Evolution of human IgH3 ' EC duplicated structures: both enhancers HS1,2 are polymorphic with variation of transcription factor's consensus sites

The enhancer complex regulatory region at the 3' of the immunoglobulin heavy cluster (IgH3'EC) is duplicated in apes along with four constant genes and the region is highly conserved throughout humans. Both human IgH3'ECs consist of three loci high sensitive (HS) to DNAse I with enhancer activity. It is thus possible that the presence of structural divergences between the two IgH3'ECs and of relative polymorphisms correspond to functional regulatory changes. To analyse the polymorphisms of these almost identical regions, it resulted mandatory to identify the presence of divergent sequences, in order to select distinctive primers for specific PCR genomic amplifications. To this aim, we first compared the two entire IgH3'ECs in silicio, utilising the updated GenBank (GB) contigs, then we analysed the two IgH3'ECs by cloning and sequencing amplicons from independent genomes. In silicio analysis showed that several inversions, deletions and short insertions had occurred after the duplication. We analysed in detail, by sequencing specific regions, the polymorphisms occurring in enhancer HS1,2-A (which lies in IgH3'EC-1, 3' to the C alpha-1 gene) and in enhancer HS1,2-B (which lies in IgH3'EC-2, 3' to C alpha-2). Polymorphisms are due to the repetition (occurring one to four times) of a 38-bp sequence present at the 3' of the core of enhancers HS1,2. The structure of both human HS1,2 enhancers has revealed not yet described polymorphic features due to the presence of variable spacer elements separating the 38-bp repetitions and to variable external elements bordering the repetition cluster. We found that one of the external elements gave rise to a divergent allele 3 in the two clusters. The frequency of the different alleles of the two loci varies in the Italian population and allele 3 of both loci are very rare. The analysis of the Callicebus moloch, Gorilla gorilla and Pan troglodytes HS1,2 enhancers showed the transformation from the ancestral structure with the 31- to the 17-by external element in hominids. The relevance of the polymorphisms in the HS1,2 enhancers is due to the variable number of binding sites for the transcription factors: NF-kappa B, CMYB, BSAP1/2, AP1/4, E47, MyoD and mu E5 and thus to the possible influence of these variations on switch, production of Ig and on maturation of B cells. (c) 2004 Elsevier B.V. All rights reserved

Naphthalenone polyketides produced by Neofusicoccum parvum , a fungus associated with grapevine Botriosphaeria dieback

A strain of Neofusicoccum parvum isolated from declining vines was pathogenic to grapevine cultivar Inzolia in Sicily. This strain produced some metabolites in liquid medium. Crude extract, through a bio-guided purification process, yielded four naphthalenone polyketides. They were identified by comparison with spectroscopic data and optical proprieties reported in literature as: (3S, 4S)-7-ethyl-3,4,8-trihydroxy-6-methoxy-3,4-dihydro-1-(2H)-naphthalenone, (3S*, 4S*)-3,4-dihydro-3,4,8-trihydroxy-7-(1-hydroxyethyl)-6-methoxy-1-(2H)-naphthalenone, (4S)-3,4-dihydro-4,8-dihydroxy-1-(2H)-naphthalenone, named botryosphaerones D and A, isosclerone, respectively, and (3S*,4S*)-3,4,5-trihydroxy-1-tetralone (1-4). Phytotoxic activity of the isolated compounds (1-4) was tested on grapevine leaves at using the leaf puncture assay. All tested compounds were phytotoxic, with botryosphaerone D showing the greatest activity. The phytotoxic effects decreased when treated leaves were exposed to light. All of the metabolites did not show in vitro antifungal activity against Diplodia seriata, Lasiodiplodia mediterranea, Neofusicoccum vitifusiforme, or Phytophthora citrophthora. This is the first report of in vitro production of botryosphaerones D and A, and 3,4,5-trihydroxy-1-tetralone by N. parvum

High-speed double layer graphene electro-absorption modulator on SOI waveguide

We report on a C-band double layer graphene electro-absorption modulator on a passive SOI platform showing 29GHz 3dB-bandwith and NRZ eye-diagrams extinction ratios ranging from 1.7 dB at 10 Gb/s to 1.3 dB at 50 Gb/s. Such high modulation speed is achieved thanks to the quality of the CVD pre-patterned single crystal growth and transfer on wafer method that permitted the integration of high-quality scalable graphene and low contact resistance. By demonstrating this high-speed CVD graphene EAM modulator integrated on Si photonics and the scalable approach, we are confident that graphene can satisfy the main requirements to be a competitive technology for photonics

Photo Thermal Effect Graphene Detector Featuring 105 Gbit s-1 NRZ and 120 Gbit s-1 PAM4 Direct Detection

The challenge of next generation datacom and telecom communication is to increase the available bandwidth while reducing the size, cost and power consumption of photonic integrated circuits. Silicon (Si) photonics has emerged as a viable solution to reach these objectives. Graphene, a single-atom thick layer of carbon5, has been recently proposed to be integrated with Si photonics because of its very high mobility, fast carrier dynamics and ultra-broadband optical properties. Here, we focus on graphene photodetectors for high speed datacom and telecom applications. High speed graphene photodetectors have been demonstrated so far, however the most are based on the photo-bolometric (PB) or photo-conductive (PC) effect. These devices are characterized by large dark current, in the order of milli-Amperes , which is an impairment in photo-receivers design, Photo-thermo-electric (PTE) effect has been identified as an alternative phenomenon for light detection. The main advantages of PTE-based photodetectors are the optical power to voltage conversion, zero-bias operation and ultra-fast response. Graphene PTE-based photodetectors have been reported in literature, however high-speed optical signal detection has not been shown. Here, we report on an optimized graphene PTE-based photodetector with flat frequency response up to 65 GHz. Thanks to the optimized design we demonstrate a system test leading to direct detection of 105 Gbit s-1 non-return to zero (NRZ) and 120 Gbit s-1 4-level pulse amplitude modulation (PAM) optical signal

