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1.  Antagonist-Induced Conformational Changes in Dopamine Transporter Extracellular Loop Two Involve Residues in a Potential Salt Bridge 
Ligand-induced changes in the conformation of extracellular loop (EL) 2 in the rat (r) dopamine transporter (DAT) were examined using limited proteolysis with endoproteinase Asp-N and detection of cleavage products by epitope-specific immunoblotting. The principle N-terminal fragment produced by Asp-N was a 19 kDa peptide likely derived by proteolysis of EL2 residue D174, which is present just past the extracellular end of TM3. Production of this fragment was significantly decreased by binding of cocaine and other uptake blockers, but was not affected by substrates or Zn2+, indicating the presence of a conformational change at D174 that may be related to the mechanism of transport inhibition. DA transport activity and cocaine analog binding were decreased by Asp-N treatment, suggesting a requirement for EL2 integrity in these DAT functions. In a previous study we demonstrated that ligand-induced protease resistance also occurred at R218 on the C-terminal side of rDAT EL2. Here using substituted cysteine accessibility analysis of human (h) DAT we confirm cocaine-induced alterations in reactivity of the homologous R219 and identify conformational sensitivity of V221. Focused molecular modeling of D174 and R218 based on currently available Aquifex aeolicus leucine transporter crystal structures places these residues within 2.9 Å of one another, suggesting their proximity as a structural basis for their similar conformational sensitivities and indicating their potential to form a salt bridge. These findings extend our understanding of DAT EL2 and its role in transport and binding functions.
PMCID: PMC4394652  PMID: 24269640
cocaine; amphetamine; methamphetamine; SCAM; molecular modeling
2.  Novel Heparan Sulfate-Binding Peptides for Blocking Herpesvirus Entry 
PLoS ONE  2015;10(5):e0126239.
Human cytomegalovirus (HCMV) infection can lead to congenital hearing loss and mental retardation. Upon immune suppression, reactivation of latent HCMV or primary infection increases morbidity in cancer, transplantation, and late stage AIDS patients. Current treatments include nucleoside analogues, which have significant toxicities limiting their usefulness. In this study we screened a panel of synthetic heparin-binding peptides for their ability to prevent CMV infection in vitro. A peptide designated, p5+14 exhibited ~ 90% reduction in murine CMV (MCMV) infection. Because negatively charged, cell-surface heparan sulfate proteoglycans (HSPGs), serve as the attachment receptor during the adsorption phase of the CMV infection cycle, we hypothesized that p5+14 effectively competes for CMV adsorption to the cell surface resulting in the reduction in infection. Positively charged Lys residues were required for peptide binding to cell-surface HSPGs and reducing viral infection. We show that this inhibition was not due to a direct neutralizing effect on the virus itself and that the peptide blocked adsorption of the virus. The peptide also inhibited infection of other herpesviruses: HCMV and herpes simplex virus 1 and 2 in vitro, demonstrating it has broad-spectrum antiviral activity. Therefore, this peptide may offer an adjunct therapy for the treatment of herpes viral infections and other viruses that use HSPGs for entry.
PMCID: PMC4436313  PMID: 25992785
There are several diseases which arise because of changes in the microbial communities in the body. Scientists continue to conduct research in a quest to find the catalysts that provoke these changes in the naturally occurring microbiota. Bacterial Vaginosis (BV) is a disease that fits the above criteria. BV afflicts approximately 29% of women in child bearing age. Unfortunately, its causes are unknown. This paper seeks to uncover the most important features for diagnosis and in turn employ classification algorithms on those features. In order to fulfill our purpose, we conducted two experiments on the data. We isolated the clinical and medical features from the full set of raw data, we compared the accuracy, precision, recall and F-measure and time elapsed for each feature selection and classification grouping. We noticed that classification results were as good or better after performing feature selection although there was a wide range in the number of features produced from the feature selection process. After comparing the experiments, the algorithms performed best on the medical dataset.
PMCID: PMC4407517  PMID: 25914861
Bacterial Vaginosis; Machine learning; Feature selection; Classification
4.  Network analysis suggests a potentially ‘evil' alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities 
Scientific Reports  2015;5:8275.
