Using random regression models to estimate genetic variation in growth pattern and its association with sexual maturity of Thai native chickens.

1. Genetic (co)variances and parameters between body weights (BW) across the growth trajectory were estimated using a univariate random regression (RR) animal model. The effect of growth rates (GH) on age at first egg (AFE) and egg weight at first egg (EWFE) were explored using a series of univariate and bivariate analyses. 2. Body weights were taken from Thai native chickens at hatch day to 168 days of age. The model included interactions between age with hatch nested within year and sex as fixed effects, and random effects of direct additive genetic, direct permanent environmental, maternal genetic and maternal permanent environmental effects. All random effects were fitted as regressions to animals' age via quadratic Legendre polynomials and fitting six classes of residual variances was identified as an optimal variance structure to estimate parameters. 3. Genetic and phenotypic variances for BW increased with increasing age. Estimated heritabilities for direct additive (h2 a) and maternal genetic (h2 m) effects on BW traits ranged from 0.34 to 0.54, and 0.04 to 0.06, respectively. Estimated variance ratios for direct (c2 ape) and maternal permanent environmental (c2 mpe) effects ranged from 0.19 to 0.48 and 0.10 to 0.12, respectively. Estimated correlations between weights at different ages were high for all random effects. 4. Estimated h2 a for six GH traits ranged from 0.06 to 0.28, while for AFE and EWFE these were 0.24 and 0.16, respectively. Estimated h2 m and c2 mpe were low for GH. Estimated genetic correlations between GH and AFE ranged from -0.22 to 0.02 and, between GH and EWFE, ranged from -0.05 to 0.40. These estimates suggested that selecting high GH chickens at 28 days of age can be expected to reduce AFE and to increase EWFE.

Correction: Two stable variants of Burkholderia pseudomallei strain MSHR5848 express broadly divergent in vitro phenotypes associated with their virulence differences.

[This corrects the article DOI: 10.1371/journal.pone.0171363.].

Two stable variants of Burkholderia pseudomallei strain MSHR5848 express broadly divergent in vitro phenotypes associated with their virulence differences.

Burkholderia pseudomallei (Bp), the agent of melioidosis, causes disease ranging from acute and rapidly fatal to protracted and chronic. Bp is highly infectious by aerosol, can cause severe disease with nonspecific symptoms, and is naturally resistant to multiple antibiotics. However, no vaccine exists. Unlike many Bp strains, which exhibit random variability in traits such as colony morphology, Bp strain MSHR5848 exhibited two distinct and relatively stable colony morphologies on sheep blood agar plates: a smooth, glossy, pale yellow colony and a flat, rough, white colony. Passage of the two variants, designated "Smooth" and "Rough", under standard laboratory conditions produced cultures composed of > 99.9% of the single corresponding type; however, both could switch to the other type at different frequencies when incubated in certain nutritionally stringent or stressful growth conditions. These MSHR5848 derivatives were extensively characterized to identify variant-associated differences. Microscopic and colony morphology differences on six differential media were observed and only the Rough variant metabolized sugars in selective agar. Antimicrobial susceptibilities and lipopolysaccharide (LPS) features were characterized and phenotype microarray profiles revealed distinct metabolic and susceptibility disparities between the variants. Results using the phenotype microarray system narrowed the 1,920 substrates to a subset which differentiated the two variants. Smooth grew more rapidly in vitro than Rough, yet the latter exhibited a nearly 10-fold lower lethal dose for mice than Smooth. Finally, the Smooth variant was phagocytosed and replicated to a greater extent and was more cytotoxic than Rough in macrophages. In contrast, multiple locus sequence type (MLST) analysis, ribotyping, and whole genome sequence analysis demonstrated the variants' genetic conservation; only a single consistent genetic difference between the two was identified for further study. These distinct differences shown by two variants of a Bp strain will be leveraged to better understand the mechanism of Bp phenotypic variability and to possibly identify in vitro markers of infection.

