Genome-Wide Association Study Identifies Major Loci for Carcass Weight on BTA14 in Hanwoo (Korean Cattle)

This genome-wide association study (GWAS) was conducted to identify major loci that are significantly associated with carcass weight, and their effects, in order to provide increased understanding of the genetic architecture of carcass weight in Hanwoo. This genome-wide association study identified one major chromosome region ranging from 23 Mb to 25 Mb on chromosome 14 as being associated with carcass weight in Hanwoo. Significant Bonferroni-corrected genome-wide associations (P<1.52×10⁻⁶) were detected for 6 Single Nucleotide Polymorphic (SNP) loci for carcass weight on chromosome 14. The most significant SNP was BTB-01280026 (P = 4.02×10⁻¹¹), located in the 25 Mb region on Bos taurus autosome 14 (BTA14). The other 5 significant SNPs were Hapmap27934-BTC-065223 (P = 4.04×10⁻¹¹) in 25.2 Mb, BTB-01143580 (P = 6.35×10⁻¹¹) in 24.3 Mb, Hapmap30932-BTC-011225 (P = 5.92×10⁻¹⁰) in 24.8 Mb, Hapmap27112-BTC-063342 (P = 5.18×10⁻⁹) in 25.4 Mb, and Hapmap24414-BTC-073009 (P = 7.38×10⁻⁸) in 25.4 Mb, all on BTA 14. One SNP (BTB-01143580; P = 6.35×10⁻¹¹) lies independently from the other 5 SNPs. The 5 SNPs that lie together showed a large Linkage disequilibrium (LD) block (block size of 553 kb) with LD coefficients ranging from 0.53 to 0.89 within the block. The most significant SNPs accounted for 6.73% to 10.55% of additive genetic variance, which is quite a large proportion of the total additive genetic variance. The most significant SNP (BTB-01280026; P = 4.02×10⁻¹¹) had 16.96 kg of allele substitution effect, and the second most significant SNP (Hapmap27934-BTC-065223; P = 4.04×10⁻¹¹) had 18.06 kg of effect on carcass weight, which correspond to 44% and 47%, respectively, of the phenotypic standard deviation for carcass weight in Hanwoo cattle. Our results demonstrated that carcass weight was affected by a major Quantitative Trait Locus (QTL) with a large effect and by many SNPs with small effects that are normally distributed.     

Periarticular Osteophytes as an Appendicular Joint Stress Marker (JSM): Analysis in a Contemporary Japanese Skeletal Collection

Objective

The aim of this study was to investigate the possibility that periarticular osteophytes plays a role as a appendicular joint stress marker (JSM) which reflects the biomechanical stresses on individuals and populations.

Methods

A total of 366 contemporary Japanese skeletons (231 males, 135 females) were examined closely to evaluate the periarticular osteophytes of six major joints, the shoulder, elbow, wrist, hip, knee, and ankle and osteophyte scores (OS) were determined using an original grading system. These scores were aggregated and analyzed statistically from some viewpoints.

Results

All of the OS for the respective joints were correlated logarithmically with the age-at-death of the individuals. For 70 individuals, in whom both sides of all six joints were evaluated without missing values, the age-standardized OS were calculated. A right side dominancy was recognized in the joints of the upper extremities, shoulder and wrist joints, and the bilateral correlations were large in the three joints on the lower extremity. For the shoulder joint and the hip joint, it was inferred by some distinctions that systemic factors were relatively large. All of these six joints could be assorted by the extent of systemic and local factors on osteophytes formation. Moreover, when the age-standardized OS of all the joints was summed up, some individuals had significantly high total scores, and others had significantly low total scores; namely, all of the individuals varied greatly in their systemic predisposition for osteophytes formation.

Conclusions

This study demonstrated the significance of periarticular osteophytes; the evaluating system for OS could be used to detect differences among joints and individuals. Periarticular osteophytes could be applied as an appendicular joint stress marker (JSM); by applying OS evaluating system for skeletal populations, intra-skeletal and inter-skeletal variations in biomechanical stresses throughout the lives could be clarified.     

