Hybrid Panel Research Articles

Development and material properties of new hybrid plywood from oil palm biomass

Shortage of wood as a raw material has forced wood-based industries to find alternative local raw materials. Currently, oil palm biomass is undergoing research and development (R & D) and appears to be the most viable alternative. This work examines the conversion of oil palm trunk (OPT) and oil palm empty fruit bunches (OPEFB) into new plywood and analyses its properties. We prepared five-ply veneer hybrid plywood (alternating layers of oil palm trunk veneer and empty fruit bunch mat) with different spread levels (300 g/m 2 and 500 g/m 2) of resins (phenol formaldehyde and urea formaldehyde). We then studied the mechanical and physical properties of the plywood. The results show that hybridisation of EFB with OPT improves some properties of plywood, such as bending strength, screw withdrawal and shear strength. The thermal properties of the plywood panels were studied by thermogravimetric analysis (TGA). The panels glued with phenol formaldehyde with a spread level of 500 g/m 2 showed better thermal stability than the other panels. Scanning electron microscope (SEM) was used to study the fibre matrix bonding and surface morphology of the plywood at different glue spread levels of the resins. The fibre–matrix bonding showed good improvement for the hybrid panel glued with 500 g/m 2 phenol formaldehyde.

Porcine skeletal muscle differentially expressed gene CMYA1: isolation, characterization, mapping, expression and association analysis with carcass traits

To investigate the differences in gene expression between some obese and lean pig breeds, differential display of mRNA was employed in our previous research. One differentially expressed EST (BI596262) was further identified as the porcine cardiomyopathy associated 1 (CMYA1) gene because of its homology to the human CMYA1 gene. The full-length DNA of the porcine CMYA1 gene encompasses 9379 bp, including a complete open reading frame encoding 1839 amino acid residues, a 158-bp 5'-untranslated region and a 630-bp 3'-untranslated region. The porcine CMYA1 gene was assigned to chromosome 13 by the radiation hybrid panel (IMpRH). The porcine CMYA1 gene was expressed only in the striated muscle. Single nucleotide polymorphism (SNP) scanning in the coding region identified one synonymous mutation (c.1053C>T) and three missense mutations, c.1394A>G (p.His465Arg), c.1751A>G (p.Asp582Gly) and c.3290C>A (p.Thr1097Asp). The allele frequencies were tested among about 200 unrelated pigs from several pig breeds. Linkage mapping was further conducted with the SNP c.1751A>G (p.Asp582Gly) in a Berkshire x Yorkshire resource family and this confirmed that porcine CMYA1 is closely linked with Sw344 (distance = 2 cM, LOD score is 129.47), an interesting region harbouring a QTL for back fat thickness. Association analysis in our experimental pig population showed that different genotypes of CMYA1 gene were associated with different back fat thicknesses (P < 0.05). Our results suggest that the porcine CMYA1 gene has effects on porcine back fat deposition and further investigation will be necessary to illustrate the underlying mechanisms.

A high resolution RH map of the bovine major histocompatibility complex

BackgroundThe cattle MHC is termed the bovine leukocyte antigen (BoLA) and, along with the MHCs of other ruminants, is unique in its genomic organization. Consequently, correct and reliable gene maps and sequence information are critical to the study of the BoLA region. The bovine genome sequencing project has produced two assemblies (Btau_3.1 and 4.0) that differ substantially from each other and from conventional gene maps in the BoLA region. To independently compare the accuracies of the different sequence assemblies, we have generated a high resolution map of BoLA using a 12,000rad radiation hybrid panel. Seventy-seven unique sequence tagged site (STS) markers chosen at approximately 50 kb intervals from the Btau 2.0 assembly and spanning the IIa-III-I and IIb regions of the bovine MHC were mapped on a 12,000rad bovine radiation hybrid (RH) panel to evaluate the different assemblies of the bovine genome sequence.ResultsAnalysis of the data generated a high resolution RH map of BoLA that was significantly different from the Btau_3.1 assembly of the bovine genome but in good agreement with the Btau_4.0 assembly. Of the few discordancies between the RH map and Btau_4.0, most could be attributed to closely spaced markers that could not be precisely ordered in the RH panel. One probable incorrectly-assembled sequence and three missing sequences were noted in the Btau_4.0 assembly. The RH map of BoLA is also highly concordant with the sequence-based map of HLA (NCBI build 36) when reordered to account for the ancestral inversion in the ruminant MHC.ConclusionThese results strongly suggest that studies using Btau_3.1 for analyses of the BoLA region should be reevaluated in light of the Btau_4.0 assembly and indicate that additional research is needed to produce a complete assembly of the BoLA genomic sequences.