Draft Genomes for Eight Burkholderia mallei Isolates from Turkey.

Burkholderia mallei, the etiologic agent of glanders, is a Gram-negative, nonmotile, facultative intracellular pathogen. Although glanders has been eradicated from many parts of the world, the threat of B. mallei being used as a weapon is very real. Here we present draft genome assemblies of 8 Burkholderia mallei strains that were isolated in Turkey.

KOOS pain as a marker for significant knee pain two and six years after primary ACL reconstruction: a Multicenter Orthopaedic Outcomes Network (MOON) prospective longitudinal cohort study.

OBJECTIVE: The prevalence of radiographic osteoarthritis (OA) after anterior cruciate ligament reconstruction (ACLR) approaches 50%, yet the prevalence of significant knee pain is unknown. We applied three different models of Knee injury and Osteoarthritis Outcome Score (KOOS) thresholds for significant knee pain to an ACLR cohort to identify prevalence and risk factors. DESIGN: Multicenter Orthopaedic Outcomes Network (MOON) prospective cohort patients with a unilateral primary ACLR and normal contralateral knee were assessed at 2 and 6 years. Independent variables included patient demographics, validated Patient Reported Outcomes (PRO; Marx activity score, KOOS), and surgical characteristics. Models included: (1) KOOS criteria for a painful knee = quality of life subscale <87.5 and ≥2 of: KOOSpain <86.1, KOOSsymptoms <85.7, KOOSADL <86.8, or KOOSsports/rec <85.0; (2) KOOSpain subscale score ≤72 (≥2 standard deviations below population mean); (3) 10-point KOOSpain drop from 2 to 6 years. Proportional odds models (alpha ≤ 0.05) were used. RESULTS: 1761 patients of median age 23 years, median body mass index (BMI) 24.8 kg/m(2) and 56% male met inclusion, with 87% (1530/1761) and 86% (1506/1761) follow-up at 2 and 6 years, respectively. At 6 years, n = 592 (39%), n = 131 (9%) and n = 169 (12%) met criteria for models #1 through #3, respectively. The most consistent and strongest independent risk factor at both time-points was subsequent ipsilateral knee surgery. Low 2-year Marx activity score increased the odds of a painful knee at 6 years. CONCLUSIONS: Significant knee pain is prevalent after ACLR; with those who undergo subsequent ipsilateral surgery at greatest risk. The relationship between pain and structural OA warrants further study.

Identification and typing of Francisella tularensis with a highly automated genotyping assay.

A PCR assay was developed to genotypically characterize Francisella tularensis and F. novicida. An integrated and partially redundant set of markers was selected to provide positive identification of these species, identify subspecies of F. tularensis and genotype 14 variable number tandem repeat (VNTR) markers. Assay performance was evaluated with 117 Francisella samples. Sample DNA was amplified, and the masses of the PCR products were determined with electrospray ionization/time of flight mass spectrometry (ESI-MS). The base compositions of the PCR amplicons were derived from these high-accuracy mass measurements and contrasted with databased information associated with each of the 25 assay markers. Species and subspecies determinations for all samples were fully concordant with results from established typing methods, and VNTR markers provided additional discrimination among samples. Sequence variants were observed with a number of assay markers, but these did not interfere with sample characterization, and served to increase the genetic diversity detected by the assay.

Identification and characterization of Francisella species from natural warm springs in Utah, USA.

