Scalable stable comb-to-tone integrated RF photonic drive for superconducting qubits.

The recent advent of quantum computing has the potential to overhaul security, communications, and scientific modeling. Superconducting qubits are a leading platform that is advancing noise-tolerant intermediate-scale quantum processors. The implementation requires scaling to large numbers of superconducting qubits, circuit depths, and gate speeds, wherein high-purity RF signal generation and effective cabling transport are desirable. Fiber photonic-enhanced RF signal generation has demonstrated the principle of addressing both signal generation and transport requirements, supporting intermediate qubit numbers and robust packaging efforts; however, fiber-based approaches to RF signal distribution are often bounded by their phase instability. Here, we present a silicon photonic integrated circuit-based version of a photonic-enhanced RF signal generator that demonstrates the requisite stability, as well as a path towards the necessary signal fidelity.

Forensic Mitochondrial DNA Analysis: Current Practice and Future Potential.

Current practices for performing forensic mitochondrial DNA (mtDNA) sequence analysis, as employed in public and private laboratories across the United States, have changed remarkably little over the past 20 years. Alternative approaches have been developed and proposed, and new technologies have emerged, but the core methods have remained relatively unchanged. Once DNA has been recovered from biological material (for example, from older skeletal remains and hair shafts), segments of the mtDNA control region are amplified using a variety of approaches, dictated by the quality of the sample being tested. The amplified mtDNA products are subjected to Sanger-based sequencing and data interpretation is performed using one of many available software packages. These relatively simple methods, at least in retrospect, have remained robust, and have stood the test of time. However, alternative methods for mtDNA analysis remain viable options (for example, linear array assays and dHPLC), and should be revisited as the desire to streamline the testing process, interpret heteroplasmy, and deconvolute mixed mtDNA profiles intensifies. Therefore, it is important to periodically reassess the alternative methods available to the mtDNA practitioner, and to evaluate newer technologies being put forth by the scientific community, for example, next-generation sequencing. Although the basic mitochondrial DNA protocols and practices of public and private laboratories are similar, an overview of the current practices of forensic mtDNA analysis is provided, helping to frame the path forward.

An Assessment of the Genetic Diversity in a Field Population of Phytophthora nicotianae with a Changing Race Structure.

One hundred fifty-three isolates of Phytophthora nicotianae that were collected over a 4-year period from a single field were subjected to amplified fragment length polymorphism (AFLP) analysis to investigate the effect of different types of resistance in tobacco (Nicotiana tabacum) on genetic diversity in the pathogen population. No race 1 isolates were detected in the field prior to initiating the study, but the race was present in multiple plots by the end of the 4-year period. There were 102 race 0 isolates and 51 race 1 isolates characterized. Seventy-six of the 153 isolates had a unique AFLP profile, whereas the remaining 77 isolates were represented by 27 AFLP profiles shared by at least two isolates. Isolates of both races were found in both the unique and shared AFLP profile groups. Twenty-three of the AFLP profiles were detected in multiple years, indicating a clonal component to the pathogen population. Race 1 isolates that were detected over multiple years were always obtained from the same plot. No race 1 profile was found in more than one plot, confirming the hypothesis that the multiple occurrences of the race throughout the field were the result of independent events and not pathogen spread. Three identical race 0 AFLP profiles occurred in noncontiguous plots, and in each case, the plots contained the same partially resistant variety. Cluster analysis provided a high level of bootstrap support for 41 isolates in 19 clusters that grouped primarily by race and rotation treatment. Estimates of genetic diversity ranged from 0.365 to 0.831 and varied depending on tobacco cultivar planted and race. When averaged over all treatments, diversity in race 1 isolates was lower than in race 0 isolates at the end of each season. Deployment of single-gene resistance initially decreased genetic diversity of the population, but the diversity increased each year, indicating the pathogen was adapting to the host genotypes deployed in the field.

Fitness of Races 0 and 1 of Phytophthora parasitica var. nicotianae.