A competitive polymerase chain reaction-based approach for the identification and semiquantification of mitochondrial DNA in differently heat-treated bovine meat and bone meal

The risk of bovine spongiform encephalopathy propagation was drastically reduced after the European Union (EU) Health Authorities adopted restrictions involving a ban on animal-derived proteins in the diet of farm animals. Currently, the EU's officially recommended method for controlling meat and bone meal (MBM) in animal feed is the microscopic method, which involves the identification of bone fragments on the basis of their morphological characteristics. Recently, we demonstrated that a polymerase chain reaction (PCR)-based assay can be used for the detection of taxon-specific DNA in MBM and animal feeds. To ensure the safe rendering of animal by-products, the EU Council requires that this material be treated at 133degreesC at 300 kPa for 20 min. Here we investigate the relationship between DNA degradation, PCR amplification, and MBM heat treatment. With a competitive PCR-based approach, we compare the amplification efficiency of bovine mitochondrial DNA target sequences of different lengths in several heat-treated MBM samples. For our method, a synthetic competitive DNA is used as an internal control for both DNA extraction and PCR reaction. A correlation between an increase in treatment temperature and a reduction in the size of the target sequences suitable for amplification was observed, suggesting progressive DNA fragmentation due to the temperature. We show that short amplicons (147 bp) can be used to detect the presence of bovine mtDNA in MBM samples treated according to the current European regulations. The use of such a competitive approach to compare amplification efficiency levels of targets of different lengths might represent a useful tool for the determination of both the amount of MBM in animal feeds and its proper heat treatment

Allele *2 of the HS1,2A enhancer of the Ig regulatory region associates with rheumatoid arthritis

Objective: To investigate the role of the HS1.2 enhancer polymorphisms as a new candidate marker for rheumatoid arthritis (RA) and to define the possible association with autoantibody positivity and clinical outcome. Methods: Genomic DNA was obtained from two cohorts of patients with RA (100 with early RA (ERA) and 114 with longstanding RA (LSRA)) and from 248 gender-matched controls from the same geographical area. Clinical and immunological characteristics were recorded for all the patients. Results: The percentage of the 2/2 genotype was higher In patients with ERA (27.0%), and In patients with LSRA (34.2%), than In controls (14.9%) (ERA: OR = 2.11 (95% Cl 1.20 to 3.70) vs controls; LSRA: OR = 2.96 (95% Cl 1.76 to 5.00) vs controls). A lower representation of allele *3 was present In patients with ERA (2.0%) than In controls (6.0%; OR = 0.32 (95% Cl 0.11 to 0.91)). No significant associations were found between polymorphisms and autoantibodies positivity. Conclusion: The HS1.2A allele *2 associates with early and longstanding RA

Increased frequency of the immunoglobulin enhancer HS1,2 allele 2 in coeliac disease

Background: Coeliac disease ( CD) is characterized by increased immunological responsiveness to ingested gliadin in genetically predisposed individuals. This genetic predisposition is not completely defined. A dysregulation of immunoglobulins (Ig) is present in CD: since antiendomysium antibodies (anti-EMA) are of the IgA class. One polymorphic enhancer within the locus control region (LCR) of the immunoglobulin heavy chain cluster at the 3' of the C alpha-1 gene was investigated. The correlation of the penetrance of the four different alleles of the HS1,2-A enhancer of the LCR-1 3' to C alpha-1 in CD patients compared to a control population was analysed. Methods: A total of 115 consecutive CD outpatients, on a gluten-free diet, and 248 healthy donors, age- and sex-matched, from the same geographical area were enrolled in the study. HS1,2-A allele frequencies were investigated by nested polymerase chain reaction (PCR). Results: The frequency of allele 2 of the enhancer HS1,2-A gene was increased by 30.8% as compared to the control frequency. The frequency of homozygosity for allele 2 was significantly increased in CD patients. Crude odds ratio ( OR) showed that those with 2/2 and 2/4 ( OR 2.63, P < 0.001 and OR 2.01, P = 0.03) have a significantly higher risk of developing the disease. In contrast, allele 1/2 may represent a protective genetic factor against CD ( OR 0.52, P = 0.01). Conclusions: These data provide further evidence of a genetic predisposition in CD. Because of the Ig dysregulation in CD, the enhancer HS1,2-A may be involved in the pathogenesis

Ultrafast, Zero-Bias, Graphene Photodetectors with Polymeric Gate Dielectric on Passive Photonic Waveguides.

We report compact, scalable, high-performance, waveguide integrated graphene-based photodetectors (GPDs) for telecom and datacom applications, not affected by dark current. To exploit the photothermoelectric (PTE) effect, our devices rely on a graphene/polymer/graphene stack with static top split gates. The polymeric dielectric, poly(vinyl alcohol) (PVA), allows us to preserve graphene quality and to generate a controllable p-n junction. Both graphene layers are fabricated using aligned single-crystal graphene arrays grown by chemical vapor deposition. The use of PVA yields a low charge inhomogeneity ∼8 × 1010 cm-2 at the charge neutrality point, and a large Seebeck coefficient ∼140 μV K-1, enhancing the PTE effect. Our devices are the fastest GPDs operating with zero dark current, showing a flat frequency response up to 67 GHz without roll-off. This performance is achieved on a passive, low-cost, photonic platform, and does not rely on nanoscale plasmonic structures. This, combined with scalability and ease of integration, makes our GPDs a promising building block for next-generation optical communication devices