Mapping of quantitative trait loci for carcass traits in a Japanese Black (Wagyu) cattle population

To detect quantitative trait loci (QTL) that influence economically important traits in a purebred Japanese Black cattle population, we performed a preliminary genome-wide scan using 187 microsatellite markers across a paternal half-sib family composed of 258 offspring. We located six QTL at the 1% chromosome-wise level on bovine chromosomes (BTA) 4, 6, 13, 14 and 21. A second screen of these six QTL regions using 138 additional paternal offspring half-sib from the same sire, provided further support for five QTL: carcass weight on BTA14 (22-39 cM), one for rib thickness on BTA6 (27-58 cM) and three for beef marbling score (BMS) on BTA4 (59-67 cM), BTA6 (68-89 cM) and BTA21 (75-84 cM). The location of QTL for subcutaneous fat thickness on BTA13 was not supported by the second screen (P > 0.05). We determined that the combined contribution of the three QTLs for BMS was 10.1% of the total variance. The combined phenotypic average of these three Q was significantly different (P < 0.001) from those of other allele combinations. Analysis of additional half-sib families will be necessary to confirm these QTL.     

Evaluation of the porcine melanocortin 4 receptor (MC4R) gene as a positional candidate for a fatness QTL in a cross between Landrace and Hampshire

Melanocortin 4 receptor (MC4R) is expressed in the appetite-regulating areas of the brain where it is central in the regulation of feed intake and energy balance. A mutation in MC4R causing an Asp298Asn substitution has been associated with fatness, high daily gain and feed intake in the pig. In a previously performed genome scan based on a Hampshire x Landrace cross, we detected one quantitative trait loci (QTL) affecting carcass fat/meat ratio and one QTL affecting the biceps femoris muscle, both close to the position of MC4R on porcine chromosome 1. In this study, the two lines were found to be close to fixation for alternative alleles of the Asp298Asn polymorphism. Additional QTL analyses supported our hypothesis of MC4R as a positional candidate gene but only for the fat/meat QTL. The Asp298Asn polymorphism was also evaluated as a selection target for daily gain in a Danish pig breeding population that included four breeds (Hampshire, Duroc, Landrace and Yorkshire). Over a 12-year period (1990-2002), a significant increase in the allele frequency of 298Asn was found in Landrace and Duroc, whereas a non-significant decrease in the 298Asn allele frequency was observed in Yorkshire. The Hampshire breed was fixed for the 298Asn allele in 1990. The high 298Asn allele frequencies in Hampshire, Landrace and Duroc are most likely due to selection for daily gain, whereas selection for daily gain in the Yorkshire breed apparently focuses on other loci.     

Endogenous NO(3) in the Root as a Source of Substrate for Reduction in the Light

An experiment was conducted to investigate the reduction of endogenous NO₃⁻, which had been taken up by plants in darkness, during the course of the subsequent light period. Vegetative, nonnodulated soybean plants (Glycine max [L]. Merrill, `Ransom') were exposed to 1.0 millimolar <sup>15</sup>NO<sub>3</sub><sup>−</sup> for 12 hours in darkness and then returned to a solution containing 1.0 millimolar <sup>14</sup>NO<sub>3</sub><sup>−</sup> for the 12 hours `chase' period in the light. Another set of plants was exposed to ¹⁵NO₃⁻ during the light period to allow a direct comparison of contributions of substrate from the endogenous and exogenous sources. At the end of the ¹⁵NO₃⁻ exposure in the dark, 70% of the absorbed ¹⁵NO₃⁻ remained unreduced, and 83% of this unreduced NO₃⁻ was retained in roots. The pool of endogenous ¹⁵NO₃⁻ in roots was depleted at a steady rate during the initial 9 hours of light and was utilized almost exclusively in the formation of insoluble reduced-N in leaves. Unlabeled endogenous NO₃⁻, which had accumulated in the root prior to the previous dark period, also was depleted in the light. When exogenous ¹⁵NO₃⁻ was supplied during the light period, the rate of assimilation progressively increased, reflecting an increased rate of uptake and decreased accumulation of NO₃⁻ in the root tissue. The dark-absorbed endogenous NO₃⁻ in the root was the primary source of substrate for whole-plant NO₃⁻ reduction in the first 6 hours of the light period, and exogenous NO₃⁻ was the primary source of substrate thereafter. It is concluded that retention of NO₃⁻ in roots in darkness and its release in the following light period is an important whole-plant regulatory mechanism which serves to coordinate delivery of substrate with the maximal potential for NO₃⁻ assimilation in photosynthetic tissues.     