The critical importance of human milk to infants and even human civilization has been well established. Yet our understanding of the milk microbiome has been limited to cataloguing OTUs and computation of community diversity. To the best of our knowledge, there has been no report on the bacterial interactions within the milk microbiome. To bridge this gap, we reconstructed a milk bacterial community network based on Hunt et al. Our analysis revealed that the milk microbiome network consists of two disconnected sub-networks. One sub-network is a fully connected complete graph consisting of seven genera as nodes and all of its pair-wise interactions among the bacteria are facilitative or cooperative. In contrast, the interactions in the other sub-network of eight nodes are mixed but dominantly cooperative. Somewhat surprisingly, the only ‘non-cooperative' nodes in the second sub-network are mutually cooperative Staphylococcus and Corynebacterium that include some opportunistic pathogens. This potentially ‘evil' alliance between Staphylococcus and Corynebacterium could be inhibited by the remaining nodes that cooperate with one another in the second sub-network. We postulate that the ‘confrontation' between the ‘evil' alliance and ‘benign' alliance and the shifting balance between them may be responsible for dysbiosis of the milk microbiome that permits mastitis.
PMCID: PMC4317708  PMID: 25651890
5.  MetAmp: combining amplicon data from multiple markers for OTU analysis 
Bioinformatics  2015;31(11):1830-1832.
Motivation: We present a novel method and corresponding application, MetAmp, to combine amplicon data from multiple genomic markers into Operational Taxonomic Units (OTUs) for microbial community analysis, calibrating the markers using data from known microbial genomes. When amplicons for multiple markers such as the 16S rRNA gene hypervariable regions are available, MetAmp improves the accuracy of OTU-based methods for characterizing bacterial composition and community structure. MetAmp works best with at least three markers, and is applicable to non-bacterial analyses and to non 16S markers. Our application and testing have been limited to 16S analysis of microbial communities.
Results: We clustered standard test sequences derived from the Human Microbiome Mock Community test sets and compared MetAmp and other tools with respect to their ability to recover OTUs for these benchmark bacterial communities. MetAmp compared favorably to QIIME, UPARSE and Mothur using amplicons from one, two, and three markers.
Availability and implementation: MetAmp is available at
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC4443678  PMID: 25630378
Many colleges and universities across the globe now offer bachelors, masters, and doctoral degrees, along with certificate programs in bioinformatics. While there is some consensus surrounding curricula competencies, programs vary greatly in their core foci, with some leaning heavily toward the biological sciences and others toward quantitative areas. This allows prospective students to choose a program that best fits their interests and career goals. In the digital age, most scientific fields are facing an enormous growth of data, and as a consequence, the goals and challenges of bioinformatics are rapidly changing; this requires that bioinformatics education also change. In this workshop, we seek to ascertain current trends in bioinformatics education by asking the question, “What are the core competencies all bioinformaticians should have at the end of their training, and how successful have programs been in placing students in desired careers?”
PMCID: PMC3935419  PMID: 24297567
7.  GA-Based Selection of Vaginal Microbiome Features Associated with Bacterial Vaginosis 
In this paper, we successfully apply GEFeS (Genetic & Evolutionary Feature Selection) to identify the key features in the human vaginal microbiome and in patient meta-data that are associated with bacterial vaginosis (BV). The vaginal microbiome is the community of bacteria found in a patient, and meta-data include behavioral practices and demographic information. Bacterial vaginosis is a disease that afflicts nearly one third of all women, but the current diagnostics are crude at best. We describe two types of classifies for BV diagnosis, and show that each is associated with one of two treatments. Our results show that the classifiers associated with the ‘Treat Any Symptom’ version have better performances that the classifier associated with the ‘Treat Based on N-Score Value’. Our long term objective is to develop a more accurate and objective diagnosis and treatment of BV.
PMCID: PMC4274626  PMID: 25541628
Bacterial Vaginosis; GEFeS
8.  Seed: a user-friendly tool for exploring and visualizing microbial community data 
Bioinformatics  2014;31(4):602-603.
