Species-specific real-time PCR detection of Colletotrichum kahawae

AIMS

Colletotrichum kahawae is a strongly aggressive pathogen causing coffee berry disease and is specific to Arabica coffee (Coffea arabica) in Africa. In this article, we developed a real-time PCR assay for the species-specific diagnosis of C. kahawae by designing the primers and a TaqMan probe derived from the single nucleotide polymorphism-rich region of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene.

METHODS AND RESULTS

DNA markers from rDNA internal transcribed spacer, actin, β-tubulin and GAPDH genes of the ex-type culture of C. kahawae and 10 reference strains of Colletotrichum species were analysed for intra- and interspecific variations. The GAPDH gene was selected to develop a species-specific DNA marker. A TaqMan real-time PCR assay for species-specific detection of C. kahawae was developed, and its accuracy was tested against type strains of other phylogenetically closely related species in the C. gloeosporioides species complex, with the detection sensitivity of 80 fg μl(-1) of genomic DNA.

CONCLUSIONS

This real-time PCR assay is highly specific and sensitive for the diagnosis of C. kahawae and can be applied in qualitative and quantitative tests.

SIGNIFICANCE AND IMPACT OF THE STUDY

This protocol allows for a rapid and sensitive detection of C. kahawae and will be useful in disease management and pest detection to prevent further spread of this pathogen.

First imaging result with an ultrahigh resolution stationary MR compatible SPECT system

In this paper, we will present the design and preliminary performance of an ultrahigh resolution stationary MR compatible SPECT (MRC-SPECT) system that is developed in our lab. The MRC-SPECT system is based on the second-generation energy-resolved photon-counting (ERPC) CdTe detectors and there are several key features associated with this system. Firstly, up to a total of twenty ERPC detectors will be assembled as a very compact ring, which provides an adequate angular sampling capability and a relatively high detection efficiency. The detectors are supported on a gantry made of high strength polyamide structure constructed using 3-D printing. This compact system can be directly operated inside an MR scanner. The detector module used in this system offers an intrinsic resolution of 350μm and an excellent energy resolution of around 3~4kev. Each ERPC detector module consists of four pixelated CdTe detectors with a total dimension of 4.5cm×2.25cm. Secondly, a die-cast platinum pinhole inserts and cast lead apertures are developed for this stationary SPECT system. Four 300/500μm diameter pinholes are used for each detector and all pinholes are mounted around a casted cylinder lead aperture tube. The inner diameter of the lead aperture tube is 6cm and the lead tube thickness is 16mm. The opposite detectors are placed 15.6cm apart and the magnification factor of this SPECT system is about 1.2. Thirdly, a comprehensive charge collection model inside strong magnetic field has been developed to account for the magnetic field induced distortion in the SPECT image. This model can accurately predict the detector's energy and spatial response to gamma ray incident events and then help to compensate for the event position recording error due to the strong magnetic field. In this development, we have made an effort to minimize the amount of magnetic materials in the system to alleviate potential interference to magnetic field inhomogeneity.

Cadmium and its epigenetic effects

Cadmium (Cd) is a toxic, nonessential transition metal and contributes a health risk to humans, including various cancers and cardiovascular diseases; however, underlying molecular mechanisms remain largely unknown. Cells transmit information to the next generation via two distinct ways: genetic and epigenetic. Chemical modifications to DNA or histone that alters the structure of chromatin without change of DNA nucleotide sequence are known as epigenetics. These heritable epigenetic changes include DNA methylation, post-translational modifications of histone tails (acetylation, methylation, phosphorylation, etc), and higher order packaging of DNA around nucleosomes. Apart from DNA methyltransferases, histone modification enzymes such as histone acetyltransferase, histone deacetylase, and methyltransferase, and microRNAs (miRNAs) all involve in these epigenetic changes. Recent studies indicate that Cd is able to induce various epigenetic changes in plant and mammalian cells in vitro and in vivo. Since aberrant epigenetics plays a critical role in the development of various cancers and chronic diseases, Cd may cause the above-mentioned pathogenic risks via epigenetic mechanisms. Here we review the in vitro and in vivo evidence of epigenetic effects of Cd. The available findings indicate that epigenetics occurred in association with Cd induction of malignant transformation of cells and pathological proliferation of tissues, suggesting that epigenetic effects may play a role in Cd toxic, particularly carcinogenic effects. The future of environmental epigenomic research on Cd should include the role of epigenetics in determining long-term and late-onset health effects following Cd exposure.