Evaluation of the Stag3 gene and the synaptonemal complex in a rat model (as/as) for male infertility

Affected males (as/as) from the mutant TT rat strain are sterile due to spermatogenesis impairment with meiotic arrest at the pachytene stage. The as locus is on rat chromosome 12, in a region that shows conserved synteny to cM 74-94 on mouse chromosome 5. Stag3, a new member of the stromalin protein family, is expressed specifically in testis and associates to the synaptonemal complex. Mouse Stag3 gene has been assigned to cM 78 on chromosome 5. In this study, we have characterized the rat Stag3 gene and examined it as a candidate for male infertility in as/as rats. The rat Stag3 cDNA is 4181 nucleotides long, contains a highly polymorphic hexanucleotide repeat in the coding region, and encodes a 1256 amino acid protein with 93 and 77% sequence identity to mouse and human Stag3 proteins, respectively. No mutations or differences in size or abundance of Stag3 mRNA were detected between as/as and control rats, suggesting that Stag3 is not responsible for the aspermic phenotype. In addition, immunohistochemistry with antibodies against SCP1 and SPC3 proteins suggest that the synaptonemal complex structures are not primarily affected in these rats.     

3-Methylaspartate ammonia-lyase as a marker enzyme of the mesaconate pathway for (S)-glutamate fermentation in Enterobacteriaceae

The enzyme 3-methylaspartase (3-methylaspartate ammonia-lyase, EC 4.3.1.2) was found in the cells of enteric bacteria, especially in the genera Citrobacter and Morganella, that were grown under anoxic and oxygen-limited conditions. The enzymes were purified to homogeneity from the cell-free extracts of 18 active strains and had similar enzymological properties such as action on columns, specific activity, molecular weight, subunit structure, and N-terminal amino acid sequence similarity. The production of the enzyme was dependent on the limitation of oxygen during growth and was arrested by aeration. The addition of external electron acceptors such as dimethylsulfoxide could support cell growth and production of the enzyme. Activities of glutamate mutase (EC 5.4.99.1) and (S)-citramalate hydrolyase (EC 4.2.1.34), key enzymes of the mesaconate pathway of (S)-glutamate fermentation in the genus Clostridium, were detected in the cells of the active strains grown under oxygen-limited conditions. Based on the results, the mesaconate pathway is proposed to explain the (S)-glutamate fermentation process observed in Enterobacteriaceae, and 3-methylaspartase could be a marker enzyme for this pathway. Received: 28 May 1997 / Accepted: 16 July 1997     

Evaluation of PM3(tm) as a Geometry Generator in Theoretical Studies of Transition-Metal-Based Catalysts for Polymerizing Olefins

The PM3(tm) method has been applied to several systems of relevance to catalytic polymerization of olefins, for catalysts containing Ti, Zr or Cr. With some exceptions, PM3(tm) calculations reproduce experimental geometries of stable, closed-shell, precursors well. For stationary points along the path of monomer insertion into a metal-alkyl bond, the comparison is made to structures obtained by optimization using various first-principle methods. Large errors are uncovered for the transient structures, in particular pertaining to metal-ethylene coordination and agostic interactions. The energy profiles for four insertion reactions are computed by gradient-corrected density functional (DFTG) methods, using molecular structures taken from PM3(tm) and first-principle geometry optimizations, respectively. The chromium case is promising, giving values for the barrier to monomer insertion of 11 and 9 kcal/mol based on PM3(tm) and DFTG geometries, respectively. The Ti- and Zr-based systems are predicted to proceed downhill based on PM3(tm) structures, whereas small barriers are found when using first-principle structures. A hybrid PM3(tm)-DFTG procedure is suggested for geometry optimization, which facilitates an accurate estimate of the barrier when applied to one of the zirconium systems.     

