The frequency of 844ins68 mutation in the cystathionine beta-synthase gene is not increased in patients with venous thrombosis

Background and Objectives. A frequent mutation in the cystathionine beta-synthase (CBS) gene (844ins68, a 68-bp insertion in the coding region of exon 8) was recently discovered. In the present study we Investigated this mutation as a candidate risk factor for venous thrombosis.Design and Methods. The prevalence of the 844ins68 CBS mutation was determined in 101 patients with objectively diagnosed deep venous thrombosis and in 101 healthy controls matched for age, sex and race. PCR amplification of a DNA fragment containing exon 8 of the CBS gene was employed to determine the genotypes, Additionally, Bsrl restriction enzyme digestion of the PCR products was performed in all samples from carriers of the insertion, to test for concurrent presence of a second mutation (T833C) in the CBS gene.Results. The insertion was found in 21 out of 101 patients (20.8%; allele frequency 0.109) and in 20 out of 101 controls (19.8%; allele frequency 0.114), yielding a relative risk for venous thrombosis related to the 844ins68 CBS mutation close to 1.0. In addition, the T833C GBS mutation was detected in all alleles carrying the 844ins68 CBS insertion, confirming the co-inheritance of the two mutations.Interpretation and Conclusions. Our findings do not support the hypothesis that the 844ins68 mutation in the CBS gene is a genetic risk factor for venous thrombosis. (C)1998, Ferrata Storti Foundation.

The frequency of 844ins68 mutation in the cystathionine β-synthase gene is not increased in patients with venous thrombosis

Background and Objectives. A frequent mutation in the cystathionine β- synthase (CBS) gene (844ins68, a 68-bp insertion in the coding region of exon 8) was recently discovered. In the present study we investigated this mutation as a candidate risk factor for venous thrombosis. Design and Methods. The prevalence of the 844ins68 CBS mutation was determined in 101 patients with objectively diagnosed deep venous thrombosis and in 101 healthy controls matched for age, sex and race. PCR amplification of a DNA fragment containing exon 8 of the CBS gene was employed to determine the genotypes. Additionally, Bsrl restriction enzyme digestion of the PCR products was performed in all samples from carriers of the insertion, to test for concurrent presence of a second mutation (T833C) in the CBS gene. Results. The insertion was found in 21 out of 101 patients (20.8%; allele frequency 0.109) and in 20 out of 101 controls (19.8%; allele frequency 0.114), yielding a relative risk for venous thrombosis related to the 844ins68 CBS mutation close to 1.0. In addition, the T833C CBS mutation was detected in all alleles carrying the 844ins68 CBS insertion, confirming the co- inheritance of the two mutations. Interpretation and Conclusions. Our findings do not support the hypothesis that the 844ins68 mutation in the CBS gene is a genetic risk factor for venous thrombosis.

A miniature insertion element transposable in Microcystis sp FACHB 854

A 186-bp sequence with imperfect terminal inverted repeats and target direct repeats but without any transposase-encoding capacity was found to be transposable in an isolate derived from Microcystis sp. FACHB 854. This miniature insertion element, designated as ISM854-1, and with its homologues present at least 10 copies in the genome of Microcystis FACHB 854, is inserted into the 8-bp long and AT-rich target sequences, but none or few in other Microcystis strains. A variant of ISM854-1, denoted ISM854-1A, has perfect inverted repeat sequences and may transpose in pairs in a structure like a composite transposon. This is the first report of non-autonomous transposition of a mini-IS in a cyanobacterium.

Evaluation of Random Delay Insertion against DPA on FPGAs

Side-channel attacks (SCA) threaten electronic cryptographic devices and can be carried out by monitoring the physical characteristics of security circuits. Differential Power Analysis (DPA) is one the most widely studied side-channel attacks. Numerous countermeasure techniques, such as Random Delay Insertion (RDI), have been proposed to reduce the risk of DPA attacks against cryptographic devices. The RDI technique was first proposed for microprocessors but it was shown to be unsuccessful when implemented on smartcards as it was vulnerable to a variant of the DPA attack known as the Sliding-Window DPA attack.Previous research by the authors investigated the use of the RDI countermeasure for Field Programmable Gate Array (FPGA) based cryptographic devices. A split-RDI technique wasproposed to improve the security of the RDI countermeasure. A set of critical parameters wasalso proposed that could be utilized in the design stage to optimize a security algorithm designwith RDI in terms of area, speed and power. The authors also showed that RDI is an efficientcountermeasure technique on FPGA in comparison to other countermeasures.In this article, a new RDI logic design is proposed that can be used to cost-efficiently implementRDI on FPGA devices. Sliding-Window DPA and realignment attacks, which were shown to beeffective against RDI implemented on smartcard devices, are performed on the improved RDIFPGA implementation. We demonstrate that these attacks are unsuccessful and we also proposea realignment technique that can be used to demonstrate the weakness of RDI implementations.

