alternative, what it requires is the transformed OLS residuals under the null hypothesis. We show that the test has a limiting standard normal distribution under the null hypothesis, and is powerful against single break, multiple breaks and smooth structural changes. The Monte Carlo experiment is conducted to highlight the merits of the proposed test relative to other popular tests for structural changes.

Electricity consumption and economic growth nexus in Zimbabwe revisited: fresh evidence from Maki cointegration

ABSTRACTThis study explores the relationship between electricity consumption, real gross domestic product per capita and carbon dioxide emissions in Zimbabwe. To achieve this, the study set off by examining the stationarity properties of the variables under review with the Zivot-Andrews (1992) unit root test that accounts for a single structural break. Subsequently, Maki (2012) cointegration test, which accounts for multiple structural breaks, is applied for equilibrium relationship between the variables under review while the long run regression of dynamic ordinary least square (DOLS) is employed for long-run coefficients as estimation procedures. In order to account for the direction of causality flow, the Toda-Yamamoto (1995) causality test is used for annual frequency data set spanning from 1971–2014. Empirical evidence from the Maki cointegration test shows that there exists a long-run equilibrium relationship between electricity consumption, carbon dioxide emissions and real gross domestic product per capita over the sampled period. The long-run regression suggests that there exist a positive statistically significant relationship between real income and electricity consumption. Thus, corroborating the electricity-led growth hypothesis. This result is supported by the causality test, as one-way causality is observed running from electricity consumption to real gross domestic product. Thus, this is suggestive to government administrators and policymakers that the Zimbabwean economy is electricity dependent. However, there is a tradeoff for environmental quality. As the increase in electricity consumption increases carbon dioxide emissions. The need for diversification of Zimbabwe energy portfolio to cleaner and environmentally friendly energy sources is recommended, given the world global consciousness for cleaner energy consumption.

Stochastic modelling of rainfall for the island of Ireland

This paper analyses a recently created continuous 305-year (1711–2016) monthly rainfall series for the island of Ireland. The findings are as follows. The excess skewness in the monthly series may be eradicated by using a Box-Cox transformation with parameter equal to 0.6: a value very similar to that found for the U.K. and its regions. There is no evidence of either an overall stochastic trend or of evolving monthly seasonal patterns, but positive linear trends are found for January, March, and December and a negative linear trend is found for July. Analysis of the seasonal and annual series (which require no transformation) confirms the implication from the monthly data that winters have become progressively wetter and summers progressively drier, with the positive linear trend for winter being twice the size of the negative summer trend. Since there is no trend in either spring or autumn rainfall, annual rainfall shows a positive linear trend. Given that the rainfall series exists for over three centuries, breaks and structural shifts in the model were investigated. Five breaks were identified, three of which occurred in the early portion of the series during the eighteenth century. However, trends were found to be much more stable from the middle of the nineteenth century. For the seasonal series, only a single break, at 1790 for the winter series, was found: it was only after this break that winters became wetter; before then, winter rainfall had a negative trend. In terms of predictability, predictions from the model were found to be more volatile during the second half of the eighteenth century and again from 1976 onwards.

A Multibreakpoint Analysis of Crude Oil Prices

Investigation of economic data is often a posterior analysis. Clearly, among applied techniques the main difference is between methods able to (reasonably) capture past issues in inherent modeling approach or not. In the present contribution, a quite recent multibreakpoint analysis of time series is proposed with the aim to overcome traditional constraints the researcher has to face. As a matter of fact, common applied methods are able to identify one (or at best two) structural break(s) in time series. By investigating oil crude prices, we propose a quite different approach applying a not (at the moment) widespread econometric technique to detect more than a single structural break in empirical data analysis. Hence, a brief discussion is developed to compare resulting outcomes with real historical facts. The aim is to test endogenous capability of the technique in pairing changes in statistical properties of oil price time series with salient chronological events.

