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2.  Dr. William Louis Rodman 
British Medical Journal  1916;1(2883):506.
PMCID: PMC2347147
PMCID: PMC1641838  PMID: 18736679
5.  Make it better but don't change anything 
With massive amounts of data being generated in electronic format, there is a need in basic science laboratories to adopt new methods for tracking and analyzing data. An electronic laboratory notebook (ELN) is not just a replacement for a paper lab notebook, it is a new method of storing and organizing data while maintaining the data entry flexibility and legal recording functions of paper notebooks. Paper notebooks are regarded as highly flexible since the user can configure it to store almost anything that can be written or physically pasted onto the pages. However, data retrieval and data sharing from paper notebooks are labor intensive processes and notebooks can be misplaced, a single point of failure that loses all entries in the volume. Additional features provided by electronic notebooks include searchable indices, data sharing, automatic archiving for security against loss and ease of data duplication. Furthermore, ELNs can be tasked with additional functions not commonly found in paper notebooks such as inventory control. While ELNs have been on the market for some time now, adoption of an ELN in academic basic science laboratories has been lagging. Issues that have restrained development and adoption of ELN in research laboratories are the sheer variety and frequency of changes in protocols with a need for the user to control notebook configuration outside the framework of professional IT staff support. In this commentary, we will look at some of the issues and experiences in academic laboratories that have proved challenging in implementing an electronic lab notebook.
PMCID: PMC2810290  PMID: 20098591
6.  Reduced inclination of cervical spine in a novel notebook screen system - implications for rehabilitation 
Professional working at computer notebooks is associated with high requirements on the body posture in the seated position. By the high continuous static muscle stress resulting from this position at notebooks, professionals frequently working at notebooks for long hours are exposed to an increased risk of musculoskeletal complaints. Especially in subjects with back pain, new notebooks should be evaluated with a focus on rehabilitative issues.
In a field study a new notebook design with adjustable screen was analyzed and compared to standard notebook position.
There are highly significant differences in the visual axis of individuals who are seated in the novel notebook position in comparison to the standard position. Also, differences are present between further alternative notebook positions. Testing of gender and glasses did not reveal influences.
This study demonstrates that notebooks with adjustable screen may be used to improve the posture. Future studies may focus on patients with musculoskeletal diseases.
PMCID: PMC3253038  PMID: 22118159
7.  From documents to datasets: A MediaWiki-based method of annotating and extracting species observations in century-old field notebooks 
ZooKeys  2012;235-253.
Part diary, part scientific record, biological field notebooks often contain details necessary to understanding the location and environmental conditions existent during collecting events. Despite their clear value for (and recent use in) global change studies, the text-mining outputs from field notebooks have been idiosyncratic to specific research projects, and impossible to discover or re-use. Best practices and workflows for digitization, transcription, extraction, and integration with other sources are nascent or non-existent. In this paper, we demonstrate a workflow to generate structured outputs while also maintaining links to the original texts. The first step in this workflow was to place already digitized and transcribed field notebooks from the University of Colorado Museum of Natural History founder, Junius Henderson, on Wikisource, an open text transcription platform. Next, we created Wikisource templates to document places, dates, and taxa to facilitate annotation and wiki-linking. We then requested help from the public, through social media tools, to take advantage of volunteer efforts and energy. After three notebooks were fully annotated, content was converted into XML and annotations were extracted and cross-walked into Darwin Core compliant record sets. Finally, these recordsets were vetted, to provide valid taxon names, via a process we call “taxonomic referencing.” The result is identification and mobilization of 1,068 observations from three of Henderson’s thirteen notebooks and a publishable Darwin Core record set for use in other analyses. Although challenges remain, this work demonstrates a feasible approach to unlock observations from field notebooks that enhances their discovery and interoperability without losing the narrative context from which those observations are drawn.
“Compose your notes as if you were writing a letter to someone a century in the future.”
Perrine and Patton (2011)
PMCID: PMC3406479  PMID: 22859891
Field notes; notebooks; crowd sourcing; digitization; biodiversity; transcription; text-mining; Darwin Core; Junius Henderson; annotation; taxonomic referencing; natural history; Wikisource; Colorado; species occurrence records
8.  LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory 
PLoS ONE  2013;8(7):e67460.
The electronic laboratory notebook (ELN) has the potential to replace the paper notebook with a marked-up digital record that can be searched and shared. However, it is a challenge to achieve these benefits without losing the usability and flexibility of traditional paper notebooks. We investigate a blog-based platform that addresses the issues associated with the development of a flexible system for recording scientific research.