Summary: In this article we present Simple Exploration of Ecological Data (Seed), a data exploration tool for microbial communities. Seed is written in R using the Shiny library. This provides access to powerful R-based functions and libraries through a simple user interface. Seed allows users to explore ecological datasets using principal coordinate analyses, scatter plots, bar plots, hierarchal clustering and heatmaps.
Availability and implementation: Seed is open source and available at
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC4325548  PMID: 25332377
9.  Transforming Growth Factor β and Insulin Signal Changes in Stromal Fibroblasts of Individual Keratoconus Patients 
PLoS ONE  2014;9(9):e106556.
Keratoconus (KC) is a complex thinning disease of the cornea that often requires transplantation. The underlying pathogenic molecular changes in this disease are poorly understood. Earlier studies reported oxidative stress, metabolic dysfunctions and accelerated death of stromal keratocytes in keratoconus (KC) patients. Utilizing mass spectrometry we found reduced stromal extracellular matrix (ECM) proteins in KC, suggesting ECM-regulatory changes that may be due to altered TGFβ signals. Here we investigated properties of stromal cells from donor (DN) and KC corneas grown as fibroblasts in serum containing DMEM: F12 or in serum-free medium containing insulin, transferrin, selenium (ITS). Phosphorylation of SMAD2/3 of the canonical TGFβ pathway, was high in serum-starved DN and KC fibroblast protein extracts, but pSMAD1/5/8 low at base line, was induced within 30 minutes of TGFβ1 stimulation, more so in KC than DN, suggesting a novel TGFβ1-SMAD1/5/8 axis in the cornea, that may be altered in KC. The serine/threonine kinases AKT, known to regulate proliferation, survival and biosynthetic activities of cells, were poorly activated in KC fibroblasts in high glucose media. Concordantly, alcohol dehydrogenase 1 (ADH1), an indicator of increased glucose uptake and metabolism, was reduced in KC compared to DN fibroblasts. By contrast, in low glucose (5.5 mM, normoglycemic) serum-free DMEM and ITS, cell survival and pAKT levels were comparable in KC and DN cells. Therefore, high glucose combined with serum-deprivation presents some cellular stress difficult to overcome by the KC stromal cells. Our study provides molecular insights into AKT and TGFβ signal changes in KC, and a mechanism for functional studies of stromal cells from KC corneas.
PMCID: PMC4172437  PMID: 25247416
10.  Mechanisms of dopamine transporter regulation in normal and disease states 
Trends in pharmacological sciences  2013;34(9):10.1016/
The dopamine transporter (DAT) controls the spatial and temporal dynamics of dopamine (DA) neurotransmission by driving reuptake of extracellular transmitter into presynaptic neurons. Many diseases such as depression, bipolar disorder, Parkinson’s disease, and attention deficit hyperactivity disorder are associated with abnormal DA levels, implicating DAT as a factor in their etiology. Medications used to treat these disorders and many addictive drugs target DAT and enhance dopaminergic signaling by suppressing transmitter reuptake. We now understand that transport and binding properties of DAT are regulated by complex and overlapping mechanisms that provide neurons the ability to modulate DA clearance in response to physiological demands. These processes are controlled by endogenous signaling pathways and affected by exogenous transporter ligands, demonstrating their importance for normal neurotransmission, drug abuse, and disease treatments. Increasing evidence supports the disruption of these mechanisms in DA disorders, implicating dysregulation of transport in disease etiologies and suggesting these processes as potential points for therapeutic manipulation of DA availability.
PMCID: PMC3831354  PMID: 23968642
cocaine; amphetamine; drug addiction; attention deficit hyperactivity disorder; bipolar disorder; Parkinson’s disease
11.  Prevalence of low back pain by anatomic location and intensity in an occupational population 
Low Back Pain (LBP) is a common and costly problem, with variation in prevalence. Epidemiological reports of rating of pain intensity and location within the low back area are rare. The objective is to describe LBP in a large, multi-center, occupational cohort detailing both point and 1-month period prevalence of LBP by location and intensity measures at baseline.
