Nucleic acid sensing by an orthogonal reporter system based on homo-DNA

We have developed an assay for single strand DNA or RNA detection which is based on the homo-DNA templated Staudinger reduction of the profluorophore rhodamine-azide. The assay is based on a three component system, consisting of a homo-DNA/DNA hybrid probe, a set of homo-DNA reporter strands and the target DNA or RNA. We present two different formats of the assay (Omega probe and linear probe) in which the linear probe was found to perform best with catalytic turnover of the reporter strands (TON: 8) and a match/mismatch discrimination of up to 19. The advantage of this system is that the reporting (homo-DNA) and sensing (DNA) domain are decoupled from each other since the two pairing systems are bioorthogonal. This allows independent optimization of either domain which may lead to higher selectivity in in vivo imaging.

Gender-specific modulation of immune system complement gene expression in marine medaka Oryzias melastigma following dietary exposure of BDE-47

BDE-47 is one of the most widely found congeners of PBDEs in marine environments. The potential immunomodulatory effects of BDE-47 on fish complement system were studied using the marine medaka Oryzias melastigma as a model fish. Three-month-old O. melastigma were subjected to short-term (5 days) and long-term (21 days) exposure to two concentrations of BDE-47 (low dose at 290 +/- 172 ng/day; high dose at 580 +/- 344 ng/day) via dietary uptake of BDE-47 encapsulated in Artemia nauplii. Body burdens of BDE-47 and other metabolic products were analyzed in the exposed and control fish. Only a small amount of debrominated product, BDE-28, was detected, while other metabolic products were all under detection limit. Transcriptional expression of six major complement system genes involved in complement activation: C1r/s (classical pathway), MBL-2 (lectin pathway), CFP (alternative pathway), F2 (coagulation pathway), C3 (the central component of complement system), and C9 (cell lysis) were quantified in the liver of marine medaka. Endogenous expression of all six complement system genes was found to be higher in males than in females (p < 0.05). Upon dietary exposure of marine medaka to BDE-47, expression of all six complement genes were downregulated in males at day 5 (or longer), whereas in females, MBl-2, CFP, and F2 mRNAs expression were upregulated, but C3 and C9 remained stable with exposure time and dose. A significant negative relationship was found between BDE-47 body burden and mRNA expression of C1r/s, CFP, and C3 in male fish (r = -0.8576 to -0.9447). The above findings on changes in complement gene expression patterns indicate the complement system may be compromised in male O. melastigma upon dietary exposure to BDE-47. Distinct gender difference in expression of six major complement system genes was evident in marine medaka under resting condition and dietary BDE-47 challenge. The immunomodulatory effects of BDE-47 on transcriptional expression of these complement components in marine medaka were likely induced by the parent compound instead of biotransformed products. Our results clearly demonstrate that future direction for fish immunotoxicology and risk assessment of immunosuppressive chemicals must include parallel evaluation for both genders.

Evaluation of a Year-Round Grazing System: Summer Cow-Calf Progress Report

A comparison was made between two different summer grazing systems. One system was the summer component of a year-round grazing system, involving the rotational stocking of smooth bromegrass--orchardgrass--birdsfoot trefoil pastures and winter stockpiles pastures with cowcalf pairs co-grazing with stocker yearlings at .75 animal units per acre. That system was compared with a minimal land system involving the rotational stocking of smooth bromegrass--orchardgrass-- birdsfoot trefoil summer pastures with cow-calf pairs grazing at .64 animal units per acre and hay removal from 25% of the pasture. Stocker yearlings or hay removal were used as management tools to remove excess forage and optimize forage quality. Hay was removed once from three fourths of the winter stockpiled pastures and one fourth of the allocated summer pastures. Cow-calf pairs grazing in the year-round system utilized on fourth of the winter stockpile pastures due to lack of forage, whereas cow-calf pairs grazing with hay removal were supplemented with harvested hay for two weeks during the summer. Grazing system did not affect cow body weight, condition score, or daily calf weight gain. Growing animal production per acre was affected by grazing system, with the minimal land system having a higher production level.