Assessment of third order smeared and zigzag theories for buckling and vibration of flat angle-ply hybrid piezoelectric panels

A recently developed improved third order theory (ITOT) for angle-ply hybrid piezoelectric plates in cylindrical bending is extended to include geometric non-linearity in the Von Karman sense. The transverse deflection is approximated non-uniformly to explicitly account for the transverse strain due to temperature and electric potential. The coupled non-linear equations of motion and the boundary conditions are derived using the extended Hamilton’s principle. The non-linear theory is used to obtain the buckling and free vibration response of symmetrically laminated hybrid angle-ply panels under inplane electro-thermomechanical loading. This theory and the third order zigzag theory with additional layerwise terms for inplane displacements are assessed in direct comparison with the exact 2D piezothermoelasticity solutions for forced harmonic response, buckling and free vibration response under initial inplane electro-thermomechanical loading. The comparison establishes the accuracy of the results of the zigzag theory and its superiority over the ITOT for the dynamic and buckling response of angle-ply hybrid panels.

Molecular characterization and chromosomal mapping of porcine brain and muscle Arnt-like protein-1 gene

As a transcription factor regulating circadian rhythm, brain and muscle Arnt-like protein-1 (BMAL1) plays an important role in lipid homeostasis. The Chinese indigenous and western pig breeds show marked difference in fat deposition, the structure and function of porcine BMAL1 (pBMAL1) between them might be different. In present study, the molecular characteristics and chromosomal location of pBMAL1 were analyzed. The results indicated that pBMAL1 cDNA had a coding region of 1,878 bp and shared 94.36, 89.85 and 89.79% identity with human, mouse and rat BMAL1, respectively, and the pBMAL1 protein had 99.20, 98.24 and 97.92% identity to those of human BMAL1b, mouse BMAL1b and rat BMAL1b, respectively. Compared with other mammals, pBMAL1 was more closely related to human BMAL1. The expression of pBMAL1 was detected in kidney, stomach, spleen, bladder, gallbladder, lumbar spinal cord, medulla oblongata, heart, longissimus dorsi muscle, liver, small intestine, large intestine, lung and backfat tissues. In adipose tissues, it was detected in mesentery fat, leaf fat, caul fat, backfat and cardiac fat, however, the expression level was not significantly different. Alternative usage of exon 2 was revealed to result in two pBMAL1 transcripts. Finally, by using a whole genome porcine radiation hybrid (RH) panel (IMpRH), the pBMAL1 gene was mapped to SSC 2p11-q21.

Polymorphisms on SSC15q21-q26 Containing QTL for reproduction in Swine and its association with litter size

Several quantitative trait loci (QTL) for important reproductive traits (ovulation rate) have been identified on the porcine chromosome 15 (SSC15). To assist in the selection of positional candidate swine genes for these QTL on SSC15, twenty-one genes had already been assigned to SSC15 in a previous study in our lab, by using the radiation hybrid panel IMpRH. Further polymorphism studies were carried out on these positional candidate genes with four breeds of pigs (Duroc, Erhualian, Dahuabai and Landrace) harboring significant differences in reproduction traits. A total of nineteen polymorphisms were found in 21 genes. Among these, seven in six genes were used for association studies, whereby NRP2 polymorphism was found to be significantly (p < 0.05) associated with litter-size traits. NRP2 might be a candidate gene for pig-litter size based on its chromosome location (Du et al., 2006), significant association with litter-size traits and relationships with Sema and the VEGF super families.