In this cross-sectional report from a prospective cohort study, 828 participants were workers enrolled from 30 facilities performing a variety of manual material handling tasks. All participants underwent a structured interview detailing pain rating and location. Symptoms in the lower extremities, demographic and other data were collected. Body mass indices were measured. Outcomes are pain rating (0–10) in five defined lumbar back areas (i) LBP in the past month and (ii) LBP on the day of enrollment. Pain ratings were reported on a 0–10 scale and subsequently collapsed with ratings of 1–3, 4–6 and 7–10 classified as low, medium and high respectively.
172 (20.8%) and 364 (44.0%) of the 828 participants reported pain on the day of enrollment or within the past month, respectively. The most common area of LBP was in the immediate paraspinal area with 130 (75.6%) participants with point prevalence LBP and 278 (77.4%) with 1-month period prevalence reported having LBP in the immediate paraspinal area. Among those 364 reporting 1-month period prevalence pain, ratings varied widely with 116 (31.9%) reporting ratings classified as low, 170 (46.7%) medium and 78 (21.4%) providing high pain ratings in any location. Among the 278 reporting 1-month period prevalence pain in the immediate paraspinal area, 89 (32.0%) reported ratings classified as low, 129 (46.4%), medium and 60 (21.6%) high pain ratings.
Pain ratings varied widely, however less variability was seen in pain location, with immediate paraspinal region being the most common. Variations may suggest different etiological factors related to LBP. Aggregation of different locations of pain or different intensities of pain into one binary classification of LBP may result in loss of information which may potentially be useful in prevention or treatment of LBP.
PMCID: PMC4153910  PMID: 25146722
Low back pain; Point prevalence; 1-month period prevalence; Intensity; Location; Epidemiological; Cross-sectional analysis
12.  Bumblebees Learn Polarization Patterns 
Current Biology  2014;24(12):1415-1420.
Foraging insect pollinators such as bees must find and identify flowers in a complex visual environment. Bees use skylight polarization patterns for navigation [1–3], a capacity mediated by the polarization-sensitive dorsal rim area (DRA) of their eye [4, 5]. While other insects use polarization sensitivity to identify appropriate habitats [6], oviposition sites, and food sources [7], to date no nonnavigational functions of polarization vision have been identified in bees. Here we investigated the ability of bumblebees (Bombus terrestris) to learn polarization patterns on artificial “flowers” in order to obtain a food reward. We show that foraging bumblebees can learn to discriminate between two differently polarized targets, but only when the target artificial “flower” is viewed from below. A context for these results is provided by polarization imaging of bee-pollinated flowers, revealing the potential for polarization patterns in real flowers. Bees may therefore have the ability to use polarization vision, possibly mediated by their polarization-sensitive DRA, both for navigation and to learn polarization patterns on flowers, the latter being the first nonnavigational function for bee polarization vision to be identified.
•Bumblebees (Bombus terrestris) learn polarization patterns on artificial “flowers”•Polarization patterns were only learned from downward-facing, pendant “flowers”•Polarization vision in bumblebees is not restricted to sun-compass navigation•Polarization patterns of petals may be a component of floral signaling
Foraging bumblebees (Bombus terrestris) learn polarization patterns on downward-facing artificial “flowers” to find food, demonstrating that their polarization vision is not restricted to sun-compass navigation. Polarization patterns occur on the petals of real flowers and may be a, hitherto overlooked, component of floral signaling.
PMCID: PMC4062934  PMID: 24909321
13.  SLC6 Transporters: Structure, Function, Regulation, Disease Association and Therapeutics 
Molecular aspects of medicine  2013;34(2-3):197-219.
The SLC6 family of secondary active transporters are integral membrane solute carrier proteins characterized by the Na+-dependent translocation of small amino acid or amino acid-like substrates. SLC6 transporters, which include the serotonin, dopamine, norepinephrine, GABA, taurine, creatine, as well as amino acid transporters, are associated with a number of human diseases and disorders making this family a critical target for therapeutic development. In addition, several members of this family are directly involved in the action of drugs of abuse such as cocaine, amphetamines, and ecstasy. Recent advances providing structural insight into this family have vastly accelerated our ability to study these proteins and their involvement in complex biological processes.
