Molecular characterization of the DDX3Y gene and its homologs in cattle

DDX3Y (also known as DBY) is a member of the DEAD box protein family, which is involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. In the human, DDX3Y is located in the AZFa interval in the Y chromosome. Deletion of the AZFa region has been shown to disrupt spermatogenesis, causing subfertility and infertility in otherwise healthy men. Here, we report the characterization of the bovine (b) DDX3Y gene and its homologs DDX3X and PL10. We found 2 transcripts for the bDDX3Y (bDDX3Y-L and -S), which correspond to the long and short transcripts of the human DDX3Y and mouse Ddx3y gene. The 2 transcripts are identical except for a 3-bp (AGT) insertion at the position of nt 2025 and an expanded 3'UTR (nt 2155-2769) in bDDX3Y-L. The bDDX3Y-S encodes a peptide of 660 amino acids (aa), while the bDDX3Y-L encodes a peptide of 661 aa as the result of an additional serine (S) insertion at the position of aa 634. Both bDDX3Y isoforms contain the conserved DEAD-box motif. The bDDX3Y is composed of 17 exons. The homologous gene on the X chromosome, bDDX3X, is highly conserved to the Y-copy at mRNA (83%) and protein (88%) levels as well as in the genomic structure. The autosomal copy, bPL10, mapped on BTA15, is a processed pseudogene with a similarity of 88.1% to bDDX3Y and 93.7% to bDDX3X mRNA, suggesting that PL10 is a retroposon of DDX3X. RT-PCR analyses showed that bDDX3Y-L, -S, bDDX3X and bPL10 were all widely expressed with predominant expression in testis and brain. Testicular section in situ hybridization revealed that sense and anti-sense RNAs of bDDX3Y-L, -S, and bDDX3X were expressed in interstitial cells. These results together with the finding that the pseudogene bPL10 is transcriptionally active in this study provide a basis for further investigating the DDX3 gene function in spermatogenesis, male fertility and gene evolution in mammals.

Molecular characterization and experimental host range of an isolate of Wissadula golden mosaic St. Thomas virus

Partial genome segments of a begomovirus were previously amplified from Wissadula amplissima exhibiting yellow-mosaic and leaf-curl symptoms in the parish of St. Thomas, Jamaica and this isolate assigned to a tentative begomovirus species, Wissadula golden mosaic St. Thomas virus. To clone the complete genome of this isolate of Wissadula golden mosaic St. Thomas virus, abutting primers were designed to PCR amplify its full-length DNA-A and DNA-B components. Sequence analysis of the complete begomovirus genome obtained, confirmed that it belongs to a distinct begomovirus species and this isolate was named Wissadula golden mosaic St. Thomas virus-[Jamaica:Albion:2005] (WGMSTV-[JM:Alb:05]). The genome of WGMSTV-[JM:Alb:05] is organized similar to that of other bipartite Western Hemisphere begomoviruses. Phylogenetic analyses placed the genome components of WGMSTV-[JM:Alb:05] in the Abutilon mosaic virus clade and showed that the DNA-A component is most closely related to four begomovirus species from Cuba, Tobacco leaf curl Cuba virus, Tobacco leaf rugose virus, Tobacco mottle leaf curl virus, and Tomato yellow distortion leaf virus. The putative Rep-binding-site motif in the common region of WGMSTV-[JM:Alb:05] was observed to be identical to that of Chino del tomate virus-Tomato [Mexico:Sinaloa:1983], Sida yellow mosaic Yucatan virus-[Mexico:Yucatan:2005], and Tomato leaf curl Sinaloa virus-[Nicaragua:Santa Lucia], suggesting that WGMSTV-[JM:Alb:05] is capable of forming viable pseudo-recombinants with these begomoviruses, but not with other members of the Abutilon mosaic virus clade. Biolistic inoculation of test plant species with partial dimers of the WGMSTV-[JM:Alb:05] DNA-A and DNA-B components showed that the virus was infectious to Nicotiana benthamiana and W. amplissima and the cultivated species Phaseolus vulgaris (kidney bean) and Lycopersicon esculentum (tomato). Infected W. amplissima plants developed symptoms similar to symptoms observed under field conditions, confirming that this virus is a causal agent of Wissadula yellow mosaic disease in W. amplissima.

