The clinical values of methylation status of P16 and APC genes in bile in diagnosis of malignant obstructive jaundice

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Background: Preoperative definitive diagnosis of malignant obstructive jaundice caused by biliary and pancreatic carcinomas still remains a major challenge. Hypermethylation of tumor suppressor genes have been implied in carcinogenesis of biliary and pancreatic malignancies. The diagnostic values of methylation status of tumor suppressor genes in bile in malignant obstructive jaundice have not been well-documented.

Methods: Bile was prospectively collected from 70 patients with obstructive jaundice treated at our hospital between November 2008 and Sepetember 2009. Forty-eight of them were proved to be malignant obstructive jaundice (biliary carcinoma in 36, pancreatic carcinoma in 8 and duodenal carcinoma in 4) by pathological examination, and 22 were benign obstructive jaundice caused by cholelithiasis. DNA was extracted from bile and modified by sodium bisulfite. Methylation-specific PCR was run to detect methylation status of P16 and APC gene promoters. Their diagnostic values in malignant obstructive jaundice were assessed.

Results: Hypermethylation of P16 promoter was presented in 72.9% (35/48) malignant obstructive jaundice, and 9% (2/22) bengin obstructive jaundice (p<0.05). Hypermethylation of APC promoter was presented in 56.2% (27/48) malignant obstructive jaundice, and 9% (2/22) bengin obstructive jaundice (p<0.05). With respect to their diagnostic values in malignant obstructive jaundice, sensitivity, specificity, positive predictivity and negative predictivity were 72.9%, 90.9%, 94.6% and 60.6%, respectively, for P16 gene; 56.2%, 90.9%, 93.1%, 48.8%, respectively, for APC gene.

Conclusions: Methylation status of P16 and APC gene promoters in bile was valuable in diagnosis of malignant obstructive jaundice, with an excellent specificity. P16 gene had a higher sensitivity than APC gene.

No significant financial relationships to disclose.

First Report of Bituminaria Witches'-Broom in Australia Caused by a 16SrII Phytoplasma

Bituminaria bituminosa (L.) Stirt. is a perennial legume known as Arabian pea that is used as a forage in arid areas and for stabilization of degraded soils. It is widely distributed in the Mediterranean Basin with wider adaptation across the Canary Islands (4). In July 2010, during a survey for phytoplasma, some Canary Island B. bituminosa plants with typical phytoplasma symptoms, including stunted growth with small leaves, shortened internodes, and bushy growth, were found in seed multiplication nurseries at Medina, Perth, Western Australia (115°48.5'E; 32°13.2'S). Two samples from plants with clear disease symptoms and two visibly healthy plants were collected and total DNA was extracted with the Illustra DNA extraction kit Phytopure (GE Healthcare) according to the manufacturer's instructions. Direct and nested PCR were used to test the presence of phytoplasma 16S rDNA in samples with universal primers P1/P7 and R16F2n/R16R2, respectively (1,3). The PCR amplifications from all diseased samples yielded an expected product of 1.8 kb by direct and 1.2 kb by nested PCR, but not from the healthy plant samples. The direct PCR product was used as a template DNA in sequencing and the DNA sequence was deposited in the NCBI GenBank (Accession No. HQ404357). Sequence homology analysis indicated there was a perfect match between the two isolates. BLAST search of the NCBI GenBank revealed that B. bituminosa phytoplasma shares >99% sequence identity with Crotalaria witches'-broom phytoplasma (Accession No. EU650181.1), pear decline phytoplasma (Accession No. EF656453.1), and Scaevola witches'-broom phytoplasma (Accession No. AB257291.1). On the basis of BLAST analyses of 16S rRNA gene sequences, B. bituminosa phytoplasma in Western Australia appears to belong to the peanut witches'-broom group (16SrII-D) of phytoplasma. Restriction fragment length polymorphism analysis was also performed on nested PCR products of two samples of B. bituminosa phytoplasma by separate digestion with HaeIII, Hind6I, HpaII, MboI, RsaI, Tru9I, and T-HB8I restriction enzymes. Samples yielded patterns similar to alfalfa witches'-broom phytoplasma (Accession No. AF438413) belonging to subgroup 16SrII-D (2). To our knowledge, this is the first report of a phytoplasma of the 16SrII-D group infecting B. bituminosa in Australia and should be referred to as "Bituminaria witches'-broom phytoplasma" (BiWB). This report also indicates that the occurrence of the phytoplasma in B. bituminosa may be widespread in the Canary Islands and other species of Bituminaria might be susceptible to infection by Bituminaria witches'-broom phytoplasma. References: (1) D. E. Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (2) A. J. Khan et al. Phytopathology 92:1038, 2002. (3) I.-M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004. (4) P. Mendez et al. Grassland Sci. Eur. 11:300, 2006.