PMCID: PMC3602807  PMID: 23506866
Neurotransmitters; Biogenic amines; Amino acids; Epigenetics; Osmolyte balance; Cocaine; SLC6
14.  Machine Learning Techniques Accurately Classify Microbial Communities by Bacterial Vaginosis Characteristics 
PLoS ONE  2014;9(2):e87830.
Microbial communities are important to human health. Bacterial vaginosis (BV) is a disease associated with the vagina microbiome. While the causes of BV are unknown, the microbial community in the vagina appears to play a role. We use three different machine-learning techniques to classify microbial communities into BV categories. These three techniques include genetic programming (GP), random forests (RF), and logistic regression (LR). We evaluate the classification accuracy of each of these techniques on two different datasets. We then deconstruct the classification models to identify important features of the microbial community. We found that the classification models produced by the machine learning techniques obtained accuracies above 90% for Nugent score BV and above 80% for Amsel criteria BV. While the classification models identify largely different sets of important features, the shared features often agree with past research.
PMCID: PMC3912131  PMID: 24498380
15.  Correction: Evidence in Sheep for Pre-Natal Transmission of Scrapie to Lambs from Infected Mothers 
PLoS ONE  2014;9(1):10.1371/annotation/f7240569-aa33-4a9c-b7f0-75be4fad9999.
PMCID: PMC3894048
16.  SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching 
Journal of data mining in genomics & proteomics  2013;4(3):10.4172/2153-0602.1000133.
With the advent of Next-Generation (NG) sequencing, it has become possible to sequence a entire genomes quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for example when performing transcriptome studies, sequencing mitochondrial genomes, or characterizing exomes. With the raw DNA-library of a complete genome it would appear to be a trivial problem to identify reads of interest. But it is not always easy to incorporate well-known tools such as BLAST, BLAT, Bowtie, and SOAP directly into a bioinformatics pipelines before the assembly stage, either due to incompatibility with the assembler’s file inputs, or because it is desirable to incorporate information that must be extracted separately. For example, in order to incorporate flowgrams from a Roche 454 sequencer into the Newbler assembler it is necessary to first extract them from the original SFF files.
We present SlopMap, a bioinformatics software utility that allows quickly identification similar to the provided reference reads from either Roche 454 or Illumnia DNA library. With simple and intuitive command-line interface along with file output formats compatible to assembly programs, SlopMap can be directly embedded to biological data processing pipeline without any additional programming work. In addition, SlopMap preserves flowgram information needed for Roche 454 assembler.
PMCID: PMC3882202  PMID: 24404406
17.  Evidence in Sheep for Pre-Natal Transmission of Scrapie to Lambs from Infected Mothers 
PLoS ONE  2013;8(11):e79433.
Natural scrapie transmission from infected ewes to their lambs is thought to occur by the oral route around the time of birth. However the hypothesis that scrapie transmission can also occur before birth (in utero) is not currently favoured by most researchers. As scrapie is an opportunistic infection with multiple infection routes likely to be functional in sheep, definitive evidence for or against transmission from ewe to her developing fetus has been difficult to achieve. In addition the very early literature on maternal transmission of scrapie in sheep was compromised by lack of knowledge of the role of the PRNP (prion protein) gene in control of susceptibility to scrapie. In this study we experimentally infected pregnant ewes of known PRNP genotype with a distinctive scrapie strain (SSBP/1) and looked for evidence of transmission of SSBP/1 to the offspring. The sheep were from the NPU Cheviot flock, which has endemic natural scrapie from which SSBP/1 can be differentiated on the basis of histology, genetics of disease incidence and strain typing bioassay in mice. We used embryo transfer techniques to allow sheep fetuses of scrapie-susceptible PRNP genotypes to develop in a range of scrapie-resistant and susceptible recipient mothers and challenged the recipients with SSBP/1. Scrapie clinical disease, caused by both natural scrapie and SSBP/1, occurred in the progeny but evidence (including mouse strain typing) of SSBP/1 infection was found only in lambs born to fully susceptible recipient mothers. Progeny were not protected from transmission of natural scrapie or SSBP/1 by washing of embryos to International Embryo Transfer Society standards or by caesarean derivation and complete separation from their birth mothers. Our results strongly suggest that pre-natal (in utero) transmission of scrapie may have occurred in these sheep.