An intron 1 polymorphism in the cholecystokinin-A receptor gene associated with schizophrenia in males

OBJECTIVE

To identify whether a genetic variation (rs1800857; IVS1-5T>C) in the neuropeptide cholecystokinin-A receptor (CCKAR) gene is a risk factor in the pathogenesis of schizophrenia.

METHOD

The variation was analysed in a case-control design comprising 508 patients with schizophrenia and 1619 control subjects. A possible functional impact of this variant on CCKAR protein synthesis through alterations in splicing was analysed in an exon-trapping assay.

RESULTS

In males only, the risk variant, IVS1-5C, was associated with a significantly increased risk of schizophrenia. Carrying one risk allele was associated with an increased risk of 1.74 (Odds Ratio, OR) and homozygosity (CC) was associated with an OR of 3.19. The variation had no impact on protein synthesis of CCKAR.

CONCLUSION

This is the first report associating the CCKAR gene variant with schizophrenia specifically in men. Our study strengthens the conclusion that a CCKAR dysfunction could be involved in the aetiology of schizophrenia.

16alpha-Bromoepiandrosterone (HE2000) limits non-productive inflammation and stimulates immunity in lungs

16alpha-Bromoepiandrosterone (HE2000) is a synthetic steroid that limits non-productive inflammation, enhances protective immunity and improves survival in clinical studies of patients with human immunodeficiency virus (HIV), malaria and tuberculosis infections. We now show that HE2000 decreased nitric oxide production by lipopolysaccharide (LPS)-stimulated RAW264.7 cells. Treatment with HE2000 also reduced non-productive inflammation associated with carrageenan-induced pleurisy and LPS-induced lung injury in mice. In the hapten-carrier reporter antigen popliteal lymph node assay, HE2000 increased absolute numbers of lymphocytes, antigen-presenting cells, hapten-specific immunoglobulin (Ig)M antibody-forming cells and shifted the interferon (IFN)-gamma/interleukin (IL)-4 balance towards IFN-gamma production. In the cystic fibrosis transmembrane conductance regulator (CFTR(-/-)) mouse model of acute Pseudomonas aeruginosa infection, treatment with HE2000 consistently reduced bacterial burden in lungs. All HE2000 effects were dose-dependent. In H1N1 infection in mice, HE2000 was safe but not effective as a monotherapy, as treatment did not effect survival. HE2000 reduced mortality related to excessive inflammation and opportunistic lung infections in animals and patients, and this might extend to those with H1N1 influenza infection.

Identification and characterization of the bovine G protein-coupled receptor GPR41 and GPR43 genes

Volatile fatty acids (VFA), including acetate, propionate, and butyrate, are not only a primary source of energy, but also regulate rumen development, insulin and glucagon secretion, and other physiological processes in cattle and sheep. The mechanism underlying the regulatory effects of VFA is unknown. Recent "reverse pharmacology" studies identified human G protein-coupled receptors GPR41 and GPR43 as receptors for short-chain fatty acids. It is possible that proteins similar to human GPR41 and GPR43 mediate the regulatory effects of VFA in cattle. In this study, we determined first, whether the bovine genome contains genes similar to the human GPR41 and GPR43 genes; second, whether and where these genes are expressed in cattle; and third, if the proteins encoded by these genes can be activated by acetate, propionate, and butyrate. A search of GenBank revealed bovine genomic sequences and expressed sequence tags highly similar to the human GPR41 and GPR43 DNA and cDNA sequences. The protein-coding and 5' untranslated regions of the bovine GPR41 and GPR43 mRNA were cloned and sequenced from spleen tissue. Based on these sequences, the bovine GPR41 gene contains 3 exons and its transcription is initiated at 2 leader exons, generating 2 GPR41 mRNA variants differing in the 5' untranslated region. The bovine GPR43 gene contains 2 exons and transcription of this gene is initiated from a single start site. The amino acid sequences deduced from the bovine GPR41 and GPR43 mRNA sequences are more than 75% identical to those of the human GPR41 and GPR43 and are predicted to encode 7 transmembrane domains, typical of G protein-coupled receptors. Both bovine GPR41 and GPR43 mRNA were detected in a variety of tissues including rumen and pancreas. In a cell system, interaction of the overexpressed bovine GPR41 or GPR43 protein with acetate, propionate, or butyrate inhibited luciferase reporter expression from a cyclic AMP-responsive promoter, suggesting that the bovine GPR41 and GPR43 proteins couple to Galpha(i/11). In total, these results demonstrate that the bovine genome encodes functional GPR41 and GPR43 genes and suggest that GPR41 and GPR43 may play a role in the regulatory effects of VFA in cattle.