Methodology/Principal Findings
We chose a blog-based approach with the journal characteristics of traditional notebooks in mind, recognizing the potential for linking together procedures, materials, samples, observations, data, and analysis reports. We implemented the LabTrove blog system as a server process written in PHP, using a MySQL database to persist posts and other research objects. We incorporated a metadata framework that is both extensible and flexible while promoting consistency and structure where appropriate. Our experience thus far is that LabTrove is capable of providing a successful electronic laboratory recording system.
LabTrove implements a one-item one-post system, which enables us to uniquely identify each element of the research record, such as data, samples, and protocols. This unique association between a post and a research element affords advantages for monitoring the use of materials and samples and for inspecting research processes. The combination of the one-item one-post system, consistent metadata, and full-text search provides us with a much more effective record than a paper notebook. The LabTrove approach provides a route towards reconciling the tensions and challenges that lie ahead in working towards the long-term goals for ELNs. LabTrove, an electronic laboratory notebook (ELN) system from the Smart Research Framework, based on a blog-type framework with full access control, facilitates the scientific experimental recording requirements for reproducibility, reuse, repurposing, and redeployment.
PMCID: PMC3720848  PMID: 23935832
9.  John P. Peters and the committee of 430 physicians. 
John Peters and his committee had a few basic goals. One was that local, state, and federal governments needed to provide money to construct facilities, support medical research and education, and care for the poor. And they wanted experts to call the shots. Over time, Peters and the committee got what they wanted for the most part: Hill-Burton money for building the hospitals, the rise of the National Institutes of Health, Medicare, Medicaid, a Veterans Administration system, and new and expanded medical schools. The experts calling the shots included David Kessler at the Food and Drug Administration and Surgeon General C. Everett Koop. In the halcyon days of American health system reform, back in 1993, Yale's Paul Beeson wrote about the Committee of 430 Physicians and its goals in the Pharos of Alpha Omega Alpha. Beeson was optimistic and he quoted from my 1991 JAMA health system reform editorial as a sharp contrast to what Fishbein had written - although coincidentally, we both quote Lincoln. My editorial began, "'with malice toward none, with charity for all...' so spoke Abraham Lincoln in his second inaugural address recognizing that he had no political consensus regarding either the constitutionality of states seceding or the morality of slavery being abolished. Nonetheless, he knew what was right and was able, through persuasive, often inspiring rhetoric, to conclude a bloody and decisive Civil War and constitute the foundation for this great republic.... Yet access to basic medical care for all of our inhabitants is still not a reality in this country. There are many reasons for this, not the least of which is a long-standing, systematic, institutionalized racial discrimination.... An aura of inevitablitiy is upon us. It is not acceptable morally, ethically, or economically for so many of our people to be medically uninsured or seriously underinsured. We can solve this problem. We have the knowledge and the resources, the skills, the time, and the moral prescience. We need only clear-cut objectives and proper organization of existing resources. Have we now the national will and leadership?" Beeson's answer to that question in 1993 was, "Yes, but not by one comprehensive act." He quoted Peters from his 1938 Annals of Internal Medicine article: "a sweeping program suddenly imposed in this country as a whole out of the head of any Jove would undoubtedly create confusion if not chaos. Thoughtful investigation and experiment promises more than grandiose projects born of emotional preconceptions. The programs must be built of an evolutionary manner, step by step." Very wise, very valid. But how long must our people wait?
PMCID: PMC2588694  PMID: 12074477
10.  Mediators between Theoretical and Practical Medieval Knowledge: Medical Notebooks from the Cairo Genizah and their Significance 
Medical History  2013;57(4):487-515.
This article presents a plethora of fragments from the medical notebooks found in the Cairo Genizah that comprise a unique source of historical data for scholarly study and for a better understanding of the ways in which medieval medical knowledge in Egypt was transferred from theory to practice and vice versa. These documents provide the most direct evidence we have for preferred practical medical recipes because they record the choices of medical practitioners in medieval Cairo. Since the language most commonly used in them was Judaeo-Arabic, they were evidently written by Jews. The medical genre in the notebooks was primarily pharmacopoeic, consisting of apparently original recipes for the treatment of various diseases. There are also a few notebooks on materia medica. The subject matter of the Genizah medical notebooks shows that they were mostly of an eclectic nature, i.e. the writers had probably learnt about these treatments and recipes from their teachers, applied them at the hospitals where they worked or copied them from the books they read. Foremost among the subjects dealt with were eye diseases, followed by skin diseases, coughs and colds, dentistry and oral hygiene, and gynaecological conditions. The writers of the Genizah notebooks apparently recorded the practical medical knowledge they wished to preserve for their future use as amateur physicians, students, traditional healers or professional practitioners.
