First complete genome sequence of infectious laryngotracheitis virus

BACKGROUND: Infectious laryngotracheitis virus (ILTV) is an alphaherpesvirus that causes acute respiratory disease in chickens worldwide. To date, only one complete genomic sequence of ILTV has been reported. This sequence was generated by concatenating partial sequences from six different ILTV strains. Thus, the full genomic sequence of a single (individual) strain of ILTV has not been determined previously. This study aimed to use high throughput sequencing technology to determine the complete genomic sequence of a live attenuated vaccine strain of ILTV. RESULTS: The complete genomic sequence of the Serva vaccine strain of ILTV was determined, annotated and compared to the concatenated ILTV reference sequence. The genome size of the Serva strain was 152,628 bp, with a G + C content of 48%. A total of 80 predicted open reading frames were identified. The Serva strain had 96.5% DNA sequence identity with the concatenated ILTV sequence. Notably, the concatenated ILTV sequence was found to lack four large regions of sequence, including 528 bp and 594 bp of sequence in the UL29 and UL36 genes, respectively, and two copies of a 1,563 bp sequence in the repeat regions. Considerable differences in the size of the predicted translation products of 4 other genes (UL54, UL30, UL37 and UL38) were also identified. More than 530 single-nucleotide polymorphisms (SNPs) were identified. Most SNPs were located within three genomic regions, corresponding to sequence from the SA-2 ILTV vaccine strain in the concatenated ILTV sequence. CONCLUSIONS: This is the first complete genomic sequence of an individual ILTV strain. This sequence will facilitate future comparative genomic studies of ILTV by providing an appropriate reference sequence for the sequence analysis of other ILTV strains

Biophotonic Methods for Brain-Computer Interfaces

Poste

Real-time PCR based on SYBR-Green I fluorescence: An alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions

BACKGROUND: Real-time PCR is increasingly being adopted for RNA quantification and genetic analysis. At present the most popular real-time PCR assay is based on the hybridisation of a dual-labelled probe to the PCR product, and the development of a signal by loss of fluorescence quenching as PCR degrades the probe. Though this so-called 'TaqMan' approach has proved easy to optimise in practice, the dual-labelled probes are relatively expensive. RESULTS: We have designed a new assay based on SYBR-Green I binding that is quick, reliable, easily optimised and compares well with the published assay. Here we demonstrate its general applicability by measuring copy number in three different genetic contexts; the quantification of a gene rearrangement (T-cell receptor excision circles (TREC) in peripheral blood mononuclear cells); the detection and quantification of GLI, MYC-C and MYC-N gene amplification in cell lines and cancer biopsies; and detection of deletions in the OPA1 gene in dominant optic atrophy. CONCLUSION: Our assay has important clinical applications, providing accurate diagnostic results in less time, from less biopsy material and at less cost than assays currently employed such as FISH or Southern blotting

Production of oriented nitrogen-vacancy color centers in synthetic diamond

The negatively charged nitrogen-vacancy (NV-) center in diamond is an attractive candidate for applications that range from magnetometry to quantum information processing. Here we show that only a fraction of the nitrogen (typically < 0.5 %) incorporated during homoepitaxial diamond growth by Chemical Vapor Deposition (CVD) is in the form of undecorated NV- centers. Furthermore, studies on CVD diamond grown on (110) oriented substrates show a near 100% preferential orientation of NV- centers along only the [111] and [-1-11] directions, rather than the four possible orientations. The results indicate that NV centers grow in as units, as the diamond is deposited, rather than by migration and association of their components. The NV unit of the NVH- is similarly preferentially oriented, but it is not possible to determine whether this defect was formed by H capture at a preferentially aligned NV center or as a complete unit. Reducing the number of NV orientations from 4 orientations to 2 orientations should lead to increased optically-detected magnetic resonance contrast and thus improved magnetic sensitivity in ensemble-based magnetometry.Comment: 13 Pages (inlcuding suplementary information), 4 figure

A 12-Channel, real-time near-infrared spectroscopy instrument for brain-computer interface applications