Accelerated evolution of lager yeast strains for improved flavour profiles

Fermented food and beverages have accompanied humans throughout history. Several species of microorganisms can transform raw materials into products with different and improved characteristics, for example alcoholic beverages (wine and beer) or dairy products, such as yogurt. In a world of constant change and competitiveness, brewers have to modulate and create new products to satisfy consumers. Therefore, the aim of my project is to generate lager yeast capable of producing molecules that improve the organoleptic profile of alcoholic beverages and understand the genetic and biochemical changes that increases the production of these aromatic molecules. The initial work has focused on the Ehrlich Pathway and the ester production. To produce changes in the genome, two approaches have been followed: one chemical way, using Radicicol, and one physical way, Heat Shock Thermal Stress (HSTS). Both ways inhibit Heat Shock proteins. Furthermore, this inhibition produces DNA damage, introducing Single sStrand Breaks (SSBs) and Double Strand Breaks (DSBs). The result of this inhbition is damage in the DNA and, furthermore, mutations in the DNA (aneuplidies and INDELS). After the Accelerated evolution, the evolved strains were plated on media containing amino acid analogues. These amino acid analogues select for cells with decreased feed-back inhibition of amino acid biosynthesis. Different mutant strains were generated with these two ways. These strains will be tested by different approaches, as growth curves, genome ploidy using cCGH and CHEF gel and qPCR analysis to measure the flux throughout the fermentation.

Detection and Mapping of dsDNA Breaks using Graphene Nanopore Transistor

Single-strand DNA (ssDNA) breaks that are often converted into DNA double-strand (dsDNA) breaks make up a vast majority of lesions a normal human cell undergoes everyday. If the repair mechanism fails, the dsDNA break can cause chromosomal instability leading to tumorigenesis. Additionally, a single break in a critical gene can cause the cell to undergo apoptosis. Existing genome sequencing techniques are not suitable for detecting such changes directly. As an alternative methodology, we propose to employ graphene-Quantum Point Contact nanopore transistor to detect and map defects in the DNA backbone, as miniscule as ssDNA breaks, efficiently using electronic sheet currents obtained across the transistor membrane. For this purpose, we use large-scale comprehensive all-atom molecular dynamics simulation techniques accompanied with electronic transport calculations, data denoising and signal detection. In all our simulations, we observe the molecule sticking in the pore at the nicked site due to strong hydrophobic attraction between the graphene membrane and the damaged-backbone. While the ionic currents calculated for the translocation of 20 base-pair dsDNA strand with a break in the backbone does not show any distinct signature from the nicked-site in the signal, a clear dip is seen in the transverse sheet current signal corresponding to the location of the breakage, thereby enabling us to detect and map these damages, electronically. We validated our methodology by detecting other sequence specific dsDNA breaks along randomly sequenced strands. We strongly believe such a detection mechanism enables the development of versatile semiconductor electronics for early cancer detection caused by structural modification of the genome.

A phase II study of M6620 and irinotecan in TP53 mutant gastric and gastroesophageal junction (GEJ) adenocarcinoma patients (pts) [NCT03641313

TPS175 Background: Progressive metastatic or unresectable gastric/GEJ adenocarcinoma pts carry dismal prognoses with a significant need for novel systemic therapies. One avenue for drug development in this disease is targeting salvage DNA repair pathways. TP53, a central gene to DNA damage repair (DDR), is mutated in 50% of gastric/GEJ cancer pts. Pre-clinical models from multiple cancer types demonstrate that cancer cells with TP53 mutations rely on the ataxia telangiectasia and Rad-3 related protein kinase (ATR) axis as a primary pathway of salvage DDR in the face of cytotoxic stress. The ATR pathway is typically triggered by single strand DNA breaks such as those generated by topoisomerase I inhibitors. Irinotecan is already known to be active in later line gastric/GEJ pts, thus, there appears to be an opportunity to combine the agent with the ATR inhibitor M6620 in TP53 mutant pts with the disease. Methods: Our trial is a single arm phase II study of M6620 plus irinotecan in progressive gastric/GEJ adenocarcinoma pts. Only pts with TP53 mutations in exon 2 and exons 4-11, as determined by next-generation sequencing from archived tissue, will be eligible. Pts will receive 180 mg/m^2 of irinotecan immediately followed by M6620 every 2 weeks; the M6620 dose will be determined based on the recommended phase 2 dose from the ongoing phase I trial. CT scans will be repeated every 2 months to assess response. The primary endpoint of the study is overall response rate (ORR), with a pre-specified target of 35%. Correlative studies will be performed on fresh tumor tissue from the first 9 pts, obtained by biopsies on day 1 of cycle 1 post-irinotecan and day 2 of cycle 2, to assess dynamic changes in the biomarkers Y-H2AX, KAP1 p-Ser 824, and p-ATR. Our study employs a Simon’s two-stage design (α = 0.1, power = 0.8) where an initial analysis will be performed after 9 pts are enrolled. If &lt; 2 pts demonstrate objective response, the trial will stop for futility. If &gt; 2 pts demonstrate response, the study will enroll 14 more pts. If ≥ 6 pts experience an objective response, the trial will achieve its efficacy threshold. Accrual will be ensuing in the near future. Clinical trial information: NCT03641313.