Evaluation of a Year-Round Grazing System: Winter Progress Report

The winter component of a year-round grazing system involving grazing of corn crop residues followed by grazing stockpiled grass-legume forages was compared at the McNay Research Farm with that of the winter component of a minimal land system that maintained cows in drylot. In the summers of 1995 and 1996, two and one cuttings of hay per year were harvested from two 15-acre fields containing “Johnston” low endophtye tall fescue and red clover. Two cuttings of hay in 1995 and one cutting in 1996 were harvested from two 15-acre fields of smooth bromegrass and red clover. Hay yields were 4,236 and 4,600 pounds of dry matter per acre for the tall fescue-red clover in 1995 and 1996, and 2,239 and 2,300 pounds of dry matter per acre for the smooth bromegrass-red clover in 1995 and 1996. Following grain harvest, four 7.5-acre fields containing corn crop residues were stocked with cows at midgestation at an allowance of 1.5 acres per cow. Forage yields at the initiation of corn crop grazing in 1995 and 1996 were 3,757 and 3,551 pounds of dry matter per acre for corn crop residues. Stockpiled forage yields were 1,748 and 2,912 pounds of dry matter for tall fescue-red clover and 1,880 and 2,187 pounds for smooth bromegrass-red clover. Corn crop residues and stockpiled forages were grazed in a strip stocking system. For comparison, 20 cows in 1995 and 16 cows in 1996 were placed in two drylots simultaneously with initiation of corn crop grazing, where they remained throughout the winter and spring grazing periods. Cows maintained in drylots or grazing corn crop residue and stockpiled forages were supplemented with hay as large round bales to maintain a body condition score of five. In both years, no seasonal differences in body weight and body condition score were observed between grazing cows or cows maintained in drylots, but grazing cows required 85% and 98% less harvested hay in years 1 and 2 than cows in drylot during the winter and spring. Because less hay was needed to maintain grazing cows, excesses of 12,354 and 5,244 pounds of hay dry matter per cow in 1995 and 1996 remained in the year-round grazing system. During corn crop grazing, organic matter yield decreased at 23.5 and 28.8 pounds of organic matter per day from grazed areas of corn crop residues in 1995 and 1996. Organic matter losses due to weathering were 6.8, 10.3, and 12.7 pounds per day in corn crop residue, tall fescue-red clover and smooth bromegrass-red clover in 1995 and 12.1, 10.7, and 12.1 in 1996. Organic matter losses from grazed and ungrazed areas of tall fescue-red clover and smooth bromegrass-red clover during stockpiled grazing were 6.9, 6.9, and 2.1, 2.9 in 1995 and 13.4, 4.3, and +6.9, 4.4 pounds per day in 1996.

Evaluation of a Year-Round Grazing System: Summer Cow-Calf Progress Report

A comparison was made between two different summer grazing systems at the McNay Research Farm. One system was the summer component of a year-round grazing system, involving the rotational stocking of smooth bromegrass-orchardgrass-birdsfoot trefoil pastures and winter stockpile pastures with cow-calf pairs co-grazing with stocker yearlings at .75 animal units per acre. That system was compared with a minimal land system involving the rotational stocking of smooth bromegrass-orchardgrass-birdsfoot trefoil summer pastures with cow-calf pairs grazing at .64 animal units per acre and hay removal from 25% of the pasture. Stocker yearlings or hay removal were used as management tools to remove excess forage and optimize forage quality. Hay was removed once from three fourths of the winter stockpiled pastures in 1996 (Yr. 1) and all the pasture in 1997 (Yr. 2). One hay removal occurred on one fourth of the allocated summer pastures in Year 1 and one half of the pastures in Year 2. In Year one, cow-calf pairs grazing in the year-round system utilized one fourth of the winter stockpile pastures due to a lack of forage on the summer pastures, whereas in Year 2 cowcalf pairs grazed winter stockpile pastures to remove forage as a second cutting of hay. Cow-calf pairs grazing with hay removal were supplemented with harvested hay for two weeks during the summer of Year 1 due to lack of grazable forage; in Year 2, no supplementation was needed. Grazing system did not affect cow body weight, condition score, or daily calf gain in either year. Growing animal production per acre was affected by grazing system, with the minimal land system having a higher production level in Year 1 and Year 2. The year-round system also produced more net winter forage than did the minimal land system in Year 1. Differences in forage yield and quality were only observed between winter stockpile forages of tall fescue-red clover and smooth bromegrass-red clover and summer pastures during the months of June, July, and August.