A first case of protease codon 35 amino acid insertion in a HIV-1 subtype B sequence detected in the Bauru region, state of São Paulo, Brazil: case report

Inserções de aminoácidos na protease têm sido raramente descritas em pacientes infectados pelo HIV. Uma destas inserções foi, recentemente, descrita no codon 35, embora seu impacto na resistência mantém-se pouco conhecido. Este trabalho apresenta um caso de uma variante viral com inserção no codon 35 da protease, descrita pela primeira vez em Bauru, São Paulo, Brasil, circulante em um homem, caucasiano, com 38 anos, o qual apresenta infecção assintomática pelo HIV desde 1997. A variante isolada mostrou uma inserção no codon 35 da protease de dois aminoácidos: uma treonina e um ácido aspártico, resultando na sequência de aminoácidos E35E_TD.

A RAB3GAP1 SINE Insertion in Alaskan Huskies with Polyneuropathy, Ocular Abnormalities and Neuronal Vacuolation (POANV) Resembling Human Warburg Micro Syndrome 1 (WARBM1)

We observed a hereditary phenotype in Alaskan Huskies, which was characterized by polyneuropathy with ocular abnormalities and neuronal vacuolation (POANV). The affected dogs developed a progressive severe ataxia, which led to euthanasia between 8 and 16 months of age. The pedigrees were consistent with a monogenic autosomal recessive inheritance. We localized the causative genetic defect to a 4 Mb interval on chromosome 19 by a combined linkage and homozygosity mapping approach. Whole genome sequencing of one affected dog, an obligate carrier and an unrelated control revealed a 218 bp SINE insertion into exon 7 of the RAB3GAP1 gene. The SINE insertion was perfectly associated with the disease phenotype in a cohort of 43 Alaskan Huskies and it was absent from 541 control dogs of diverse other breeds. The SINE insertion induced aberrant splicing and led to a transcript with a greatly altered exon 7. RAB3GAP1 loss-of-function variants in humans cause Warburg Micro Syndrome 1 (WARBM1), which is characterized by additional developmental defects compared to canine POANV, whereas Rab3gap1 deficient mice have a much milder phenotype than either humans or dogs. Thus the RAB3GAP1 mutant Alaskan Huskies provide an interesting intermediate phenotype that may help to better understand the function of RAB3GAP1 in development. Furthermore, the identification of the presumed causative genetic variant will enable genetic testing to avoid the non-intentional breeding of affected dogs.

A transposable element insertion in APOB causes cholesterol deficiency in Holstein cattle

Cholesterol deficiency, a new autosomal recessive inherited genetic defect in Holstein cattle, has been recently reported to have an influence on the rearing success of calves. The affected animals show unresponsive diarrhea accompanied by hypocholesterolemia and usually die within the first weeks or months of life. Here, we show that whole genome sequencing combined with the knowledge about the pedigree and inbreeding status of a livestock population facilitates the identification of the causative mutation. We resequenced the entire genomes of an affected calf and a healthy partially inbred male carrying one copy of the critical 2.24-Mb chromosome 11 segment in its ancestral state and one copy of the same segment with the cholesterol deficiency mutation. We detected a single structural variant, homozygous in the affected case and heterozygous in the non-affected carrier male. The genetic makeup of this key animal provides extremely strong support for the causality of this mutation. The mutation represents a 1.3kb insertion of a transposable LTR element (ERV2-1) in the coding sequence of the APOB gene, which leads to truncated transcripts and aberrant splicing. This finding was further supported by RNA sequencing of the liver transcriptome of an affected calf. The encoded apolipoprotein B is an essential apolipoprotein on chylomicrons and low-density lipoproteins, and therefore, the mutation represents a loss of function mutation similar to autosomal recessive inherited familial hypobetalipoproteinemia-1 (FHBL1) in humans. Our findings provide a direct gene test to improve selection against this deleterious mutation in Holstein cattle.