Single and Double Strand Sperm DNA Damage: Different Reproductive Effects on Male Fertility.

Reproductive diseases have become a growing worldwide problem and male factor plays an important role in the reproductive diagnosis, prognosis and design of assisted reproductive treatments. Sperm cell holds the mission of carrying the paternal genetic complement to the oocyte in order to contribute to an euploid zygote with proper DNA integrity. Sperm DNA fragmentation had been used for decades as a male fertility test, however, its usefulness have arisen multiple debates, especially around Intracytoplasmic Sperm Injection (ICSI) treatments. In the recent years, it has been described that different types of sperm DNA breaks (single and double strand DNA breaks) cause different clinical reproductive effects. On one hand, single-strand DNA breaks are present extensively as a multiple break points in all regions of the genome, are related to oxidative stress and cause a lack of clinical pregnancy or an increase of the conception time. On the other hand, double-strand DNA breaks are mainly localized and attached to the sperm nuclear matrix as a very few break points, are possibly related to a lack of DNA repair in meiosis and cause a higher risk of miscarriage, low embryo quality and higher risk of implantation failure in ICSI cycles. The present work also reviews different studies that may contribute in the understanding of sperm chromatin as well as treatments to prevent sperm DNA damage.

Investigation of the charge transport in model single molecule junctions based on expanded bipyridinium molecular conductors

In this work the charge transport and energetics of a photochemically addressable single molecule switch based on the expanded bipyridinium core linked to an anchoring group with a controlled torsion angle θ was investigated. Electrochemical and UV-VIS absorption spectroscopy techniques complemented by the analysis based on density functional theory (DFT) show that for selected molecules the energy and shape of the LUMO is insensitive to the value of θ, but the difference in torsion angle θ leads to a sizable shift of the LUMO energy and single molecule conductance value in a metal-molecule-metal junction for these molecules as shown by the combination of experimental single molecule break junction technique and theoretical non-equilibrium Green's function (NEGF)/DFT approach. The conductance switching ratio calculated from the cos2 θ law is in a perfect agreement with the value obtained from the NEGF approach. Our combined experimental and theoretical approach paves the way for investigating expanded bipyridinium systems with multiple photochemically addressable units potentially achieving greater conductance switching ratios.

Effect of Slip-Weakening Distance on Seismic\u2013Aseismic Slip Patterns

In order to explain the seismic–aseismic slip patterns observed on megathrust faults, numerical simulations were carried out using the quasi-dynamic asperity fault model with the slip-dependent friction and stress-dependent healing. Two friction law parameters, strength and slip-weakening distance, are interpreted in the subduction channel context. The parameters are treated as random fields with specified characteristics. Their distributions define heterogeneities of the interplate frictional coupling. The higher strength regions accumulate stresses, whereas the slip-weakening distance lengths control the stress release rates. The simulation results indicate that the slip-dependent asperity model reproduces key features of real megathrust fault behavior. First, stable and unstable slip movements can occur at the same locations, even if the friction parameters are fixed. Second, two rupture styles, single asperity breaks and wide, smooth, propagating rupture fronts, can be distinguished. The latter style is responsible for large slips near the free surface, where lower fault strengths are expected. The reason for these effects is that slip instabilities depend both on local friction and on the system stiffness, which is related to the slipping area size and distribution of slips. It is also shown that the high-strength interplate patches, such as subducted seamounts, can both promote and restrain large earthquakes, depending on the slip-weakening distance lengths.