AIMS: To characterize Francisella isolated from two natural warm springs in Utah and compare them to a strain isolated from a patient with probable exposure to one of the springs in 2001. METHODS AND RESULTS: A total of 39 presumptive Francisella isolates were obtained from two springs, Wasatch Hot Spring and Hobo Warm Spring, just north of Salt Lake City, Utah. All isolates were characterized by a combination of biochemical and molecular analyses, including novel PCR/electrospray ionization-mass spectrometry (ESI-MS) typing assays. Thirty-one were identified as F. philomiragia, while the remaining eight were identified as F. tularensis ssp. novicida. Phylogenetic analysis of the 16S rRNA sequences revealed 27 isolates, which clustered with F. philomiragia, albeit into two distinct clades. The remaining isolates clustered along with other F. tularensis strains including the Utah clinical isolate. Testing with the PCR/ESI-MS assays confirmed the identities of the isolates, but both yielded DNA signatures distinct from that of the clinical isolate. CONCLUSION: We were successful in isolating several Francisella strains from natural warm springs; however, none appeared to genetically match the original 2001 clinical isolate. SIGNIFICANCE AND IMPACT OF THE STUDY: This work highlights the presence of viable, potentially pathogenic Franscisella species living in the unique environmental niche of natural warm springs.

Modeling the relationship between scanned rump and 12th-rib fat in young temperate and tropical bovines: model development and evaluation.

A decision support tool for predicting subcutaneous fat depths called BeefSpecs, based on the Davis growth model (DGM), has been developed by the Cooperative Research Centre for Beef Genetic Technologies. Currently, the DGM predicts 12th-rib fat thickness (RFT, mm). To allow predictions of fat thickness at the P8 rump (P8FT, mm) site, the standard carcass fat measurement in the Australian beef industry, a relationship was developed between ultrasound RFT and P8FT in steers and heifers from temperate (Angus, Hereford, Shorthorn, and Murray Grey) and tropical (Brahman, Belmont Red, and Santa Gertrudis) breed types. Model development involved fitting various combinations of sex, breed type (BrT), BW, age, and RFT to produce 6 models. The models were challenged with data from 3 independent data sets: 1) Angus steers from 2.4 generations of divergent selection for and against residual feed intake; 2) 2 tropically adapted genotypes [Brahman and tropically adapted composites (combinations of Belmont Red, Charbray, Santa Gertrudis, Senepol, and Brahman breeds)]; and 3) a study using sires from Charolais, Limousin, Belgian Blue, and Black and Red Wagyu breeds and 3 genetic lines of Angus to create divergence in progeny in terms of genetic potential for intramuscular fat percent and retail beef yield. When challenged with data from Angus cattle, the mean biases (MB, mm) for models A to F were -1.23, -0.56, -0.56, -0.02, 0.14, and 0.04, and the root mean square errors of predictions (mm) were 1.53, 0.97, 0.97, 0.92, 0.93, and 0.91, respectively. When challenged with data from Brahman cattle, MB were 0.04, -0.22, -0.14, 0.05, -0.11, and 0.02 and root mean square errors of predictions were 1.30, 1.29, 1.27, 1.23, 1.37, and 1.29, respectively. Generally, model accuracy indicated by MB tended to be less for model E, which contained age rather than BW as a covariate. Models B and C were generally robust when challenged with data from Angus, Brahman, and Tropical Composite cattle as well as crossbred cattle with temperate sires. Model D, which did not contain age, performed the most consistently and was selected for inclusion in the DGM: P8FT, mm = -3.6 (+/-0.14) + 1.3 (+/-0.13) x sex + 0.11 (+/-0.13) x BrT + 0.014 (+/-4.8E(-4)) x BW + 0.96 (+/-0.01) x RFT - 0.73 (+/-0.08) x sex x BrT - 3.8E(-3) (+/-4.2E(-4)) x sex x BW - 0.09 (+/-0.01) x sex x RFT + 1.3E(-3) (+/-3.7E(-4)) x BrT x BW + 0.24 (+/-0.01) x BrT x RFT (adjusted R(2) = 0.86; SE = 0.013). Model D has been implemented in BeefSpecs to predict P8FT.

Avian cholera in a southern giant petrel (Macronectes giganteus) from Antarctica.