PMCID: PMC3832582  PMID: 24260219
18.  mcaGUI: microbial community analysis R-Graphical User Interface (GUI) 
Bioinformatics  2012;28(16):2198-2199.
Summary: Microbial communities have an important role in natural ecosystems and have an impact on animal and human health. Intuitive graphic and analytical tools that can facilitate the study of these communities are in short supply. This article introduces Microbial Community Analysis GUI, a graphical user interface (GUI) for the R-programming language (R Development Core Team, 2010). With this application, researchers can input aligned and clustered sequence data to create custom abundance tables and perform analyses specific to their needs. This GUI provides a flexible modular platform, expandable to include other statistical tools for microbial community analysis in the future.
Availability: The mcaGUI package and source are freely available as part of Bionconductor at
Supplementary Information: Supplementary data and figures are available at Bioinformatics online.
PMCID: PMC3413388  PMID: 22692220
19.  Gut microbial colonisation in premature neonates predicts neonatal sepsis 
Neonatal sepsis due to intestinal bacterial translocation is a major cause of morbidity and mortality. Understanding microbial colonisation of the gut in prematurity may predict risk of sepsis to guide future strategies to manipulate the microbiome.
Prospective longitudinal study of premature infants. Stool samples were obtained weekly. DNA was extracted and the V6 hypervariable region of 16S rRNA was amplified followed by high throughput pyrosequencing, comparing subjects with and without sepsis.
Six neonates were 24–27 weeks gestation at birth and had 18 samples analysed. Two subjects had no sepsis during the study period, two developed late-onset culture-positive sepsis and two had culture-negative systemic inflammation. 324 350 sequences were obtained. The meconium was not sterile and had predominance of Lactobacillus, Staphylococcus and Enterobacteriales. Overall, infants who developed sepsis began life with low microbial diversity, and acquired a predominance of Staphylococcus, while healthy infants had more diversity and predominance of Clostridium, Klebsiella and Veillonella.
In very low birth weight infants, the authors found that meconium is not sterile and is less diverse from birth in infants who will develop late-onset sepsis. Empiric, prolonged antibiotics profoundly decrease microbial diversity and promote a microbiota that is associated not only with neonatal sepsis, but the predominant pathogen previously identified in the microbiome. Our data suggest that there may be a ‘healthy microbiome’ present in extremely premature neonates that may ameliorate risk of sepsis. More research is needed to determine whether altered antibiotics, probiotics or other novel therapies can re-establish a healthy microbiome in neonates.
PMCID: PMC3724360  PMID: 22562869
20.  Odontogenic ameloblast-associated protein (ODAM) inhibits growth and migration of human melanoma cells and elicits PTEN elevation and inactivation of PI3K/AKT signaling 
BMC Cancer  2013;13:227.
The Odontogenic Ameloblast-associated Protein (ODAM) is expressed in a wide range of normal epithelial, and neoplastic tissues, and we have posited that ODAM serves as a novel prognostic biomarker for breast cancer and melanoma. Transfection of ODAM into breast cancer cells yields suppression of cellular growth, motility, and in vivo tumorigenicity. Herein we have extended these studies to the effects of ODAM on cultured melanoma cell lines.
The A375 and C8161 melanoma cell lines were stably transfected with ODAM and assayed for properties associated with tumorigenicity including cell growth, motility, and extracellular matrix adhesion. In addition, ODAM–transfected cells were assayed for signal transduction via AKT which promotes cell proliferation and survival in many neoplasms.
ODAM expression in A375 and C8161 cells strongly inhibited cell growth and motility in vitro, increased cell adhesion to extracellular matrix, and yielded significant cytoskeletal/morphologic rearrangement. Furthermore, AKT activity was downregulated by ODAM expression while an increase was noted in expression of the PTEN (phosphatase and tensin homolog on chromosome 10) tumor suppressor gene, an antagonist of AKT activation. Increased PTEN in ODAM-expressing cells was associated with increases in PTEN mRNA levels and de novo protein synthesis. Silencing of PTEN expression yielded recovery of AKT activity in ODAM-expressing melanoma cells. Similar PTEN elevation and inhibition of AKT by ODAM was observed in MDA-MB-231 breast cancer cells while ODAM expression had no effect in PTEN-deficient BT-549 breast cancer cells.