RELIABILITY MODEL OF OPTICAL CIRCULAR NET WITH WAVE DIVISION

It is considered the possibility of construction of the high‑speed object local net based on new domestic highly efficient clustered on‑board computing platform on the basis of 64‑bit Elbrus (BC‑3416) processor with use of original high‑reliability physical environment. Increasing of the optical object local net reliability is ensured by automatic restoration of such net in the case of single break of communication link using dual‑redundant communication lines by wave lengths (wave compression) instead of fibers duplication as it was made in traditional nets. An analytical model is presented to assess the reliability indicators of the proposed fault‑tolerant fiber‑optic circular net with wave separation, wave channels redundancy and self‑recovery. Use of circular optic net allows to provide the symmetry of transmitting directions capacity, increasing of transmission speed with use of wave compression principle.

Investigation on the Thermal Performance of a 363 kV Vacuum Circuit Breaker Using a 3D Coupled Model

Multi-break vacuum circuit breakers (VCBs) are the most potential approach for applying VCBs to high voltage power system. However, it has higher thermal stability requirements than normal single break VCBs due to its complex structure and high rated current. In this paper, a novel 363 kV/5000 A/63 kA SF6 gas insulate (GI) VCB with series and parallel structure is proposed. To analyze its temperature rise, a 3D coupled electromagnetic-thermal-fluid model is established based on actual size and calculated by finite element method under rated condition, which enables prediction of the temperature distribution of the contacts of VCB and bus bar. In the numerical model, the vacuum chamber is modelled as solid material with temperature dependent effective thermal conductivity while skin effect, nonlinear property of conductor resistivity and turbulence model are taken into consideration. The simulation results show that the hot spot is the contacts of VCB with a temperature of 102.2 K, while the temperature of busbars reach at 92.3 K. In addition, the influences of contact resistance, short circuit current on the temperature rise are discussed. Finally, the simulation results are validated by temperature rise experiment on prototype. Using the proposed model, the temperature rise and hot spot area can be predicted in advance, which could finally facilitate the design and performance evaluation of the 363 kV GI-VCB.

How wildebeest walk on the wilder side

![Graphic][1] Imagine, for a minute, that you're taking a stroll through the Kalahari desert under the unforgiving heat of a summer sun. Now imagine that stroll lasting for 5 days and covering an impressive 80 km. Finally, imagine undertaking this epic desert trek without a single break for

Human capital and export diversification as new determinants of energy demand in the United States

This paper investigates how education and export diversification contribute to energy demand by also incorporating the role of natural resource, oil prices and income in driving energy demand function for the United States (U.S.) economy. In doing so, we apply the unit root test of Kim and Perron (2009) and the bootstrapping autoregressive-distributed lag (ARDL) cointegration approach developed by McNown etal. (2018), which accommodates the presence of a single unknown structural break in the series. The empirical results confirm that the variables are cointegrated in a long-run relationship. Education is negatively linked to energy demand, and export diversification also decreases this demand in the long-run. On the other hand, economic growth increases energy consumption, while oil prices reduce energy demand in the long-run. Natural resource production affects energy consumption positively. Further, the Vector Error Correction Mechanism (VECM)'s Granger causality analysis reveals a feedback effect between education and energy demand. Export diversification causes energy demand, and in return, energy demand causes export diversification. A bidirectional causality also exists between economic growth and energy demand. The paper also discusses the potential implications of the results.

The Pneumatic Retinopexy versus Vitrectomy for the Management of Primary Rhegmatogenous Retinal Detachment Outcomes Randomized Trial (PIVOT)

