A study of electron recombination using highly ionizing particles in the ArgoNeuT Liquid Argon TPC

Electron recombination in highly ionizing stopping protons and deuterons is studied in the ArgoNeuT detector. The data are well modeled by either a Birks model or a modified form of the Box model. The dependence of recombination on the track angle with respect to the electric field direction is much weaker than the predictions of the Jaffe columnar theory and by theoretical-computational simulations.

Characterization of template switching and recombination during Moloney murine leukemia virus replication

Retroviruses uniquely co-package two copies of their genomic RNA within each virion. The two copies are used as templates for synthesis of the proviral DNA during the process of reverse transcription. Two template switches are required to complete retroviral DNA synthesis by the retroviral enzyme, reverse transcriptase. With two RNA genomes present in the virion, reverse transcriptase can make template switches utilizing only one of the RNA templates (intramolecular) or utilizing both RNA templates (intermolecular) during the process of reverse transcription. The results presented in this study show that during a single cycle of Moloney murine leukemia virus replication, both nonrecombinant and recombinant proviruses predominantly underwent intramolecular minus- and plus-strand transfers during the process of reverse transcription. This is the first study to examine the nature of the required template switches occurring during MLV replication and these results support the previous findings for SNV, and the hypothesis that the required template switches are ordered events. This study also determined rates for deletion and a rate of recombination for a single cycle of MLV replication. The rates reported here are comparable to the rates previously reported for both SNV and MLV. ^

The role of ATM in the cell cycle control of V(D)J recombination

Lymphocyte development requires the assembly of diversified antigen receptor complexes generated by the genetically programmed V(D)J recombination event. Because germline DNA is cut, introducing potentially dangerous double-stranded breaks (DSBs) and rearranged prior to repair, its activity is limited to the non-cycling stages of the cell cycle, G0/G1. The potential involvement of a key mediator, Ataxia Telangiectasia Mutated or ATM, in the DNA damage response (DDR) and cell cycle checkpoints has been implicated in recombination, but its role is not fully understood. Thymic lymphomas from ATM deficient mice contain clonal chromosomal translocations involving the T-cell antigen receptor (TCR). A previous report found ATM and its downstream target p53 associated with V(D)J intermediates, suggesting the DDR senses recombination. In this study, we sought to understand the role of ATM in V(D)J recombination. Developing thymocytes from ATM deficient mice were analyzed according to the cell cycle to detect V(D)J intermediates. Examination of all TCR loci in the non-cycling (G0/G1) and cycling (S/G2/M) fractions revealed the persistence of intermediates in ATM deficient thymocytes, contrary to the wild-type in which intermediates are found only during G0/G1. Further analysis found no defect in end-joining of intermediates, nor were they detected in developed T-cells. Based upon the presence of persisting intermediates, the recombination initiating nuclease Rag-2 was examined; strict regulation limits it to G 0/G1. Rag-2 regulation was not affected by an ATM deficiency as Rag-2 expression remained contained within G0/G 1, indicating recombination is not continuous. To determine if an ATM deficiency affects recognition of V(D)J breaks, sites of recombination identified by a TCR locus or Rag expression were analyzed according to co-localization with a DDR factor phosphorylated immediately after DNA damage, phosphorylated H2AX (γH2AX). No differences in co-localization were found between the wild-type and ATM deficiency, demonstrating ATM deficient lymphocytes retain the ability to recognize DSBs. Together, these results suggest ATM is necessary in the cell cycle regulation of recombination but not essential for the identification of V(D)J breaks. ATM ensures the containment of intermediates within G0/G1 and maintains genomic stability of developing lymphocytes, emphasizing its fundamental role in preventing tumorigenesis.^

Molecular fingerprinting and amplicon sequencing of the bacterial biofilm on settlement tiles deployed along natural pH gradients in Papua New Guinea