Yohimbine anxiogenesis in the elevated plus maze is disrupted by bilaterally disconnecting the bed nucleus of the stria terminalis from the central nucleus of the amygdala

The α2 adrenergic receptor antagonist yohimbine (YO) is a sympathomimetic drug that crosses the blood-brain barrier after systemic administration. YO promotes increased transmitter release from noradrenergic (NA) axon terminals in the central nucleus of the amygdala (CEA), bed nucleus of the stria terminalis (BST), hypothalamus, and other brain regions implicated in physiological and behavioral responses to stressful and threatening stimuli. YO is potently anxiogenic in humans and experimental animals, including rats. To determine whether direct connections between the CEA and anterolateral group of BST nuclei (algBST) are necessary for YO anxiogenesis in rats, neurotoxic ibotenate lesions of the CEA in one hemisphere and the ipsi- or contralateral algBST were conducted to disrupt CEA-algBST communication uni- or bilaterally. Sham-lesioned controls received microinjections of vehicle into the CEA and algBST. Two weeks later, behavior was assessed in the elevated plus maze (EPMZ) in rats after i.p. saline or YO (1.0mg/kg). Central ibotenate lesion placement and extent was assessed post-mortem in NeuN-immunolabeled tissue sections. The ability of YO to increase anxiety-like behavior in the EPMZ was similarly robust in rats with sham lesions or ipsilateral CEA-algBST lesions. Conversely, YO anxiogenesis in the EPMZ was disrupted in rats with asymmetric lesions designed to bilaterally disconnect the CEA and algBST, whereas neither unilateral nor bilateral disconnecting lesions altered EPMZ behavior in rats after i.p. saline. We conclude that the anxiogenic effects of increased NA signaling in rats after YO require direct CEA-algBST interactions that do not shape EPMZ behavior under baseline conditions.

First Report of Flower Anthracnose Caused by Colletotrichum karstii in White Phalaenopsis Orchids in the United States

In October 2010, a Colletotrichum species was isolated from white Phalaenopsis flowers growing in a greenhouse in San Francisco, CA. This Phalaenopsis is a common commercial orchid hybrid generated mostly likely from Phalaenopsis amabilis and P. aphrodite. The white petals showed anthracnose-like lesions where necrotic tissue is surrounded by a ring of green tissue. The green halo tissues around the necrotic tissue contain functional chloroplasts. One-centimeter disks were cut around the necrotic sites and surface-sterilized with 95% ethanol and 0.6% sodium hypochlorite. The disks were placed on potato dextrose agar (PDA) medium to establish cultures. Pure cultures were obtained by subculturing hyphal tips onto fresh PDA plates. The generated colonies had white aerial mycelia and orange conidial mass. The color of the reverse colony varies between colorless and pale orange. Microscopic observations identified the conidia as cylindrical, straight, and rounded at both ends. In addition, the conidia were approximately 15.0 to 18.0 μm long and 5.0 to 6.5 μm in diameter. These observed morphological features suggested that these isolates possessed the same characteristics as previously described for Colletotrichum karstii, a species considered as part of the C. boninense species complex (1). Four putative independent Colletotrichum isolates were recovered (DED9596, DED9597, DED9598, and DED9599). To confirm the Colletotrichum isolates as the causative pathogen, healthy white Phalaenopsis flowers (five total) in a whole plant were sprayed with a conidial suspension (approximately 1.2 × 10⁶ conidia/ml) of the isolates and incubated at 20°C and 100% relative humidity with cycles of 16 h light and 8 h of darkness. Approximately 1 ml of conidial suspension solution was used for each flower. The plants were watered regularly and flowers were sprayed with sterile double-distilled water daily. As negative controls, five flowers in a whole plant were sprayed with water. Fifteen to twenty days after inoculation, lesions started to form on the petals sprayed with the putative Colletotrichum isolates. All controls remained healthy. The Colletotrichum-inoculated flowers remained alive and did not die as a result of the infection. This same experiment was repeated and the same results were obtained. DNA was extracted from the necrotic regions of the petals infected by the pure cultures of the four isolates and used to sequence the 18S rRNA ITS (internal transcribed spacer) region. All four isolates gave identical ITS sequences. Analysis of the obtained representative sequences (GenBank Accession No. JQ277352) suggested that the isolated pathogen as C. karstii. Using the published ITS data for the C. boninense species complex (1), a phylogenetic tree was generated via the maximum likelihood method. This created tree places the isolates in the same group as C. karstii. This type of C. karstii infection in Phalaenopsis orchid petals was not documented in the U.S. before, although it has been reported in China and Thailand (2). To our knowledge, this is the first report of infection and green island formation caused by C. karstii on orchid flower in the United States. References: (1) Damm et al. Studies in Mycology 73:1, 2012. (2) Yang et al. Cryptogamie Mycologie 32:229, 2011.