Evaluation of a Year-Round Grazing System: Winter Progress Report

The winter component of a year-round grazing system involving grazing of corn crop residues followed by grazing stockpiled grass legume forages was compared at the McNay Research Farm with that of the winter component of a minimal land system that maintained cows in drylot,. In the summer of 1995, two cuttings of hay were harvested from two 15-acre fields containing “Johnston” endophyte-free tall fescue and red clover, and two cuttings of hay were taken from two 15-acre fields of smooth bromegrass and red clover. Hay yields were 4,236 and 4,600 pounds of dry matter per acre for the tall fescue--red clover and smooth bromegrass--red clover. Following grain harvest four 7.5-acre fields containing corn crop residue were stocked with cows at midgestation at an allowance of 1.5 acres per cow. Forage yields at the initiation of corn crop grazing were 3,766pounds of dry matter per acre for corn crop residue, 1,748 pounds for tall fescue--red clover, and 1,.880 pounds for smooth bromegrass--red clover. Corn crop residues and stockpiled forages were grazed in a strip stocking system. For comparison, 20 cows were placed in two drylots simultaneously to the initiation of corn crop grazing where they remained throughout the winter and spring grazing seasons. Cows maintained in drylot or grazing corn crop residue and stockpiled forages were supplemented with hay as large round bales to maintain a body condition score of five. No seasonal differences in body weight and body condition were observed between grazing cows or cows maintained in drylot, but grazing cows required 87% and 84% less harvested hay than cows in drylot during the winter and spring respectively. Because less hay was needed to maintain grazing cows, an excess of 11,905 and 12,803 pounds of hay dry matter per cow remained in the year-round grazing system. During corn crop grazing, organic matter yield decreased at 27.3 pounds of organic matter per day from grazed areas of corn crop residue. Organic matter losses due to weathering were 9.4, 12.9, and 15.8 pounds per day in corn crop residue, tall fescue-red clover and smooth bromegrass-red clover. Organic matter losses from grazed and ungrazed areas during stockpiled grazing were 7.3 and 6.9 for tall fescue--red clover and 2.1, 2.9 for smooth bromegrass--red clover.

A novel mutation L260P of the steroidogenic acute regulatory protein gene in three unrelated patients of Swiss ancestry with congenital lipoid adrenal hyperplasia.

CONTEXT Lipoid congenital adrenal hyperplasia (CAH) is the most severe form of CAH leading to impaired production of all adrenal and gonadal steroids. Mutations in the gene encoding steroidogenic acute regulatory protein (StAR) cause lipoid CAH. OBJECTIVE We investigated three unrelated patients of Swiss ancestry who all carried novel mutations in the StAR gene. All three subjects were phenotypic females with absent Müllerian derivatives, 46,XY karyotype, and presented with adrenal failure. METHODS AND RESULTS StAR gene analysis showed that one patient was homozygous and the other two were heterozygous for the novel missense mutation L260P. Of the heterozygote patients, one carried the novel missense mutation L157P and one had a novel frameshift mutation (629-630delCT) on the second allele. The functional ability of all three StAR mutations to promote pregnenolone production was severely attenuated in COS-1 cells transfected with the cholesterol side-chain cleavage system and mutant vs. wild-type StAR expression vectors. CONCLUSIONS These cases highlight the importance of StAR-dependent steroidogenesis during fetal development and early infancy; expand the geographic distribution of this condition; and finally establish a new, prevalent StAR mutation (L260P) for the Swiss population.

