Exploring the Use of Cytochrome Oxidase c Subunit 1 (COI) for DNA Barcoding of Free-Living Marine Nematodes

BackgroundThe identification of free-living marine nematodes is difficult because of the paucity of easily scorable diagnostic morphological characters. Consequently, molecular identification tools could solve this problem. Unfortunately, hitherto most of these tools relied on 18S rDNA and 28S rDNA sequences, which often lack sufficient resolution at the species level. In contrast, only a few mitochondrial COI data are available for free-living marine nematodes. Therefore, we investigate the amplification and sequencing success of two partitions of the COI gene, the M1-M6 barcoding region and the I3-M11 partition.MethodologyBoth partitions were analysed in 41 nematode species from a wide phylogenetic range. The taxon specific primers for the I3-M11 partition outperformed the universal M1-M6 primers in terms of amplification success (87.8% vs. 65.8%, respectively) and produced a higher number of bidirectional COI sequences (65.8% vs 39.0%, respectively). A threshold value of 5% K2P genetic divergence marked a clear DNA barcoding gap separating intra- and interspecific distances: 99.3% of all interspecific comparisons were >0.05, while 99.5% of all intraspecific comparisons were <0.05 K2P distance.ConclusionThe I3-M11 partition reliably identifies a wide range of marine nematodes, and our data show the need for a strict scrutiny of the obtained sequences, since contamination, nuclear pseudogenes and endosymbionts may confuse nematode species identification by COI sequence

Field-effect transistors assembled from functionalized carbon nanotubes

We have fabricated field effect transistors from carbon nanotubes using a novel selective placement scheme. We use carbon nanotubes that are covalently bound to molecules containing hydroxamic acid functionality. The functionalized nanotubes bind strongly to basic metal oxide surfaces, but not to silicon dioxide. Upon annealing, the functionalization is removed, restoring the electronic properties of the nanotubes. The devices we have fabricated show excellent electrical characteristics.Comment: 5 pages, 6 figure

Colorectal cancer linkage on chromosomes 4q21, 8q13, 12q24, and 15q22

A substantial proportion of familial colorectal cancer (CRC) is not a consequence of known susceptibility loci, such as mismatch repair (MMR) genes, supporting the existence of additional loci. To identify novel CRC loci, we conducted a genome-wide linkage scan in 356 white families with no evidence of defective MMR (i.e., no loss of tumor expression of MMR proteins, no microsatellite instability (MSI)-high tumors, or no evidence of linkage to MMR genes). Families were ascertained via the Colon Cancer Family Registry multi-site NCI-supported consortium (Colon CFR), the City of Hope Comprehensive Cancer Center, and Memorial University of Newfoundland. A total of 1,612 individuals (average 5.0 per family including 2.2 affected) were genotyped using genome-wide single nucleotide polymorphism linkage arrays; parametric and non-parametric linkage analysis used MERLIN in a priori-defined family groups. Five lod scores greater than 3.0 were observed assuming heterogeneity. The greatest were among families with mean age of diagnosis less than 50 years at 4q21.1 (dominant HLOD = 4.51, α = 0.84, 145.40 cM, rs10518142) and among all families at 12q24.32 (dominant HLOD = 3.60, α = 0.48, 285.15 cM, rs952093). Among families with four or more affected individuals and among clinic-based families, a common peak was observed at 15q22.31 (101.40 cM, rs1477798; dominant HLOD = 3.07, α = 0.29; dominant HLOD = 3.03, α = 0.32, respectively). Analysis of families with only two affected individuals yielded a peak at 8q13.2 (recessive HLOD = 3.02, α = 0.51, 132.52 cM, rs1319036). These previously unreported linkage peaks demonstrate the continued utility of family-based data in complex traits and suggest that new CRC risk alleles remain to be elucidated. © 2012 Cicek et al

Low-frequency Current Fluctuations in Individual Semiconducting Single-Wall Carbon Nanotubes

We present a systematic study on low-frequency current fluctuations of nano-devices consisting of one single semiconducting nanotube, which exhibit significant 1/f-type noise. By examining devices with different switching mechanisms, carrier types (electrons vs. holes), and channel lengths, we show that the 1/f fluctuation level in semiconducting nanotubes is correlated to the total number of transport carriers present in the system. However, the 1/f noise level per carrier is not larger than that of most bulk conventional semiconductors, e.g. Si. The pronounced noise level observed in nanotube devices simply reflects on the small number of carriers involved in transport. These results not only provide the basis to quantify the noise behavior in a one-dimensional transport system, but also suggest a valuable way to characterize low-dimensional nanostructures based on the 1/f fluctuation phenomenon

Impact of Cigarette Smoking Status on Pain Intensity Among Veterans With and Without Hepatitis C