First Report of Leaf Disease on Cinnamomum subavenium Caused by Colletotrichum fioriniae in China

Cinnamomum subavenium Miq. (Lauraceae) is a subtropical arbor plant widely distributed in southwest China. It has a long history of cultivation and has been widely used in traditional Chinese medicine, food flavors, and industrial materials. In August 2010, a serious leaf disease was observed on wild Cinnamomum subavenium growing in Gutianshan Nature Reserve, Zhejiang, China. Lesions were approximately 1.0 cm in diameter and the margin of the lesions was light to dark brown and the middle was gray to pale yellowish. Necrotic lesions were surface disinfected with 1% sodium hypochlorite for 1 min and 70% ethanol for 3 min, and isolations were made from lesion edges onto potato dextrose agar (PDA). Three plants were tested and a fungus was consistently isolated from lesions. Colonies of this fungus on PDA were at first gray becoming pinkish gray with age, with salmon pink conidial masses, and the reverse of the colony was pink. The growth rate was 10.82 to 11.95 mm per day (average = 11.58 ± 0.25, n = 6) on PDA at 25°C. Conidia were oblong or cylindrical with acute ends, occasionally guttulate, hyaline, 7.5 to 14.5 × 2.5 to 4.3 μm (average = 11.25 ± 0.5 × 3.4 ± 0.4, n = 30). These characteristics matched the description of Colletotrichum fioriniae (Marcelino & Gouli) R.G. Shivas & Y.P. Tan (2). DNA was extracted from one isolate and the rDNA-internal transcribed spacer (ITS) region was amplified and sequenced using primers ITS1 and ITS4 (1). The ITS sequence of the isolate (GenBank Accession No. JN208890) shared 100% identity to the holotype of C. fioriniae (Accession No. EF464594). The pathogenicity of C. fioriniae on Cinnamomum subavenium was confirmed through inoculation. Three freshly harvested, healthy leaves were washed under running tap water, immersed in 5% sodium hypochlorite for 3 min and 70% ethanol for 1 min, rinsed three times in sterilized water, and finally dried with sterilized tissue paper. Plant leaves were inoculated with a concentration of 2.5 × 10⁶ spores/ml. Sterilized water was used for controls. All the leaves inoculated with C. fioriniae were symptomatic with round to elliptical lesions with a brown margin 14 days postinoculation. The fungus, reisolated from symptomatic leaf tissue, had the same morphological and cultural characteristics of C. fioriniae. Although C. gloeosporioides has been reported from several species in the genus Cinnamomum ( http://nt.ars-grin.gov/fungaldatabases/ ), to our knowledge, this is the first report of leaf disease on Cinnamomum subavenium caused by a Colletotrichum species. References: (1) H. Prihastuti et al. Fungal Divers. 39:89, 2009. (2) R. G. Shivas and Y. P. Tan. Fungal Divers. 39:111, 2009.