Bacterial biofilms provide cues for the settlement of marine invertebrates such as coral larvae, and are therefore important for the resilience and recovery of coral reefs. This study aimed to better understand how ocean acidification may affect the community composition and diversity of bacterial biofilms on surfaces under naturally reduced pH conditions. Settlement tiles were deployed at coral reefs in Papua New Guinea along pH gradients created by two CO2 seeps, and upper and lower tiles surfaces were sampled 5 and 13 months after deployment. Automated Ribosomal Intergenic Spacer Analysis were used to characterize more than 200 separate bacterial communities, complemented by amplicon sequencing of the bacterial 16S rRNA gene of 16 samples. The bacterial biofilm consisted predominantly of Alpha-, Gamma- and Deltaproteobacteria, as well as Cyanobacteria, Flavobacteriia and Cytophaga, whereas putative settlement-inducing taxa only accounted for a small fraction of the community. Bacterial biofilm composition was heterogeneous with approximately 25% shared operational taxonomic units between samples. Among the observed environmental parameters, pH only had a weak effect on community composition (R² ~ 1%) and did not affect community richness and evenness. In contrast, there were strong differences between upper and lower surfaces (contrasting in light exposure and grazing intensity). There also appeared to be a strong interaction between bacterial biofilm composition and the macroscopic components of the tile community. Our results suggest that on mature settlement surfaces in situ, pH does not have a strong impact on the composition of bacterial biofilms. Other abiotic and biotic factors such as light exposure and interactions with other organisms may be more important in shaping bacterial biofilms than changes in seawater pH.

Near infrared high efficiency InAs/GaAsSb QDLEDs: band alignment and carrier recombination mechanisms

The development of high efficiency laser diodes (LD) and light emitting diodes (LED) covering the 1.0 to 1.55 μm region of the spectra using GaAs heteroepitaxy has been long pursued. Due to the lack of materials that can be grown lattice-macthed to GaAs with bandgaps in the 1.0 to 1.55 μm region, quantum wells (QW) or quantum dots (QD) need be used. The most successful approach with QWs has been to use InGaAs, but one needs to add another element, such as N, to be able to reach 1.3/1.5μm. Even though LDs have been successfully demonstrated with the QW approach, using N leads to problems with compositional homogeneity across the wafer, and limited efficiency due to strong non-radiative recombination. The alternative approach of using InAs QDs is an attractive option, but once again, to reach the longest wavelengths one needs very large QDs and control over the size distribution and band alignment. In this work we demonstrate InAs/GaAsSb QDLEDs with high efficiencies, emitting from 1.1 to 1.52 μm, and we analyze the band alignment and carrier loss mechanisms that result from the presence of Sb in the capping layer.

3-D modeling of perimeter recombination in GaAs diodes and its influence on concentrator solar cells

This paper describes a complete modelling of the perimeter recombination of GaAs diodes which solves most unknowns and suppresses the limitations of previous models. Because of the three dimensional nature of the implemented model, it is able to simulate real devices. GaAs diodes on two epiwafers with different base doping levels, sizes and geometries, namely square and circular are manufactured. The validation of the model is achieved by fitting the experimental measurements of the dark IV curve of the manufactured GaAs diodes. A comprehensive 3-D description of the occurring phenomena affecting the perimeter recombination is supplied with the help of the model. Finally, the model is applied to concentrator GaAs solar cells to assess the impact of their doping level, size and geometry on the perimeter recombination.

Analysis of perimeter recombination in the subcells of GaInP/GaAs/Ge triple-junction solar cells

This paper studies the recombination at the perimeter in the subcells that constitute a GaInP/GaAs/Ge lattice-matched triple-junction solar cell. For that, diodes of different sizes and consequently different perimeter/area ratios have been manufactured in single-junction solar cells resembling the subcells in a triple-junction solar cell. It has been found that neither in GaInP nor in Ge solar cells the recombination at the perimeter is significant in devices as small as 500 μm × 500μm(2.5 ⋅ 10 − 3 cm2) in GaInP and 250μm  × 250μm (6.25 ⋅ 10 − 4cm2) in Ge. However, in GaAs, the recombination at the perimeter is not negligible at low voltages even in devices as large as 1cm2, and it is the main limiting recombination factor in the open circuit voltage even at high concentrations in solar cells of 250 μm  × 250μm (6.25 ⋅ 10 − 4 cm2) or smaller. Therefore, the recombination at the perimeter in GaAs should be taken into account when optimizing triple-junction solar cells.