International Criminal Courts as an Architect of Sustainable Peace in Post-Conflict Societies

The theory behind international law courts and tribunals has existed for some time however a vast cavity existed in their practical implementation. Their genesis arrived in the aftermath of World War II through the Nuremberg and Tokyo tribunals. Since these post WWII trials newly created international institutions include the International Criminal Court (ICC, 2002), ad hoc tribunals for Rwanda (International Criminal Tribunal for Rwanda ICTR, 1994) and the former Yugoslavia (International Criminal Tribunal for the Former Yugoslavia ICTY, 1993) the Special Court for Sierra Leone (SCSL, 2000) and a variety of hybrid panels or chambers.There is a sense that conducting more criminal trials in more provinces afflicted by atrocity will lead to more justice and peace, so long as those trials conform to due process standards. Criminal trials can serve to articulate and emphasize legal norms – typically human rights that were violated in contexts of civil war or oppression. In articulating and emphasizing such norms, criminal trials can serve as important steps toward the ending of a culture of impunity and the transition to a society based on the rule of law. They also derive legitimacy because, in the wake of atrocity, national institutions may be annihilated, corrupt, politicised, biased, or too insecure. Therefore there is an argument that international criminal courts can nurture the progression to sustainable peace in vulnerable post-conflict societies.

Damping Characteristics of Cylindrical Laminates with Viscoelastic Layer Considering Temperature- and Frequency-Dependence

The vibration and damping characteristics of the cylindrical hybrid panels with viscoelastic layers were investigated by using a full layerwise shell finite element method which can consider temperature and frequency dependent material properties. The present layerwise shell theory can accurately represent the zig-zag in-plane and out-of-plane displacements of multilayered hybrid structures and can fully consider the transverse shear and normal strains and the perfect cylindrical geometry. The remarkable differences of the frequency response functions of cylindrical hybrid panels including constrained layer damping and co-cured sandwiched models were observed. Present results show that the damping mechanics of hybrid panels with viscoelastic layers may be greatly affected by their temperature and frequency dependent material properties and that the present full layerwise theory can be used to accurately predict the vibration and damping characteristics of hybrid shells with viscoelastic layers.

Chromosomal localization of 13 candidate genes for human obesity in the pig genome

Thirteen candidate genes for human obesity were selected for cytogenetic mapping by FISH in the pig genome. Among them, 6 genes were assigned to chromosomes for the first time (NR3C1, GNB3, ADRB1, ADRB2, ADRB3 and UCP1). Location of the other 7 genes (INSIG2, LIPIN1, PLIN, NAMPT, ADIPOQ, UCP2 and UCP3), earlier mapped by somatic cell hybridization or with the use of a radiation hybrid panel, was verified (INSIG2) or more precisely described. The genes were assigned to the following chromosomes: INSIG2 to SSC15q12, LIPIN1 to SSC3q26, NR3C1 to SSC2q29, PLIN to SSC7q15, GNB3 to SSC5q21, NAMPT to SSC9q23, ADIPOQ to SSC13q41, ADRB1 to SSC14q28, ADRB2 to SSC2q29, ADRB3 to SSC15q13-14, UCP1 to SSC8q21-22, and both UCP2 and UCP3 to SSC9p24. Most of the genes were located within known QTL for pig fatness traits.

Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis) chromosome 20

BackgroundFluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification dissociation curve analysis, or differentiation of amplicon length or sequence composition. Despite the current era of whole-genome sequencing, mapping tools such as radiation hybrid DNA panels remain useful aids for sequence assembly, focused resequencing efforts, and for building physical maps of species that have not yet been sequenced. For placement of specific, individual genes or markers on a map, low-throughput methods remain commonplace. Typically, PCR amplification of DNA from each panel cell line is followed by gel electrophoresis and scoring of each clone for the presence or absence of PCR product. To improve sensitivity and efficiency of radiation hybrid panel analysis in comparison to gel-based methods, we adapted fluorescence-based real-time PCR and dissociation curve analysis for use as a novel scoring method.ResultsAs proof of principle for this dissociation curve method, we generated new maps of river buffalo (Bubalus bubalis) chromosome 20 by both dissociation curve analysis and conventional marker scoring. We also obtained sequence data to augment dissociation curve results. Few genes have been previously mapped to buffalo chromosome 20, and sequence detail is limited, so 65 markers were screened from the orthologous chromosome of domestic cattle. Thirty bovine markers (46%) were suitable as cross-species markers for dissociation curve analysis in the buffalo radiation hybrid panel under a standard protocol, compared to 25 markers suitable for conventional typing. Computational analysis placed 27 markers on a chromosome map generated by the new method, while the gel-based approach produced only 20 mapped markers. Among 19 markers common to both maps, the marker order on the map was maintained perfectly.ConclusionDissociation curve analysis is reliable and efficient for radiation hybrid panel scoring, and is more sensitive and robust than conventional gel-based typing methods. Several markers could be scored only by the new method, and ambiguous scores were reduced. PCR-based dissociation curve analysis decreases both time and resources needed for construction of radiation hybrid panel marker maps and represents a significant improvement over gel-based methods in any species.

Predictors of Clinical Outcome to Pentostatin, Cyclophosphamide and Rituximab (PCR) Followed by Campath for Relapsed/Refractory CLL – A Study of the Eastern Cooperative Oncology Group, E2903.

Background: This is an initial report of a correlative laboratory study of an ECOG clinical trial, E2903, to investigate an array of prognostic factors that are potentially associated with the clinical outcome in previously treated, high risk Chronic Lymphocytic Leukemia (CLL) patients. The ultimate goal of this study is to develop a prognostic model for this group of patients.Method: We have previously reported (ASH, 2007) on initial clinical and toxicity results using a combination of PCR followed by Campath. To date we have clinical response data on 37 patients and have conducted correlative prognostic factor analysis on these patients at entry to the study. The prognostic parameters assessed were fluorescence interphase hybridization (FISH) panel, CD38, ZAP-70 and IGVH (mutated vs. unmutated) status and plasma levels of pro- and anti-angiogenic cytokines. In addition, features such as clinical stage, age, sex and laboratory parameters including total white blood count, absolute lymphocyte count (ALC) and beta 2 microglobulin (b2m) were studied as predictors of response to PCR.Results: As of July 2008, the response data for the first 41 (the accrual goal is 110) patients who started the induction treatment are available. Of these 41, 3 patients are ineligible and one patient had no response data. The median age was 63 (range 51–76) with 29 males and 8 females, median b2m was 4 (range 2–28), 11 (31%) were Rai stage 0–2, and 26 (69%) were Rai 3–4. The median number of prior treatments was 2 (range 1–5); 15 of 23 (65%) patients tested for IGVH were unmutated, while on FISH analysis 4 had del 6q, 8 had del 11q, 4 had del 17p and 30 patients had complex FISH defects (>1 defect). Despite the prevalence of high risk features in this cohort of patients, 17 out of 37 responded (best response=partial response), 18 were stable and 2 had progressive disease with an overall response rate of 46%. Prognostic parameters most strongly associated with a clinical response included CD38 negative (p=0.008), ZAP-70 negative status (p=0.01) and mutated status (p=0.03). Responses were independent of age, sex, b2m, ALC, number of prior therapy or FISH defects. Responders showed a prolonged progression-free survival (PFS) compared to the PFS of non-responders (i.e., 2-yr PFS 29% vs. 0%, respectively, p<0.0001). Prognostic parameters most strongly associated with PFS included being both ZAP-70 negative (p=0.0009) and CD38 negative (p=0.004). Also, ZAP-70 negative and CD38 negative status was a strong predictor of favorable PFS (p=0.002). Mutated status was borderline significant (p=0.07) in univariate analysis and there was no obvious correlation of baseline angiogenic cytokine plasma levels with PFS. These results also hold in a multivariable Cox model. In the Cox model, mutated status was significantly associated with PFS (HR=0.2, p=0.01).Conclusion: We believe that the PCR regimen is highly effective at inducing responses in previously treated relapsed or refractory CLL patients who carry high risk prognostic markers. Thus, while no CRs were seen all but 2 patients had a PR or were stable after 6 cycles of PCR. The prognostic parameters most strongly associated with predictors of clinical outcome appear to be ZAP-70, CD38 and mutation status. The ability to attain a response also appears to be important for achieving a prolonged PFS. In summary, we believe that the strong clinical activity of PCR in a high risk group of CLL patients provides more evidence for pursuing the regimen as a platform for other combinations. In addition, we have generated a first level prognostic model that will continue to be refined as we proceed to complete this trial.