The efficacy and safety of vildagliptin in patients with type 2 diabetes: a meta-analysis of randomized clinical trials

WHAT IS KNOWN AND OBJECTIVE

Dipeptidyl peptidase-4 (DPP-4) inhibitors are a relatively new class of drugs for the management of type 2 diabetes (T2DM). Vildagliptin is an oral DPP-4 inhibitor approved in more than 70 countries. The purpose of this meta-analysis is to provide an update on the clinical efficacy and safety of vildagliptin in patients with T2DM.

METHODS

A literature search identified 30 randomized controlled trials comparing vildagliptin with comparators (placebo or other hypoglycaemic agents). Meta-analyses were conducted for HbA1c, weight, fasting plasma glucose (FPG), hypoglycaemia and other adverse events. The outcomes of HbA1c, weight and FPG were analysed as weighted mean differences (WMD), and the number of ADRs events as relative risks (RR).

RESULTS

Compared with placebo, vildagliptin lowered HbA1c {WMD, -0·77% [95% confidence interval (CI), -0·96% to -0·58%] for 100 mg/day of vildagliptin and -0·58% [95% CI, -0·72% to -0·44%] for 50 mg/day of vildagliptin}. The effect was non-inferior to thiazolidinediones, sulfonylureas and α-glycosidase inhibitors, but inferior to metformin. Compared with placebo, treatment with 50 mg/day of vildagliptin caused neutral weight changes, while 100 mg/day of vildagliptin resulted in slight weight gain [0·95 kg (95% CI, 0·73-1·17 kg)]. In addition, compared to comparators, vildagliptin was not associated with an increase in overall risk for any adverse events [RR, 0·97 (95% CI, 0·94-0·99)]. The incidence of hypoglycaemia was low with vildagliptin, and the risk with vildagliptin was not significantly different from the comparators [0·85 (95% CI, 0·49-1·47)]. The use of vildagliptin did not display any increased risks of infection [1·03 (95% CI, 0·94-1·13) for nasopharyngitis and 1·07 (95% CI, 0·90-1·27) for upper respiratory tract infection].

WHAT IS NEW AND CONCLUSION

Vildagliptin is effective in glycaemic control with a low risk of hypoglycaemia and other adverse reactions. This may have an important impact on patient adherence to this medication.

P4-12-13: A Multi-Center Randomized Controlled Double Blind Trial Assessing the Effect of Acupuncture in Reducing Musculoskeletal Symptoms in Breast Cancer Patients Taking Aromatase Inhibitors: First Interim Analysis

Background: Aromatase inhibitors (AIs) are recommended as first-line adjuvant hormonal therapy in postmenopausal women with hormone-receptor-positive breast cancer, as monotherapy or sequential therapy after tamoxifen. AI-associated musculoskeletal symptoms (AIMSS) occur in approximately 50% of women receiving AIs and in some may result in discontinuation of treatment. Symptom management is essential to ensure that breast cancer patients receive the full recommended duration of AI therapy. We conducted a randomized, placebo-controlled trial to evaluate the effect of acupuncture on AIMSS and report the first interim analysis.

Method: Postmenopausal women with early stage breast cancer, experiencing AIMSS, who had not had acupuncture in the year prior to the study, were eligible. Patients were randomized to 8 weekly acupuncture or sham acupuncture. Health assessment questionnaire disability index (HAQ-DI ranging 0–3.0) and pain visual analog scale (VAS ranging 0–100) were used to assess clinical musculoskeletal disorder severity at weeks 0, 4, 8, and 12 or 24. Change in HAQ-DI (ΔHAQ-DI) and VAS scores (ΔVAS) from baseline were compared between patients receiving acupuncture versus sham acupuncture using exact Wilcoxon rank sum test. Serum samples were collected for measurements of estrogens and beta endorphin concentrations and cytokine profile before and after the intervention to evaluate the etiology of AIMSS and the mechanism of acupuncture in treating AIMSS.