Functional copies of a human gene can be directly isolated by transformation-associated recombination cloning with a small 3′ end target sequence

Unique, small sequences (sequence tag sites) have been identified at the 3′ ends of most human genes that serve as landmarks in genome mapping. We investigated whether a single copy gene could be isolated directly from total human DNA by transformation-associated recombination (TAR) cloning in yeast using a short, 3′ unique target. A TAR cloning vector was constructed that, when linearized, contained a small amount (381 bp) of 3′ hypoxanthine phosphoribosyltransferase (HPRT) sequence at one end and an 189-bp Alu repeat at the other end. Transformation with this vector along with human DNA led to selective isolations of the entire HPRT gene as yeast artificial chromosomes (YACs) that extended from the 3′ end sequence to various Alu positions as much as 600 kb upstream. These YACs were retrofitted with a NeoR and a bacterial artificial chromosome (BAC) sequence to transfer the YACs to bacteria and subsequently the BACs to mouse cells by using a Neo selection. Most of the HPRT isolates were functional, demonstrating that TAR cloning retains the functional integrity of the isolated material. Thus, this modified version of TAR cloning, which we refer to as radial TAR cloning, can be used to isolate large segments of the human genome accurately and directly with only a small amount of sequence information.

The high mobility group protein Abf2p influences the level of yeast mitochondrial DNA recombination intermediates in vivo

Abf2p is a high mobility group (HMG) protein found in yeast mitochondria that is required for the maintenance of wild-type (ρ+) mtDNA in cells grown on fermentable carbon sources, and for efficient recombination of mtDNA markers in crosses. Here, we show by two-dimensional gel electrophoresis that Abf2p promotes or stabilizes Holliday recombination junction intermediates in ρ+ mtDNA in vivo but does not influence the high levels of recombination intermediates readily detected in the mtDNA of petite mutants (ρ−). mtDNA recombination junctions are not observed in ρ+ mtDNA of wild-type cells but are elevated to detectable levels in cells with a null allele of the MGT1 gene (Δmgt1), which codes for a mitochondrial cruciform-cutting endonuclease. The level of recombination intermediates in ρ+ mtDNA of Δmgt1 cells is decreased about 10-fold if those cells contain a null allele of the ABF2 gene. Overproduction of Abf2p by ≥ 10-fold in wild-type ρ+ cells, which leads to mtDNA instability, results in a dramatic increase in mtDNA recombination intermediates. Specific mutations in the two Abf2p HMG boxes required for DNA binding diminishes these responses. We conclude that Abf2p functions in the recombination of ρ+ mtDNA.

Heteroduplex joint formation in Escherichia coli recombination is initiated by pairing of a 3′-ending strand

The formation of heteroduplex joints in Escherichia coli recombination is initiated by invasion of double-stranded DNA by a single-stranded homologue. To determine the polarity of the invasive strand, linear molecules with direct terminal repeats were released by in vivo restriction of infecting chimeric phage DNA and heteroduplex products of intramolecular recombination were analyzed. With this substrate, the invasive strand is expected to be incorporated into the circular crossover product and the complementary strand is expected to be incorporated into the reciprocal linear product. Strands of both polarities were incorporated into heteroduplex structures, but only strands ending 3′ at the break were incorporated into circular products. This result indicates that invasion of the 3′-ending strand initiates the heteroduplex joint formation and that the complementary 5′-ending strand is incorporated into heteroduplex structures in the process of reciprocal strand exchange. The polarity of the invasive strand was not affected by recD, recJ, or xonA mutations. However, xonA and recJ mutations increased the proportion of heteroduplexes containing 5′-ending strands. This observation suggests that RecJ exonuclease and exonuclease I may enhance recombination by degrading the displaced strands during branch migration and thereby causing strand exchange to be unidirectional.