PMCID: PMC3865955  PMID: 24069914
Cairo Genizah; History of Medicine; Jewish; Medieval Middle East; Middle Ages; Notebook
11.  Cytological and Biochemical Effects of St. John’s Wort Supplement (A Complex Mixture of St. John’s Wort, Rosemary and Spirulina) on Somatic and Germ Cells of Swiss Albino Mice 
Commercially available St. John’s wort supplement (SJWS) composed of an herbal mixture of St. John’s Wort (SJW), Rosemary (RM) and Spirulina (SP) is used as a dietary supplement for the treatment of psychiatric disorders. Although the minor ingredients, (RM and SP) are proven antioxidants, their quantity is quite insignificant as compared to the SJW, which is the major ingredient. Most of the toxic effects of SJWS are attributed to the main constituents of SJW which differ due to the influence of light (hypericin) and variations in temperature above freezing point (hyperforin). However, there are no reports on toxicity of SJWS maintained at room temperature in pharmacies and supermarkets. In view of the folkloric importance, immense (prescribed or unprescribed) use and a paucity of literature on SJWS, it was found worthwhile to (1) determine the genotoxic effects of SJWS in somatic and germ cells of mice and (2) investigate the role of biochemical changes, as a possible mechanism. The protocol included the oral treatment of mice with different doses (380, 760 and 1520 mg/kg/day) of SJWS for 7 days. The following experiments were conducted: (i) cytological studies on micronucleus test, (ii) cytogenetic analysis for meiotic chromosomes, (iii) cytological analysis of spermatozoa abnormalities, (iv) quantification of proteins and nucleic acids in hepatic and testicular cells and (v) estimation of malondialdehyde (MDA) and nonprotein sulfhydryl (NP-SH) in hepatic and testicular cells. The treatment increased the frequency of micronuclei in polychromatic erythrocytes (PCE) in the femora. It caused aberrations in chromosomes of testes and induced spermatozoa abnormalities. These changes might be attributed to the epigenetic mechanisms as revealed by an increase in concentrations of MDA and depletion of nucleic acids and NP-SH levels in both hepatic and testicular cells observed in the present study. Since, the samples of SJWS used were not drawn from extremities of light and temperature; the observed effect might not be related to the main constituents of SJW. However, these changes might be ascribed to the combined effect of terpenes, tannins, quercetin and flavonoids present in SJW.
PMCID: PMC3700001  PMID: 19151436
St. John’s Wort Supplement; cytology; somatic cells; germ cells; nucleic acids; malondialdehyde; nonprotein sulfhydryl groups
12.  John R. Paul and the Definition of Preventive Medicine 
John R. Paul, Professor of Preventive Medicine at the Yale University School of Medicine, wrote numerous monographs and papers defining and delimiting the field of preventive medicine and its fundamental science, clinical epidemiology. For Dr. Paul, preventive medicine was part of the continuum of clinical medicine; others believed that it was a separate entity deserving of departmental status. This paper discusses Dr. Paul's definition and philosophy of preventive medicine in contrast to other disciplines, such as social medicine and public health.
PMCID: PMC2596460  PMID: 6758366
13.  John N. Brady (1952-2009): a Generous Spirit 
Journal of Virology  2009;83(14):6975-6976.
John N. Brady, Chief of the Virus Tumor Biology Section of the Laboratory of Cellular Oncology, National Institutes of Health, died of cancer on 27 April 2009. John was a stellar member of the virology community. He was a longtime Journal of Virology reviewer and a member of the editorial board. He will be missed. Fatah Kashanchi of the George Washington University Medical Center has written John's memorial. Fatah worked with John at the NIH and published more than 30 papers with him. Fatah thanks all the people who contributed to John's obituary, including Kuan-Teh Jeang, Lou Laimins, Mary Loeken, Renaud Mehieux, Paul Lambert, Graziella Piras, Scott Gitlin, Paul Lindholm, Nadia Rosenthal, Sergi Nekhai, Brian Wigdahl, David Price, Susan J. Marriott, Cynthia Masison, Jurgen Dittmer, Eric Verdin, Bassel E. Sawaya, and John's longtime assistants Janet Duvall Grimm and Michael Radonovich, who gave immense support to all the individuals who went through John's lab.