3D Face Reconstruction from 2D Pictures: First Results of a Web-Based Computer Aided System for Aesthetic Procedures

The human face is a vital component of our identity and many people undergo medical aesthetics procedures in order to achieve an ideal or desired look. However, communication between physician and patient is fundamental to understand the patient’s wishes and to achieve the desired results. To date, most plastic surgeons rely on either “free hand” 2D drawings on picture printouts or computerized picture morphing. Alternatively, hardware dependent solutions allow facial shapes to be created and planned in 3D, but they are usually expensive or complex to handle. To offer a simple and hardware independent solution, we propose a web-based application that uses 3 standard 2D pictures to create a 3D representation of the patient’s face on which facial aesthetic procedures such as filling, skin clearing or rejuvenation, and rhinoplasty are planned in 3D. The proposed application couples a set of well-established methods together in a novel manner to optimize 3D reconstructions for clinical use. Face reconstructions performed with the application were evaluated by two plastic surgeons and also compared to ground truth data. Results showed the application can provide accurate 3D face representations to be used in clinics (within an average of 2 mm error) in less than 5 min.

Characterization of the Agrobacterium tumefaciens VirB2 pilin of the VirB/D4 Type IV Secretion System

The Agrobacterium tumefaciens VirB/D4 type IV secretion system (T4SS) delivers oncogenic T-DNA and effector proteins to susceptible plant cells. This leads to the formation of tumors termed Crown Galls. The VirB/D4 T4SS is comprised of 12 subunits (VirB1 to VirB11 and VirD4), which assemble to form two structures, a secretion channel spanning the cell envelope and a T-pilus extending from the cell surface. In A. tumefaciens, the VirB2 pilin subunit is required for assembly of the secretion channel and is the main subunit of the T-pilus. The focus of this thesis is to define key reactions associated with the T4SS biogenesis pathway involving the VirB2 pilin. Topology studies demonstrated that VirB2 integrates into the inner membrane with two transmembrane regions, a small cytoplasmic loop, and a long periplasmic loop comprised of covalently linked N and C termini. VirB2 was shown by the substituted cysteine accessibility method (SCAM) to adopt distinct structural states when integrated into the inner membrane and when assembled as a component of the secretion channel and the T-pilus. The VirB4 and VirB11 ATPases were shown by SCAM to modulate the structural state of membrane-integrated VirB2 pilin, and evidence was also obtained that VirB4 mediates extraction of pilin from the membrane. A model that VirB4 functions as a pilin dislocase by an energy-dependent mechanism was further supported by coimmunoprecipitation and osmotic shock studies. Mutational studies identified two regions of VirB10, an N-terminal transmembrane domain and an outer membrane-associated domain termed the antennae projection, that contribute selectively to T-pilus biogenesis. Lastly, characterization of a VirB10 mutant that confers a ‘leaky’ channel phenotype further highlighted the role of VirB10 in gating substrate translocation across the outer membrane as well as T-pilus biogenesis. Results of my studies support a working model in which the VirB4 ATPase catalyzes dislocation of membrane-integrated pilin, and distinct domains of VirB10 coordinate pilin incorporation into the secretion channel and the extracellular T-pilus.