Clinicopathological Variables Associated with Lymph Node Metastasis and Prognostic Factors in pT2 Gastric Cancer

This retrospective study investigated the clinicopathological variables associated with lymph node metastasis and prognosis in 325 patients with pT2 gastric cancer in order to set out a foundation for the surgical management of this condition. Univariate and multivariate analyses identified factors that were predictive of lymph node metastasis. Cox regression analysis evaluated the effect of prognostic factors on survival. Tumour location, maximum tumour diameter, lymphatic invasion and total retrieved lymph nodes (tLN) were revealed as independent factors for lymph node metastasis in pT2a gastric cancer, whereas histological type, lymphatic invasion and tLN were associated with lymph node metastasis in patients with pT2b gastric cancer. Maximum tumour diameter, lymphatic invasion and metastatic lymph node (mLN) ratio, but not tLN, were independent prognostic factors in pT2a cancer. Maximum tumour diameter and mLN ratio, but not tLN, were independent prognostic factors in pT2b cancer. Overall, it is concluded that maximum tumour diameter and mLN ratio are important prognostic factors in pT2 gastric cancer.

Cryopreservation of embryogenic callus of Dioscorea bulbifera by vitrification

Cryopreservation of callus of Dioscorea bulbifera by vitrification was optimized. Calli of Dioscorea bulbifera were pretreated in liquid Murashige and Skoog (MS) medium supplemented with 2 mg L(-1) kinetin (KT), 0.5 mg L(-1) NAA, 0.5 mg L(-1) 2,4-D and 0.2 M sucrose for 5 d under continuous light (36 microM m(-2) s(-1)) at 25 + or - 1 degree C. The material was then loaded with 60 percent vitrification solution (PVS2) for 20 min at room temperature and dehydrated with 100 percent PVS2 for 30 min at 0 degree C. After changing the solution with fresh PVS2, the calli were directly immersed in liquid nitrogen and conserved for 1- 360 d. After rapid thawing in a water-bath at 35 degree C, the calli were washed three times with liquid MS medium supplemented with 2 mg L(-1) KT, 0.5 mg L(-1) NAA, 0.5 mg L(-1) 2, 4-D and 1.2 M sucrose and then transferred onto solid MS medium supplemented with KT 2 mg L(-1), NAA 0.5 mg per liter, 0.09 M sucrose and 0.75 percent agar. The cultures were kept in the dark for 2 days prior to exposure to the light (12 h light-dark cycle). The TTC test showed that 80-90 percent of the calli survived this cryoprocedure and there was a 60-70 percent regeneration of plantlets from the calli. The regenerated material did not exhibit any morphological variations.

Notched stress-strain behavior of a conventional and a sequentially annealed highly crosslinked UHMWPE

Contemporary total joint replacement designs contain stress-risers such as fillets, grooves, and undercuts; therefore, it is of interest to analyze the behavior of UHMWPEs in the presence of such design-related stress-risers. This study examined the engineering and true axial stress-strain behavior of smooth cylindrical and notched cylindrical test specimens, under applied axial tensile loading (2 displacement rates, 37 degrees C) for a conventional and a highly crosslinked second generation UHMWPE. Both materials were prepared from ram extruded GUR 1050. The conventional material (30 kGy) was gamma sterilized at 30 kGy in an inert N(2) environment. The sequentially annealed material (SA) was gamma irradiated at 30 kGy and annealed for 8h at 130 degrees C. The irradiation-annealing process was repeated two more times for an overall irradiation dose of 90 kGy. Differential scanning calorimetry (DSC) was utilized to investigate changes in crystallinity and lamellar thickness distributions upon loading. Fractographic analysis of scanning electron microscope (SEM) images of fracture surfaces was performed to investigate changes in fracture micromechanism with notching. Both the 30 kGy and SA materials, in the smooth condition, demonstrated substantial ductility and orientation hardening. With the introduction of a notch, both materials demonstrated an elevation in the yield stress (notch strengthening) and a reduction in the ultimate stress and ultimate strain at both displacement rates. Additionally, it was found that the uniaxial stress-state (smooth condition) allowed for greater changes in crystallinity and the lamellar thickness distributions, when compared to the untested materials, than the triaxial stress-state induced by the notched geometry.