PMCID: PMC2704784  PMID: 19474098
14.  eCAT: Online electronic lab notebook for scientific research 
eCAT is an electronic lab notebook (ELN) developed by Axiope Limited. It is the first online ELN, the first ELN to be developed in close collaboration with lab scientists, and the first ELN to be targeted at researchers in non-commercial institutions. eCAT was developed in response to feedback from users of a predecessor product. By late 2006 the basic concept had been clarified: a highly scalable web-based collaboration tool that possessed the basic capabilities of commercial ELNs, i.e. a permissions system, controlled sharing, an audit trail, electronic signature and search, and a front end that looked like the electronic counterpart to a paper notebook.
During the development of the beta version feedback was incorporated from many groups including the FDA's Center for Biologics Evaluation & Research, Uppsala University, Children's Hospital Boston, Alex Swarbrick's lab at the Garvan Institute in Sydney and Martin Spitaler at Imperial College. More than 100 individuals and groups worldwide then participated in the beta testing between September 2008 and June 2009. The generally positive response is reflected in the following quote about how one lab is making use of eCAT: "Everyone uses it as an electronic notebook, so they can compile the diverse collections of data that we generate as biologists, such as images and spreadsheets. We use to it to take minutes of meetings. We also use it to manage our common stocks of antibodies, plasmids and so on. Finally, perhaps the most important feature for us is the ability to link records, reagents and experiments."
By developing eCAT in close collaboration with lab scientists, Axiope has come up with a practical and easy-to-use product that meets the need of scientists to manage, store and share data online. eCAT is already being perceived as a product that labs can continue to use as their data management and sharing grows in scale and complexity.
PMCID: PMC2809322  PMID: 20334629
15.  An automated and reproducible workflow for running and analyzing neural simulations using Lancet and IPython Notebook 
Lancet is a new, simulator-independent Python utility for succinctly specifying, launching, and collating results from large batches of interrelated computationally demanding program runs. This paper demonstrates how to combine Lancet with IPython Notebook to provide a flexible, lightweight, and agile workflow for fully reproducible scientific research. This informal and pragmatic approach uses IPython Notebook to capture the steps in a scientific computation as it is gradually automated and made ready for publication, without mandating the use of any separate application that can constrain scientific exploration and innovation. The resulting notebook concisely records each step involved in even very complex computational processes that led to a particular figure or numerical result, allowing the complete chain of events to be replicated automatically. Lancet was originally designed to help solve problems in computational neuroscience, such as analyzing the sensitivity of a complex simulation to various parameters, or collecting the results from multiple runs with different random starting points. However, because it is never possible to know in advance what tools might be required in future tasks, Lancet has been designed to be completely general, supporting any type of program as long as it can be launched as a process and can return output in the form of files. For instance, Lancet is also heavily used by one of the authors in a separate research group for launching batches of microprocessor simulations. This general design will allow Lancet to continue supporting a given research project even as the underlying approaches and tools change.
PMCID: PMC3874632  PMID: 24416014
IPython; pandas; reproducibility; workflow; simulation; batch computation; provenance; big data
16.  A novel collaborative e-learning platform for medical students - ALERT STUDENT 
BMC Medical Education  2014;14:143.
The increasing complexity of medical curricula would benefit from adaptive computer supported collaborative learning systems that support study management using instructional design and learning object principles. However, to our knowledge, there are scarce reports regarding applications developed to meet this goal and encompass the complete medical curriculum. The aim of ths study was to develop and assess the usability of an adaptive computer supported collaborative learning system for medical students to manage study sessions.
A study platform named ALERT STUDENT was built as a free web application. Content chunks are represented as Flashcards that hold knowledge and open ended questions. These can be created in a collaborative fashion. Multiple Flashcards can be combined into custom stacks called Notebooks that can be accessed in study Groups that belong to the user institution. The system provides a Study Mode that features text markers, text notes, timers and color-coded content prioritization based on self-assessment of open ended questions presented in a Quiz Mode. Time spent studying and Perception of knowledge are displayed for each student and peers using charts. Computer supported collaborative learning is achieved by allowing for simultaneous creation of Notebooks and self-assessment questions by many users in a pre-defined Group. Past personal performance data is retrieved when studying new Notebooks containing previously studied Flashcards. Self-report surveys showed that students highly agreed that the system was useful and were willing to use it as a reference tool.