Deployment of tobacco (Nicotiana tabacum) varieties with complete resistance to race 0 of Phytophthora parasitica var. nicotianae has led to a rapid increase in the field populations of race 1 in North Carolina. In a field study, population levels of race 1 decreased relative to race 0 when cultivars with partial resistance to both races were planted, suggesting that race 1 isolates were less fit than race 0 isolates. Experiments were conducted to quantify differences in aggressiveness and survivability of the two races. Tobacco varieties with low, moderate, or high levels of partial resistance were inoculated with 60 pathogen isolates, and symptom development was monitored for 3 weeks. Race 0 isolates were more aggressive than race 1 isolates on cultivars with moderate or high levels of partial resistance; incubation periods were shorter and root rot severity was greater with race 0 isolates. Isolates of race 1, however, caused greater stunting of plants with moderate and high levels of partial resistance than race 0 isolates. Field microplots were infested with either a single race or an equal mixture of each race. Soil samples were collected at the end of two growing seasons and again the following spring. Pathogen populations declined from 40 to 80% during winter months, but population declines for race 0 were lower than for race 1 in each treatment over each winter. Race shifts from race 1 to race 0 that were observed in the presence of cultivars with partial resistance appear to be primarily the result of differences in aggressiveness of the races, with a possible minor effect of enhanced overwintering survival of race 0 compared with race 1.

Managing the Race Structure of Phytophthora parasitica var. nicotianae with Cultivar Rotation.

Deployment of tobacco cultivars with single-gene, complete resistance to race 0 of the tobacco black shank pathogen, Phytophthora parasitica var. nicotianae, has resulted in a rapid increase in the occurrence of race 1 of the pathogen in North Carolina. Cultivar-rotation studies were conducted in three fields to assess how different levels and types of resistance affected the race structure and population dynamics of the pathogen when deployed in fields initially containing single or mixed races of the pathogen. In a field with both races present, a high level of partial resistance in cv. K 346 was most effective in reducing disease and decreasing the proportion of race 1 in the pathogen population. The deployment of complete resistance in cv. NC 71 resulted in intermediate levels of disease control and race 1 became the predominate race. The cv. K 326, with a low level of partial resistance, had the highest levels of disease, and race 0 was the dominant race recovered. In a field where no race 1 was detected initially, disease incidence was high with the use of partial resistance. Complete resistance was very effective in suppressing disease, but race 1 was recovered after only one growing season. By the end of the third growing season, race 1 was recovered from most treatments where single-gene resistance was deployed. A high level of partial resistance was most effective in suppressing disease in a field where race 1 initially was the predominant race. A rotation between cultivars with single-gene resistance and cultivars with a high level of partial resistance should provide the most effective approach to black shank management. This rotation will reduce disease incidence and minimize race shifts in the pathogen and, over time, should prolong the usefulness of the Ph gene for black shank control in commercial production of tobacco.

Mitochondrial DNA Heteroplasmy.

Heteroplasmy, the presence of more than one type of mitochondrial DNA (mtDNA) in an individual, holds implications for forensic analysis of specimens such as blood, hair, and skeletal material. That is, what can we conclude about the likelihood that heteroplasmic specimens could or could not be from known individuals? Originally believed to be quite rare in healthy individuals, we now know that heteroplasmy exists at some level in all tissues on a predominantly homoplasmic background. A substantial body of general literature covers the biological origins of heteroplasmy, especially its transmission to new offspring and during life, the methodology for its detection, and its distribution in different tissues. In addition, the forensic community has contributed many observations on the characteristic appearance of heteroplasmy in relevant regions of the mtDNA control region and its appropriate treatment in forensic science. As a result of this growing understanding of a relatively simple biological phenomenon, we conclude that heteroplasmy can be expected to play a role in forensic interpretation on a regular basis, and that knowledge of its biological underpinnings contribute to just, conservative, and scientifically appropriate interpretational guidelines.

Forensic mitochondrial DNA analysis: two years of commercial casework experience in the United States.

AIM: To describe mitochondrial DNA (mtDNA) forensic casework experience in a commercial laboratory in the United States. METHODS: Frequency statistics were kept for two years on all aspects of mtDNA forensic cases, including types of clientele, types of samples, levels of sample success and failure, site heteroplasmy, length heteroplasmy, contamination, rates of failures to exclude, and match statistics using a mtDNA sequence database. RESULTS: Low sample failure rate was observed, especially since an "ancient DNA" approach was used for samples with degraded DNA. Levels of contamination were low, and the observed site and length heteroplasmy did not confound the interpretation of results. The data collected from mtDNA haplotypes developed in casework showed extremely high diversity of haplotypes consistent with other formally developed databases. CONCLUSIONS: MtDNA forensic analysis in the private sector was successfully applied to many different types of samples overall, with minimal rates of complication due to sample handling challenges (degraded DNA, minimal samples, contamination) and sequence-specific phenomena (site and length heteroplasmy).

Diversity and heterogeneity in mitochondrial DNA of North American populations.