The long-term impact of ferritin level on treatment and complications of type 2 diabetes

AIM

To investigate if high-serum ferritin has long-term impact on response to treatment and the development of diabetic complications in patients with type 2 diabetes.

RESEARCH DESIGN AND METHODS

We analysed the record of 90 consecutive type 2 diabetic subjects who had serum ferritin level determined soon after diagnosis of diabetes and who also had long-term follow-up data.

RESULTS

Patients with higher serum ferritin level had slightly worse triglyceride, blood pressure and liver enzyme levels at the end of follow up. However, ferritin level had no impact on the initial or final requirements for diabetic medication and the development of diabetic complications.

CONCLUSIONS

Although elevated serum ferritin is a marker of insulin resistance and chronic inflammation, it is not necessarily a bad prognostic indicator that should affect the clinician's approach to management.

Over 4000 nm bandwidth of mid-IR supercontinuum generation in sub-centimeter segments of highly nonlinear tellurite PCFs

We report broad bandwidth, mid-IR supercontinuum generation using a sub-cm (8 mm) length of highly nonlinear tellurite microstructured photonic crystal fiber (PCF). We pump the fiber at telecommunication wavelengths by using 1550 nm, 100 fs pulses of energy E=1.9 nJ. When coupled in the PCF, these pulses result in a supercontinuum (SC) bandwidth of 4080 nm extending from 789 to 4870 nm measured at 20 dBm below the peak spectral power. This bandwidth is comparable or in excess of previously reported spectra for other nonlinear glass fiber formulations despite the significantly shorter fiber length. In addition, besides offering a convenient pump wavelength, short fiber lengths enable smoother SC spectra, lower dispersion, and reduced material absorption at longer wavelengths making the use of this PCF particularly interesting.

Molecular characterization of the bovine chromodomain Y-like genes

The human chromodomain protein, Y-like (CDYL) gene family consists of three members, one on the Y chromosome (CDY) and two on autosomes (CDYL and CDYL2). Studies in the human and mouse showed that genes in the CDYL family are abundantly expressed in testis and play an important role in spermatogenesis. In this study, we have characterized the bovine CDYL (bCDYL) and CDYL2 (bCDYL2) genes. We found that bCDYL and bCDYL2 are very similar to the human orthologues at both mRNA (79% and 85%) and protein (89% and 93%) levels. However, the similarity between the bCDYL and bCDYL2 proteins is low (41%). The bCDYL gene is composed of nine exons, and the bCDYL2 has seven exons. The bCDYL and bCDYL2 genes were mapped by radiation hybrid mapping to bovine chromosomes (BTA) 24 and 18 respectively. The bCDYL gene has four transcript variants that produce four protein isoforms. RT-PCR expression analysis in 12 bovine tissues showed that bCDYL variant 2 was expressed in the testis only, bCDYL variants 1, 3 and 4 were expressed predominantly in the testis and at very low or undetectable levels in the remaining tissues and bCDYL2 was expressed ubiquitously. Examination of bovine testis with in situ hybridization revealed that the bCDYL and bCDYL2 transcripts were found mainly in spermatids, though the amounts of transcripts varied among genes/variants. In addition, antisense transcripts were detected in bCDYL variants 2/3 and 4, as well as in the bCDYL2 gene.

NOD2-expressing bone marrow-derived cells appear to regulate epithelial innate immunity of the transplanted human small intestine

BACKGROUND

Intestinal allograft rejection resembles Crohn's disease clinically and pathologically. An understanding of its mechanism could impact this life-saving procedure, as well as provide insight into the pathophysiology of inflammatory bowel disease. The NOD2 protein has been implicated as a key player in intestinal immune health, as a consequence of the discovery of three polymorphisms linked with Crohn's disease. An investigation was carried out to determine whether epithelial immune function and graft survival were influenced by NOD2 mutations in an intestinal transplant population.

