Protein Fragment Motif Finder (PFMFind) is a system that enables e cient discovery of relationships between short fragments of protein sequences using similarity search. It supports queries based on amino acid similarity matrices and position specific score matrices (PSSMs) obtained through an iterative procedure. PSSM construction is customisable through plugins written in Python. PFMFind consists of a GUI client, an index for fast similarity search and a relational database for storing search results and sequence annotations. It is written mostly in Python. The components of PFMFind communicate through TCP/IP sockets and can be located on different physical machines. PFMFind is freely available for download (under a GPL licence) from http://pfmfind.stojmirovic.org
similarity search; indexing; protein fragments
Background. University students were studied prospectively to determine the incidence of and risk factors for acquisition of primary Epstein–Barr virus (EBV) infection and the virologic and immune correlates of disease severity.
Methods. EBV antibody–negative freshmen participated in monthly surveillance until graduation. If antibodies developed, proximate samples were assayed for viral load by polymerase chain reaction. Lymphocyte and natural killer (NK) cell numbers and activation were measured by flow cytometry, and plasma cytokine levels were measured by a multiplex assay.
Results. Of 546 students screened, 202 (37%) were antibody negative; 143 antibody-negative students were enrolled. During a median of 3 years of observation, 66 subjects experienced primary infection. Of these, 77% had infectious mononucleosis, 12% had atypical symptoms, and 11% were asymptomatic. Subjects reporting deep kissing with or without coitus had the same higher risk of infection than those reporting no kissing (P < .01). Viremia was transient, but median oral shedding was 175 days. Increases were observed in numbers of NK cells and CD8+ T-cells but not in numbers of CD4+ T-cells during acute infection. Severity of illness correlated positively with both blood EBV load (P = .015) and CD8+ lymphocytosis (P = .0003).
Conclusions. Kissing was a significant risk for primary EBV infection. A total of 89% of infections were symptomatic, and blood viral load and CD8+ lymphocytosis correlated with disease severity.
IL-1; S. pneumoniae; coagulation; fibrinogen; innate immunity
Cystic fibrosis related diabetes is the most common co-morbidity in persons with CF. ISPAD guidelines recommend annual OGTT screening starting at age 10. The OGTT might be recommended in younger children if, as in adults, it provided clinically relevant prognostic information. A database review was performed to determine whether OGTT findings in children with CF predict subsequent clinical course.
A retrospective matched-pair cohort study was based on OGTTs performed 1998–2003. Children age 6–9 were classified as normal glucose tolerance (NGT) or abnormal glucose tolerance (AGT). AGT were matched by age and gender to NGT. Clinical status was assessed at baseline and 5 years later. In a separate investigation, diabetes and prior AGT status of children aged 10–18 were used to assess predictions derived from the cohort study.
In 1998–2003, 39 of 94 children had AGT. Of these, 31 had sufficient follow-up data to be included. Both at baseline and 5 years later there was no significant difference in height, weight, BMI or lung function between AGT and NGT. Diabetes developed in 13 AGT (42%) and one NGT (3%) (odds ratio (OR) 11, p= 0.0009). Age of diabetes onset was 12±1 years in boys and 11±1 in girls, compared to ~23 years in the general CF population. Fifteen current children age 10–18 who had AGT before age 10 have diabetes, close to the prediction of 19.
Abnormal glucose tolerance in children with CF age 6–9 years identifies those at high risk for progression to early onset diabetes.
Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure.
GWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress.
Haplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance.
GWAS; Frost tolerance; Barley
To investigate the association of concussion with cognitive ability (CA) and educational level (EL).
Epidemiological—cross-linkage of national computer registers.
130 420 young men appearing before the Danish draft board during the period 2006–2010.
Primary and secondary outcome measures
CA test scores, EL and occurrence of concussion during the period 2004–2009, treated either in an A&E unit or upon admission to a hospital ward.
The 3067 men who had suffered a concussion had lower CAs (mean=96.5, SD=15, 95% CI 95.0 to 97.0) than the total cohort and they were lower for 1452 who were admitted to a hospital ward (mean CA=95.8, SD=15, 95% CI 95.1 to 96.6) than for 1615 who were treated only at an A&E unit (mean CA=97.1, SD=15, 95% CI 96.3 to 98.0). Multiple logistic regressions revealed that the effects for EL were stronger than those for CA. Among 127 353 men not sustaining a concussion, 48% attended a ‘gymnasium’ (sixth-form college), among men treated for a concussion at an A&E unit, this falls to 36% and among men hospitalised for a concussion to 30%. Transfer to a gymnasium, if it happens, almost invariably does so before the 18th birthday. Among 701 men suffering a concussion and admitted to a hospital department after this date, only 26% (n=182) were previously transferred to a gymnasium. Among the 804 men treated at an A&E unit after their 18th birthday, 33% (n=265) had done so. These two percentages are significantly below the corresponding non-concussed population (48%).