AsaGEI2b: a new variant of a genomic island identified in the Aeromonas salmonicida subsp. salmonicida JF3224 strain isolated from a wild fish in Switzerland.

Aeromonas salmonicida subsp. salmonicida is the causal agent of furunculosis in salmonids. We recently identified a group of genomic islands (AsaGEI) in this bacterium. AsaGEI2a, one of these genomic islands, has almost exclusively been identified in isolates from North America. To date, Aeromonas salmonicida subsp. salmonicida JF3224, a strain isolated from a wild brown trout (Salmo trutta) caught in Switzerland, was the only European isolate that appeared to bear AsaGEI2a. We analyzed the genome of JF3224 and showed that the genomic island in JF3224 is a new variant of AsaGEI, which we have called AsaGEI2b. While AsaGEI2b shares the same integrase gene and insertion site as AsaGEI2a, it is very different in terms of many other features. Additional genomic investigations combined with PCR genotyping revealed that JF3224 is sensitive to growth at 25°C, leading to insertion sequence-dependent rearrangement of the locus on the pAsa5 plasmid that encodes a type three secretion system, which is essential for the virulence of the bacterium. The analysis of the JF3224 genome confirmed that AsaGEIs are accurate indicators of the geographic origins of A. salmonicida subsp. salmonicida isolates and is another example of the susceptibility of the pAsa5 plasmid to DNA rearrangements.

Structure and function of the Bacillus hybrid enzyme GluXyn-1: Native-like jellyroll fold preserved after insertion of autonomous globular domain

The 1,3–1,4-β-glucanase from Bacillus macerans (wtGLU) and the 1,4-β-xylanase from Bacillus subtilis (wtXYN) are both single-domain jellyroll proteins catalyzing similar enzymatic reactions. In the fusion protein GluXyn-1, the two proteins are joined by insertion of the entire XYN domain into a surface loop of cpMAC-57, a circularly permuted variant of wtGLU. GluXyn-1 was generated by protein engineering methods, produced in Escherichia coli and shown to fold spontaneously and have both enzymatic activities at wild-type level. The crystal structure of GluXyn-1 was determined at 2.1 Å resolution and refined to R = 17.7% and R(free) = 22.4%. It shows nearly ideal, native-like folding of both protein domains and a small, but significant hinge bending between the domains. The active sites are independent and accessible explaining the observed enzymatic activity. Because in GluXyn-1 the complete XYN domain is inserted into the compact folding unit of GLU, the wild-type-like activity and tertiary structure of the latter proves that the folding process of GLU does not depend on intramolecular interactions that are short-ranged in the sequence. Insertion fusions of the GluXyn-1 type may prove to be an easy route toward more stable bifunctional proteins in which the two parts are more closely associated than in linear end-to-end protein fusions.

Inactive conformation of the serpin α1-antichymotrypsin indicates two-stage insertion of the reactive loop: Implications for inhibitory function and conformational disease

The serpins are a family of proteinase inhibitors that play a central role in the control of proteolytic cascades. Their inhibitory mechanism depends on the intramolecular insertion of the reactive loop into β-sheet A after cleavage by the target proteinase. Point mutations within the protein can allow aberrant conformational transitions characterized by β-strand exchange between the reactive loop of one molecule and β-sheet A of another. These loop-sheet polymers result in diseases as varied as cirrhosis, emphysema, angio-oedema, and thrombosis, and we recently have shown that they underlie an early-onset dementia. We report here the biochemical characteristics and crystal structure of a naturally occurring variant (Leu-55–Pro) of the plasma serpin α1-antichymotrypsin trapped as an inactive intermediate. The structure demonstrates a serpin configuration with partial insertion of the reactive loop into β-sheet A. The lower part of the sheet is filled by the last turn of F-helix and the loop that links it to s3A. This conformation matches that of proposed intermediates on the pathway to complex and polymer formation in the serpins. In particular, this intermediate, along with the latent and polymerized conformations, explains the loss of activity of plasma α1-antichymotrypsin associated with chronic obstructive pulmonary disease in patients with the Leu-55–Pro mutation.