METHODS

The NOD2 genotypes of 34 transplants performed consecutively over the past 3 years were determined. The NOD2 genotypes were related to clinical outcomes and the expression of certain intestinal antimicrobial peptides (AMPs) believed to protect the epithelium.

RESULTS

An unexpectedly high percentage of recipients, 35%, possessed NOD2 polymorphisms, while 8.6% of donors had comparable mutations. The likelihood of allograft failure was about 100-fold higher in recipients with mutant NOD2 alleles compared with recipients with wild-type NOD2 loci. Rejection in NOD2 mutant recipients was characterised by decreased expression of certain Paneth cell and enterocyte AMPs, prior to the onset of epithelial injury and inflammation.

CONCLUSIONS

Crohn's disease-associated polymorphisms in the NOD2 gene in the recipient represent a critical immunological risk factor for intestinal allograft rejection. Compromised epithelial defences precede visible epithelial injury and inflammatory infiltration. The association of impaired epithelial immunity with the recipient's genotype suggests that certain NOD2-expressing cells of haematopoietic origin play a role in the process, perhaps by regulating expression of certain epithelial AMPs within the allograft.

Pathogens in Crassostrea ariakensis and other Asian oyster species: implications for non-native oyster introduction to Chesapeake Bay

With the drastic decline of eastern oyster Crassostrea virginica populations in the Chesapeake Bay due to over-fishing, diseases and habitat destruction, there is interest in Maryland and Virginia in utilizing the non-native oyster species Crassostrea ariakensis for aquaculture, fishery resource enhancement, and ecological restoration. The International Council for the Exploration of the Sea (ICES) recommends that non-native species be examined for ecological, genetic and disease relationships in the native range prior to a deliberate introduction to a new region. Therefore, a pathogen survey of C. ariakensis and other sympatric oyster species was conducted on samples collected in the PR China, Japan and Korea using molecular diagnostics and histopathology. Molecular assays focused on 2 types of pathogens: protistan parasites in the genus Perkinsus and herpesviruses, both with known impacts on commercially important molluscan species around the world, including Asia. PCR amplification and DNA sequence data from the internal transcribed spacer region of the rRNA gene complex revealed the presence of 2 Perkinsus species not currently found in USA waters: P. olseni and an undescribed species. In addition, 3 genetic strains of molluscan herpesviruses were detected in oysters from several potential C. ariakensis broodstock acquisition sites in Asia. Viral gametocytic hypertrophy, Chlamydia-like organisms, a Steinhausia-like microsporidian, Perkinsus sp., Nematopsis sp., ciliates, and cestodes were also detected by histopathology.

Improved COBAS TaqMan hepatitis C virus test (Version 2.0) for use with the High Pure system: enhanced genotype inclusivity and performance characteristics in a multisite study

We have evaluated the COBAS TaqMan hepatitis C virus (HCV) test (version 2.0) for use with the High Pure system (HCVHPS V2), a new, revised real-time reverse transcription-PCR assay developed to improve the genotype quantitation of version 1.0 (HCVHPS V1). Revisions were made in the wash buffer and in the reverse transcription temperature. The genotype inclusivity of HCVHPS V2 was evaluated at three different sites, using HCVHPS V2, HCVHPS V1, and the COBAS AMPLICOR HCV MONITOR test (version 2.0) (CAHCM). The fully automated COBAS Ampliprep/COBAS TaqMan HCV test was also used in one of the participating laboratories. The mean differences in HCV RNA values between HCVHPS V2 and CAHCM and between HCVHPS V2 and HCVHPS V1 ranged from -0.21 to 0.13 log and from 0.24 to 1.27 log, respectively, with >0.5-log differences for genotypes 2, 3, 4, and 5. With a NIBSC panel of HCV genotypes 1 through 6, the measured HCVHPS V2 values were within 0.25 log of the nominal values for all 6 genotypes. When serial dilutions of genotype-specific clinical HCV specimens were tested, the assay showed a limit of detection between 10 and 20 IU/ml and a linear range of 25 IU/ml to 3.91 x 10(8) IU/ml. Clinical and analytical specificities of 100% were demonstrated with 100 HCV-seronegative specimens as well as with 12 non-HCV members of Flaviviridae and 22 additional microorganisms. These data indicate that HCVHPS V2 is a robust and accurate test for the quantitation of all six HCV genotypes and useful in monitoring viral load in all clinical HCV specimens.