Taken together, the results suggest that lower CA and, in particular, lower EL are risk factors for sustaining a concussion, the risk increasing with the severity of the injury.
Epidemiology; Trauma Management
Two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. In one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. In the opposing model, conflicts between mutualist and host are largely resolved and the interaction is characterized by evolutionary stasis. We tested these opposing frameworks in two lineages of mutualistic rhizobia, Sinorhizobium fredii and Bradyrhizobium japonicum. To examine genes demonstrably important for host-interactions we coupled the mining of genome sequences to a comprehensive functional screen for type III effector genes, which are necessary for many Gram-negative pathogens to infect their hosts. We demonstrate that the rhizobial type III effector genes exhibit a surprisingly high degree of conservation in content and sequence that is in contrast to those of a well characterized plant pathogenic species. This type III effector gene conservation is particularly striking in the context of the relatively high genome-wide diversity of rhizobia. The evolution of rhizobial type III effectors is inconsistent with the molecular arms race paradigm. Instead, our results reveal that these loci are relatively static in rhizobial lineages and suggest that fitness conflicts between rhizobia mutualists and their host plants have been largely resolved.
Rhizobia are an important group of bacteria that can enter into mutually beneficial symbiotic interactions with legume plants to fix atmospheric nitrogen. However, in order to do so, a complex dialog involving the exchange of chemical and molecular signals must occur between partners. Some species of beneficial rhizobia employ a type III secretion system, a well-characterized virulence mechanism used by pathogens to inject bacterial-encoded type III effector proteins directly into host cells to coerce the host into accommodating the microbe. In this study, we generated draft genome sequences and employed computational as well as experimental methods to identify type III effectors from eight strains representing Sinorhizobium fredii and Bradyrhizobium japonicum. We demonstrate that the type III effector genes of these rhizobial species are highly conserved in content with little diversity between strains. This work is an important step towards understanding the roles for type III secretion systems and their effectors in mutualistic interactions.
Renal transplant recipients regularly fail to take their prescribed immunosuppressive medications, frequently leading to adverse outcomes.
Medication vials incorporating electronic monitor circuits in their caps compiled prospective data files on the azathioprine dosing patterns of 180 adult renal transplant recipients monitored up to 4 years. These patients were followed for a mean of 8.7 years posttransplantation.
Patients were divided into three groups by the medication doses missed during the first 6 months posttransplant. These initial dosing patterns remained remarkably consistent up to 4 years. Patients (n=47) missing the most doses (≥5%) experienced earlier and more frequent acute rejection episodes (P=0.025). This group also demonstrated significantly longer interdose intervals (P=0.005), with more frequent (P<0.001) and longer (P<0.001) “drug holidays.” A patient subgroup with early declining medication adherence (n=23) experienced dramatically poorer outcomes, with significantly increased acute rejection (P<0.001), chronic rejection (P=0.034), graft loss before death (P<0.001), and death (P=0.04). In all tertiles there was a trend toward missing more medication over time.
Excellent posttransplant medication adherence is critical to improved outcomes. Individual dosing patterns are established early after hospital discharge and remain remarkably consistent, despite gradual erosion in adherence over time. The later consequences of medication nonadherence, especially early declines in adherence, include increased frequencies of rejection, graft loss, and death.
Transplantation; Medication; Adherence; Compliance; Rejection
The United States is currently in an age of obesity and inactivity despite increasing public awareness and scientific knowledge of detrimental long-term health effects of this lifestyle. Behavior-tracking diaries offer an effective strategy for physical activity adherence and weight management. Furthermore, Web-based physical activity diaries can engage meaningful partners in people’s social networks through fun online gaming interactions and generate motivational mechanisms for effective behavioral change and positive health outcomes.
Wellness Partners (WP) is a Web-based intervention in the form of a physical activity diary with social networking and game features. Two versions were designed and developed for the purpose of this study—“Diary” only and “Diary+Game”. The objectives of this study included pilot testing the research process of this intervention design, implementation, evaluation, and exploring the effectiveness of social gaming features on adult participants’ physical activity and anthropometric measures.