A southern giant petrel (Macronectes giganteus) was found dead at Potter Peninsula, King George Island, South Shetland, Antarctica. The adult male was discovered approximately 48 hr after death. Macroscopic and microscopic lesions were compatible with avian cholera and the bacterium Pasteurella multocida subsp. gallicida, serotype A1 was isolated from lung, heart, liver, pericardial sac, and air sacs. In addition, Escherichia coli was isolated from pericardial sac and air sacs. This is the first known report of avian cholera in a southern giant petrel in Antarctica.

Abundance and characteristics of the recreational water quality indicator bacteria Escherichia coli and enterococci in gull faeces.

AIMS: To evaluate the numbers and selected phenotypic and genotypic characteristics of the faecal indicator bacteria Escherichia coli and enterococci in gull faeces at representative Great Lakes swimming beaches in the United States. METHODS AND RESULTS: E. coli and enterococci were enumerated in gull faeces by membrane filtration. E. coli genotypes (rep-PCR genomic profiles) and E. coli (Vitek GNI+) and enterococci (API rapid ID 32 Strep and resistance to streptomycin, gentamicin, vancomycin, tetracycline and ampicillin) phenotypes were determined for isolates obtained from gull faeces both early and late in the swimming season. Identical E. coli genotypes were obtained only from single gull faecal samples but most faecal samples yielded more than one genotype (median of eight genotypes for samples with 10 isolates). E. coli isolates from the same site that clustered at >/=85% similarity were from the same sampling date and shared phenotypic characteristics, and at this similarity level there was population overlap between the two geographically isolated beach sites. Enterococcus API(R) profiles varied with sampling date. Gull enterococci displayed wide variation in antibiotic resistance patterns, and high-level resistance to some antibiotics. CONCLUSIONS: Gull faeces could be a major contributor of E. coli (10(5)-10(9) CFU g(-1)) and enterococci (10(4)-10(8) CFU g(-)1) to Great Lakes recreational waters. E. coli and enterococci in gull faeces are highly variable with respect to their genotypic and phenotypic characteristics and may exhibit temporal or geographic trends in these features. SIGNIFICANCE AND IMPACT OF THE STUDY: The high degree of variation in genotypic or phenotypic characteristics of E. coli or enterococci populations within gull hosts will require extensive sampling for adequate characterization, and will influence methods that use these characteristics to determine faecal contamination sources for recreational waters.

Applying nitrogen site-specifically using soil electrical conductivity maps and precision agriculture technology.

Soil texture varies significantly within many agricultural fields. The physical properties of soil, such as soil texture, have a direct effect on water holding capacity, cation exchange capacity, crop yield, production capability, and nitrogen (N) loss variations within a field. In short, mobile nutrients are used, lost, and stored differently as soil textures vary. A uniform application of N to varying soils results in a wide range of N availability to the crop. N applied in excess of crop usage results in a waste of the grower"s input expense, a potential negative effect on the environment, and in some crops a reduction of crop quality, yield, and harvestability. Inadequate N levels represent a lost opportunity for crop yield and profit. The global positioning system (GPS)-referenced mapping of bulk soil electrical conductivity (EC) has been shown to serve as an effective proxy for soil texture and other soil properties. Soils with a high clay content conduct more electricity than coarser textured soils, which results in higher EC values. This paper will describe the EC mapping process and provide case studies of site-specific N applications based on EC maps. Results of these case studies suggest that N can be managed site-specifically using a variety of management practices, including soil sampling, variable yield goals, and cropping history.

Cytokine and adhesion molecule expression in SCID mice reconstituted with CD4+ T cells.

