Rapid isolation of blood plasma using a cascaded inertial microfluidic device.

Blood, saliva, mucus, sweat, sputum, and other biological fluids are often hindered in their ability to be used in point-of-care (POC) diagnostics because their assays require some form of off-site sample pre-preparation to effectively separate biomarkers from larger components such as cells. The rapid isolation, identification, and quantification of proteins and other small molecules circulating in the blood plasma from larger interfering molecules are therefore particularly important factors for optical blood diagnostic tests, in particular, when using optical approaches that incur spectroscopic interference from hemoglobin-rich red blood cells (RBCs). In this work, a sequential spiral polydimethylsiloxane (PDMS) microfluidic device for rapid (∼1 min) on-chip blood cell separation is presented. The chip utilizes Dean-force induced migration via two 5-loop Archimedean spirals in series. The chip was characterized in its ability to filter solutions containing fluorescent beads and silver nanoparticles and further using blood solutions doped with a fluorescent protein. Through these experiments, both cellular and small molecule behaviors in the chip were assessed. The results exhibit an average RBC separation efficiency of ∼99% at a rate of 5.2 × 106 cells per second while retaining 95% of plasma components. This chip is uniquely suited for integration within a larger point-of-care diagnostic system for the testing of blood plasma, and the use of multiple filtering spirals allows for the tuning of filtering steps, making this device and the underlying technique applicable for a wide range of separation applications.

History of the Athens Canadian Random Bred and the Athens Random Bred control populations.

The University of Georgia maintains two meat-type chicken control strains: the Athens Random Bred (ARB) and the Athens Canadian Random Bred (ACRB). The Athens Random Bred was developed from colored plumage commercial meat chicken strains in 1956. The ACRB is a replicate population of the Ottawa Meat Control strain which was developed in 1955 from white plumage commercial meat-type chickens. These genetic lines have been extremely valuable research resources and have been used extensively to provide comparative context to modern meat-type strains. The ACRB may be the oldest pedigreed control commercial meat-type chicken still in existence today. This paper reviews the history of the breed backgrounds for both control populations and reviews research utilizing the ACRB.

Epilepsy and respiratory chain defects in children with mitochondrial encephalopathies.

OBJECTIVE: The purpose of this study was to determine the relationship between epilepsy and respiratory chain defects in children with mitochondrial encephalopathies (ME). STUDY DESIGN: We conducted a retrospective review of the medical records of children referred for evaluation of an ME. Only patients assigned a definite diagnosis of ME using modified Walker criteria and with a respiratory chain defect were included. Clinical data pertaining to the ME and epilepsy type were collected. Mitochondria were isolated by subcellular fractionation from a vastus lateralis muscle biopsy and studies were performed using polarographic and spectroscopic techniques for the quantitative determination of NADH and cytochrome components of the respiratory chain. RESULTS: A total of 38 children with ME were identified. Seizures were present in 61%. Sixteen of 23 children with epilepsy (70%) had refractory epilepsy associated with a progressive encephalopathy. Children with epilepsy had a significantly higher incidence of complex I defects than children without epilepsy (p<0.01). Complex III and IV defects were significantly higher in patients without epilepsy (p<0.01 and p<0.05, respectively) than in those with epilepsy. CONCLUSIONS: Epilepsy is an important component of ME. The higher incidence of complex I defects in patients with epilepsy suggests a possible relationship between mitochondrial oxidative stress dysfunction and epileptogenic process.

Exon skipping mutations in collagen VI are common and are predictive for severity and inheritance.