We conducted a field experiment with randomized crossover design. Assessments occurred at baseline, first follow-up (FU, 5-8 weeks after using one version of WP), and second FU (5-8 weeks of using the other version of WP). In the control condition, participants started with the “Diary” version of WP while in the experimental condition, participants started with the “Diary+Game” version of WP. A total of 54 adults (egos) ages 44-88, and their family and friends (alters) ages 17-69 participated in the study in ego-network groups. Both egos and their alters completed online surveys about their exercise habits. In addition, egos completed anthropometric measurements of BMI, fat percentage, and fat mass by bioimpedance.
From October 2009 to May 2010, flyers, emails, and Web advertisements yielded 335 volunteers who were screened. Rolling recruitment resulted in enrollment of 142 qualified participants in 54 ego-network groups, which were randomly assigned to a study condition. The final analytic sample included 87 individuals from 41 groups. Data were collected from December 2009 to August 2010, and data analysis was completed in 2011. Overall, the participants were given access to the intervention for 10-13 weeks. Statistical analysis suggested an increase in self-reported exercise frequency (mean days per week) from baseline (2.57, SD 1.92) to first FU (3.21, SD 1.74) in both conditions. Stronger effects were seen in the condition where Diary+Game was played first, especially in network groups with larger age variation between the alters and egos. Overall, the decrease in egos’ BMI was statistically significant from baseline to first FU, with greater decrease for those in the Diary+Game first condition (-0.26 vs -0.16 in the Diary first condition).
The Wellness Partners program increased physical activity among participants and resulted in health benefits among the egos. Web-based diary interventions designed with social gaming features hold potential to promote active lifestyles for middle-age adults and people in their social networks.
physical activity; social networking; diary; game; Web-based intervention; behavior change intervention
Chlorthalidone (CTD) reduces 24-hour blood pressure more effectively than hydrochlorothiazide (HCTZ), but whether this influences electrocardiographic left ventricular hypertrophy (LVH) is uncertain. One source of comparative data is the Multiple Risk Factor Intervention Trial (MRFIT), which randomly assigned 8,012 hypertensive men to special intervention (SI) or usual care (UC). SI participants could use CTD or HCTZ initially; previous analyses have grouped clinics by their main diuretic used (C-clinics: CTD; H-clinics: HCTZ). After 48 months, SI participants receiving HCTZ were recommended to switch to CTD, in part, because higher mortality was observed for SI compared to UC participants in H-clinics, while the opposite was found in C-clinics. In this analysis, we examined change in continuous measures of electrocardiographic LVH using both an ecologic analysis by previously-reported C- or H-clinic groupings, and an individual participant analysis where use of CTD or HCTZ by SI participants was considered and updated annually. Through 48 months, differences between SI and UC in LVH were larger for C-clinics compared to H-clinics (Sokolow-Lyon: −93.9 vs −54.9 μV, P=0.049; Cornell voltage: −68.1 vs −35.9 μV, P=0.019; Cornell voltage product: −4.6 vs −2.2 μV/ms, P=0.071; left ventricular mass: −4.4 vs −2.8 gm, P=0.002). At the individual participant level, Sokolow-Lyon and left ventricular mass were significantly lower for SI men receiving CTD compared to HCTZ through 48 months and 84 months of follow-up. Our findings on LVH support the idea that greater blood pressure reduction with CTD than HCTZ may have led to differences in mortality observed in MRFIT.
hydrochlorothiazide; chlorthalidone; left ventricular hypertrophy; hypertension; blood pressure; electrocardiography
We previously found that microalbuminuria (MA) is present in 14% of patients with long-standing cystic fibrosis–related diabetes (CFRD). However, others have reported much higher rates of MA in CF patients with and without diabetes (32–67%), suggesting this test is not sufficiently specific for diabetic nephropathy screening in CF. We investigated transient (TMA) and persistent (PMA) microalbuminuria in CF patients to resolve these contradictory findings.
RESEARCH DESIGN AND METHODS
We reviewed 1,449 outpatient urinary albumin measurements from 467 patients aged ≥10 years, which were collected over a decade. TMA was defined as a single episode of MA that subsequently was resolved. PMA was defined as two consecutive or two out of three consecutive measurements in the MA range.