Results: Between May 2008 and June 2011, 48 patients were enrolled, 2 patients were not evaluable due to noncompliance to treatment and lost to follow up, 10 were still receiving treatment and therefore not evaluable. Thirty-six were evaluable, and were equally distributed between the real and sham acupuncture groups. Baseline characteristics were balanced between the two groups with regard to age, race, and body mass index (BMI) with the exception that baseline mean HAQ-DI was higher in the acupuncture group (0.9 vs 0.55, p=0.04). White/Black/Asian: 26/7/3, Median (range): age: 61 (45-82); BMI (kg/m2): 31.1 (22.9−59.6). At week 8, both groups showed a wide range of ΔHAQ-DI (ΔHAQ-DI =HAQ-DIweek8-HAQ-DIbaseline): from −1.38 to 0.5 in the acupuncture group versus from −1 to 0.12 in sham acupuncture group. There was no statistically significant difference in mean ΔHAQ-DI between the real and sham acupuncture groups (−0.33 vs −0.33, p=0.87). Eleven patients in each group (61%) reported decreased HAQ-DI scores, which correlated with improved function. There was no difference in mean ΔVAS between the real and sham acupuncture groups (−9.27 vs −13.82, p=0.67). No significant side effects were reported. Changes in other time points and in serum biomarkers will be presented at the meeting.

Conclusions: The majority of breast cancer patients experiencing AIMSS who participated in our study reported a reduced HAQ-DI score both from acupuncture and sham acupuncture. We did not observe significant differences between responses to real versus sham acupuncture after 8 weekly treatments. The study remains open to accrual to reach 50 evaluable patients.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P4-12-13.

On acetyl-CoA as a gauge of cellular metabolic state

Many activities within a cell must be intimately coordinated with its metabolic state. Understanding these connections to metabolism is critical to deciphering the regulation of a variety of cellular processes. However, despite intensive research in these areas, the precise mechanisms by which a cell monitors its metabolic state remain controversial and poorly understood. Herein, we discuss the thesis that intracellular levels of the metabolite acetyl-CoA represent a critical gauge of cellular metabolic state, which is cleverly monitored by the cell through dynamic acetylation modifications to direct a variety of outputs connected to energy metabolism, cell growth, and survival.

Activation of Notch1 signaling in stromal fibroblasts inhibits melanoma growth by upregulating WISP-1

The tumor microenvironment is emerging as an important target for cancer therapy. Fibroblasts (Fbs) within the tumor stroma are critically involved in promoting tumor growth and angiogenesis through secretion of soluble factors, synthesis of extracellular matrix and direct cell-cell interaction. In this work, we aim to alter the biological activity of stromal Fbs by modulating the Notch1 signaling pathway. We show that Fbs engineered to constitutively activate the Notch1 pathway significantly inhibit melanoma growth and tumor angiogenesis. We determine that the inhibitory effect of 'Notch-engineered' Fbs is mediated by increased secretion of Wnt-induced secreted protein-1 (WISP-1) as the effects of Notch1 activation in Fbs are reversed by shRNA-mediated blockade of WISP-1. When 'Notch-engineered' Fbs are co-grafted with melanoma cells in SCID mice, shRNA-mediated blockade of WISP-1 reverses the tumor-suppressive phenotype of the 'Notch-engineered' Fbs, significantly increases melanoma growth and tumor angiogenesis. Consistent with these findings, supplement of recombinant WISP-1 protein inhibits melanoma cell growth in vitro. In addition, WISP-1 is modestly expressed in melanoma-activated Fbs but highly expressed in inactivated Fbs. Evaluation of human melanoma skin biopsies indicates that expression of WISP-1 is significantly lower in melanoma nests and surrounding areas filled with infiltrated immune cells than in the adjacent dermis unaffected by the melanoma. Overall, our study shows that constitutive activation of the Notch1 pathway confers Fbs with a suppressive phenotype to melanoma growth, partially through WISP-1. Thus, targeting tumor stromal Fbs by activating Notch signaling and/or increasing WISP-1 may represent a novel therapeutic approach to combat melanoma.