MOLECULAR MECHANISMS UNDERLYING THE TRANSCRIPTIONAL REGULATION OF T HELPER 17 AND REGULATORY T CELLS

CD4+ T helper (Th) lymphocytes are vital for integrating immune responses by orchestrating the function of other immune cell types. Naïve Th cells can differentiate into different effector subsets that are characterized by their cytokine profile and immune regulatory functions. These subsets include Th1, Th2, Th17, natural and inducible regulatory T cells (nTreg and iTreg respectively), among others. We focused our investigation on two Th lineages, Th17 and regulatory T cells, with opposing functions in the immune system. These subsets have been suggested to be reciprocally regulated since they both require TGF-b for their development. We investigated the role of the Treg-associated master transcription factor Foxp3, and found that Foxp3 inhibits Th17 cell generation by preventing the transcriptional activity of the two main Th17-specific transcription factors, nuclear orphan receptors RORa and RORgt. At the molecular level, we identified two different functional domains in Foxp3 required for such inhibition: the LQALL sequence in exon 2 and the TIP60/HDAC7 binding domain. These domains could be crucial to either prevent the association of the nuclear receptors to coactivators or to recruit histone deacetylases to RORa- or RORgt-target genes. Since TGF-b is a common cytokine required for the commitment towards both Th lineages, we determined the role of the TGF-b-dependent signaling pathway in the generation of each subset. By using mice with deficiencies in signaling molecules downstream of TGF-b, we found that while Smad2, Smad3 and Smad4 are required for the generation of iTreg cells, only Smad2 is indispensable for the induction of IL-17-producing cells, suggesting that TGF-b induces these T helper lineages through differential signaling pathways. Thus, our findings describe novel transcriptional regulatory mechanisms that control the generation of two T helper lineages with opposing functions. These findings could provide novel therapeutic targets to treat diseases where the balance of these T cells is dysregulated, such as in autoimmunity, chronic infectious diseases and cancer.

The effectiveness of a needleless intravenous system in prevention of percutaneous injury in two hospitals

This study assessed if hospital-wide implementation of a needleless intravenous connection system reduces the number of reported percutaneous injuries, overall and those specifically due to intravenous connection activities.^ Incidence rates were compared before and after hospital-wide implementation of a needleless intravenous system at two hospitals, a full service general hospital and a pediatric hospital. The years 1989-1991 were designated as pre-implementation and 1993 was designated as post-implementation. Data from 1992 were not included in the effectiveness evaluation to allow employees to become familiar with use of the new device. The two hospitals showed rate ratios of 1.37 (95% CI = 1.22-1.54, p $\le$.0001) and 1.63 (95% CI = 1.34-1.97, p $\le$.0001), or a 27.1% and a 38.6% reduction in overall injury rate, respectively. Rate ratios for intravenous connection injuries were 2.67 (95% CI = 1.89-3.78, p $\le$.0001) and 3.35 (95% CI = 1.87-6.02, p $\le$.0001), or a 62.5% and a 69.9% reduction in injury rate, respectively. Rate ratios for all non-intravenous connection injuries were calculated to control for factors other than device implementation that may have been operating to reduce the injury rate. These rate ratios were lower, 1.21 and 1.44, demonstrating the magnitude of injury reduction due to factors other than device implementation. It was concluded that the device was effective in reduction of numbers of reported percutaneous injuries.^ Use-effectiveness of the system was also assessed by a survey of randomly selected device users to determine satisfaction with the device, frequency of use and barriers to use. Four hundred seventy-eight surveys were returned for a response rate of 50.9%. Approximately 94% of respondents at both hospitals expressed satisfaction with the needleless system and recommended continued use. The survey also revealed that even though over 50% of respondents report using the device "always" or "most of the time" for intravenous medication administration, flushing lines, and connecting secondary intravenous lines, needles were still being used for these same activities. Compatibility, accessibility and other technical problems were reported as reasons for using needles for these activities. These problems must be addressed, by both manufacturers and users, before the needleless system will be effective in prevention of all intravenous connection injuries. ^

An evaluation of the personal response system program for the elderly in Harris County, Texas