Solid phase synthesis of a fully active analogue of cholecystokinin using the acid-stable Boc-Phe (p-CH2) SO3H as a substitute for Boc-Tyr(SO3H) in CCK8

Substitution of the -OSO3H group in the sulfated-tyrosine by the non-hydrolyzable-CH2SO3H group was the first described modification of the sulfate ester that does not affect CCK8 activity. In addition to its capacity to mimic the sulfated tyrosine residue, the amino acid Phe(p-CH2SO3Na) was shown to be stable in acidic media, including HF containing mixtures. The synthesis of Boc-Phe(p-CH2SO3Na)-OH in racemic and resolved forms and its introduction into the sequence of CCK8 by solid phase using standard Boc/benzyl synthesis conditions and BOP as coupling reagent is now reported. The two CCK8 analogues containing the L- or the D-Phe(p-CH2SO3Na) residue, obtained in satisfactory yields, were separated by HPLC and the stereochemistry of Phe(p-CH2SO3Na) residue in each peptide was established by NMR spectroscopy and confirmed by a separate solid phase synthesis in which the pure L isomer was used. Both CCK8 analogues displayed high affinities for peripheral and central receptors (KI approximately 1 nM) and proved to be full agonists in the stimulation of pancreatic amylase secretion. The "stabilized-CCK8 peptide", easily prepared by solid phase, could replace the native peptide in biochemical and pharmacological studies. Moreover the modified amino acid Phe (p-CH2SO3Na) could also be used in solid phase synthesis to prepare a wide variety of CCK analogues and more generally, peptides analogues containing the acid-labile O-sulfated tyrosine.     

Quinazoline-2,4(1H,3H)-dione as a substitute for thymine in triple-helix forming oligonucleotides: a reassessment.

A major limitation in triple-helix formation arises from the weak energy of interaction between the third strand and the double-stranded target. We tried to increase the stacking interaction contribution within the third strand by extending the aromatic domain of thymine. We report here the use of 2,4-quinazolinedione as a substitute for thymine in the canonical TA*T triplet. The synthesis and the characterization of the quinazoline beta nucleoside Q and of its phosphoramidite derivative is described. Triple-helix- forming oligonucleotides incorporating Q have been prepared and their ability to form triplexes has been evaluated by UV-monitored thermal denaturation measurements. The introduction of one or multiple Q residues, either contiguous or remote from each other, slightly destabilized triple-stranded structures, whatever the nucleic acid base composition (pyrimidine or GT) of the third strand.     

Transcriptomic Identification of ADH1B as a Novel Candidate Gene for Obesity and Insulin Resistance in Human Adipose Tissue in Mexican Americans from the Veterans Administration Genetic Epidemiology Study (VAGES)

Type 2 diabetes (T2D) is a complex metabolic disease that is more prevalent in ethnic groups such as Mexican Americans, and is strongly associated with the risk factors obesity and insulin resistance. The goal of this study was to perform whole genome gene expression profiling in adipose tissue to detect common patterns of gene regulation associated with obesity and insulin resistance. We used phenotypic and genotypic data from 308 Mexican American participants from the Veterans Administration Genetic Epidemiology Study (VAGES). Basal fasting RNA was extracted from adipose tissue biopsies from a subset of 75 unrelated individuals, and gene expression data generated on the Illumina BeadArray platform. The number of gene probes with significant expression above baseline was approximately 31,000. We performed multiple regression analysis of all probes with 15 metabolic traits. Adipose tissue had 3,012 genes significantly associated with the traits of interest (false discovery rate, FDR ≤ 0.05). The significance of gene expression changes was used to select 52 genes with significant (FDR ≤ 10^-4) gene expression changes across multiple traits. Gene sets/Pathways analysis identified one gene, alcohol dehydrogenase 1B (ADH1B) that was significantly enriched (P < 10^-60) as a prime candidate for involvement in multiple relevant metabolic pathways. Illumina BeadChip derived ADH1B expression data was consistent with quantitative real time PCR data. We observed significant inverse correlations with waist circumference (2.8 x 10^-9), BMI (5.4 x 10^-6), and fasting plasma insulin (P < 0.001). These findings are consistent with a central role for ADH1B in obesity and insulin resistance and provide evidence for a novel genetic regulatory mechanism for human metabolic diseases related to these traits.     