A placenta-specific receptor for the fusogenic, endogenous retrovirus-derived, human syncytin-2

Syncytin-2 is an envelope gene from the human endogenous retrovirus FRD (HERV-FRD) co-opted by an ancestral primate host, conserved in evolution over >40 Myr, specifically expressed in the placenta, and with a cell-cell fusogenic activity likely contributing to placenta morphogenesis. Here, using the GeneBridge4 human/Chinese hamster radiation hybrid panel, we mapped and identified the human receptor for syncytin-2. This receptor-namely Major Facilitator Superfamily Domain Containing 2 (MFSD2)-belongs to a large family of presumptive carbohydrate transporters with 10-12 membrane-spanning domains, is located at chromosomal position 1p34.2, and is conserved in evolution. An expression vector for MFSD2 confers fusogenicity to otherwise insusceptible cells upon transfection of syncytin-2. It also confers infectivity to syncytin-2 pseudotypes, consistent with this protein being the receptor for the ancestrally acquired HERV-FRD family of endogenous retroviruses. At variance with the human gene, neither mouse nor rat MFSD2 can mediate membrane fusion, which is consistent with the fact that the envelope-derived syncytin genes co-opted by rodents during evolution are not orthologous to the human syncytin genes. Remarkably, a real-time quantitative RT-PCR analysis of MFSD2 in various human tissues demonstrates specific expression in the placenta, as well as in the human BeWo choriocarcinoma cell line, which discloses enhancement of receptor expression upon induction by forskolin of cell-cell fusion and syncytium formation. In situ hybridization of human placental tissue using an MFSD2-specific probe further unambiguously demonstrates receptor expression at the level of the syncytiotrophoblast, again consistent with a role in placenta morphogenesis.

Molecular characterization, chromosomal localization and association analysis with back-fat thickness of porcine LPIN2 and LPIN3

The products of mammalian LPIN2 and LPIN3 are phosphatidate phosphatase type 1 enzymes, which play an important role in the de novo biosynthesis of triacylglycerol, phosphatidylcholine and phosphatidylethanolamine. In this study, we obtained a 2,985-bp cDNA sequence of porcine LPIN2, which contains a 2,676-bp open reading frame flanked by an 11-bp 5'UTR and a 298-bp 3'UTR, and a 2,843-bp cDNA sequence of porcine LPIN3, which contains a 111-bp 5'UTR, a 2,580-bp open reading frame and a 152-bp 3'UTR. RT-PCR analysis showed that both LPIN2 and LPIN3 mRNA were ubiquitously expressed with a very high level in liver. By using the somatic cell hybrid panel (SCHP) and the radiation hybrid (IMpRH) panel, porcine LPIN2 and LPIN3 were assigned to 6q24-(1/2)q31 and 17(1/2)q21-q23, respectively. One T2193C single nucleotide polymorphism in LPIN2 was identified and was detected by Hin6I PCR-RFLP. Association analysis showed that different genotypes of LPIN2 were associated with back-fat thickness between the 6th and 7th ribs (P < 0.01).