Ethanol-induced neurodegeneration in NRSF/REST neuronal conditional knockout mice

The transcription regulator, neuron-restrictive silencer factor (NRSF), also known as repressor element-1 silencing transcription factor (REST), plays an important role in neurogenesis and various neuronal diseases such as ischaemia, epilepsy, and Huntington's disease. In these disease processes, neuronal loss is associated with abnormal expression and/or localization of NRSF. Previous studies have demonstrated that NRSF regulates the effect of ethanol on neuronal cells in vitro, however, the role of NRSF in ethanol-induced neuronal cell death remains unclear. We generated nrsf conditional knockout mice using the Cre-loxP system to disrupt neuronal expression of nrsf and its truncated forms. At postnatal day 6, ethanol significantly increased the expression of REST4, a neuron-specific truncated form of NRSF, in the brains of wild type mice, and this effect was diminished in nrsf conditional knockout mice. The apoptotic effect of ethanol was pronounced in multiple brain regions of nrsf conditional mutant mice. These results indicate that NRSF, specifically REST4, may protect the developing brain from ethanol, and provide new evidence that NRSF can be a therapeutic target in foetal alcohol syndrome (FAS).

Transforming growth factor beta 1 plays an important role in inducing CD4(+)CD25(+)forhead box P3(+) regulatory T cells by mast cells

The role of mast cells (MCs) in the generation of adaptive immune responses especially in the transplant immune responses is far from being resolved. It is reported that mast cells are essential intermediaries in regulatory T cell (T(reg)) transplant tolerance, but the mechanism has not been clarified. To investigate whether bone marrow-derived mast cells (BMMCs) can induce T(regs) by expressing transforming growth factor beta 1 (TGF-β1) in vitro, bone marrow cells obtained from C57BL/6 (H-2(b) ) mice were cultured with interleukin (IL)-3 (10 ng/ml) and stem cell factor (SCF) (10 ng/ml) for 4 weeks. The purity of BMMCs was measured by flow cytometry. The BMMCs were then co-cultured with C57BL/6 T cells at ratios of 1:2, 1:1 and 2:1. Anti-CD3, anti-CD28 and IL-2 were administered into the co-culture system with (experiment groups) or without (control groups) TGF-β1 neutralizing antibody. The percentages of CD4(+)CD25(+)forkhead box P3 (FoxP3)(+) T(regs) in the co-cultured system were analysed by flow cytometry on day 5. The T(reg) percentages were significantly higher in all the experiment groups compared to the control groups. These changes were deduced by applying TGF-β1 neutralizing antibody into the co-culture system. Our results indicated that the CD4(+) T cells can be induced into CD4(+)CD25(+)FoxP3(+) T cells by BMMCs via TGF-β1.

14,15-Epoxyeicosatrienoic acid induces the proliferation and anti- apoptosis of human carcinoma cell

BACKGROUND AND THE PURPOSE OF THE STUDY

Epoxyeicosatrienoic acids (EETs), which are cytochrome P450 epoxygenase metabolites of arachidonic acid, have anti-inflammatory effects, modulate smooth muscle proliferation, and inhibit smooth muscle migration. This study was designed to determine whether exogenous EETs have any effect on the cell proliferation and apoptosis of carcinoma cell as well as the possible signaling pathways of EETs in this regulation.

METHODS

The effects of EETs on the proliferation and anti-apoptosis of human carcinoma cells were measured by MTT assay and flowcytometric analysis, and the regulation of PPARγ, epithelial growth factor receptor (EGFR), extracellular signal-regulated kinase (ERK), phosphatidylinositol 3 (PI3)-Kinase/AKT pathways was investigated by reverse transcriptase polymerase chain reaction (RT-PCR) and western blot analysis.

RESULTS

Results of this study suggested that 14, 15-EET may activate the expression of PPARγ in Tca-8113 cells. 14,15-EET may stimulate cell proliferation, and increase the percentage of cells during S-G2-M phase in Tca-8113 cells significantly. The levels of EGFR, ERK, and PI3 kinase/AKT proteins were significantly induced by treatment of 14, 15-EET and 14,15-EET/AUDA, but no significant changes were observed by addition of GW9662.