The objectives of this study were to quantify colonic cytokine and endothelial cell adhesion molecule (ECAM) expression in the colons of severe combined immunodeficient (SCID) mice reconstituted with different subsets of CD4+ T lymphocytes. We found that animals injected with CD45RBhigh but not CD45RBlow T cells or phosphate-buffered saline (PBS) developed clinical evidence of colitis at 6-8 weeks following reconstitution, as assessed by loss of body weight, development of loose stools and/or diarrhea, and histopathology. Concurrent with the onset of distal bowel inflammation was enhanced expression of a variety of Th1 and macrophage-derived cytokines including interferon gamma, tumor necrosis factor-alpha, interleukin (IL)-1beta, IL-6, IL-12, and IL-18 lymphotoxin-beta. In addition, message levels and vascular surface expression of ICAM-1, VCAM-1, and MAdCAM-1 were all significantly enhanced in the colitic SCID mice reconstituted with CD45RBhigh T cells compared with SCID mice reconstituted with PBS or CD45RBlow T cells that did not develop disease. Significant increases in some of these ECAMs were also noted in the cecum and stomach and to a lesser degree in the small bowel. Our data confirm that reconstitution of SCID mice with CD45RBhigh but not CD45RBlow T cells induces chronic colitis, and that the colonic inflammation is associated with enhanced expression of proinflammatory cytokines and different ECAMs in the colon. Furthermore, our studies demonstrate that reconstitution of SCID mice with CD45RBhigh T cells enhances ECAM expression in tissues distant from the site of active inflammation.

Genetic analyses of live-animal ultrasound and abattoir carcass traits in Australian Angus and Hereford cattle.

In order to estimate genetic parameters, abattoir carcass data on 1,713 Angus and 1,007 Hereford steers and heifers were combined with yearling live-animal ultrasound measurements on 8,196 Angus and 3,405 Hereford individuals from seedstock herds. Abattoir measures included carcass weight (CWT), percentage of retail beefyield (RBY), near-infrared measured intramuscular fat percentage (CIMF), preslaughter scanned eye muscle area (CEMA), and subcutaneous fat depth at the 12th rib (CRIB) and at the P8 site (CP8). Ultrasound scans on yearling animals included 12th-rib fat depth (SRIB), rump fat depth at the P8 site (SP8), eye muscle area (SEMA), and percentage of intramuscular fat (SIMF). Records on CWT were adjusted to 650-d slaughter age, and the remaining abattoir traits were adjusted to 300-kg CWT. Scan data were analyzed treating records on males and females as different traits. Multivariate analyses were performed on a variety of trait combinations using animal model and REML algorithm. Heritability (h2) estimates for CWT, RBY, CIMF, CP8, CRIB, and CEMA were .31, .68, .43, .44, .28, and .26, respectively, for Angus and .54, .36, .36, .08, .27, .38, respectively, for Hereford. Pooled across sexes, h2 estimates for SIMF, SP8, SRIB, and SEMA were .33, .55, .51, and .42, respectively, for Angus and .20, .31, .18, and .38, respectively, for Hereford. Genetic correlations (r(g)) between the same pair of carcass traits measured at yearling through scanning and directly at the abattoir were moderate to strongly positive, suggesting that selection using yearling ultrasound measurements of seedstock cattle should result in predictable genetic improvement for abattoir carcass characteristics. Estimates of r(g) between the scanned fat measurements and RBY were negative, ranging from -.85 for Angus heifers to -.05 for Hereford heifers. Also, the estimates of r(g) between SEMA and the fat records measured at the abattoir were negative and ranged from -.94 in Hereford heifers to -.02 in Angus heifers.

Septicemic pasteurellosis in free-ranging neonatal pronghorn in Oregon.