Dimensioning and Efficiency Evaluation of Hybrid Solar Systems for Energy Production

Hybrid panels (HY) for joint production of thermal and electricalenergy are available on the market. The main contribution of this workis to evaluate the performance of hybrid systems and to determine thefield of application. Mathematical models of panels are used to evalu-ate thermal and electrical behaviour. Software produced by the authorscalculates the energy production of these devices in several operatingsituations; a comparison to that of photovoltaic (PV) and thermal (TH)systems is performed. Moreover, the economic validity of such an invest-ment is evaluated. Finally, a simplified criterion has been developed tocalculate the best subdivision of the available deployment surface amongTH, PV and HY panels.

Cytogenetic Abnormalities Detected by Fluorescence In Situ Hybridization on Paraffin-Embedded Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma Lymphoid Tissue Biopsy Specimens

Cytogenetic fluorescence in situ hybridization (FISH) panels are a major prognostic tool in chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), but few data exist on using paraffin-embedded extramedullary tissue biopsy specimens for these purposes. Isolated whole nuclei were extracted from 20 paraffin-embedded tissue biopsy specimens with CLL/SLL and analyzed using a standard CLL FISH panel. FISH studies were successful in 18 (90%) of 20 cases, and chromosomal abnormalities were detected in 18 (100%) of the technically successful cases. Deletion 13q14.3 was most frequent (10 [56%]; isolated in 8 and with other abnormalities in 2), followed by trisomy 12 (5 [28%]), deletion 11q22.3 (4/16 [25%]), 14q32 (IGH@) translocation (3 [17%]), and deletion 17p13.1 (1/16 [6%]). One case with IGH@ translocation showed a BCL2 translocation partner. No cases showed 6q23 deletion. Results of this FISH panel performed on 42 additional peripheral blood (PB)/bone marrow (BM) CLL specimens were similar except for a significantly greater frequency of deletion 13q14.3 in combination with other aberrations. Cytogenetic FISH studies using paraffin-embedded tissue biopsy specimens in CLL/SLL had a high yield and, with 1 exception, demonstrated a profile similar to cases diagnosed in PB/BM.

A 4,103 marker integrated physical and comparative map of the horse genome

A comprehensive second-generation whole genome radiation hybrid (RH II), cytogenetic and comparative map of the horse genome (2n = 64) has been developed using the 5000rad horse × hamster radiation hybrid panel and fluorescence in situ hybridization (FISH). The map contains 4,103 markers (3,816 RH; 1,144 FISH) assigned to all 31 pairs of autosomes and the X chromosome. The RH maps of individual chromosomes are anchored and oriented using 857 cytogenetic markers. The overall resolution of the map is one marker per 775 kilobase pairs (kb), which represents a more than five-fold improvement over the first-generation map. The RH II incorporates 920 markers shared jointly with the two recently reported meiotic maps. Consequently the two maps were aligned with the RH II maps of individual autosomes and the X chromosome. Additionally, a comparative map of the horse genome was generated by connecting 1,904 loci on the horse map with genome sequences available for eight diverse vertebrates to highlight regions of evolutionarily conserved syntenies, linkages, and chromosomal breakpoints. The integrated map thus obtained presents the most comprehensive information on the physical and comparative organization of the equine genome and will assist future assemblies of whole genome BAC fingerprint maps and the genome sequence. It will also serve as a tool to identify genes governing health, disease and performance traits in horses and assist us in understanding the evolution of the equine genome in relation to other species.

Dimensioning and Efficiency Evaluation of Hybrid Solar Systems for Energy Production

Nowadays hybrid panels for joint production of thermal and electrical energy are available on the market. The main contribution of this work is to evaluate the performances of hybrid systems and to determine the field of application. Mathematical models of panels are considered to evaluate thermal and electrical behavior of the problem. A software produced by the authors is shown that calculates the energy production of these devices in several operating situations; a comparison to that of photovoltaic and thermal systems is performed. Moreover, the economic validity of a such investment is evaluated. Finally a simplified criterion has been developed to calculate the best subdivision of the available deployment surface among thermal, photovoltaic, and hybrid panels.