The platform employs various instructional design and learning object principles in a computer supported collaborative learning platform for medical students that allows for study management. The application broadens student insight over learning results and supports informed decisions based on past learning performance. It serves as a potential educational model for the medical education setting that has gathered strong positive feedback from students at our school.
This platform provides a case study on how effective blending of instructional design and learning object principles can be brought together to manage study, and takes an important step towards bringing information management tools to support study decisions and improving learning outcomes.
PMCID: PMC4131539  PMID: 25017028
Medical education; Computer supported collaborative learning; E-learning; Information management; Memory retention; Computer-assisted instruction; Tailored learning; Student-centered learning; Spaced repetition
17.  Innate immune markers that distinguish red deer (Cervus elaphus) selected for resistant or susceptible genotypes for Johne’s disease 
Veterinary Research  2013;44(1):5.
While many factors contribute to resistance and susceptibility to infectious disease, a major component is the genotype of the host and the way in which it is expressed. Johne’s disease is a chronic inflammatory bowel disease affecting ruminants and is caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP). We have previously identified red deer breeds (Cervus elaphus) that are resistant; have a low rate of MAP infection and do not progress to develop Johne’s disease. In contrast, susceptible breeds have a high rate of MAP infection as seen by seroconversion and progress to develop clinical Johne’s disease. The aim of this study was to determine if immunological differences exist between animals of resistant or susceptible breeds. Macrophage cultures were derived from the monocytes of deer genotypically defined as resistant or susceptible to the development of Johne’s disease. Following in vitro infection of the cells with MAP, the expression of candidate genes was assessed by quantitative PCR as well as infection rate and cell death rate. The results indicate that macrophages from susceptible animals show a significantly higher upregulation of inflammatory genes (iNOS, IL-1α, TNF-α and IL-23p19) than the macrophages from resistant animals. Cells from resistant animals had a higher rate of apoptosis at 24 hours post infection (hpi) compared to macrophages from susceptible animals. The excessive expression of inflammatory mRNA transcripts in susceptible animals could cause inefficient clearing of the mycobacterial organism and the establishment of disease. Controlled upregulation of inflammatory pathways coupled with programmed cell death in the macrophages of resistant animals may predispose the host to a protective immune response against this mycobacterial pathogen.
PMCID: PMC3574005  PMID: 23347398
18.  Genome-Wide Sequence Variation among Mycobacterium avium Subspecies paratuberculosis Isolates: A Better Understanding of Johne’s Disease Transmission Dynamics 
Mycobacterium avium subspecies paratuberculosis (M. ap), the causative agent of Johne’s disease, infects many farmed ruminants, wild-life animals, and recently isolated from humans. To better understand the molecular pathogenesis of these infections, we analyzed the whole-genome sequences of several M. ap and M. avium subspecies avium (M. avium) isolates to gain insights into genomic diversity associated with variable hosts and environments. Using Next-generation sequencing technology, all six M. ap isolates showed a high percentage of similarity (98%) to the reference genome sequence of M. ap K-10 isolated from cattle. However, two M. avium isolates (DT 78 and Env 77) showed significant sequence diversity (only 87 and 40% similarity, respectively) compared to the reference strain M. avium 104, a reflection of the wide environmental niches of this group of mycobacteria. Within the M. ap isolates, genomic rearrangements (insertions/deletions) were not detected, and only unique single nucleotide polymorphisms (SNPs) were observed among M. ap isolates. While more of the SNPs (~100) in M. ap genomes were non-synonymous, a total of ~6,000 SNPs were detected among M. avium genomes, most of them were synonymous suggesting a differential selective pressure between M. ap and M. avium isolates. In addition, SNPs-based phylo-genomics had a enough discriminatory power to differentiate between isolates from different hosts but yet suggesting a bovine source of infection to other animals examined in this study. Interestingly, the human isolate (M. ap 4B) was closely related to a M. ap isolate from a dairy facility, suggesting a common source of infection. Overall, the identified phylo-genomes further supported the idea of a common ancestor to both M. ap and M. avium isolates. Genome-wide analysis described here could provide a strong foundation for a population genetic structure that could be useful for the analysis of mycobacterial evolution and for the tracking of Johne’s disease transmission among animals.