The prevalence of TMA that subsequently was resolved in CF patients was similar to the general population. It was found in 7.6% of patients, including 5% of youth (aged 10–17 years) and 9% of adults. PMA was found in 6.1% of the overall CF population, including 2% of youth and 8% of adults. The odds of PMA were increased sevenfold in patients with CFRD (95% CI 2.5–20, P = 0.0002) and 48-fold in patients with both CFRD and organ transplant (95% CI 13–177, P < 0.0001). The five patients with PMA in the absence of CFRD or transplant included two youths with presumed benign orthostatic MA and three adults with hypertension.
The spot urine albumin-to-creatinine ratio is specific enough to be a valid screening test for diabetic kidney disease in CFRD.
Head motion is a fundamental problem in functional MRI, and is often a limiting factor in its clinical implementation. This work presents a rigid-body motion correction strategy for echo-planar imaging (EPI) sequences that uses micro radio-frequency coil “active markers” for real-time, slice-by-slice prospective correction. Before the acquisition of each EPI-slice, a short tracking pulse-sequence measures the positions of three active markers integrated into a headband worn by the subject; the rigid-body transformation that realigns these markers to their initial positions is then fed back to dynamically update the scan-plane, maintaining it at a fixed orientation relative to the head. Using this method, prospectively-corrected EPI time-series are acquired on volunteers performing in-plane and through-plane head motions, with results demonstrating increased image stability over conventional retrospective image-realignment. Implications of this improvement for BOLD fMRI applications is assessed, as well as the benefit of non-rigid-body distortion-correction to reduce the remaining signal variation.
functional magnetic resonance imaging; fMRI; EPI; motion correction; prospective; real-time; active marker; device tracking; RF-coil; micro-coil; geometric distortion
Enhanced recovery program (ERP) was implemented to optimize the hospital stay in total hip arthroplasty. This study assessed the effects of optimizing preoperative and perioperative care using enhanced recovery (ER) on patients undergoing Total hip arthroplasty.
Materials and Methods:
We compared a prospective group of 64 patients on the ER program with a historic cohort of 63 patients that received conventional care (non ER).
ER patients were discharged earliest from hospital [mean length of stay (LOS) 5.3 days, median 4; P < 0.001] as compared to a mean of 8.3 days among non ER patients. Comparison based on American Association of Anesthesiologists (ASA) grades, preoperative hemoglobin, and body mass index (BMI) revealed that patients with ASA grade 3, preoperative hemoglobin of <14 g/dl, and BMI >30 on ER program spent shorter time in hospital as compared to the non ER's conventionally treated patients with more favorable physiological parameters of ASA grade 1 and 2, preoperative hemoglobin of >14 g/dl, and BMI <30.
The ER protocol is universally beneficial and confers an advantage regardless of the patients’ preoperative condition.
Enhanced recovery program; length of stay; total hip arthroplasty
Hereditary and sporadic neurodegenerative ataxias are movement disorders that affect the cerebellum. Robust and objective biomarkers are critical for treatment trials of ataxias. In addition, such biomarkers may help discriminate between ataxia subtypes because these diseases display substantial overlap in clinical presentation and conventional MRI. Profiles of 10–13 neurochemical concentrations obtained in vivo by high field proton magnetic resonance spectroscopy (1H MRS) can potentially provide ataxia-type specific biomarkers. We compared cerebellar and brainstem neurochemical profiles measured at 4 T from 26 patients with spinocerebellar ataxias (SCA1, N=9; SCA2, N=7; SCA6, N=5) or cerebellar multiple system atrophy (MSA-C, N=5) and 15 age-matched healthy controls. The Scale for the Assessment and Rating of Ataxia (SARA) was used to assess disease severity. The patterns of neurochemical alterations relative to controls differed between ataxia types. Myo-inositol levels in the vermis, myo-inositol, total N-acetylaspartate, total creatine, glutamate, glutamine in the cerebellar hemispheres and myo-inositol, total N-acetylaspartate, glutamate in the pons were significantly different between patient groups (Bonferroni corrected p<0.05). The best MRS predictors were selected by a tree classification procedure and lead to 89% accurate classification of all subjects while the SARA scores overlapped considerably between patient groups. Therefore, this study demonstrated multiple neurochemical alterations in SCAs and MSA-C relative to controls and the potential for these neurochemical levels to differentiate ataxia types. Studies with higher numbers of patients and other ataxias are warranted to further investigate the clinical utility of neurochemical levels as measured by high-field MRS as ataxia biomarkers.