Whole-Genome Scanning by Array Comparative Genomic Hybridization as a Clinical Tool for Risk Assessment in Chronic Lymphocytic Leukemia

Array-based comparative genomic hybridization (array CGH) provides a powerful method for simultaneous genome-wide scanning and prognostic marker assessment in chronic lymphocytic leukemia (CLL). In the current study, commercially available bacterial artificial chromosome and oligonucleotide array CGH platforms were used to identify chromosomal alterations of prognostic significance in 174 CLL cases. Tumor genomes were initially analyzed by bacterial artificial chromosome array CGH followed by confirmation and breakpoint mapping using oligonucleotide arrays. Genomic changes involving loci currently interrogated by fluorescence in situ hybridization (FISH) panels were detected in 155 cases (89%) at expected frequencies: 13q14 loss (47%), trisomy 12 (13%), 11q loss (11%), 6q loss (7.5%), and 17p loss (4.6%). Genomic instability was the second most commonly identified alteration of prognostic significance with three or more alterations involving loci not interrogated by FISH panels identified in 37 CLL cases (21%). A subset of 48 CLL cases analyzed by six-probe FISH panels (288 total hybridizations) was concordant with array CGH results for 275 hybridizations (95.5%); 13 hybridizations (4.5%) were discordant because of clonal populations that comprised less than 30% of the sample. Array CGH is a powerful, cost-effective tool for genome-wide risk assessment in the clinical evaluation of CLL.

Mapping and Expression Analysis of Chicken NDRG1 and NDRG3 Genes

N-myc downstream-regulated genes 1 and 3 (NDRG1 and NDRG3) are members of the alpha/beta hydrolase superfamily. Phylogenetic analysis of the family demonstrated that human NDRG1 and 3 belong to a subfamily. The mapping and gene expression patterns of these genes represent one step toward further investigation into their possible roles in the chicken (Gallus gallus). To map these genes in the chicken chromosome, a 6000 rads chicken-hamster radiation hybrid panel (ChickRH6) was used. Primers were designed according to the published human sequences for amplification of those two genes. We compared the corresponding human mRNA sequences with the predicted coding sequences of the chicken NDRG1 and 3 genes and found that the assembled contigs shared a high percentage of similarity with the human genes. PCR of samples from ChickRH6 revealed that the locations of NDRG1 and 3 are linked to the markers MYC (58 cRs away, LOD score 4.52) and SEQ0265 (10 cRs away, LOD score 17.81), respectively. This result adds two new markers to the chicken RH map, and it reinforces that the RH technique is indeed a powerful tool for mapping genes due to its rapidity, precision, convenience, and reproducibility. In addition, we detected the gene expression and distribution of chicken NDRG1 and 3 in seven tissues, including heart, liver, spleen, lung, muscle, brain, and thymus, by RT-PCR, and found that NDRG1 is relatively ubiquitously expressed in all the tested tissues and highly expressed in heart and liver, whereas NDRG3 is high in heart, muscle, and brain.

Molecular Characterization and Expression Pattern of the Porcine STARS, a Striated Muscle-Specific Expressed Gene

STARS (striated muscle activator of Rho signaling) promotes the nuclear localization of MRTFs and mediates SRF transcription, which provides a potential muscle-specific mechanism for linking changes in the actin cytoskeleton structure with muscle gene expression. In this study, the full-length cDNA of the porcine STARS was cloned. The open reading frame of this gene contains 1,155 bp and encodes a protein of 384 amino acids, which is 79, 73, and 77% identical with human, mouse, and rat STARS genes, respectively. RT-PCR revealed that STARS is specifically expressed in heart and skeletal muscles. STARS is also distinctly different in different muscle developmental stages. The result indicates that its expression increased gradually from 33 dpc (days postcoitum) to postnatal muscles, and peaked 28 days postnatal. The porcine STARS was mapped to SSC4p13 using the somatic cell hybrid panel and the radiation hybrid panel IMpRH (LOD score 11.98). The data show that STARS is closely linked to marker SW871. A T/G single nucleotide polymorphism in the coding sequence, detected as Bsh1236I PCR-RFLP, displays allele frequency differences in six pig breeds.