BP neural network classification for bleeding detection in wireless capsule endoscopy

Bleeding in the digestive tract is one of the most common gastrointestinal tract (GI) diseases, as well as the complication of some fatal diseases. Wireless capsule endoscopy (WCE) allows physicians to noninvasively examine the entire GI tract. However it is very laborious and time-consuming to inspect large numbers of WCE images, which limits the wider application of WCE. It is therefore important to develop an automatic and intelligent computer-aided bleeding detection technique. In this paper, a new method aimed at bleeding detection in WCE images is proposed. Colour texture features distinguishing the bleeding regions from non-bleeding regions are extracted in RGB and HSI colour spaces; then a neural network using the colour texture features as the feature vector inputs is designed to recognize the bleeding regions. The experiments demonstrate that the bleeding regions can be correctly recognized and clearly marked out. The sensitivity of the algorithm is 93% and the specificity is 96%.

A micro creeping robot for colonoscopy based on the earthworm

Minimally Invasive Surgery (MIS) has become one of the most important research areas in the field of medical engineering. Robotic colonoscopy is a typical medical procedure that complies with the requirements of MIS. In this paper, a new novel miniature robot for intestinal inspection based on the earthworm is described; its diameter and length are 7.5 mm and 120 mm respectively. The micro robot is driven by a DC motor which has good performance and sufficient power. In this paper the structure and locomotion mechanism of this robot are introduced; the mechanical model is built; and simulation is carried out. The control system and software design are also discussed in detail. Some actuating characteristic experiments have been performed, where the micro robot creeps in declining rubber tubes. The experimental results are in accord with simulation results, and show that this kind of robot can move reliably in horizontal and certain declining tubes. This research has laid a foundation for the application of the miniature robot endoscope.

A novel c.545-546insG mutation in the loricrin gene correlates with a heterogeneous phenotype of loricrin keratoderma

BACKGROUND

Loricrin keratoderma (LK) is a group of congenital skin abnormalities characterized by the common features of honeycomb palmoplantar keratoderma and diffused ichthyosiform dermatosis. Earlier studies have shown that LK is associated with genetic defects of the loricrin gene.

OBJECTIVES

To determine the correlation between a loricrin mutation and a heterogeneous phenotype of loricrin keratoderma.

METHODS

We obtained DNA samples from a large family in which affected members showed more severe hyperkeratosis on the dorsal parts of their hands, mild palmoplantar keratoderma with no honeycomb-like manifestations and generalized ichthyosis. Screening of the loricrin gene was performed by direct sequencing of the entire coding region. Plasmids encoding the green fluorescent protein-tagged human loricrin were constructed and transferred to 293A cells for subcellular localization analyses.

RESULTS

Molecular analyses of the loricrin gene identified a novel insertion mutation c.545-546insG that resulted in a frameshift after codon 182. This mutation was predicted to produce a mutant protein with a frameshift of its C-terminal sequence of amino acids that embeds a newly generated nuclear localization signal (NLS), and to be 22 amino acids longer than the wild-type protein due to a delayed termination codon. The NLSs appear to result in an accumulation of mutant loricrin within nuclei.

CONCLUSIONS

Our results extend the repertoire of loricrin mutations underlying LK, provide further evidence that heterogeneous phenotypes of LK may be the result of genetic heterogeneity of loricrin mutations, and demonstrate that nuclear accumulation of mutant loricrin is due to the nuclear targeting sequences in the mutant C-terminus.