Neurochemical profile; Magnetic resonance spectroscopy; SCA; Multiple system atrophy; Ataxia
It is hypothesized that exercise can lead to a decrease in breast cancer risk through several hormonal and non-hormonal mechanisms. The Women in Steady Exercise Research (WISER) study investigated the effects of aerobic exercise on premenopausal sex hormone levels.
391 sedentary, healthy, young eumenorrheic women were randomized into an exercise intervention of 30 minutes of aerobic exercise 5 times a week for approximately 16 weeks (n=212), or into a control group (n=179). Serum levels of estradiol, estrone sulfate, testosterone, and sex hormone binding globulin (SHBG), all in the midfollicular phase, and of progesterone, in the midluteal phase, were measured at baseline and at the end of the 16-week period.
Compared to the controls (n=153), exercisers (n=166) experienced significant increases in aerobic fitness, lean body mass, and decreases in percent body fat. There were no significant changes in body weight and menstrual cycle length between or within groups. Progesterone decreased significantly in exercisers; however, this reduction was similar to that of the control group. No significant changes between or within groups were found for any of the other sex hormones or SHBG.
In premenopausal women, 16 weeks of 150 minutes per week of moderate aerobic exercise in young women did not significantly alter sex hormone or SHBG levels.
Any favorable effects that moderate aerobic exercise without an associated weight change may have on breast cancer risk in premenopausal women are unlikely to be a consequence of changes in levels of sex hormones or SHBG.
Aerobic Exercise; Sex Hormones; Premenopausal Women; Randomized Clinical Trial; Breast Cancer Risk
Rift Valley fever virus (RVFV) is a major human and animal pathogen associated with severe disease including hemorrhagic fever or encephalitis. RVFV is endemic to parts of Africa and the Arabian Peninsula, but there is significant concern regarding its introduction into non-endemic regions and the potentially devastating effect to livestock populations with concurrent infections of humans. To date, there is little detailed data directly comparing the host response to infection with wild-type or vaccine strains of RVFV and correlation with viral pathogenesis. Here we characterized clinical and systemic immune responses to infection with wild-type strain ZH501 or IND vaccine strain MP-12 in the C57BL/6 mouse. Animals infected with live-attenuated MP-12 survived productive viral infection with little evidence of clinical disease and minimal cytokine response in evaluated tissues. In contrast, ZH501 infection was lethal, caused depletion of lymphocytes and platelets and elicited a strong, systemic cytokine response which correlated with high virus titers and significant tissue pathology. Lymphopenia and platelet depletion were indicators of disease onset with indications of lymphocyte recovery correlating with increases in G-CSF production. RVFV is hepatotropic and in these studies significant clinical and histological data supported these findings; however, significant evidence of a pro-inflammatory response in the liver was not apparent. Rather, viral infection resulted in a chemokine response indicating infiltration of immunoreactive cells, such as neutrophils, which was supported by histological data. In brains of ZH501 infected mice, a significant chemokine and pro-inflammatory cytokine response was evident, but with little pathology indicating meningoencephalitis. These data suggest that RVFV pathogenesis in mice is associated with a loss of liver function due to liver necrosis and hepatitis yet the long-term course of disease for those that might survive the initial hepatitis is neurologic in nature which is supported by observations of human disease and the BALB/c mouse model.
Rift Valley fever virus (RVFV) is a deadly virus that is found primarily in sub-Saharan Africa. However, mosquitoes that are capable of transmitting RVFV have a worldwide distribution. RVF affects a broad range of animal species and is known to cause encephalitis or hemorrhagic fever in humans with survivors having long-term health effects such as a loss of vision. There is no vaccine currently approved for use in humans. In this study we evaluated the host response to infection with either a RVFV vaccine strain or a wild-type strain to identify similarities or differences that could be exploited for development of therapeutics or improved vaccines. While mice infected with the vaccine strain did not develop disease and survived, infection with the wild-type strain caused severe disease with a fatal outcome. Analyzing multiple clinical factors and the host immune response over the course of infection allowed us to identify potential host factors associated with disease progression during wild-type virus infection. This work also provides support for a current vaccine candidate, MP-12, in demonstrating a limited and protective host response to infection.
The Strength and Difficulties Questionnaire (SDQ) is a brief behavioural five factor instrument developed to assess emotional and behavioural problems in children and adolescents. The aim of the current study was to evaluate the psychometric properties for parent and teacher ratings in the Danish version of SDQ for different age groups of boys and girls.