Variation in the mitochondrial DNA (mtDNA) control region as detected by sequence-specific oligonucleotide (SSO) probes is described for 2282 individuals from African-American, European-American, and Hispanic subpopulations from five broadly defined regions of North America (Northeast, Southeast, Central, Northwest, Southwest). Population diversity estimates were uniformly high for all subpopulations and for each major ethnic group. Only the Pennsylvania Hispanic group was remarkable with respect to its mitochondrial DNA types, having both six low frequency population specific types (ranging from 1.2-8.6%) and three high frequency shared types (10-20% each). There was no statistically significant subpopulation heterogeneity present within any of the three major groups at either the subpopulation level or the regional level (p > 0.01). However, statistically significant heterogeneity was measured when comparing the three major groups to each other, with the variance component attributable to this large division accounting for 18.60% of the total variance (p < 0.001). Overall mtDNA is a satisfactory forensic typing locus within broadly defined African-American, European-American, and Hispanic groups from North America, based on the high diversity estimates and absence of heterogeneity, as characterized by SSO typing.

Identification of Sources of Resistance to Four Species of Root-knot Nematodes in Tobacco.

Resistance to the southern root-knot nematode, Meloidogyne incognita races 1 and 3, has been identified, incorporated, and deployed into commercial cultivars of tobacco, Nicotiana tabacum. Cultivars with resistance to other economically important root-knot nematode species attacking tobacco, M. arenaria, M. hapla, M. javanica, and other host-specific races of M. incognita, are not available in the United States. Twenty-eight tobacco genotypes of diverse origin and two standard cultivars, NC 2326 (susceptible) and Speight G 28 (resistant to M. incognita races 1 and 3), were screened for resistance to eight root-knot nematode populations of North Carolina origin. Based on root gall indices at 8 to 12 weeks after inoculation, all genotypes except NC 2326 and Okinawa were resistant to M. arenaria race 1, and races 1 and 3 of M. incognita. Except for slight root galling, genotypes resistant to M. arenaria race 1 responded similarly to races 1 and 3 of M. incognita. All genotypes except NC 2326, Okinawa, and Speight G 28 showed resistance to M. javanica. Okinawa, while supporting lower reproduction of M. javanica than NC 2326, was rated as moderately susceptible. Tobacco breeding lines 81-R-617A, 81-RL- 2K, SA 1213, SA 1214, SA 1223, and SA 1224 were resistant to M. arenaria race 2, and thus may be used as sources of resistance to this pathogen. No resistance to M. hapla and only moderate resistance to races 2 and 4 of M. incognita were found in any of the tobacco genotypes. Under natural field infestations of M. arenaria race 2, nematode development on resistant tobacco breeding lines 81-RL-2K, SA 1214, and SA 1215 was similar to a susceptible cultivar with some nematicide treatments; however, quantity and quality of yield were inferior compared to K 326 plus nematicides.

Genetic evidence for the proto-Austronesian homeland in Asia: mtDNA and nuclear DNA variation in Taiwanese aboriginal tribes.

Previous studies of mtDNA variation in indigenous Taiwanese populations have suggested that they held an ancestral position in the spread of mtDNAs throughout Southeast Asia and Oceania (Melton et al. 1995; Sykes et al. 1995), but the question of an absolute proto-Austronesian homeland remains. To search for Asian roots for indigenous Taiwanese populations, 28 mtDNAs representative of variation in four tribal groups (Ami, Atayal, Bunun, and Paiwan) were sequenced and were compared with each other and with mtDNAs from 25 other populations from Asia and Oceania. In addition, eight polymorphic Alu insertion loci were analyzed, to determine if the pattern of mtDNA variation is concordant with nuclear DNA variation. Tribal groups shared considerable mtDNA sequence identity (P>.90), where gene flow is believed to have been low, arguing for a common source or sources for the tribes. mtDNAs with a 9-bp deletion have considerable mainland-Asian diversity and have spread to Southeast Asia and Oceania through a Taiwanese bottleneck. Only four Taiwanese mtDNA haplotypes without the 9-bp deletion were shared with any other populations, but these shared types were widely dispersed geographically throughout mainland Asia. Phylogenetic and principal-component analyses of Alu loci were concordant with conclusions from the mtDNA analyses; overall, the results suggest that the Taiwanese have temporally deep roots, probably in central or south China, and have been isolated from other Asian populations in recent history.

Extent of heterogeneity in mitochondrial DNA of sub-Saharan African populations.