The apparent anti-neoplastic effects of ODAM in cultured melanoma and breast cancer cells are associated with increased PTEN expression, and suppression of AKT activity. This association should serve to clarify the clinical import of ODAM expression and any role it may serve as an indicator of tumor behavior.
PMCID: PMC3651709  PMID: 23648148
21.  Susceptibility of Young Sheep to Oral Infection with Bovine Spongiform Encephalopathy Decreases Significantly after Weaning 
Journal of Virology  2012;86(21):11856-11862.
Bovine spongiform encephalopathy (BSE) is a transmissible spongiform encephalopathy (TSE) (or prion disease) that is readily transmissible to sheep by experimental infection and has the shortest incubation period in animals with the ARQ/ARQ PRNP genotype (at codons 136, 154, and 171). Because it is possible that sheep in the United Kingdom could have been infected with BSE by being fed contaminated meat and bone meal supplements at the same time as cattle, there is considerable interest in the responses of sheep to BSE inoculation. Epidemiological evidence suggests that very young individuals are more susceptible to TSE infection; however, this has never been properly tested in sheep. In the present study, low doses of BSE were fed to lambs of a range of ages (∼24 h, 2 to 3 weeks, 3 months, and 6 months) and adult sheep. The incidence of clinical BSE disease after inoculation was high in unweaned lambs (∼24 h and 2 to 3 weeks old) but much lower in older weaned animals The incubation period was also found to be influenced by the genotype at codon 141 of the PRNP gene, as lambs that were LF heterozygotes had a longer mean incubation period than those that were homozygotes of either type. The results suggest that sheep in the United Kingdom would have been at high risk of BSE infection only if neonatal animals had inadvertently ingested contaminated supplementary foodstuffs.
PMCID: PMC3486293  PMID: 22915816
22.  Estimating population diversity with CatchAll 
Bioinformatics  2012;28(7):1045-1047.
Motivation: The massive data produced by next-generation sequencing require advanced statistical tools. We address estimating the total diversity or species richness in a population. To date, only relatively simple methods have been implemented in available software. There is a need for software employing modern, computationally intensive statistical analyses including error, goodness-of-fit and robustness assessments.
Results: We present CatchAll, a fast, easy-to-use, platform-independent program that computes maximum likelihood estimates for finite-mixture models, weighted linear regression-based analyses and coverage-based non-parametric methods, along with outlier diagnostics. Given sample ‘frequency count’ data, CatchAll computes 12 different diversity estimates and applies a model-selection algorithm. CatchAll also derives discounted diversity estimates to adjust for possibly uncertain low-frequency counts. It is accompanied by an Excel-based graphics program.
Availability: Free executable downloads for Linux, Windows and Mac OS, with manual and source code, at
PMCID: PMC3315724  PMID: 22333246
23.  Study protocol title: a prospective cohort study of low back pain 
Few prospective cohort studies of workplace low back pain (LBP) with quantified job physical exposure have been performed. There are few prospective epidemiological studies for LBP occupational risk factors and reported data generally have few adjustments for many personal and psychosocial factors.
A multi-center prospective cohort study has been incepted to quantify risk factors for LBP and potentially develop improved methods for designing and analyzing jobs. Due to the subjectivity of LBP, six measures of LBP are captured: 1) any LBP, 2) LBP ≥ 5/10 pain rating, 3) LBP with medication use, 4) LBP with healthcare provider visits, 5) LBP necessitating modified work duties and 6) LBP with lost work time. Workers have thus far been enrolled from 30 different employment settings in 4 diverse US states and performed widely varying work. At baseline, workers undergo laptop-administered questionnaires, structured interviews, and two standardized physical examinations to ascertain demographics, medical history, psychosocial factors, hobbies and physical activities, and current musculoskeletal disorders. All workers’ jobs are individually measured for physical factors and are videotaped. Workers are followed monthly for the development of low back pain. Changes in jobs necessitate re-measure and re-videotaping of job physical factors. The lifetime cumulative incidence of low back pain will also include those with a past history of low back pain. Incident cases will exclude prevalent cases at baseline. Statistical methods planned include survival analyses and logistic regression.