The Danish versions of the SDQ were distributed to a total of 71,840 parent and teacher raters of 5-, 7- and 10- to 12-year-old children included in four large scale Danish cohorts. The internal reliability was assessed and exploratory factor analyses were carried out to replicate the originally proposed five factor structure. Mean scores and percentiles were examined in order to differentiate between low, medium and high levels of emotional and behavioural difficulties.
The original five factor structure could be substantially confirmed. The Conduct items however did not solely load on the proposed Conduct scale and the Conduct scale was further contaminated by non-conduct items. Positively worded items tended to load on the Prosocial scale. This was more so the case for teachers than for parents. Parent and teacher means and percentiles were found to be lower compared to British figures but similar to or only slightly lower than those found in the other Nordic countries. The percentiles for girls were generally lower than for boys, markedly so for the teacher hyperactivity ratings.
The study supports the usefulness of the SDQ as a screening tool for boys and girls across age groups and raters in the general Danish population.
Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome.
We hypothesized that a whey protein diet would result in greater weight loss and improved body compositioncompared to standard weight loss diets. Weight change, body composition, and renin angiotensin aldosterone system activity in midlife adults was compared between diet groups. Eighteen subjects enrolled ina5 month study of8 weeks controlled food intake followed by 12 weeks ad libitum intake. Subjects were randomized to one of three treatment groups: control diet (CD) (55% carbohydrate: 15% protein: 30% fat), mixed protein (MP) (40% carbohydrate: 30% protein: 30% fat), or whey protein (WP) (40% carbohydrate: 15% mixed protein: 15% whey protein: 30% fat). Measurements included weight, metabolic measures, body composition by dual energy x-ray absorptiometry (DXA), and resting energy expenditure. No statistically significant differences in total weight loss or total fat loss were observed between treatments, however, a trend toward greater total weight loss (p = 0.08) and total fat loss (p=0.09) was observed in the WP group compared to the CD group. Fat loss in the leg and gynoid regions was greater (p < 0.05) in the WP group than the CD group. No RAAS mediated response was observed, but a decrease in systolic blood pressure was significantly greater (p <0.05) in the WP group compared to the CD group. In summary, increased whey protein intake did not result in statistically significant differences in weight loss or in total fat loss, but significant differences in regional fat loss and in decreased blood pressure were observed in the WP group.
adults; fat loss; weight loss; whey protein; satiety; resting energy expenditure
Phage display is used to discover peptides or proteins with a desired target property—most often, affinity for a target selector molecule. Libraries of phage clones displaying diverse surface peptides are subject to a selection process designed to enrich for the target behavior, and subsequently propagated to restore phage numbers. A recurrent problem is enrichment of clones, called target-unrelated phage (TUPs), that lack the target behavior. Many TUPs are propagation-related; they have mutations conferring a growth advantage, and are enriched during the propagations accompanying selection. Unlike other filamentous phage libraries, fd-tet-based libraries are relatively resistant to propagation-related TUP corruption. Their minus strand origin is disrupted by a large cassette that simultaneously confers resistance to tetracycline and imposes a rate-limiting growth defect that cannot be bypassed with simple mutations. Nonetheless, a new type of propagation-related TUP emerged in the output of in vivo selections from an fd-tet library. The founding clone had a complex rearrangement that restored the minus strand origin while retaining tetracycline resistance. The rearrangement involved two recombination events, one with a contaminant having a wild-type minus strand origin. The founder’s infectivity advantage spread by simple recombination to clones displaying different peptides. We propose measures for minimizing TUP corruption.
Phage display; target-unrelated peptides; phage propagation; filamentous phage libraries; affinity selection; recombination
Based on epidemiological data, it is believed that human-to-human transmission plays an important role in Nipah virus outbreaks. No experimental data are currently available on the potential routes of human-to-human transmission of Nipah virus. In a first dose-finding experiment in Syrian hamsters, it was shown that Nipah virus was predominantly shed via the respiratory tract within nasal and oropharyngeal secretions. Although Nipah viral RNA was detected in urogenital and rectal swabs, no infectious virus was recovered from these samples, suggesting no viable virus was shed via these routes. In addition, hamsters inoculated with high doses shed significantly higher amounts of viable Nipah virus particles in comparison with hamsters infected with lower inoculum doses. Using the highest inoculum dose, three potential routes of Nipah virus transmission were investigated in the hamster model: transmission via fomites, transmission via direct contact and transmission via aerosols. It was demonstrated that Nipah virus is transmitted efficiently via direct contact and inefficiently via fomites, but not via aerosols. These findings are in line with epidemiological data which suggest that direct contact with nasal and oropharyngeal secretions of Nipah virus infected individuals resulted in greater risk of Nipah virus infection. The data provide new and much-needed insights into the modes and efficiency of Nipah virus transmission and have important public health implications with regards to the risk assessment and management of future Nipah virus outbreaks.