Variation in the mitochondrial DNA (mtDNA) control region as detected by sequence-specific oligonucleotide (SSO) probes is described for 381 individuals from nine sub-Saharan African populations. Population diversity estimates for SSO types ranged from 0.23 to 0.97, while 102 SSO types were detected, none of these types was shared by more than four populations. Eighteen types occurred in > or = 10% of individuals in some populations; of these, 11 were population-specific. One type occurred in 15% of the total sample, but was shared among only three populations. African SSO types were characterized by high frequencies of blank variants, indicating that there was additional variation present at the nucleotide sequence level in regions where SSO probes hybridize. Analyses of molecular variance (AMOVA) incorporating genetic distances between SSO types showed that 30% of the total variation was due to differences among populations, indicating that there is statistically significant heterogeneity (p < 0.001). An AMOVA on mtDNA control region nucleotide sequence data from 12 populations showed that including all additional variation present at the sequence level increased the variance due to population subdivision to 34% (p < 0.001). Overall, when considering both the low diversity within some populations and high heterogeneity among populations, SSO typing of mtDNA may not be a desirable forensic DNA typing method for continental African populations. Further mtDNA sampling of African-derived populations of North America should be carried out to determine how much of the continental African mtDNA variation is of forensic significance. However, the existence of extensive mtDNA control region nucleotide sequence variation in African populations means that control region sequencing is still appropriate in forensic cases requiring mtDNA analysis.

Extent of heterogeneity in mitochondrial DNA of European populations.

Variation in the mitochondrial DNA (mtDNA) control region as detected by sequence-specific oligonucleotide (SSO) probes is described for 595 individuals from six European or European-derived populations. Estimates of diversity for mtDNA types exceed 0.91 in all populations, while 50% of the 158 types which were observed occur only once. Of 68 shared types, most occur rarely (< 3% of the total population); only one type occurs at a frequency greater than 10%, and it is present at comparable frequencies in all six populations (18-29%). An analysis of molecular variance (AMOVA) incorporating genetic distances between types shows that 100% of the variation present in the total sample is attributable to within-population diversity, while there are essentially no between-population differences. Another AMOVA was performed for the first hypervariable region SSO sites only, which included this sample plus an additional 537 SSO types from mine more European populations that were inferred from published mtDNA control region sequence data. Similar results were obtained, with over 99% of the variation overall attributable to within-population differences, and less than 1% of the variation attributable to between-population differences. The Saami were the most different from other populations, which had been observed in an earlier study of nucleotide sequence data. Overall, there is no statistically significant heterogeneity for European populations (p > 0.001), and these groups are virtually indistinguishable with respect to mtDNA SSO types. These results demonstrate the utility of mtDNA typing for forensic investigations.

Sources of Inoculum and Management for Rhizoctonia solani Damping-off on Tobacco Transplants under Greenhouse Conditions.

Damping-off and target spot are important diseases of tobacco transplants produced under greenhouse conditions. Identification of sources of inoculum for these diseases caused by Rhizoctonia solani is an important first step in disease management. Control strategies based on sanitation and the eradication of primary inoculum were studied. Potting mix and Styrofoam trays used in transplant production were assayed to determine if they were sources of primary inoculum. Eleven sources of potting mix were sampled over a 2-year period. None of the mixes contained viable inoculum of R. solani. R. solani was isolated from previously used trays after 1 year of storage by removing and plating pieces of Styrofoam from individual tray cells on alkaline water agar (AWA). Sclerotia and melanized hyphae of R. solani were observed in the cracks present in the cells of the trays. Dry heat (70 to 80°C for 2 h) and chemical (sodium hypochlorite and sodium chloride) treatments reduced the levels of inoculum on trays up to 45% compared to controls, but only methyl bromide and steam treatments (80°C for 0.5 to 2.0 h) eradicated inoculum of R. solani from trays. Elimination of primary inoculum from previously used trays effectively controlled target spot and stem rot diseases caused by R. solani.

Extent of heterogeneity in mitochondrial DNA of ethnic Asian populations.

Variation in the mitochondrial DNA (mtDNA) control region as detected by sequence-specific oligonucleotide (SSO) probes is described for 993 individuals in 11 ethnic Asian populations. Estimates of diversity for mtDNA types exceed 0.94 in all populations, while 53% of the 255 types that were observed occur only once. Of 96 shared types, four occur at frequencies of greater than 10% but less than 17% in any one population. There is statistically significant heterogeneity among these 11 populations, however, an analysis of variance incorporating genetic distances between types shows that at least 95% of the variation present in the total sample is attributable to within-population diversity, while only 5% is due to between-population differences. Overall, heterogeneity with respect to mtDNA SSO types is grossly correlated with geographic distance between populations; the most extreme heterogeneity was observed between populations from East Asia and populations from West Asia. With respect to population genetics, the control region of mtDNA exhibits satisfactory qualities as a DNA typing locus.