CONCLUSION

These findings suggest that exogenous 14,15-EET has potent inhibitory effect on proliferation, and could induce apoptosis in Tca-8113 cell, and these changes are related to the expression of PPARγ, the activation of EGFR, ERK, and PI3 kinase/AKT proteins.

Progress towards discovery of antifibrotic drugs targeting synthesis of type I collagen

Type I collagen is the most abundant protein in human body. Fibrosis is characterized by excessive synthesis of type I collagen in parenchymal organs. It is a leading cause of morbidity and mortality worldwide, about 45% of all natural deaths are attributable to some fibroproliferative disease. There is no cure for fibrosis. To find specific antifibrotic therapy targeting type I collagen, critical molecular interactions regulating its synthesis must be elucidated. Type I and type III collagen mRNAs have a unique sequence element at the 5' end, the 5' stem-loop. This stem-loop is not found in any other mRNA. We cloned LARP6 as the protein which binds collagen 5' stem-loop with high affinity and specificity. Mutation of the 5' stem-loop or knock down of LARP6 greatly diminishes collagen expression. Mice with mutation of the 5' stem-loop are resistant to development of liver fibrosis. LARP6 associates collagen mRNAs with filaments composed of nonmuscle myosin; disruption of these filaments abolishes synthesis of type I collagen. Thus, LARP6 dependent collagen synthesis is the specific mechanism of high collagen expression seen in fibrosis. We developed fluorescence polarization (FP) method to screen for drugs that can inhibit binding of LARP6 to 5' stem-loop RNA. FP is high when LARP6 is bound, but decreases to low levels when the binding is competed out. Thus, by measuring decrease in FP it is possible to identify chemical compounds that can dissociate LARP6 from the 5' stem-loop. The method is simple, fast and suitable for high throughput screening.

Processed pseudogenes are located preferentially in regions of low recombination rates in the human genome

The aim of this article is to demonstrate possible recombination-associated evolutionary forces affecting the genomic distribution of processed pseudogenes. The relationship between recombination rate and the distribution of processed pseudogenes is analysed in the human genome. The results show that processed pseudogenes preferentially accumulate in regions of low recombination rates and this correlation cannot be explained by indirect relationships with GC content and gene density. Several explanatory models for the observation are discussed. A model of selection against ectopic recombination is tested based on the difference in distribution pattern between two classes of processed pseudogenes, which differ in the possibility of stimulating ectopic recombination. Our results indicate that the correlation between processed pseudogene density and recombination rate is probably results, in part, from the selection against ectopic recombination between closely located homologous processed pseudogenes. We also found a length effect in processed pseudogene distribution, namely long processed pseudogenes are located more preferentially in regions of low recombination rates than short ones.

Differentiation of Chlamydia trachomatis lymphogranuloma venereum-related serovars from other serovars using multiplex allele-specific polymerase chain reaction and high-resolution melting analysis

Lymphogranuloma venereum (LGV) is a sexually transmitted infection caused by Chlamydia trachomatis serovars L1, L2 and L3. Consequently, more specific and sensitive detection methods that are rapid and inexpensive are necessary to differentiate between C. trachomatis serovars. The purpose of this study was to identify and differentiate LGV-related C. trachomatis serovars from rectal swabs using high-resolution melting analysis (HRMA) and multiplex allele-specific polymerase chain reaction (MAS-PCR). Fifteen clinical samples from patients in Sydney were first screened and confirmed as C. trachomatis by using the COBAS®AMPLICOR PCR analyser. The same samples were assayed for C. trachomatis and LGV by HRMA and MAS-PCR of the polymorphic membrane protein H ( pmpH) gene. Both methods indicated that two of 15 samples were serovar L2 and the remainder (13/15) other C. trachomatis serovars. Both HRMA and MAS-PCR are inexpensive, rapid, easy methods that are useful tools for the identification of LGV in clinical and research laboratories.