Mutations in the genes encoding collagen VI (COL6A1, COL6A2, and COL6A3) cause Bethlem myopathy (BM) and Ullrich congenital muscular dystrophy (UCMD), two related conditions of differing severity. BM is a relatively mild dominantly inherited disorder characterized by proximal weakness and distal joint contractures. UCMD was originally regarded as an exclusively autosomal recessive condition causing severe muscle weakness with proximal joint contractures and distal hyperlaxity. We and others have subsequently modified this model when we described UCMD patients with heterozygous in-frame deletions acting in a dominant-negative way. Here we report 10 unrelated patients with a UCMD clinical phenotype and de novo dominant negative heterozygous splice mutations in COL6A1, COL6A2, and COL6A3 and contrast our findings with four UCMD patients with recessively acting splice mutations and two BM patients with heterozygous splice mutations. We find that the location of the skipped exon relative to the molecular structure of the collagen chain strongly correlates with the clinical phenotype. Analysis by immunohistochemical staining of muscle biopsies and dermal fibroblast cultures, as well as immunoprecipitation to study protein biosynthesis and assembly, suggests different mechanisms each for exon skipping mutations underlying dominant UCMD, dominant BM, and recessive UCMD. We provide further evidence that de novo dominant mutations in severe UCMD occur relatively frequently in all three collagen VI chains and offer biochemical insight into genotype-phenotype correlations within the collagen VI-related disorders by showing that severity of the phenotype depends on the ability of mutant chains to be incorporated in the multimeric structure of collagen VI.

Accounting for inherent variability of growth in microbial risk assessment.

Risk assessments of pathogens need to account for the growth of small number of cells under varying conditions. In order to determine the possible risks that occur when there are small numbers of cells, stochastic models of growth are needed that would capture the distribution of the number of cells over replicate trials of the same scenario or environmental conditions. This paper provides a simple stochastic growth model, accounting only for inherent cell-growth variability, assuming constant growth kinetic parameters, for an initial, small, numbers of cells assumed to be transforming from a stationary to an exponential phase. Two, basic, microbial sets of assumptions are considered: serial, where it is assume that cells transform through a lag phase before entering the exponential phase of growth; and parallel, where it is assumed that lag and exponential phases develop in parallel. The model is based on, first determining the distribution of the time when growth commences, and then modelling the conditional distribution of the number of cells. For the latter distribution, it is found that a Weibull distribution provides a simple approximation to the conditional distribution of the relative growth, so that the model developed in this paper can be easily implemented in risk assessments using commercial software packages.

Five patients with a recently described novel leukoencephalopathy with brainstem and spinal cord involvement and elevated lactate.

Recently, a novel leukoencephalopathy syndrome was described in eight patients with a distinct pattern of MRI abnormalities. Here we describe the clinical, laboratory, and MRI findings in five new, unrelated patients. The clinical picture was homogeneous with onset in childhood, a slowly progressive course, variable mental deficits, signs of pyramidal and cerebellar dysfunction and sometimes dorsal column dysfunction. In two patients, a minor head trauma was followed by neurological deterioration and fever. No underlying metabolic defect was found. In two patients serum lactate was elevated, but no evidence of a mitochondrial defect was found. MRI showed variably extensive, diffuse, or spotty cerebral white matter abnormalities and a selective involvement of particular brainstem tracts. The tracts involved included the pyramidal tracts, sensory tracts, superior and inferior cerebellar peduncles, and intraparenchymal trajectories of the trigeminal nerve. In four patients spinal MRI was performed and revealed involvement of tracts over the entire length depicted. Single voxel proton MRS in three patients revealed increased lactate within the abnormal white matter. The uniform and highly characteristic MRI findings, in combination with the similarities in clinical and MRS findings, provide evidence for a distinct nosological entity.

Genetic variation among isolates of White spot syndrome virus.