The Personal Response System Program at Huffington Center on Aging, Baylor College of Medicine, provides emergency call systems for elderly people living independently in Houston, Texas. The goal of the project was to complete a formative evaluation of the Personal Response System Program. The specific aims of the evaluation were three-fold. One aim was to evaluate participant health status and level of disability. The second aim was to develop a health care cost estimation strategy. Finally, a preliminary cost-effectiveness analysis was completed to evaluate the program's impact on health care costs and health status among the elderly target population. ^ The evaluation was a longitudinal, randomized experimental design. After the screening of 120 volunteers for eligibility, clients were asked to complete a written questionnaire and a monthly health service contact diary. Volunteers were contacted by telephone interviewers to collect health status information from 100 eligible clients (83%) on three occasions during the six months of follow-up. ^ Initially, volunteers were randomized to two experimental groups. The two groups were found to be comparable at the beginning of the study. No significant differences were detected related to health status, level of disability, or history of physician visits at baseline. However, the group with the Personal Response System (PRS) device had more adverse health events, higher IADL scores, more frequent use of walkers, lower average health status scores, and fewer community volunteers hours than the usual care comparison group. ^ The health care costs were estimated based on an algorithm adapted from the American Medical Association guidelines. Average total health care costs for the group with the PRS device ($912) were greater than the usual care group ($464). However, median health care values for the PRS group ($263) were similar to the usual care comparison group ($234). The preliminary findings indicated that the use of the PRS device was not associated with health care cost savings. ^ In the preliminary cost-effectiveness analysis, use of the personal response system was found to be associated with increased mental health status among elderly clients. The cost-effectiveness evaluation indicated that the associated cost for six months was $710 per unit increase in mental component score when the $150 PRS subscription was included. However, clients with the PRS device were found to have a greater decline in physical health status during the six-month follow-up. The beneficial effect on mental health status was found to be in contrast to negative findings associated with changes in physical health status. The implications for future research relate to the need to identify risk factors among geriatric populations to better target groups that would most likely benefit from PRS Program enrollment. ^

Cloning and genetic characterization of Skb1: A novel regulator of Shk1 and mitosis in Schizosaccharomyces pombe

A partial skb1 gene was originally isolated in a yeast two-hybrid screen for Shk1-interacting polypeptides. Shk1 is one of two Schizosaccharomyces pombe p21Cdc42/Rac-activated kinases (PAKs) and is an essential component of the Ras1-dependent signal transduction pathways regulating cell morphology and mating responses in fission yeast. After cloning the skb1 gene we found the Skb1 gene product to be a novel, nonessential protein lacking homology to previously characterized proteins. However the identification of Skb1 homologs in C. elegans, S. cerevisiae, and H. sapiens reveals evolution has conserved the skb1 gene. Fission yeast cells carrying a deletion of skb1 exhibit a defect in cell size but not mating abilities. This defect is suppressed by high copy shk1. Fission yeast overexpressing skb1 were found to undergo cell division at a length 1.5X greater than normal. In the two-hybrid system, Skb1 interacts with a subdomain of the Shk1 regulatory region distinct from that with which Cdc42 interacts, and forms a ternary complex with Shk1 and Cdc42. By use of yeast genetics, we have established a role for Skb1 as a positive regulator of Shk1. Co-overexpression of shk1 with skb1 was found to suppress the morphology defect, but not the sterility, of ras1Δ fission yeast. Thus, the function of Skb1 is restricted to a morphology control pathway. We determined that Skb1 functions as a negative regulator of mitosis and does this through a Shk1-dependent mechanism. The mitotic regulatory function of Skb1 and Shk1 was also partially dependent upon Wee1, a direct negative regulator of the cyclin-dependent kinase Cdc2. The role for Skb1 and Shk1 as mitotic regulators is the first connection from a PAK protein to control of the cell cycle. Furthermore, Skb1 is the first non-Cdc42/Rac PAK modulator to be identified. ^