Understanding how viruses are transmitted plays an important role in our ability to intervene in virus outbreaks. Over the last decade, Nipah virus has caused multiple outbreaks in Malaysia, India and especially Bangladesh. Fruit bats form the natural reservoir for Nipah virus; from the bats the virus is introduced into the human population, either directly or via an intermediate host. Epidemiological data suggest that upon introduction into the human population the virus has the ability to spread from person-to-person. We performed experimental studies in a hamster model to investigate if we could mimic human-to-human transmission and to determine the route of transmission through which Nipah virus spread between people. We discovered that Nipah virus-infected hamsters predominantly shed virus via excretions from the nose and lungs. In transmission experiments, we showed that Nipah virus is efficiently transmitted via direct contact. Fomite transmission was inefficient and transmission via aerosols did not occur. The elucidation of the mode of Nipah virus transmission has important public health implications because it allows a targeted and experiment-based assessment of intervention strategies and surveillance for emerging Nipah virus strains better adapted to human-to-human transmission.
While glucose tolerance abnormalities are common in cystic fibrosis (CF), impaired fasting glucose (IFG) has scarcely been explored. No studies have examined the relation between IFG and clinical status.
RESEARCH DESIGN AND METHODS
Data were retrieved from the University of Minnesota CF database on oral glucose tolerance tests (OGTTs) performed in 1996–2005. Subjects were identified as normal glucose tolerance (NGT), impaired glucose tolerance (IGT), or CF–related diabetes without fasting hyperglycemia (CFRD FH−). Patients with fasting hyperglycemia were excluded. The presence of IFG was assessed within each category. In a separate case-control cohort study, subjects with IFG were matched to CF control subjects by age, sex, and OGTT class to explore outcomes.
For the total population (n = 310), the prevalence of IFG was 22%, and by OGTT class was NGT 14%, IGT 31%, CFRD FH− 53%. Within the cohort study, mortality was significantly reduced in IFG (two vs. nine deaths, odds ratio [OR] = 0.2 [95% CI 0.04–0.9]). IFG did not confer increased risk of progression to diabetes (OR 0.66 [0.29–1.48]). Lung function was better in pediatric IFG subjects with IGT and not significantly worse in adults with IGT or adults and children with NGT and CFRD FH−. BMI was not significantly different in IFG subjects versus control subjects.
Contrary to expectations in patients with CF, IFG appeared to be associated with improved survival and was not associated with worse nutritional or pulmonary status or increased progression to fasting hyperglycemia.
Ebolavirus belongs to the family filoviridae and causes severe hemorrhagic fever in humans with 50–90% lethality. Detailed understanding of how the viruses attach to and enter new host cells is critical to development of medical interventions. The virus displays a trimeric glycoprotein (GP1,2) on its surface that is solely responsible for membrane attachment, virus internalization and fusion. GP1,2 is expressed as a single peptide and is cleaved by furin in the host cells to yield two disulphide-linked fragments termed GP1 and GP2 that remain associated in a GP1,2 trimeric, viral surface spike. After entry into host endosomes, GP1,2 is enzymatically cleaved by endosomal cathepsins B and L, a necessary step in infection. However, the functional effects of the cleavage on the glycoprotein are unknown.
We demonstrate by antibody binding and Hydrogen-Deuterium Exchange Mass Spectrometry (DXMS) of glycoproteins from two different ebolaviruses that although enzymatic priming of GP1,2 is required for fusion, the priming itself does not initiate the required conformational changes in the ectodomain of GP1,2. Further, ELISA binding data of primed GP1,2 to conformational antibody KZ52 suggests that the low pH inside the endosomes also does not trigger dissociation of GP1 from GP2 to effect membrane fusion.
The results reveal that the ebolavirus GP1,2 ectodomain remains in the prefusion conformation upon enzymatic cleavage in low pH and removal of the glycan cap. The results also suggest that an additional endosomal trigger is necessary to induce the conformational changes in GP1,2 and effect fusion. Identification of this trigger will provide further mechanistic insights into ebolavirus infection.