White spot syndrome virus (WSSV), member of a new virus family called Nimaviridae, is a major scourge in worldwide shrimp cultivation. Geographical isolates of WSSV identified so far are very similar in morphology and proteome, and show little difference in restriction fragment length polymorphism (RFLP) pattern. We have mapped the genomic differences between three completely sequenced WSSV isolates, originating from Thailand (WSSV-TH), China (WSSV-CN) and Taiwan (WSSV-TW). Alignment of the genomic sequences of these geographical isolates revealed an overall nucleotide identity of 99.32%. The major difference among the three isolates is a deletion of approximately 13 kb (WSSV-TH) and 1 kb (WSSV-CN), present in the same genomic region, relative to WSSV-TW. A second difference involves a genetically variable region of about 750 bp. All other variations >2 bp between the three isolates are located in repeat regions along the genome. Except for the homologous regions ( hr1, hr3, hr8 and hr9), these variable repeat regions are almost exclusively located in ORFs, of which the genomic repeat regions in ORF75, ORF94 and ORF125 can be used for PCR based classification of WSSV isolates in epidemiological studies. Furthermore, the comparison identified highly invariable genomic loci, which may be used for reliable monitoring of WSSV infections and for shrimp health certification.

Intracellular distribution of cowpea mosaic virus movement protein as visualised by green fluorescent protein fusions.

Cowpea mosaic virus (CPMV) derivatives expressing movement protein (MP) green fluorescent protein (GFP) fusions (MP:GFP) were used to study the intracellular targeting and localization of the MP in cowpea protoplasts and plants. In protoplasts, a virus coding for a wild type MP:GFP (MPfGFP) induced the formation of fluorescent tubular structures, which shows that subcellular targeting and tubule formation are not affected by fusion of GFP to the C-terminus of the MP. In plants, MPfGFP infections were mostly confined to single epidermal cells and failed to achieve a systemic infection, probably because the fusion of GFP to the MP interfered with MP-virion interaction. MP:GFP mainly accumulated in fluorescent spots in the cell wall of epidermal cells of inoculated leaves, which may represent short tubular structures in modified plasmodesmata. At the cuticle-side of epidermal cells tubular structures were detected indicating that tubule formation in plants, as in protoplasts, does not require the presence of functional plasmodesmata. Furthermore, results were obtained which indicate that CPMV MP:GFP is able to traffic from cell-to-cell by itself. The possible significance of this finding is discussed.

Effect of long-term divergent selection on growth characteristics in Japanese quail.

The current study was undertaken to examine the effect of long-term selection for 4-wk BW on growth characteristics in divergent lines of Japanese quail and their control. Growth rate was significantly higher in males than females in all the lines. There was a significant increase in growth rate of the females selected for increased 4-wk BW over the control females, as well as a significant decline in growth rate of males selected for decreased 4-wk BW compared to their control counterparts. It appeared that selection for increased 4-wk BW did not alter the rate of growth in the males compared to the control males; however, in the females, selection for increased 4-wk BW resulted in an increase in growth rate. On the other hand, selection for decreased 4-wk BW resulted in a decline in growth rate in males but not in the females. The dynamics of the growth curve parameters indicate that selection for decreased 4-wk BW shifted the growth curve for females as well as altering the trajectories of growth in both sexes. However, selection for increased 4-wk BW only resulted in altering the trajectory of growth in the males. Long-term selection resulted in asymmetry of response in the low and high lines. In addition, different genes may respond differently to the same selection pressure in opposite directions. The use of the 4-parameter Richards model to analyze growth data from such an experiment provided a better understanding of how selection can alter the rate and trajectory of growth to affect the genetically determined growth potential of quail. Consequently selection for increased or decreased 4-wk BW affected the sexes differently.

Analysis of censored survival data in Japanese quail divergently selected for growth and their control.

The aim of the current study was to characterize and quantify risk factors involved in juvenile mortality in divergently selected and control lines of Japanese quail. Survival analysis and Cox proportional hazards regression were used to describe mortality in the three experimental lines with hatch weight and posthatch BW evaluated as risk factors. Survival function distribution indicated that the proportional mortality was highest in the line selected for high 4-wk BW compared to the low and control lines. In all the experimental lines mortality declined when posthatch BW increased; however, the magnitude of reduction was highest in the control line compared to the divergently selected lines (57 vs. 22%). Any factor that influences growth after hatching may likely have a direct impact on mortality. Lack of accessibility to water, feed, warmth, and potential negative social interaction are factors that could affect mortality immediately after hatch. The posthatch BW at time of mortality used as a risk factor indicated that the divergently selected lines have about the same risk and are less sensitive to reduced BW compared to the control population. Through survival analysis, the present study has demonstrated that factors causing reduction in posthatch BW are likely risk factors for mortality in growing birds.