As part of a study to determine the cause(s) of population decline and low survival of pronghorn (Antilocapra americana) neonates on Hart Mountain National Antelope Refuge (HMNAR), Oregon (USA), 55 of 104 neonates captured during May 1996 and 1997 were necropsied (n = 28, 1996; n = 27, 1997) to determine cause of death. Necropsies were conducted on fawns that died during May, June, or July of each year. The objectives of this study were to report the occurrence and pathology of pasteurellosis in neonates and determine if the isolated strain of Pasteurella multocida was unique. Septicemic pasteurellosis, caused by P. multocida, was diagnosed as the cause of death for two neonates in May and June 1997. Necropsy findings included widely scattered petechial and ecchymotic hemorrhages found over a large portion of the subcutaneous tissue, meninges of the brain, epicardium, skeletal muscle, and serosal surface of the thorasic and abdominal cavities. Histological examination of lung tissues revealed diffuse congestion and edema and moderate to marked multifocal infiltrate of macrophages, neutrophils, and numerous bacteria within many terminal bronchioles and alveoli. Pasteurella multocida serotypes A:3,4, and B:1 were isolated from several tissues including lung, intestinal, thorasic fluid, and heart blood. Each B:1 isolate had DNA restriction endonuclease fingerprint profiles distinct from isolates previously characterized from domestic cattle, swan (Olor spp.), moose (Alces alces), and pronghorn from Montana (USA). This is the first report of pasteurellosis in pronghorn from Oregon and the B:1 isolates appear to be unique in comparison to DNA fingerprint profiles from selected domestic and wild species.

Erysipelas in a free-ranging Hawaiian crow (Corvus hawaiiensis).

We describe a case of erysipelas in a free-ranging endangered Hawaiian crow. The partially scavenged carcass exhibited gross emaciation and petechial hemorrhages in both lungs. Microscopy revealed multiple necrotic foci associated with gram-positive rods in the liver and adrenal, diffuse acute proximal tubular necrosis of kidney, diffuse necrosis and inflammation of proventricular mucosa associated with gram-positive rods, and multiple intravascular aggregates of gram-positive rods associated with thrombi. Culture of the kidney revealed the bacterium to be Erysipelothrix rhusiopathiae. The implications of this finding to free-ranging crows remain unclear.

Advances in nucleic acid-based detection methods.

Laboratory techniques based on nucleic acid methods have increased in popularity over the last decade with clinical microbiologists and other laboratory scientists who are concerned with the diagnosis of infectious agents. This increase in popularity is a result primarily of advances made in nucleic acid amplification and detection techniques. Polymerase chain reaction, the original nucleic acid amplification technique, changed the way many people viewed and used nucleic acid techniques in clinical settings. After the potential of polymerase chain reaction became apparent, other methods of nucleic acid amplification and detection were developed. These alternative nucleic acid amplification methods may become serious contenders for application to routine laboratory analyses. This review presents some background information on nucleic acid analyses that might be used in clinical and anatomical laboratories and describes some recent advances in the amplification and detection of nucleic acids.

Postpneumonectomy tension chylothorax.

Chylous leak from the thoracic duct into the pleural space may occur after any type of thoracic surgery. This is a serious, often life-threatening entity. Two cases of postpneumonectomy chylothorax with hemodynamic compromise are reported. Early recognition, pathophysiology, and optimal management of this problem are discussed.

Biochemical characteristics of the heterophile transplantation antigen (HT-A).

The Heterophile Transplantation Antigen (HT-A) is a clinically important antigen which is found in some human kidneys and on the erythrocytes and in the serum of rats and some other mammals. Recent reports suggest the possibility that the anti-HT-A antibodies responsible for graft rejection may cross react with one or more HL-A specificities. The ideal way to investigate this possibility would be to perform careful serological and biochemical comparisons of purified HT-A and HL-A. We report here the first stage of these investigations, the examination of the biochemical properties of HT-A. The HT-A molecule of rat plasma is apparently a glycoprotein with a molecular weight greater than 1,000,000. The HT-A antigenic determinant site seems to reside in the carbohydrate portion of the glycoprotein. The native HT-A molecule is apparently susceptible to proteolytic enzymes of rat plasma and serum and is cleaved by these enzymes to produce a fragment with a lower apparent molecular weight and a larger fragment which coelutes with lipoproteins during Sepharose CL-4B chromatography. The data presented here should allow development of a rational purification scheme for the HT-A glycoprotein of rat plasma to be used in further studies in the relationship between HT-A and HL-A.