Selection and Characterization of Aspartokinase Feedback-Insensitive Mutants of Azotobacter vinelandii.

Aspartokinase feedback-insensitive mutants of Azotobacter vinelandii were selected as resistant to l-threonine, (beta)-hydroxynorvaline, or S-(2-aminoethyl)-l-cysteine. l-Threonine-resistant strains were classified into three groups based on their ability to transport l-threonine and their growth response to O-methylthreonine and (beta)-hydroxynorvaline. Most of the mutants were transport defective; however, some were desensitized to feedback regulation.

Polynesian genetic affinities with Southeast Asian populations as identified by mtDNA analysis.

Polynesian genetic affinities to populations of Asia were studied using mtDNA markers. A total of 1,037 individuals from 12 populations were screened for a 9-bp deletion in the intergenic region between the COII and tRNA(Lys) genes that approaches fixation in Polynesians. Sequence-specific oligonucleotide probes that identify specific mtDNA control region nucleotide substitutions were used to describe variation in individuals with the 9-bp deletion. The 9-bp deletion was not observed in northern Indians, Bangladeshis, or Pakistanis but was seen at low to moderate frequencies in the nine other Southeast Asian populations. Three substitutions in the control region at positions 16217, 16247, and 16261 have previously been observed at high frequency in Polynesian mtDNAs; this "Polynesian motif" was observed in 20% of east Indonesians with the 9-bp deletion but was observed in only one additional individual. mtDNA types related to the Polynesian motif are highest in frequency in the corridor from Taiwan south through the Philippines and east Indonesia, and the highest diversity for these types is in Taiwan. These results are consistent with linguistic evidence of a Taiwanese origin for the proto-Polynesian expansion, which spread throughout Oceania by way of Indonesia.

Temporal efficacy of selected nematicides on meloidogyne species on tobacco.

Aldicarb, ethoprop, and fenamiphos were evaluated for their efficacy in controlling various species of root-knot nematodes on flue-cured tobacco and for their residual activity, as determined through periodic sampling and bioassays of soil taken from field plots. Field experiments were conducted at five locations over 2 years with flue-cured tobacco. Soil in plots treated with nematicides were formed into high, wide beds before transplanting with 'Coker 371-Gold' or 'K 326' tobacco. Residual control of Meloidogyne spp. was greatest (P

Chemotactic Behavior of Azotobacter vinelandii.

Chemotaxis was exhibited by Azotobacter vinelandii motile cells. Exposure of cells to sudden increases in attractant concentration suppressed the frequency of tumbling and resulted in smooth swimming. Cells responded chemotactically to a chemical gradient produced during metabolism. Motility occurred over a temperature range of 25 to 37 degrees C with an optimum pH range of between pH 7.0 and 8.0. The average speed of motile cells was determined to be 74 mum/s or 37 body lengths per s. The speed of cells appeared to increase as a function of attractant concentration. Chemotactic systems for fructose, glucose, xylitol, and mannitol were inducible. A. vinelandii exhibited chemotaxis for a number of compounds, including hexoses, hexitols, pentitols, pentoses, disaccharides, and amino sugars. We conclude from these studies that A. vinelandii exhibits a temporal chemotactic sensing system.

Effects of Nematicides and Cuitivars on Rotylenchulus reniformis and Flue-cured Tobacco Yield.

Main plots of tobacco cultivars were split into subplots treated or not treated with 1,3-D + chloropicrin. Some differences (P = 0.05) occurred for tobacco yield, value, and R. reniformis populations among the 12 cultivars tested. Treatment increased yields an average of 8.5%, but a significant cultivar x fumigation interaction did not occur. In a nematicide test, six of nine non-fumigant and fumigant nematicides significantly increased the value of tobacco cv. Coker 371-Gold by an average of $1,475/ha and decreased populations of Rotylenchulus reniformis. Similar results were not obtained using the cv. K 326 in another year. Nematode population levels often declined from the first sampling to the second, especially when initial numbers were relatively high. These are the first reported field studies involving management of R. reniformis on tobacco in the United States.