Effect of triplet repeat expansion on chromatin structure and expression of DMPK and neighboring genes, SIX5 and DMWD, in myotonic dystrophy.

Myotonic dystrophy (DM), an autosomal dominant neuromuscular disease, is associated with expansion of a polymorphic (CTG)n repeat in the 3'-untranslated region of the DM protein kinase (DMPK) gene. The repeat expansion results in decreased levels of DMPK mRNA and protein, but the mechanism for this decreased expression is unknown. Loss of a nuclease-hypersensitive site in the region of the repeat expansion has been observed in muscle and skin fibroblasts from DM patients, indicating a change in local chromatin structure. This change in chromatin structure has been proposed as a mechanism whereby the expression of DMPK and neighboring genes, sine oculis homeobox (Drosophila) homolog 5 (SIX5) and dystrophia myotonica-containing WD repeat motif (DMWD), might be affected. We have developed a polymerase chain reaction (PCR)-based method to assay the chromatin sensitivity of the region adjacent to the repeat expansion in somatic cell hybrids carrying either normal or affected DMPK alleles and show that hybrids carrying expanded alleles exhibit decreased sensitivity to PvuII digestion in this region. Semiquantitative multiplex reverse transcriptase PCR (RT/PCR) assays of gene expression from the chromosomes carrying the expanded alleles showed marked reduction of DMPK mRNA, partial inhibition of SIX5 expression from a congenital DM chromosome, and no reduction of DMWD mRNA. Nested RT/PCR analysis of DMPK mRNA from somatic cell hybrids carrying the repeat expansions revealed that most of the DMPK transcripts expressed from the expanded alleles lacked exons 13 and 14, whereas full-length transcripts were expressed predominantly from the normal alleles. These results suggest that the CTG repeat expansion leads to a decrease in DMPK mRNA levels by affecting splicing at the 3' end of the DMPK pre-mRNA transcript.

A new polymorphism in the proteolipid protein (PLP1) gene and its use for carrier detection of PLP1 gene duplication in Pelizaeus-Merzbacher disease.

Pelizaeus Merzbacher Disease (PMD) is an X-linked recessive dysmyelinating disorder of the central nervous system. Most patients have point mutations in exons of the proteolipid protein (PLP1) gene or duplication of a genomic region that includes the PLP1 gene. We identified a common MspI polymorphism in intron 1 of the PLP1 gene and used it to determine carrier status for PLP1 gene duplication in PMD by using a quantitative PCR approach.

A comparative study of embryonic development of Japanese quail selected for different patterns of postnatal growth.

Patterns of early embryonic development have traditionally been viewed as invariant within vertebrate taxa. It has been argued that the specific differences which are found arise during the later stages of development. These differences may be a result of allometry, heterochrony or changes in relative growth rates. To test whether early embryonic development is indeed invariant, or whether selection of adult characteristics can alter embryonic growth, we compared embryonic development in birds selected for different patterns of postnatal growth. Using quail lines selected for high and low body mass, we compared somite formation, and muscle and feather development. We obtained data that showed changes in the rate of myotome formation in the brachial somites which contribute to muscle formation in the limbs and thorax. We think these observations are connected with intraspecific changes in adult morphology, ie., breast muscle size. Our findings suggest that selection for late ontogenetic/adult stages affects early embryonic development.

Modeling non-linear survival curves to calculate thermal inactivation of salmonella in poultry of different fat levels.