Genetic analysis of pod and seed resistance to pea weevil in a Pisum sativum×P. fulvum interspecific cross

Interspecific populations derived from crossing cultivated field pea, Pisum sativum, with the wild pea relative, Pisum fulvum, were scored for pod and seed injury caused by the pea weevil, Bruchus pisorum. Pod resistance was quantitatively inherited in the F2 population, with evidence of transgressive segregation. Heritability of pod resistance between F2 and F3 generations was very low, suggesting that this trait would be difficult to transfer in a breeding program. Seed resistance was determined for the F2 population by testing F3 seed tissues of individual F2 plants and pooling data from seed reaction for each F2 plant (inferred F2 genotype). Segregation for seed resistance in the F2 population of the cross Pennant/ATC113 showed a trigenic mode of inheritance, with additive effects and dominant epistasis towards susceptibility. Seed resistance was conserved over consecutive generations (F2 to F5) and successfully transferred to a new population by backcross introgression. Seed resistance in the backcross introgressed population segregated in a 63 : 1 ratio, supporting the three-gene inheritance model. It is proposed that complete resistance to pea weevil is controlled by three major recessive alleles assigned pwr1, pwr2, and pwr3, and complete susceptibility by three major dominant alleles assigned PWR1, PWR2, and PWR3. It is recommended that large populations (>300 F2 plants) would be required to effectively transfer these recessive alleles to current field pea cultivars through hybridisation and repeated backcrossing.

Enhancement of genetic diversity in canola-quality Brassica napus and B. juncea by interspecific hybridisation

Reciprocal crosses were made between Brassica napus cv. Mystic (canola) and B. juncea JN29 (near canola quality). The F1 hybrids were selfed and backcrossed in all possible combinations to parent plants. The greatest number of selfed fertile progeny were obtained when Mystic was the maternal parent, and its F1 was most successful in backcrosses to Mystic or JN29 as maternal or paternal parent. The predominant morphological type of fertile progeny was B. napus, but several B. juncea morphological types occurred in F2 and BC1-derived lines. F2 : 3 and BC1S0 : 1 progeny showed transgressive segregation for agronomic and seed quality traits in two contrasting field environments. Several of the B. juncea-type progeny had improved seed quality (lower total seed glucosinolates and higher % oleic acid) over the B. juncea parent. Selfing of interspecific hybrids between canola-quality B. napus and B. juncea has the potential to greatly enhance genetic diversity in canola-quality progeny of both species, without the loss of donor alleles that normally occurs with repeated backcrossing.

Noninvasive measurement of phenylalanine by iontophoretic extraction in patients with phenylketonuria

Phenylketonuria is an autosomal recessive disorder characterized by elevated concentrations of phenylalanine. Elevated phenylalanine concentrations can impair intellectual functions and the disease is treated with a lifelong diet and frequent monitoring of plasma phenylalanine concentrations. Previous in vitro studies have demonstrated the feasibility of iontophoretically enhanced transdermal transport of phenylalanine. Here we evaluate the feasibility of transdermal iontophoretic extraction of phenylalanine in vivo. Phenylalanine was iontophoretically extracted from the skin of healthy volunteers and of patients with phenylketonuria for up to 6 h and concentrations were compared with those measured in plasma. The amount of phenylalanine iontophoretically extracted from the skin declined over time, suggesting contribution of phenylalanine from the skin in the initial extraction. Phenylalanine iontophoretically extracted from skin correlated with plasma phenylalanine levels at plasma levels above 300 micromol/L. This correlation supports the feasibility of iontophoretic phenylalanine extraction for monitoring phenylketonuria.

Population genetics of Plasmodium resistance genes in Anopheles gambiae: no evidence for strong selection

Anopheles mosquitoes are the primary vectors for malaria in Africa, transmitting the disease to more than 100 million people annually. Recent functional studies have revealed mosquito genes that are crucial for Plasmodium development, but there is presently little understanding of which genes mediate vector competence in the wild, or evolve in response to parasite-mediated selection. Here, we use population genetic approaches to study the strength and mode of natural selection on a suite of mosquito immune system genes, CTL4, CTLMA2, LRIM1, and APL2 (LRRD7), which have been shown to affect Plasmodium development in functional studies. We sampled these genes from two African populations of An. gambiae s.s., along with several closely related species, and conclude that there is no evidence for either strong directional or balancing selection on these genes. We highlight a number of challenges that need to be met in order to apply population genetic tests for selection in Anopheles mosquitoes; in particular the dearth of suitable outgroup species and the potential difficulties that arise when working within a closely-related species complex.