PMCID: PMC3234532  PMID: 22163226
Mycobacteria; paratuberculosis; Johne’s disease; whole-genome sequencing; genomics; pathogenesis
19.  St. John’s Wort inhibit adipocyte differentiation and induces insulin resistance in adipocytes 
Adipocytes are insulin sensitive cells that play a major role in energy homeostasis. Obesity is the primary disease of fat cells and a major risk factor for the development of Type II diabetes, cardiovascular disease, and metabolic syndrome. Obesity and its related disorders result in dysregulation of the mechanisms that control adipocyte gene expression and function. To identify potential novel therapeutic modulators of adipocytes, we screened 425 botanical extracts for their ability to modulate adipogenesis and insulin sensitivity. We observed that less than 2% of the extracts had substantial effects on adipocyte differentiation of 3T3-L1 cells. Two of the botanical extracts that inhibited adipogenesis were extracts from St. John’s Wort (SJW). Our studies revealed that leaf and flower, but not root, extracts isolated from SJW inhibited adipogenesis as judged by examining PPARγ and adiponectin levels. We also examined the effects of these SJW extracts on insulin sensitivity in mature 3T3-L1 adipocytes. Both leaf and flower extracts isolated from SJW substantially inhibited insulin sensitive glucose uptake. The specificity of the observed effects was demonstrated by showing that treatment with SJW flower extract resulted in a time and dose dependent inhibition of insulin stimulated glucose uptake. SJW is commonly used in the treatment of depression. However, our studies have revealed that SJW may have a negative impact on adipocyte related diseases by limiting differentiation of preadipocytes and significantly inducing insulin resistance in mature fat cells.
PMCID: PMC3019118  PMID: 19646953
20.  Bioactive xanthones from the roots of Hypericum perforatum (common St John’s wort) 
Extracts of Hypericum perforatum L. (common St John’s wort; Hypericaceae) are sold as phytopharmaceuticals and herbal supplements to treat mild to moderate depression and as food additives. Extensively cultivated in Europe, plants can be infected by anthracnose (Colletotrichum gloeosporioides), a virulent fungal pathogen that causes tissue necrosis and dramatically decreases crop value. Such infections triggered the production of new secondary metabolites, specifically xanthones, in cell culture experiments.
Bioassay-guided fractionation of H. perforatum root extracts, testing for growth inhibition of plant pathogenic fungi from the genera Colletotrichum, Botrytis, Fusarium and Phomopsis, was performed. In vitro anti-inflammatory activity through inhibition of COX-1, COX-2 and 5-LOX-catalyzed LTB4 formationwas also evaluated. Extracts were analyzed by various chromatographic means and structure elucidation was performed using data from nuclear magnetic resonance and mass spectrometry.
Researchers have previously described constituents from the aerial parts of this species, but few reports describe secondary metabolites found in underground parts, of particular interest because the lower stem and upper root are often sites of fungal infection. Thiswork resulted in the isolation of three xanthones: 1,6-dihydroxy-5-methoxy-4′,5′-dihydro-4′,4′,5′-trimethylfurano-(2′,3′:3,4)-xanthone; 4,6-dihydroxy-2,3-dimethoxyxanthone; and cis-kielcorin, one of which possessed novel bioactivity against species of Phomopsis and inhibited 5-LOX-mediated LTB4 formation.
PMCID: PMC3318991  PMID: 21218475
Hypericaceae; Colletotrichum; anthracnose; Phomopsis; xanthones; anti-inflammatory
21.  St John’s Wort protein, p27SJ, regulates the MCP-1 promoter 
Molecular immunology  2008;45(15):4028-4035.
St. John's Wort is commonly known for its antiviral, antidepressant, and cytotoxic properties, but traditionally St. John's Wort has also been used to treat inflammation. In this study, we sought to characterize the mechanisms used by St. John's Wort to treat inflammation by examining the effect of the recently isolated protein from St. John's Wort, p27SJ on the expression of MCP-1. By employing an adenovirus expression vector, we demonstrate that a low concentration of p27SJ upregulates the MCP-1 promoter through the transcription factor C/EBPβ. In addition, we found that C/EBPβ-homologous protein (CHOP) or siRNA-C/EBPβ significantly reduced the ability of p27SJ to activate MCP-1 gene expression. Results from protein-protein interaction studies illustrate the existence of a physical interaction between p27SJ and C/EBPβ in microglial cells. The use of chromatin immunoprecipitation assay (ChIP) led to the identification of a new cis-element that is responsive to C/EBPβ within the MCP-1 promoter. Association of C/EBPβ with MCP-1 DNA was not affected by the presence of p27SJ. The biological activity of MCP-1 produced by cultures of adenovirus-p27SJ transduced cells was increased relative to controls as measured by the transmigration of human Jurkat cells. Thus, we conclude that at high concentration, p27SJ is a potential agent that may be developed as a modulator of MCP-1 leading to the inhibition of the cytokine-mediated inflammatory responses.