Survival curves of a cocktail of eight serotypes of Salmonella in ground poultry of different fat levels (1-12%), when heated rapidly to specified temperatures (58-65 degrees C), were examined. Because many of the survival curves were concave, values for two parameters: the asymptotic D-value and the "lag" times were estimated and used to develop secondary models for estimating the time needed to obtain a 7 log10 relative reduction as a function of fat level and temperature. To compute the necessary time, at a given temperature and fat level, the estimated lag time should be added to the product of 7 and the estimated asymptotic D-value. A model was also developed for estimating the standard error of the estimated times, so that upper confidence bounds for the necessary times can be computed. It was found that lag times increase with higher fat levels. The effect of fat on D-values depended on the species; it is estimated that, for a given increase of fat level, the increase of the D-value would be greater for ground chicken than that for ground turkey. In addition, there was a statistically significant species effect on D-values, with higher D-values for ground turkey than for ground chicken at the higher temperatures studied. The thermal death curves displayed a non-linear tendency, however, for estimation purposes, a linear curve was assumed. There was not a statistically significant interaction effect of fat levels and temperatures on D-values, thus, for modeling, it was assumed that z-values were not dependent on the fat levels. The z-values for ground chicken and turkey were estimated to be 5.5 degrees C and 6.1 degrees C, respectively, and are statistically significantly different. These findings should have substantial practical importance to food processors of cooked poultry, allowing them to vary their thermal treatment of ready-to-eat poultry products in a safe manner.

Mutations in noncoding regions of the proteolipid protein gene in Pelizaeus-Merzbacher disease.

BACKGROUND: Pelizaeus-Merzbacher disease (PMD) is an X-linked recessive dysmyelinating disorder of the CNS. Duplications or point mutations in exons of the proteolipid protein (PLP) gene are found in most patients. OBJECTIVE: To describe five patients with PMD who have mutations in noncoding regions of the PLP gene. METHODS: Quantitative multiplex PCR and Southern blot analyses were used to detect duplication of the PLP gene, and DNA sequence analysis, including exon-intron borders, was used to detect mutation of the PLP gene. RESULTS: Duplication of the PLP gene was ruled out, and mutations were identified in noncoding regions of five patients in four families with PMD. In two brothers with a severe form of PMD, a G to T transversion at IVS6+3 was detected. This mutation resulted in skipping of exon 6 in the PLP mRNA of cultured fibroblasts. A patient who developed nystagmus at 16 months and progressive spastic ataxia at 18 months was found to have a 19-base pair (bp) deletion of a G-rich region near the 5' end of intron 3 of the PLP gene. A patient with a T to C transition at IVS3+2 and a patient with an A to G transition at IVS3+4 have the classic form of PMD. These, like the 19-bp deletion, are in intron 3, which is involved in PLP/DM20 alternative splice site selection. CONCLUSIONS: Mutations in introns of the PLP gene, even at positions that are not 100% conserved at splice sites, are an important cause of PMD.

Epitopes for chicken monoclonal antibodies in spleens of selected Japanese quail lines.

A line of Japanese quail selected for high plasma cholesterol is highly susceptible to diet-induced atherosclerosis. Lymphocyte epitopes recognized by mouse anti-chicken monoclonal antibodies (c-mAb), TCR-1, TCR-2, TCR-3. CD-3, CD-4, CD-8, and BU-1a/b were reacted with spleens from quail selected for high (HL) and low (LL) plasma total cholesterol and their nonselected controls (CL). Cross reactivity to c-mAb and effect of line and gender were immunohistochemically evaluated. Chicken spleens were positive controls. Quail were immunologically stimulated with either sheep red blood cells (SRBC) or Brucella abortus 2 weeks before spleens were removed. Quail spleen epitopes of all lines recognized TCR-3 and CD-8 c-mAb, but no other c-mAb. Number of reacting cells and staining intensity to the TCR-3 c-mAb were greater in the HL than in the LL regardless of the stimulating Ag or dose used. For the CD-8 c-mAb, there were no differences among lines in birds receiving SRBC. In B. abortus-immunized birds, sex x line interactions indicated that males of the HL and CL had lower responses than females but LL males were not different than females. TCR-3 and CD8 c-mAb may be useful in studying immunological mechanisms for atherosclerosis in Japanese quail.