Micro robot prototype for colonoscopy and in vitro experiments

For actively diagnosing the colon's pathologies micro-invasively or non-invasively, an autonomous prototype of the earthworm-like robot for colonoscopy was designed according to the principle of bionics, and manufactured using precision process technology. In vitro experiments in pig colon were carried out. The micro robot was driven directly by an electromagnetic linear driver. The mobile cells were joined with joints of two degrees of freedom, and the whole body was flexible. The direction of movement and the angle of imaging can be controlled by the shape memory alloy (SMA). In experiments, locomotion efficient and locomotion ability was analysed carefully. Locomotion force and velocity were tested. In vitro experiments in pig colon demonstrated that the micro robot can navigate though the colon by itself reliably and freely, which will be useful for the application of the robot to colonoscopy in the clinic.

Vascular endothelial growth factor gene polymorphisms associated with prognosis for patients with gastric cancer

BACKGROUND

The present study analyzed vascular endothelial growth factor (VEGF) gene polymorphisms and their impact on the prognosis for patients with gastric cancer.

PATIENTS AND METHODS

Five hundred and three consecutive patients with surgically resected gastric adenocarcinoma were enrolled in the present study. The genomic DNA was extracted from paraffin-embedded tissue and four VEGF (-460T > C, -116G > A, +405G > C, and +936C > T) gene polymorphisms were determined using a polymerase chain reaction-restriction fragment length polymorphism assay.

RESULTS

The survival analysis showed no association of three VEGF gene polymorphisms with the prognosis. For the +936C > T polymorphism, the T/T genotype, however, had a worse overall survival (OS) compared with the C/C genotype (P = 0.037). The -460 T/C or C/C genotype was a poor prognostic factor in patients with stage 0 or I gastric cancer (OS: hazard ratio (HR) = 3.96, disease-free survival (DFS): HR = 4.87). In the haplotype analysis, the CACC haplotype was associated with a significantly worse survival when compared with the TGGC haplotype (OS: HR = 1.72, DFS: HR = 1.73).

CONCLUSIONS

VEGF gene polymorphisms were found to be an independent prognostic marker for patients with gastric cancer. Consequently, the analysis of VEGF gene polymorphisms can help identify patient subgroups at high risk of a poor disease outcome.

An adaptive markov model-based method to cluster validation in image segmentation

The number of class should be detected as part of the parameter estimation procedure prior to image segmentation for segmentation algorithms. It is very important in theory and application for estimating the class number correctly. In this paper, an adaptive total energy criterion (ATEC) to cluster validation is proposed based on the Markov random field (MRF) in the image segmentation. The criterion is composed of two parts: one part is inner-energy, which describes the difference of data in the same class; another is inter-class energy, which describes the edge information. The correct class number can be obtained by minimizing the ATEC. The parameters are estimated by expectation maximum (EM) algorithm and maximum psedu-likelihood (MPL) algorithm. The complex computation is optimized by the mixture of simulated algorithm (SA) and iterated conditional mode (ICM). The experiments show that the class number can be automatically detected by adjusting the hyper-parameter in MRF. As a by-product, the segmentation can be obtained by the maximum a posteriori (MAP).

Molecular evolution and intragenic recombination of the merozoite surface protein MSP-3alpha from the malaria parasite Plasmodium vivax in Thailand

The merozoite surface antigens of malaria parasites are prime anti-morbidity/mortality vaccine candidates. However, their highly polymorphic nature requires extensive surveys of parasite populations to validate vaccine designs. Previous studies have found 3 molecular types (A, B and C) of the Plasmodium vivax merozoite surface protein 3a (PvMSP-3alpha) among parasite field populations. Here we analysed complete PvMSP-3alpha sequences from 17 clinical P. vivax isolates from Thailand and found that the nucleotide diversity was as high as that from samples widely separated by time and space. The polymorphic sites were not randomly distributed but concentrated in the N-terminal Ala-rich domain (block 2A), which is partially deleted in type B and C sequences. The size variations among type A sequences were due to small indels occurring in block 2A, whereas type B and C sequences were uniform in length with each type having a different large deletion. Analysis of synonymous and non-synonymous substitutions suggested that different selection forces were operating on different regions of the molecule. The numerous recombination sites detected within the Ala-rich domain suggested that intragenic recombination was at least partially responsible for the observed genetic diversity of the PvMSP-3alpha gene. Phylogenetic analysis failed to link any alleles to a specific geographical origin, even when different domains of PvMSP-3alpha were used for analysis. The highly polymorphic nature and lack of geographical clustering of isolates suggest that more systematic investigations of the PvMSP-3alpha gene are needed to explore its evolution and vaccine potential.