The use of the S haplotype-specific F-box protein gene,SFB, as a molecular marker for S-haplotypes and self-compatibility in Japanese apricot (Prunus mume)

Japanese apricot (Prunus mume) exhibits the S-RNase-based gametophytic self-incompatibility system as do other self-incompatible Prunus species. This report identifies the S haplotype-specific F-box protein gene (SFB), a candidate gene for pollen-S, of Japanese apricot, which leads to the development of a molecular typing system for S-haplotype in this fruit species. Both 5- and 3-RACE (rapid amplification of cDNA ends) were performed with SFB gene-specific oligonucleotide primers to clone Pm-SFB¹ and Pm-SFB⁷ of 'Nanko (S¹S⁷)'. As in the case of SFB of other Prunus species, Pm-SFB¹ and Pm-SFB⁷ showed a high level of S-haplotype-specific sequence polymorphism and their expression was specific to pollen. Genomic DNA-blot analyses of 11 Japanese apricot cultivars with the Pm-SFB probes under low stringency conditions yielded RFLP bands specific to the S¹- to S⁸-haplotypes as well as a self-compatible S^f-haplotype. A practical usage of SFB as a molecular marker for S-haplotypes and self-compatibility in Japanese apricot is discussed.Communicated by H.F. LinskensThe nucleotide sequences reported in this paper have been submitted to the EMBL/GenBank/DDBJ database under accession numbers, AB101440 and AB101441, for SFB¹ and SFB⁷, respectively     

In vitro and in vivo evaluation of a Technetium-99m-labeled cyclic RGD peptide as a specific marker of alpha(V)beta(3) integrin for tumor imaging

Three amino acids residues, Arg-Gly-Asp (RGD), in vitronectin and fibronectin show affinity for alpha(V)beta(3) integrins expressed in vascular endothelial cells. That tumor growth can upregulate the expression of these integrins on tumor cells for invasion and metastasis and in tissue neovasculature suggests the potential of developing radiolabeled RGD peptides as antagonists of alpha(V)beta(3) integrins for broad spectrum tumor specific imaging. The polypeptide RGD-4C, which contains four cysteine residues for cyclization, has shown preferential localization on integrins at sites of tumor angiogenesis. Both RGD-4C and RGE (Arg-Gly-Glu)-4C (as control) were purchased and conjugated with 6-hydrazinopyridine-3-carboxylic acid (HYNIC) for 99mTc radiolabeling. After purification of the conjugated peptides by a C18 Sep-Pak cartridge with 20% methanol, both peptides were radiolabeled using tricine. For cell binding studies, both 99mTc peptides were further purified by SE HPLC. High specific radioactivity of labeled cyclized RGD/E (cyclized RGD/E will be simplified as RGD/E through out the text) of about 20 Ci/micromol was achieved. Both 99mTc complexes were stable in the labeling solution for over 24 h at room temperature. In the human umbilical vein endothelial (HUVE) cell studies, the binding at 1 h of radiolabeled RGD/E was determined at 4 degrees C and at concentrations in the picomolar to nanomolar range. Under these conditions, cell accumulation of 99mTc in the case of RGD was as much as 16 times greater than the control RGE. As a check on specificity, 7 nM of native cyclized RGD blocked 50% of the binding of 99mTc-labeled RGD to cells. The binding percentage of 99mTc-labeled RGD to purified alpha(V)beta(3) integrin protein, as determined by SE HPLC, increased with the concentration of the integrin while 99mTc-labeled RGE showed no binding. The association constant for 99mTc-RGD was modest at 7 x 10(6) M(-)(1). In both human renal adenocarcinoma (ACHN) and human colon cancer cell line (LS174T) nude mouse tumor models, the accumulation of 99mTc-labeled RGD/E exhibited no statistical difference. In conclusion, possibly because of limited numbers of alpha(V)beta(3) integrin receptors per tumor cell and low binding affinity, radiolabeled RGD peptides may have limitations as tumor imaging agents.     