A continuous wave near-infrared spectroscopy (NIRS) instrument for brain-computer interface (BCI) applications is presented. In the literature, experiments have been carried out on subjects with such motor degenerative diseases as amyotrophic lateral sclerosis, which have demonstrated the suitability of NIRS to access intentional functional activity, which could be used in a BCI as a communication aid. Specifically, a real-time, multiple channel NIRS tool is needed to realise access to even a few different mental states, for reasonable baud rates. The 12-channel instrument described here has a spatial resolution of 30mm, employing a flexible software demodulation scheme. Temporal resolution of ~100ms is maintained since typical topographic imaging is not needed, since we are only interested in exploiting the vascular response for BCI control. A simple experiment demonstrates the ability of the system to report on haemodynamics during single trial mental arithmetic tasks. Multiple trial averaging is not required

Student- and school-level belonging and commitment and student smoking, drinking and misbehaviour

Objectives: It has been suggested that students are healthier in schools where more students are committed to school. Previous research has examined this only using a proxy measure of value-added education (a measure of whether school-level attendance and attainment are higher than predicted by students’ social profile), finding associations with smoking tobacco, use of alcohol and illicit drugs, and violence. These findings do not provide direct insights into the associations between school-level aggregate student commitment and health behaviours, and may simply reflect the proxy measure being residually confounded by unmeasured student characteristics. We examined the previously used proxy measure of value-added education, as well as direct measures at the level of the school and the student of lack of student commitment to school to see whether these were associated with students’ self-reported smoking tobacco, alcohol use and school misbehaviour. Design: Cross-sectional survey. Setting: A total of 40 schools in south-east England. Methods: Multi-level analyses. Results: There were associations between school- and student-level measures of lack of commitment to school and tobacco smoking, alcohol use and school misbehaviour outcomes, but the proxy measure of school-level commitment, value-added education, was not associated with these outcomes. A sensitivity analysis focused only on violent aspects of school misbehaviour found a pattern of associations identical to that found for the measure of misbehaviour. Conclusion: Our study provides the first direct evidence in support of the Theory of Human Functioning and School Organisation

Age-Induced Diminution of Free Radical Scavenging Capacity in Bee Pollens and the Contribution of Constituent Flavonoids

Bee-collected pollen (“bee pollen”) is promoted as a health food with a wide range of nutritional and therapeutic properties. The objective of the current study is to evaluate the contribution made through the free radical scavenging capability of bee-collected floval pollens by their flavonoid/phenolics constituents, and to determine whether this capability is affected by aging. The free radical scavenging effectiveness of a bee pollen (EC50) as measured by the DPPH method is shown to be determined by the nature and levels of the constituent floral pollens, which can be assayed via their phenolics profiles by HPLC. Each pure floral pollen has been found to possess a consistent EC50 value, irrespective of its geographic origin or date of collection, and the EC50 value is determined to a large extent (ca. 50%) by the nature and the levels of the pollen's flavonoids and phenolic acids. Non-phenolic antioxidants, possibly proteins, account for the balance of the activity. Pollen aging over 3 years is demonstrated to reduce the free radical scavenging activity by up to 50% in the most active floral pollens, which tend to contain the highest levels of flavonoids/phenolic acids. It is suggested that the freshness of a bee pollen may be determined from its free radical scavenging capacity relative to that of fresh bee pollen containing the same floral pollen mix

Death from early colorectal cancer is predicted by the presence of transcripts of the REG gene family

An intrinsic component of colorectal carcinogenesis may be the capacity to activate regenerative responses simultaneously with inhibition of apoptosis. Since apoptosis is known to be inhibited in colorectal cancer, this study sought evidence for the activation of the REG family of genes which are considered to be activated during regeneration of intestinal mucosa. Transcripts for the REG gene were found in 53% of colorectal cancers and for the PAP gene in 60% of colorectal cancers, by RT-PCR. Using in situ hybridization, the REG transcripts were found to be present in the tumour cells themselves rather than inflammatory or stromal cells. There were no significant correlations between the expression of these two genes and tumour stage, age or sex of the patient population or tumour site. However, in patients with non-metastatic disease who underwent ostensibly curative surgery, the expression of REG alone and co-expression of REG with PAP had a highly significantly adverse effect on survival. These data provide support for the concept that, in some tumours, carcinogenesis involves a regenerative process which co-exists with apoptotic inhibition and may provide a valuable selective indicator of the need for adjuvant therapy in those patients with early-stage colorectal cancer whose disease is destined to recur after curative surgery. © 2000 Cancer Research Campaig