RAMP based fingerprinting and assessment of relationships among Australian narrow-leafed lupin (Lupinus angustifolius L.) cultivars

Narrow-leafed lupin is a major winter grain legume crop in the Australian farming system and a number of commercial cultivars are currently available to growers. A significant level of polymorphism was detected in narrow-leafed lupin cultivars by the randomly amplified microsatellite polymorphism (RAMP) approach, suggesting that cultivars harbour considerable DNA variation. Seventy-seven cultivar-specific markers were found among the 23 lupin cultivars examined and a dichotomous fingerprinting key was developed for the molecular identification of lupin cultivars. Cluster analysis of pairwise distance matrix computed from RAMP profiles grouped the 23 cultivars into 4–5 clusters, which generally agreed with their pedigree relationships.

Geographical patterns of genetic variation in the world collections of wild annual Cicer characterized by amplified fragment length polymorphisms

Cicer reticulatum, C. echinospermum, C. bijugum, C. judaicum, C. pinnatifidum, C. cuneatum and C. yamashitae are wild annual Cicer species and potential donors of valuable traits to improve chickpea (C. arietinum). As part of a large project to characterize and evaluate wild annual Cicer collections held in the world gene banks, AFLP markers were used to study genetic variation in these species. The main aim of this study was to characterize geographical patterns of genetic variation in wild annual Cicer germplasm. Phylogenetic analysis of 146 wild annual Cicer accessions (including two accessions in the perennial C. anatolicum and six cultivars of chickpea) revealed four distinct groups corresponding well to primary, secondary and tertiary gene pools of chickpea. Some possible misidentified or mislabelled accessions were identified, and ILWC 242 is proposed as a hybrid between C. reticulatum and C. echinospermum. The extent of genetic diversity varied considerably and was unbalanced between species with greatest genetic diversity found in C. judaicum. For the first time geographic patterns of genetic variation in C. reticulatum, C. echinospermum, C. bijugum, C. judaicum and C. pinnatifidum were established using AFLP markers. Based on the current collections the maximum genetic diversity of C. reticulatum, C. echinospermum, C. bijugum and C. pinnatifidum was found in southeastern Turkey, while Palestine was the centre of maximum genetic variation for C. judaicum. This information provides a solid basis for the design of future collections and in situ conservation programs for wild annual Cicer.

Chloroplast DNA inheritance and variation in Leucadendron species (Proteaceae) as revealed by PCR-RFLP

The inheritance of chloroplast DNA (cpDNA) in Leucadendron species was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. A total of 100 progeny from five interspecific crosses involving seven parental species were tested, and all progeny exhibited the cpDNA restriction fragment pattern of the female parent, indicating that cpDNA in Leucadendron is maternally inherited. PCR-RFLP was also employed to study cpDNA variation among 21 Leucadendron species. Parsimony analysis using a heuristic search resulted in a phylogenetic tree that showed limited agreement to the taxonomic classification of Leucadendron species, based on morphological characteristics. The incongruence between cpDNA phylogenetic and taxonomic groupings in Leucadendron may be due to reticulate evolution involving a combination of hybridization and introgression, convergent evolution and/or lineage sorting at the interspecific, intersubsectional and intersectional levels.