Radiolabeling and preliminary biological evaluation of a (99m)Tc(CO)(3) labeled 3,3'-(benzylidene)-bis-(1H-indole-2-carbohydrazide) derivative as a potential SPECT tracer for in vivo visualization of necrosis

N,N'-bis(diethylenetriamine pentaacetic acid)-3,3'-(benzylidene)-bis-(1H-indole-2-carbohydrazide) (bis-DTPA-BI) was radiolabeled with (99m)Tc(CO)(3). The resulting (99m)Tc(CO)(3)-bis-DTPA-BI was characterized (LC-MS) and evaluated as a potential SPECT tracer for imaging of necrosis in Wistar rats with a reperfused partial liver infarction and Wistar rats with ethanol induced muscular necrosis. To study the specificity, uptake of (99m)Tc(CO)(3)-bis-DTPA-BI was also studied in a mouse model of Fas-mediated hepatic apoptosis. The obtained results indicate that (99m)Tc(CO)(3)-bis-DTPA-BI displays selective uptake in necrotic tissue and can be used for in vivo visualization of necrosis by SPECT.     

Ru(bpy)(3)](2+) as a reference in transient absorption spectroscopy: differential absorption coefficients for formation of the long-lived (3)MLCT excited state

Transient absorption spectroscopy and other time-resolved methods are commonly used to study chemical reactions and biological processes induced by absorption of light. In order to scale the signal amplitude or to compare results obtained under different conditions, it is advisable to use a reference system, a standard of convenient and well-defined properties. Finding Tris(bipyridine)ruthenium(ii), [Ru(bpy)(3)](2+), a suitable candidate for a transient-absorption spectroscopy reference due to its favourable photochemical properties, we have determined accurate relative values of differential molar absorption coefficients (Δε) for light-induced formation of the metal-to-ligand charge transfer (MLCT) excited triplet state at several relevant wavelengths (wavelengths of commercially available lasers) in the UV and visible regions. We have also attempted to determine the absolute value of Δε close to the wavelength of maximum bleaching (～450 nm) and we propose to narrow down the interval of conceivable values for Δε(450) from the broad range of published values (-0.88 × 10(4) M(-1)cm(-1) to -1.36 × 10(4) M(-1)cm(-1)) to -1.1 × 10(4) M(-1)cm(-1)± 15%. Having ourselves successfully applied [Ru(bpy)(3)](2+) as a standard in a recent time-resolved study of enzymatic DNA repair, we would like to encourage other scientists to use this convenient tool as a reference in their future spectroscopic studies on time scales from picoseconds to hundreds of nanoseconds.     

Weight change in intensive insulin therapy for type 2 diabetes mellitus as a function of glycosylated hemoglobin (A1C) level achieved: The deep south diabetes program

Background: The Deep South Diabetes Program (DSDP) conducted a retrospective study to evaluate weight changes associated with intensive basal-bolus insulin therapy. Results of the effectiveness of the treatment algorithm that was used in this study were published in the April 2008 issue of Insulin.Objectives: The current study was designed to further evaluate the results of the DSDP study. The primary objective was to determine the quantitative relationship between weight gain and the patient's final glycosylated hemoglobin (A1C) level achieved. A secondary objective was to gain a qualitative understanding of the treatment parameters underlying the quantitative results.Methods: Further evaluation of the DSDP treatment algorithm in terms of weight management and A1C levels for achieving normoglycemia or near-normoglycemia was performed retrospectively using data collected in the original DSDP study. This evaluation included all patients who elected intensive basal-bolus insulin therapy and who sustained the treatment for up to 4 years. Glargine was the primary basal insulin, and aspart was the primary bolus insulin. The quantitative relationships among net weight change, net A1C change, and final A1C level achieved were evaluated. A qualitative evaluation of glycemic variability and behavioral variables was made from video recordings of patient visits during the original DSDP study and further observation of study participants after completion of the study.Results: Quantitative evaluation of change in weight as a function of A1C level achieved at the end of the study showed that for the group of patients who achieved normoglycemia, the mean change in weight was a reduction proportional to the corresponding mean reduction in A1C. For the groups of patients who did not achieve normoglycemia or near-normoglycemia, the mean change in weight was an increase proportional to the corresponding mean reduction in A1C.Conclusions: When normoglycemia was achieved and sustained using the DSDP's intensive insulin therapy, the weight gain typically seen with conventional insulin therapy did not occur. Weight gain or loss during intensive insulin therapy using the DSDP treatment algorithm was a function of A1C level achieved.