The optimal surgery to repair rhegmatogenous retinal detachment (RRD) is unknown. The purpose of this trial was to compare outcomes of pneumatic retinopexy (PnR) versus pars plana vitrectomy (PPV) for the management of primary RRD. Prospective, randomized controlled trial. Patients with RRD demonstrating a single retinal break or a group of breaks in detached retina within 1 clock hour above the 8- and 4-o'clock meridians, with any number, location and size of retinal breaks or lattice degeneration in attached retina. Patients were randomized to undergo either PnR or PPV. Macula-on and macula-off patients were assigned to intervention group by stratified randomization and were treated within 24 and 72 hours, respectively. The primary outcome was 1-year Early Treatment Diabetic Retinopathy Study (ETDRS) visual acuity (VA). Important secondary outcomes were subjective visual function (25-item National Eye Institute Visual Function Questionnaire), metamorphopsia score (M-CHARTS), and primary anatomic success. One hundred seventy-six patients were recruited between August 2012 and May 2016. ETDRS VA after PnR exceeded that after PPV by 4.9 letters at 12 months (79.9±10.4 letters vs. 75.0±15.2 letters; P= 0.024). Mean ETDRS VA also was superior for the PnR group compared with the PPV group at 3 months (78.4±12.3 letters vs. 68.5±17.8 letters) and 6 months (79.2±11.1 letters vs. 68.6±17.2 letters). Composite 25-item National Eye Institute Visual Function Questionnaire scores were superior for PnR at 3 and 6 months. Vertical metamorphopsia scores were superior for the PnR group compared with the PPV group at 12 months (0.14±0.29 vs. 0.28±0.42; P= 0.026). Primary anatomic success at 12 months was achieved by 80.8% of patients undergoing PnR versus 93.2% undergoing PPV (P= 0.045), with 98.7% and 98.6%, respectively, achieving secondary anatomic success. Sixty-five percent of phakic patients in the PPV arm underwent cataract surgery in the study eye before 12 months versus 16% in the PnR group (P < 0.001). Pneumatic retinopexy should be considered the first line treatment for RRD in patients fulfilling Pneumatic Retinopexy versus Vitrectomy for the Management of Primary Rhegmatogenous Retinal Detachment Outcomes Randomized Trial (PIVOT) recruitment criteria. Pneumatic retinopexy offers superior VA, less vertical metamorphopsia, and reduced morbidity when compared with PPV.

Acceleration of cancer science with genome editing and related technologies.

Genome editing includes various edits of the genome, such as short insertions and deletions, substitutions, and chromosomal rearrangements including inversions, duplications, and translocations. These variations are based on single or multiple DNA double‐strand break (DSB)‐triggered in cellulo repair machineries. In addition to these “conventional” genome editing strategies, tools enabling customized, site‐specific recognition of particular nucleic acid sequences have been coming into wider use; for example, single base editing without DSB introduction, epigenome editing with recruitment of epigenetic modifiers, transcriptome engineering using RNA editing systems, and in vitro detection of specific DNA and RNA sequences. In this review, we provide a quick overview of the current state of genome editing and related technologies that multilaterally contribute to cancer science.

Bleomycin-induced genotoxicity in vitro in human peripheral blood lymphocytes evidenced as complex chromosome- and chromatid-type aberrations

Bleomycin is a chemotherapeutic and a radiomimetic drug which induces single and double-strand breaks in DNA by forming free radicals. We demonstrate in this study the capacity of bleomycin in inducing complex chromosome- and chromatid-type aberrations. Human peripheral blood was exposed to different concentrations of bleomycin (0, 10, 20, 30 and 40 μg/mL) and the aberrations induced were studied. The chromosomal-type aberrations studied were dicentrics, tricentrics, tetracentrics, centric rings and acentric fragments. The chromatid-type aberrations studied were double minutes, terminal lesions and terminal deletions. Though the overall trends that we obtained in the dose-dependent mitotic index and the chromosome- and chromatid-type aberrations conform to the reported literature, we could observe enhanced numbers and the types of such damages in this study. We could notice that chromosome-type aberrations were more than the chromatid-type aberrations. The enhanced numbers and the types of aberrations induced pave way for enhancing the sensitivity of genotoxic assays. Also, with more numbers and type of aberrations available, it would be useful to study the mechanisms of genotoxicity of drugs and in understanding phenomena such as “tolerance induction” to chronic exposure to such mutagens.

Assays on DNA Damage and Repair in CLL.

Assays that measure DNA damage and repair are critical in evaluating the extent to which therapeutic agents damage DNA and in identifying whether DNA repair can limit the toxicity of chemotherapy. The COMET assays described in this guide should help readers evaluate single and double-strand breaks cause by chemotherapeutic agents and also monitor the ability of the cells to repair such damage. The EJDR assay described is a valuable tool to assess the ability of drugs and DNA repair proteins to modulate DNA repair capacity. Finally, the immunofluorescence assay described should allow accurate assessments of DNA damage and the kinetics of repair as measured by Ɣ-H2AX foci. This procedure can also be used to mechanistically investigate the recruitment of specific DNA damage and repair proteins in CLL cells.