Validation of an RT-PCR multi-gene prognostic signature for distant metastasis in node negative (N-), ER positive (ER+) breast cancer patients using FFPE sections

21009

Background: We sought to validate a previously developed 14-gene prognostic signature and a metastasis score (MS) that predicted distant metastasis in N-, ER+ breast cancer patients in an independent sample set of patients without systemic treatment. The genes consisted primarily of proliferation genes involved in p53 and TNF signaling pathways. Methods: : A cohort of 294 N-, ER+ breast cancer patients from Guy's Hospitals, London, UK without systemic therapy were tested. The cohort had a mean age of 55.5 yrs with 49% > 55 yrs, mean tumor size of 1.93 (max. 3) cm, and a median follow up of 14.3 yrs. The primary endpoint was distant metastasis free survival. RT-PCR was carried out on fixed sections. The MS was calculated. Results: The mean MS (SD) was 0.44 (0.59) with a range of -1.31 to 2.0. Hazard of distant metastasis increased 3.02 fold (95% CI 1.91–4.76, p <0.0001) per unit increase in MS from Cox model. The pre-determined cut point of zero was used to stratify patients into low- and high-risk groups. The 5-yr distant-metastasis-free survival rate (DMFSR) for low- and high-risk groups were 1 and 0.86 (SE 0.024); the 10-yr DMFSR were 0.97 (0.021) and 0.77 (0.030), respectively. Univariate Cox regression analyses indicated that MS (hazard ratio (HR) 5.65, 95% CI 2.05–15.56, p=0.008), tumor size (HR 1.62, p=0.0047) and tumor grade (HR 2.52, p=0.036) were significant but age was not. Multivariate Cox regression indicated that the signature had independent prognostic value with a HR of 4.71 (1.42–15.61, p=0.011) after adjusting for age, tumor size and grade. AUC of MS at 5-and 10-yr were 0.78 (0.71–0.85, p<0.001) and 0.73 (0.66–0.80, p<0.001) with sensitivities of 1 and 0.96 and specificities of 0.31 and 0.31 at zero cut point, respectively. The differential risk between the median MS scores of the lowest and highest deciles was 8-fold. Conclusions: A previously defined RT-PCR prognostic signature for N-, ER+ patients has been confirmed. A metastasis score that quantifies distant metastasis risk, not confounded with treatment effect can complement treatment response predictors. Insight on natural history of tumors is critical for evaluating impact of therapy.

No significant financial relationships to disclose.

Echocardiographic risk stratification for early surgery with endocarditis: a cost-effectiveness analysis

BACKGROUND

Despite widespread acceptance of echocardiography for diagnosis of infective endocarditis, few investigators have evaluated its utility as a risk-stratification tool to aid therapeutic decision-making.

METHODS

A decision tree and Markov analysis model were constructed using published and institutional data to estimate the cost-effectiveness of an echocardiographic risk-stratification strategy for infective endocarditis. The models compared surgery for high-risk patients based on clinical factors ("standard care") and surgery for high-risk patients based on echocardiographic findings ("echocardiography-guided").

RESULTS

The cost per patient for standard care and echocardiography-guided strategies was $47,766 and $53,669, respectively. The expected quality-adjusted life years (QALY) for standard care and echocardiography-guided strategies were 5.86 years and 6.10 years, respectively. Compared with standard care, the echocardiography-guided strategy cost an additional $23,867 per QALY saved. In one-way sensitivity analyses, the incremental cost of this strategy remained <$50,000/QALY across a broad range of scenarios. Baseline stroke risk had the greatest effect on cost-effectiveness. For populations with stroke risk less than 3.65%, the echocardiography-guided strategy was not cost-attractive (ICER >$50,000/QALY). At stroke risk between 3.65% and 14%, the ICER for the echocardiography-guided strategy was attractive (<$50,000 /QALY). The echocardiography-guided strategy became economically dominant at any baseline stroke risk greater than 18.3%.

CONCLUSION

Echo-guided risk stratification for early surgery in patients with large vegetations is a cost-attractive treatment strategy for IE, as it improves outcome for an incremental cost <$50,000/QALY.