Data analysis of a prospective cohort study of low back pain is underway and has successfully enrolled over 800 workers to date.
PMCID: PMC3599364  PMID: 23497211
Epidemiology; Ergonomics; Cohort; Low back pain; NIOSH lifting equation
24.  Estimation of viral richness from shotgun metagenomes using a frequency count approach 
Microbiome  2013;1:5.
Viruses are important drivers of ecosystem functions, yet little is known about the vast majority of viruses. Viral shotgun metagenomics enables the investigation of broad ecological questions in phage communities. One ecological characteristic is species richness, which is the number of different species in a community. Viruses do not have a phylogenetic marker analogous to the bacterial 16S rRNA gene with which to estimate richness, and so contig spectra are employed to measure the number of virus taxa in a given community. A contig spectrum is generated from a viral shotgun metagenome by assembling the random sequence reads into groups of sequences that overlap (contigs) and counting the number of sequences that group within each contig. Current tools available to analyze contig spectra to estimate phage richness are limited by relying on rank-abundance data.
We present statistical estimates of virus richness from contig spectra. The program CatchAll ( was used to analyze contig spectra in terms of frequency count data rather than rank-abundance, thus enabling formal statistical analyses. Also, the influence of potentially spurious low-frequency counts on richness estimates was minimized by two methods, empirical and statistical. The results show greater estimates of viral richness than previous calculations in nearly all environments analyzed, including swine feces and reclaimed fresh water.
CatchAll yielded consistent estimates of richness across viral metagenomes from the same or similar environments. Additionally, analysis of pooled viral metagenomes from different environments via mixed contig spectra resulted in greater richness estimates than those of the component metagenomes. Using CatchAll to analyze contig spectra will improve estimations of richness from viral shotgun metagenomes, particularly from large datasets, by providing statistical measures of richness.
PMCID: PMC3869190  PMID: 24451229
Phage; Metagenomics; Virome; Ecology; Richness; CatchAll; Singleton
25.  Transitional States of Acrosomal Exocytosis and Proteolytic Processing of the Acrosomal Matrix in Guinea Pig Sperm 
In this study, we adapted a FluoSphere bead-binding assay to study the exposure and release of guinea pig sperm acrosomal components during the course of capacitation and acrosomal exocytosis. Prior to capacitation or the initiation of exocytosis, acrosomal proteins were not accessible to FluoSpheres coated with antibodies against two acrosomal matrix (AM) proteins, AM67 and AM50; during the course of capacitation and ionophore-induced acrosomal exocytosis, however, we detected the transient exposure of the solid-phase AM proteins on the surface of guinea pig sperm using the antibody-coated fluorescent beads. Several different transitional stages leading to complete acrosomal exocytosis were classified, and we propose these represent true, functional intermediates since some of the AM proteins are orthologues of mouse proteins that bind the zona pellucida of unfertilized eggs. In addition, we present evidence that implicates acrosin in the proteolytic processing of AM50 during AM disassembly. Thus, we propose that the transitional states of acrosomal exocytosis involve early binding of AM proteins to the zona pellucida (by what visually appear to be “acrosome-intact” sperm), maintenance of zona pellucida binding that coincides with the progressive exposure of AM proteins, and gradual proteolytic disassembly of the AM to allow sperm movement through the zona pellucida. We feel this “transitional states” model provides a more refined view of acrosomal function that supports a move away from the widely-held, overly simplistic, and binary “acrosome-reaction” model, and embraces a more dynamic view of acrosomal exocytosis that involves intermediate stages of the secretory process in zona pellucida binding and penetration.
PMCID: PMC3220745  PMID: 21919109
acrosin; acrosomal exocytosis; acrosomal matrix; acrosome

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