PMCID: PMC2570374  PMID: 18649942
22.  The Ex Situ Comparison of Two Improved St. John’s wort (Hypericum perforatum) Cultivars with an Iranian Wild Population 
Acta horticulturae  2011;925:163-170.
This research is part of an ongoing selection and breeding effort to target Iranian genotypes of Hypericum perforatum with the potential to produce higher amounts of desired secondary metabolites and greater resistance to fungal pathogens. There is a significant interest in the development of such cultivars to supply materials to the local pharmaceutical industries. For this reason, two improved cultivars of H. perforatum (“Gold” and “Veperikon”) were compared with a wild Iranian population (Ardabile population) under common garden conditions in Iran. Plants were cultivated from seed in a greenhouse and seedlings were transplanted after one month to the field plots. The statistical design of this study was a Randomized Complete Block Design with three replications. During the period of full flowering, selected phenological (number of days to flowering), morphological (plant height, mean leaf area, number of black glands/leaf) and chemical (hypericin and pseudohypericin content) characteristics were assessed. Our observations were that the “Veperikon” cultivar is very sensitive to soil-borne diseases. All transplanted seedlings were infected by the plant pathogenic fungus Colletotrichum gloeosporioides, which caused necrosis of the whole plant. Both the “Gold” cultivar and plants from the wild population persisted despite mild infections with C. gloeosporioides and produced flowering shoots at both the first and second years after cultivation. The “Gold” cultivar was superior to the Ardabile population in terms of phenological and morphological characteristics. The average naphthodianthrone content (% dry weight of tissue) for the wild Iranian population was 0.04(±0.01)%, but for the “Gold” cultivar, 0.33(±0.43)%. These data indicate that selection and directed cultivation of Iranian H. perforatum plants can result in plants with improved morphological, phenological and chemical characteristics.
PMCID: PMC3364716  PMID: 22661825
Hypericaceae; breeding lines; phenology; morphology; naphthodianthrones; hypericin; Colletotrichum gloeosporioides
23.  Evaluation of two mutants of Mycobacterium avium subsp. paratuberculosis as candidates for a live attenuated vaccine for Johne’s disease 
Vaccine  2011;29(29-30):4709-4719.
Control of Johne’s disease, caused by Mycobacterium avium subsp. paratuberculosis, has been difficult because of a lack of an effective vaccine. To address this problem we used targeted gene disruption to develop candidate mutants with impaired capacity to survive ex vivo and in vivo to test as a vaccine. We selected relA and pknG, genes known to be important virulence factors in Mycobacterium tuberculosis and Mycobacterium bovis, for initial studies. Deletion mutants were made in a wild type Map (K10) and its recombinant strain expressing the green fluorescent protein (K10-GFP). Comparison of survival in an ex vivo assay revealed deletion of either gene attenuated survival in monocyte-derived macrophages compared to survival of wild-type K10. In contrast, study in calves revealed survival in vivo was mainly affected by deletion of relA. Bacteria were detected in tissues from wild-type and the pknG mutant infected calves by bacterial culture and PCR at three months post infection. No bacteria were detected in tissues from calves infected with the relA mutant (P < 0.05). Flow cytometric analysis of the immune response to the wild-type K10-GFP and the mutant strains showed deletion of either gene did not affect their capacity to elicit a strong proliferative response to soluble antigen extract or live Map. Quantitative RT-PCR revealed genes encoding IFN-γ, IL-17, IL-22, T-bet, RORC, and granulysin were up-regulated in PBMC stimulated with live Map three months post infection compared to the response of PBMC pre-infection. A challenge study in kid goats showed deletion of pknG did not interfere with establishment of an infection. As in calves, deletion of relA attenuated survival in vivo. The mutant also elicited an immune response that limited colonization by challenge wild type Map. The findings show the relA mutant is a good candidate for development of a live attenuated vaccine for Johne’s disease.