Habitat characteristics of Anopheles gambiae s.s. larvae in a Kenyan highland

Anopheline larval habitats associated with a swamp, were examined in a highland area (1910 m elevation) of western Kenya. A significant association was found between occurrence of Anopheles gambiae Giles s.s. (Diptera: Culicidae) larvae and two factors, habitat size and vegetation type. Over 80% of An. gambiae s.s. larvae were found in small isolated pools, characterized by short plants, occurring in both swamp margins and roadside ditches. However, Anopheles gambiae s.s. was not found in habitats marked by papyrus and floating plants. The larval habitat of An. gambiae s.s. was characterized by warmer daytime temperatures of water, which were significantly affected by habitat size and plant size. The density of indoor resting An. gambiae s.s. was 0.22 per house and negatively associated with distance from the swamp. These results indicate that the practice of swamp cultivation, in populated areas of the African highlands, increases availability and enhances habitat conditions for the malaria vector.

Population genetic structure of Anopheles arabiensis mosquitoes in Ethiopia and Eritrea

This study examined the population genetic structure of the major malaria vector, Anopheles arabiensis mosquitoes, in Ethiopia and Eritrea. Ethiopia and Eritrea have great geographical diversity, with high mountains, rugged plateaus, deep gorges, and rolling plains. The plateau is bisected diagonally by the Great Rift Valley into the Northwestern Highlands and the Southeastern Highlands. Five A. arabiensis populations from the Northwestern Highlands region and two populations from high-altitude sites in the Great Rift Valley were genotyped using six microsatellite markers to estimate the genetic diversity and population genetic structure of A. arabiensis. We found that A. arabiensis populations from the Northwestern Highlands and the Great Rift Valley region showed a similar level of genetic diversity. The genetic differentiation (F(ST)) of the five mosquito populations within the Northwestern Highlands region was 0.038 (P <.001), while the two populations within the Great Rift Valley showed little genetic differentiation (F(ST) = 0.007, P <.01). The degree of genetic differentiation between the Northwestern Highlands region and the Great Rift Valley region was small but statistically significant (F(ST) = 0.017, P <.001). The population genetic structure of A. arabiensis in the study area did not follow the isolation-by-distance model (r(2) = 0.014, P >.05). The low F(ST) estimates for A. arabiensis populations in Ethiopia and Eritrea are consistent with the general population genetic structure of this species in East Africa based on other molecular markers.

AFLP-based genetic linkage map for the red flour beetle (Tribolium castaneum)

The red flour beetle (Tribolium castaneum) is a major pest of stored grain and grain products and a popular model species for a variety of ecological, evolutionary, and developmental biology studies. Development of a linkage map based on reproducible and highly polymorphic molecular markers would greatly facilitate research in these disciplines. We have developed a genetic linkage map using 269 amplified fragment length polymorphism (AFLP) markers. Ten previously known random amplified polymorphic DNA (RAPD) markers were used as anchor markers for linkage group assignment. The linkage map was constructed through genotyping two independent F(2) segregating populations with 48 AFLP primer combinations. Each primer combination generated an average of 4.6 AFLP markers eligible for linkage mapping. The length of the integrated map is 573 cM, giving an average marker resolution of 2.0 cM and an average physical distance per genetic distance of 350 kb/cM. A cluster of loci on linkage group 3 exhibited significant segregation distortion. We have also identified six X-linked and two Y-linked markers. Five mapped AFLP fragments were sequenced and converted to sequence-tagged site (STS) markers.

A microsatellite map of the African human malaria vector Anopheles funestus

Microsatellite markers and chromosomal inversion polymorphisms are useful genetic markers for determining population structure in Anopheline mosquitoes. In Anopheles funestus (2N = 6), only chromosome arms 2R, 3R, and 3L are known to carry polymorphic inversions. The physical location of microsatellite markers with respect to polymorphic inversions is potentially important information for interpreting population genetic structure, yet none of the available marker sets have been physically mapped in this species. Accordingly, we mapped 32 polymorphic A. funestus microsatellite markers to the polytene chromosomes using fluorescent in situ hybridization (FISH) and identified 16 markers outside of known polymorphic inversions. Here we provide an integrated polytene chromosome map for A. funestus that includes the breakpoints of all known polymorphic inversions as well as the physical locations of microsatellite loci developed to date. Based on this map, we suggest a standard set of 16 polymorphic microsatellite markers that are distributed evenly across the chromosome complement, occur predominantly outside of inversions, and amplify reliably. Adoption of this set by researchers working in different regions of Africa will facilitate metapopulation analyses of this primary malaria vector.