Ebolavirus causes often fatal hemorrhagic fever in humans and nonhuman primates. During infection, the virus is internalized into the low pH endosomes prior to the delivery of viral RNA to the infected cell. Cleavage by endosomal cathepsins of the heavily glycosylated mucin-like domain and glycan cap from the ebolavirus surface glycoprotein GP1,2 is an essential step in infection. The effect of cleavage and the low pH of the endosomes on the conformation of GP1,2 is as yet unknown. To investigate the effect of priming, we cleaved the mucin-like domain and glycan cap of Zaire ebolavirus (ZEBOV) GP1,2 with thermolysin and engineered a mutant of Sudan ebolavirus (SEBOV) GP1,2 that is cleaved with furin. We demonstrate by DXMS and antibody binding studies that cleavage of the mucin domain and glycan cap and incubation at low pH are insufficient to trigger the conformational changes of GP1,2 that effect fusion. Unraveling the trigger that leads to the conformational change of GP1,2 to its fusogenic form will enhance the understanding of ebolavirus infection and pinpoint key sites for therapeutic intervention.
Insulin-like growth factor 1 (IGF-1) and IGF binding protein 3 (IGFBP-3) have been associated with increased risk of breast cancer.
We report our findings on the effects of 16 weeks of aerobic exercise on IGF axis proteins, insulin, glucose and insulin resistance of 319 young sedentary women. Demographics, health surveys, body composition, dietary intake and blood samples were collected at baseline and 16 weeks. IGF-1 and IGF binding proteins 1, 2, and 3 were measured by ELISA’s.
Exercise adherence was 88% and the dropout rates for the exercise and control groups were 21.7% and 14.5%, respectively. There was a small significant change from baseline in IGFBP-3 concentrations. IGFBP-3 levels decreased in controls and increased in exercisers. The between group difference was significant. No other changes were noted.
Sixteen weeks of exercise had minimum or no effect on IGF proteins of young women.
Our study supports findings from previous studies conducted in older populations and raises the question of what type of intervention is needed to change circulating levels of IGF proteins in humans.
IGF-1; IGFBP-3; insulin; exercise; randomized controlled trial
Zaire ebolavirus (ZEBOV) infections are associated with high lethality in primates. ZEBOV primarily targets mononuclear phagocytes, which are activated upon infection and secrete mediators believed to trigger initial stages of pathogenesis. The characterization of the responses of target cells to ZEBOV infection may therefore not only further understanding of pathogenesis but also suggest possible points of therapeutic intervention. Gene expression profiles of primary human macrophages exposed to ZEBOV were determined using DNA microarrays and quantitative PCR to gain insight into the cellular response immediately after cell entry. Significant changes in mRNA concentrations encoding for 88 cellular proteins were observed. Most of these proteins have not yet been implicated in ZEBOV infection. Some, however, are inflammatory mediators known to be elevated during the acute phase of disease in the blood of ZEBOV-infected humans. Interestingly, the cellular response occurred within the first hour of Ebola virion exposure, i.e. prior to virus gene expression. This observation supports the hypothesis that virion binding or entry mediated by the spike glycoprotein (GP1,2) is the primary stimulus for an initial response. Indeed, ZEBOV virions, LPS, and virus-like particles consisting of only the ZEBOV matrix protein VP40 and GP1,2 (VLPVP40-GP) triggered comparable responses in macrophages, including pro-inflammatory and pro-apoptotic signals. In contrast, VLPVP40 (particles lacking GP1,2) caused an aberrant response. This suggests that GP1,2 binding to macrophages plays an important role in the immediate cellular response.
Ebola virus causes a severe hemorrhagic fever syndrome in man with high case-fatality rates. Following infection, monocytes and macrophages are among the first cells targeted by the virus. These cells respond by increasing expression of inflammatory cytokines and chemokines that contribute towards pathogenesis. In order to more thoroughly characterize the host response to Ebola infection, primary human macrophages were infected with Zaire ebolavirus and samples harvested for transcriptional changes after 1 or 6 hours post infection. Whereas previous studies have analyzed a relatively small subset of host genes, this study examined the transcriptional profile of over 10,000 genes and employed rigorous pathway analyses to the datasets. Ebola virus was found to significantly regulate the expression of over 88 host genes. These changes occurred within the first hours of infection. Subsequent experiments demonstrated that virus replication was not necessary for activation. Indeed, noninfectious virus-like particles expressing the ebolavirus glycoprotein and matrix proteins were sufficient stimuli to induce activation.