Evaluation Of Recombinant Research Articles

Evaluation ofrecombination detection methods forviral sequencing.

Recombination is a key evolutionary driver in shaping novel viral populations and lineages. When unaccounted for, recombination can impact evolutionary estimations or complicate their interpretation. Therefore, identifying signals for recombination in sequencing data is a key prerequisite to further analyses. A repertoire of recombination detection methods (RDMs) have been developed over the past two decades; however, the prevalence of pandemic-scale viral sequencing data poses a computational challenge for existing methods. Here, we assessed eight RDMs: PhiPack (Profile), 3SEQ, GENECONV, recombination detection program (RDP) (OpenRDP), MaxChi (OpenRDP), Chimaera (OpenRDP), UCHIME (VSEARCH), and gmos; to determine if any are suitable for the analysis of bulk sequencing data. To test the performance and scalability of these methods, we analysed simulated viral sequencing data across a range of sequence diversities, recombination frequencies, and sample sizes. Furthermore, we provide a practical example for the analysis and validation of empirical data. We find that RDMs need to be scalable, use an analytical approach and resolution that is suitable for the intended research application, and are accurate for the properties of a given dataset (e.g. sequence diversity and estimated recombination frequency). Analysis of simulated and empirical data revealed that the assessed methods exhibited considerable trade-offs between these criteria. Overall, we provide general guidelines for the validation of recombination detection results, the benefits and shortcomings of each assessed method, and future considerations for recombination detection methods for the assessment of large-scale viral sequencing data.

Genetic characterization and recombination analysis of atypical porcine pestivirus

Atypical porcine pestivirus (APPV) is recognised as the etiology of congenital tremor (CT) Type A-II and poses a challenge to pig production. Here, we described a CT case in piglets caused by APPV infection in central China in 2017. Interestingly, different from a previous report, more CT litters were observed in the second and third parity sows compared to the first and fourth parity. Evolutionary analysis and recombination evaluation were conducted for the isolate and 61 APPV genomes were available in GenBank. Phylogenetic analysis revealed a high level of genetic variation of APPV and the coexistence of three clades (Clades I–III) in China. The isolate was clustered into Clade I, which seemed to be prevalent worldwide and displayed higher genetic variability (Subgroups 1–4) compared with Clade II and Clade III, both of which were only reported in China. Notably, three putative recombinants were identified and characterized in APPV. The recombination events occurred in inter-clades (Clade II and III) or intra-clades (Clade I). To the best of our knowledge, this study presents the first evidence of homologous recombination within Pestivirus K. These results provide new clinical presentations of APPV infection and may be helpful in better understanding the large amount of genetic variations in this genus.

Effect of charge trapping on effective carrier lifetime in compound semiconductors: High resistivity CdZnTe

The dominant problem limiting the energy resolution of compound semiconductor based radiation detectors is the trapping of charge carriers. The charge trapping affects energy resolution through the carrier lifetime more than through the mobility. Conventionally, the effective carrier lifetime is determined using a 2-step process based on measurement of the mobility-lifetime product (μτ) and determining drift mobility using time-of-flight measurements. This approach requires fabrication of contacts on the sample. A new RF-based pulse rise-time method, which replaces this 2-step process with a single non-contact direct measurement, is discussed. The application of the RF method is illustrated with high-resistivity detector-grade CdZnTe crystals. The carrier lifetime in the measured CdZnTe, depending on the quality of the crystals, was between about 5 μs and 8 μs. These values are in good agreement with the results obtained using conventional 2-step approach. While the effective carrier lifetime determined from the initial portion of the photoresponse transient combines both recombination and trapping in a manner similar to the conventional 2-step approach, both the conventional and the non-contact RF methods offer only indirect evaluation of the effect of charge trapping in the semiconductors used in radiation detectors. Since degradation of detector resolution is associated not with trapping but essentially with detrapping of carriers, and, in particular, detrapping of holes in n-type semiconductors, it is concluded that evaluation of recombination and detrapping during photoresponse decay is better suited for evaluation of compound semiconductors used in radiation detectors. Furthermore, based on previously reported data, it is concluded that photoresponse decay in high resistivity CdZnTe at room temperature is dominated by detrapping of carriers from the states associated with one type of point defect and by recombination of carriers at one type of extended defects. The recombination at the extended defects produces long, logarithmic decay limiting substantially performance of CdZnTe detectors. This decay is associated with the “electrostatic trapping” of excess holes by the Schottky-type depletion space-charge regions formed around the defects.

Surface recombination evaluation of a silicon wafer by using the photoluminescence intensity ratio method for solar cell applications