Objective: Chronic pain is a significant problem in patients living with hepatitis C virus (HCV). Tobacco smoking is an independent risk factor for high pain intensity among veterans. This study aims to examine the independent associations with smoking and HCV on pain intensity, as well as the interaction of smoking and HCV on the association with pain intensity. Design/Particpants: Cross-sectional analysis of a cohort study of veterans of Operations Enduring Freedom/Iraqi Freedom/New Dawn (OEF/OIF/OND) who had at least one visit to a Veterans Health Administration (VHA) primary care clinic between 2001 and 2014. Methods: HCV was identified using ICD-9 codes from electronic medical records (EMRs). Pain intensity, reported on a 0-10 numeric rating scale, was categorized as none/mild (0-3) and moderate/severe (4-10). Results: Among 654,841 OEF/OIF/OND veterans (median age [interquartile range] = 26 [23-36] years), 2,942 (0.4%) were diagnosed with HCV. Overall, moderate/severe pain intensity was reported in 36% of veterans, and 37% were current smokers. The adjusted odds of reporting moderate/severe pain intensity were 1.23 times higher (95% confidence interval [CI] = 1.14-1.33) for those with HCV and 1.26 times higher (95% CI = 1.25-1.28) for current smokers. In the interaction model, there was a significant Smoking Status x HCV interaction (P = 0.03). Among veterans with HCV, smoking had a significantly larger association with moderate/severe pain (adjusted odds ratio [OR] = 1.50, P \u3c 0.001) than among veterans without HCV (adjusted OR = 1.26, P \u3c 0.001). Conclusions: We found that current smoking is more strongly linked to pain intensity among veterans with HCV. Further investigations are needed to explore the impact of smoking status on pain and to promote smoking cessation and pain management in veterans with HCV

Enhanced Logic Performance with Semiconducting Bilayer Graphene Channels

Realization of logic circuits in graphene with an energy gap (EG) remains one of the main challenges for graphene electronics. We found that large transport EGs (>100 meV) can be fulfilled in dual-gated bilayer graphene underneath a simple alumina passivation top gate stack, which directly contacts the graphene channels without an inserted buffer layer. With the presence of EGs, the electrical properties of the graphene transistors are significantly enhanced, as manifested by enhanced on/off current ratio, subthreshold slope and current saturation. For the first time, complementary-like semiconducting logic graphene inverters are demonstrated that show a large improvement over their metallic counterparts. This result may open the way for logic applications of gap-engineered graphene.Comment: Accepted by ACS Nan

Genetic Structure of Xiphinema pachtaicum

The dagger nematodes Xiphinema pachtaicum and X. index are two of the most widespread and frequently occurring Xiphinema spp. co-infesting vineyards and other crops and natural habitats worldwide. Sexual reproduction is rare in these species. The primary objective of this study was to determine the genetic structure of X. pachtaicum and X. index populations using eight and seven populations, respectively, from different "wine of denomination of origin (D.O.) zones" in Spain and Sardinia (Italy), by studying mitochondria! (cytochrome oxidase c subunit 1 or COI) and nuclear (D2-D3 expansion segments of 28S rDNA) markers. Both Xiphinema spp. showed low intraspecific divergence among COI sequences, ranging from 0.2% (1 base substitution) to 2.3% (10 substitutions) in X. pachtaicum and from 0.2% (I base substitution) to 0.4% (2 substitutions) in X. index. Population genetic structure was strong for both species. Nevertheless, molecular differences among grapevine-growing areas were not significant, and intrapopulation diversity was very low. It is hypothesized that this genetic homogeneity in the nematode populations reflects their predominant parthenogenetic reproduction mode and low dispersal abilities. Our results also show that X. pachtaicum populations in Spain have possibly been established from two different populations of origin. Results also demonstrated that the two DNA regions studied are suitable diagnostic markers for X. index and X. pachtaicum

Ecology and Biogeography of Free-Living Nematodes Associated with Chemosynthetic Environments in the Deep Sea: A Review

Background: Here, insight is provided into the present knowledge on free-living nematodes associated with chemosynthetic environments in the deep sea. It was investigated if the same trends of high standing stock, low diversity, and the dominance of a specialized fauna, as observed for macro-invertebrates, are also present in the nematodes in both vents and seeps. Methodology: This review is based on existing literature, in combination with integrated analysis of datasets, obtained through the Census of Marine Life program on Biogeography of Deep-Water Chemosynthetic Ecosystems (ChEss). Findings: Nematodes are often thriving in the sulphidic sediments of deep cold seeps, with standing stock values ocassionaly exceeding largely the numbers at background sites. Vents seem not characterized by elevated densities. Both chemosynthetic driven ecosystems are showing low nematode diversity, and high dominance of single species. Genera richness seems inversely correlated to vent and seep fluid emissions, associated with distinct habitat types. Deep-sea cold seeps and hydrothermal vents are, however, highly dissimilar in terms of community composition and dominant taxa. There is no unique affinity of particular nematode taxa with seeps or vents. Conclusions: It seems that shallow water relatives, rather than typical deep-sea taxa, have successfully colonized the reduced sediments of seeps at large water depth. For vents, the taxonomic similarity with adjacent regular sediments is much higher, supporting rather the importance of local adaptation, than that of long distance distribution. Likely the ephemeral nature of vents, its long distance offshore and the absence of pelagic transport mechanisms, have prevented so far the establishment of a successful and typical vent nematode fauna. Some future perspectives in meiofauna research are provided in order to get a more integrated picture of vent and seep biological processes, including all components of the marine ecosystem