Percutaneous insertion of Dual Growth Rods using a new mobile bearing implant

Growth rods are commonly used for the treatment of scoliosis in the immature spine. Many variations have been proposed but breakage of implants is a common problem. Growth rod insertion commonly involves large exposures at initial insertion followed by multiple smaller procedures for lengthening. We present our early experiences using a percutaneous technique of insertion of a new titanium mobile bearing implant (Medtronic Inc). The implant allows some rotatory motion in the middle of the construct thus reducing construct stresses and thus possibly reducing rod breakage risk. Based on this small initial series with 12 months follow-up, percutaneous insertion of growth rods using the new implant is a safe and reliable technique although the infection rate in our sample was of note. This may be related to the titanium wear and inflammation seen in the soft tissues at time of operation and visualised on histology. No implants have required removal due to infection, and all infections were treated with debridement at next lengthening and suppressive antibiotics. Propionibacterium is one of the commonest infections seen with spinal implants and sometimes does not respond to simple antibiotic suppression. The technique allows preservation of the soft tissues until definitive fusion is needed and may lead to a decrease in hospital stay. The implant is low profile and seems to offer advantages over other systems on the market. Further follow up is needed to look at longer term outcomes with this new implant type.

The effect of insertion time on the axial pullout strength of anterior vertebral body screws

Top screw pullout occurs when the screw is under too much axial force to remain secure in the vertebral body. In vitro biomechanical pullout tests are commonly done to find the maximum fixation strength of anterior vertebral body screws. Typically, pullout tests are done instantaneously where the screw is inserted and then pulled out immediately after insertion. However, bone is a viscoelastic material so it shows a time dependent stress and strain response. Because of this property, it was hypothesised that creep occurs in the vertebral trabecular bone due to the stress caused by the screw. The objective of this study was therefore to determine whether the axial pullout strength of anterior vertebral body screws used for scoliosis correction surgery changes with time after insertion. This study found that there is a possible relationship between pullout strength and time; however more testing is required as the sample numbers were quite small. The design of the screw is made with the knowledge of the strength it must obtain. This is important to prevent such occurrences as top screw pullout. If the pullout strength is indeed decreased due to creep, the design of the screw may need to be changed to withstand greater forces.

A time-variant medical data trustworthiness assessment model

Electronic Health Record (EHR) systems are being introduced to overcome the limitations associated with paper-based and isolated Electronic Medical Record (EMR) systems. This is accomplished by aggregating medical data and consolidating them in one digital repository. Though an EHR system provides obvious functional benefits, there is a growing concern about the privacy and reliability (trustworthiness) of Electronic Health Records. Security requirements such as confidentiality, integrity, and availability can be satisfied by traditional hard security mechanisms. However, measuring data trustworthiness from the perspective of data entry is an issue that cannot be solved with traditional mechanisms, especially since degrees of trust change over time. In this paper, we introduce a Time-variant Medical Data Trustworthiness (TMDT) assessment model to evaluate the trustworthiness of medical data by evaluating the trustworthiness of its sources, namely the healthcare organisation where the data was created and the medical practitioner who diagnosed the patient and authorised entry of this data into the patient’s medical record, with respect to a certain period of time. The result can then be used by the EHR system to manipulate health record metadata to alert medical practitioners relying on the information to possible reliability problems.

The variant concept of transportation disadvantaged : evidence from Aydin, Turkey and Yamaga, Japan

Transportation disadvantaged groups, in the previous studies, are defined as those who are low income earners, family dependent, limited access to private motor vehicles and public transport services, and also those who oblige to spend relatively more time and money on their trips. Additionally those disable, young and elderly are considered among the natural groups of transportation disadvantaged. Although in general terms this definition seems correct, it is not specific enough to become a common universal definition that could apply to all urban contexts. This paper investigates whether travel difficulty perceptions vary and so does the definition of transportation disadvantaged in socio-culturally different urban contexts. For this investigation the paper undertakes a series of statistical analysis in the case study of Yamaga, Japan, and compares the findings with a previous case study, where the same methodology, hypothesis, and assumptions were utilized in a culturally and demographically different settlement of Aydin, Turkey. After comparing the findings observed in Aydin with the statistical analysis results of Yamaga, this paper reveals that there can be no explicitly detailed universal definition of transportation disadvantaged. The paper concludes by stating characteristics of transportation disadvantage is not globally identical, and policies and solutions that work in a locality may not show the same results in another socio-cultural context.