Photoluminescence (PL) was one of the useful characterization techniques for direct-band-gap and high-quantum-efficiency materials in the past. PL is now used to characterize silicon epitaxial layers or wafers in a nondestructive and contactless way at room temperature. In this research, we use a Silicon Photoenhanced Recombination (SiPHER) PL system with a 532 nm or a 827 nm wavelength. The high-intensity laser source of 1 μm or 1 mm in diameter was able to map the entire wafer at modest resolution or scan a smaller area at higher resolution. This PL system detects two signals, the PL intensity and the surface reflectance (SR) intensity, from the test sample. The PL intensity strongly depends on the surface recombination velocity, bulk lifetime, and trap density. The SR intensity depends on surface condition, layer thickness and optical properties. We have determined the carrier distribution in semiconductors following light excitation and use these distributions to calculate the PL signals to extract various surface recombination velocities and other recombination components. We focus on how the surface recombination varies widely even in high-lifetime wafers or layers because it depends on the state of the surface, i.e., bare, passivated, contaminated, oxidized, etc. The surface recombination velocity (Sr) has a major effect on the lifetime. If the number of bulk traps is low; hence, the Sr can be extracted from the PL measurement. To determine the Sr, we measured the PL intensity ratio (RPL) and optical reflection at the two exciting wavelengths. We prepared various treated surface samples and measured the PL, SR, and RPL; then, we quantized surface recombination velocity for each sample. The values of the Sr were 2 × 104, 6 × 104, and 8 × 104 cm/s for the control, the soft scrubbed sample, and the hard-scratched sample, respectively.

Towards the Genotyping of Fungi: Methods, Benefits and Challenges

Several fungi have recently been described as capable to recombine and drive large genetic diversity in clinical samples and in the environment. Among the genotyping methods, microsatellite analysis is frequently reported as preferred for studying local epidemiology, but single nucleotide polymorphisms represent the best markers for evaluation of recombination, linkage and aneuploidy. The future of typing analyses may reside in strategies capable of cataloging the whole genome and complete microbial diversity. The present review focuses the current strategies employed for fungal genotyping and evaluation of genetic diversity, and the challenges of next generation sequencing with regard to this topic. Typing methods establish the genetic identity of fungal isolates and allow clarification of outbreaks and transmission of strains between individuals, comparison of chronic colonization versus patients carrying unrelated strains, detection of co-evolution of pathogenic and/or drug-resistant strains. The next advances in molecular mycology may revolutionize clinics and redesign concepts of microbial evolution.

Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination

BackgroundMost of the DNA variations found in bacterial species are in the form of single nucleotide polymorphisms (SNPs), but there is some debate regarding how much of this variation comes from mutation versus recombination. The nitrogen-fixing symbiotic bacteria Rhizobium etli is highly variable in both genomic structure and gene content. However, no previous report has provided a detailed genomic analysis of this variation at nucleotide level or the role of recombination in generating diversity in this bacterium. Here, we compared draft genomic sequences versus complete genomic sequences to obtain reliable measures of genetic diversity and then estimated the role of recombination in the generation of genomic diversity among Rhizobium etli.ResultsWe identified high levels of DNA polymorphism in R. etli, and found that there was an average divergence of 4% to 6% among the tested strain pairs. DNA recombination events were estimated to affect 3% to 10% of the genomic sample analyzed. In most instances, the nucleotide diversity (π) was greater in DNA segments with recombinant events than in non-recombinant segments. However, this degree of recombination was not sufficiently large to disrupt the congruence of the phylogenetic trees, and further evaluation of recombination in strains quartets indicated that the recombination levels in this species are proportionally low.ConclusionOur data suggest that R. etli is a species composed of separated lineages with low homologous recombination among the strains. Horizontal gene transfer, particularly via the symbiotic plasmid characteristic of this species, seems to play an important role in diversity but the lineages maintain their evolutionary cohesiveness.

Time-Resolved Transient Grating Spectroscopy for Studies of Nonequilibrium Carrier Dynamics in Wide Band-Gap Semiconductors

Using interdisciplinary fields relevant to a highly excited semiconductor — nonequilibrium phenomena in high density plasma, light-induced changes of optical properties, and dynamic holography, we developed time-resolved four-wave mixing technique for monitoring the spatial and temporal carrier dynamics in wide band-gap semiconductors. This opened a new possibility to analyse fast electronic processes in a non-destructive “all-optical” way, i.e. without any electrical contacts. This technique allowed evaluation of recombination and transport processes and the determination of important carrier parameters which directly reveal the material quality: carrier lifetime, bipolar diffusion coefficients, surface recombination rate, nonlinear recombination rate, diffusion length, threshold of stimulated recombination. The recent experimental studies of differently grown group III-nitrides (heterostructures and free standing films) as well silicon carbide epilayers by nondegenerate picosecond four-wave mixing are presented.

Segregation of 12 isozyme genes among doubled haploid lines derived from a japonica x indica cross of rice (Oryza sativa L.)

The segregation of 12 heterozygous isozyme markers was analyzed among F2 plants and 51 anther culture (AC)-derived lines obtained from the japonica × indica cross of rice, IRAT 177 × Apura. All the lines except two were homozygous products of recombination of the two parental phenotypes. Doubled haploid (DH) lines derived from plants regenerated from the same callus were identical, confirming previously obtained results in rice. Surprisingly, some lines derived from different calli were also identical, suggesting a phenomenon of early callus fragmentation. All these observations at the isozyme level were confirmed by field evaluation. Deviations of segregations from the expected 1 : 1 ratio were observed at 4 loci among the DH lines. Among these, two were also noted among the F2 plants. The two other distortions, both in favor of the japonica allele, were observed specifically in the AC-derived materials. Although this concerns a small proportion of the genes under study, it suggests that the embryogenic microsporal population does not represent a random gametic array. On the other hand, evaluation of recombination between isozyme genes located on chromosome 6 appears consistent with F2 data and data previously recorded on the other japonica × indica crosses. The potential use of isozymes in breeding doubled haploids derived from remote crosses in rice is discussed.