PMCID: PMC3114198  PMID: 21565243
Mycobacterium avium subsp. paratuberculosis; Johne’s disease; paratuberculosis; Crohn’s disease; live vaccine
24.  The Treatment of Minor Depression with St. John’s Wort or Citalopram: Failure to Show Benefit over Placebo 
Journal of psychiatric research  2011;45(7):931-941.
This paper presents new data addressing two important controversies in psychiatry: the construct of Minor Depression (MinD) and the efficacy of St. John’s Wort for milder forms of depressive disorders. Data are from a three-arm, 12 week, randomized clinical trial of investigating the efficacy of St. John’s Wort (810 mg/day), citalopram (20 mg/day), or placebo for acute treatment of MinD. Due to a high placebo response on all outcome measures, neither St. John’s Wort nor citalopram separated from placebo on change in depressive symptom severity, quality of life, or well-being. However, systematic assessment of potential adverse effects (AEs) led to three important observations: (1) prior to the administration of study compound, 60% of subjects endorsed items that would be characterized as AEs once study compound was administered, (2) St. John’s Wort and citalopram were each associated with a significant number of new or worsening AEs during treatment, and (3) using a structured interview for identifying AEs at baseline and during treatment is informative. MinD was not responsive to either a conventional antidepressant or a nutraceutical, and both compounds were associated with a notable side effects burden. Other treatment approaches for MinD should be investigated.
PMCID: PMC3137264  PMID: 21632064
25.  Evaluation of an indigenous ELISA for diagnosis of Johne’s disease and its comparison with commercial kits 
Indian Journal of Microbiology  2007;47(3):251-258.
Country lacks sensitive and indigenous diagnostic kits for the screening of goats and sheep against Johne’s disease. Therefore an indigenous ELISA kit was developed using protoplasmic antigen from native Mycobacterium avium subspecies paratuberculosis ‘Bison Type’ strain of goat origin (Kit 1). In the present study, kit 1 and two commercial kits (kit 2 and 3) were evaluated with respect to ‘Gold Standard’ fecal culture in 71 animals (55 goats and 16 sheep). Kit 1 using indigenous antigen (protoplasmic antigen) was sensitive at very low concentration (0.1 μgm / well) as compared to purified commercial protoplasmic antigen (4 μgm / well) used in kit 2, in the Type 1 reactors (strong positive as positive). Screening of 71 animals by fecal culture detected 38.0% animals (goats-40.0%, sheep-31.2%) as positive (clinical shedders of bacilli) from these farm animals. Of the farm animals located at Central Institute for Research on Goats, herds of goat were endemic whereas, sheep flocks were comparatively resistant to Johne’s disease. The 29.5 and 61.9, 15.4 and 57.7 and 4.2 and 14.0% animals (goats and sheep) were in the category of sero-reactors type 1 and 2 of the ELISA kits 1, 2 and 3, respectively. In the type 1 sero-reactors, sensitivity and specificity of kit 1, 2 and 3 was 53.7 and 86.0, 17.8 and 86.0 and 3.5 and 94.7%, respectively. Indigenous ELISA test (kit 1) was significantly superior for the screening of goatherds and sheep flocks against JD as compared to commercial ELISA kits (Kit 2 and 3). In comparison to kit 2 and 3, kit 1 had highest sensitivity, comparable specificity and substantial to nearly perfect proportional agreement (Kappa Scores) with respect to ‘Gold standard’ fecal culture in goats and sheep. Disease being endemic in herds and flocks screened using ELISA kits, Type I sero-rectors had better correlation with fecal culture in comparison to Type II sero-reactors therefore, used for estimation of sero-prevalence. Newly developed Indigenous ELISA kit was simple, inexpensive, sensitive and reliable for screening of goats and sheep population against Johne’s disease. The study reports high prevalence of Johne’s disease in farm goatherds and sheep flocks, using sensitive tests (fecal culture and ELISA kit). Results of Type 1 reaction in kit 1 were optimally correlated with culture and were good for estimating the sero-prevalence. For controlling Johne’s disease in endemic herds initial removal of the animals in strong positive category (Tyep 1 reactors), may help to remove heavy shedders.
PMCID: PMC3450340  PMID: 23100673
Johne’s disease; Mycobacterium avium subsp. paratuberculosis; Protoplasmic antigen; Diagnosis; Fecal culture; ELISA kit

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