Awesome References to Ocimum Biosolutions


I started to write a post on the Gene Logic database references and I realized that we have a lot more than that, so I thought that while I was at it, I could put together some of the recent references to other products that we have.  I am hoping that one of you very smart folks will point out those that I am not aware of and let me build this awesome collection.

I shall start with 2011 first…. yes we already have some that appeared this year….

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Articles in 2011

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a Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK

this paper references our Campylobacter jejuni chip

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2. Determination of drug susceptibility patterns and genotypes of Mycobacterium tuberculosis isolates from Kanpur district, North India

and Devendra Singh ChauhanbE-mail The Corresponding Author
We have a wonderful spoligotyping kit that has been used by a large number of researchers worldwide. This publication references those kits that were manufactured by Ocimum Biosolutions.
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3. Establishing reference genes for use in real-time quantitative PCR analysis of early equine embryos

primers used in equine studies… nice

I am wondering if this is too much information overload for one day, but it isn’t every Sunday that I get all to myself so I shall indulge in some of this fun stuff more.

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4.  Pathology of Camel Tuberculosis and Molecular Characterization of Its Causative Agents in Pastoral Regions of Ethiopia

Gezahegne Mamo2,3*, Gizachew Bayleyegn2, Tesfaye Sisay Tessema2, Mengistu Legesse1,3, Girmay Medhin1, Gunnar Bjune3, Fekadu Abebe3, Gobena Ameni1

1 Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia, 2 Faculty of Veterinary Medicine, Addis Ababa University, Debre Zeit, Ethiopia, 3 Department of General Practice and Community Medicine, Faculty of Medicine, Institute of Health and Society, University of Oslo, Oslo, Norway

I found this especially interesting as the study of camel tuberculosis in Ethiopia.

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5. Functional Promoter Polymorphisms Govern Differential Expression of HMG-CoA Reductase Gene in Mouse Models of Essential Hypertension

[HTML] from plos.orgPJ Sonawane, BS Sahu, BK Sasi, P Geedi… – PloS one, 2011 – dx.plos.org
… The following oligos and their complementary strands were obtained from Ocimum Biosolutions,
India

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6. Genetic Alliance Registry and BioBank: a novel disease advocacy-driven research solution

Sharon F Terry1,2, Elizabeth J Horn1, Joan Scott3,4 & Patrick F Terry2,3,5

† Author for correspondence
The Genetic Alliance Registry and BioBank was founded in 2003 on the principal that a shared infrastructure would facilitate easy flow of resources and accelerate disease-specific research.
The article mentions Gene Logic as a partner for Biorepository, TRIMS registry, Genesis data mining software, Clinical questionnaire interface

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7. A Phase II Trial of Paclitaxel and Carboplatin in Women With Advanced or Recurrent Uterine Carcinosarcoma

RA Lacour, E Euscher, EN Atkinson… – International …, 2011 – pdfs.journals.lww.com
 Likewise, defects in DNA mismatch repair and TP53 have been recognized as factors in uterine
CS tu- morigenesis.23 This, along with the suggestion of PARP over- expression in uterine CS
(ASCENTA database; Gene Logic, Gaithersburg, Md), brings the exploration of novel

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8. [HTML] Identifying Consensus Disease Pathways in Parkinson’s Disease Using an Integrative Systems Biology Approach

[HTML] from plos.orgYJK Edwards, GW Beecham, WK Scott, S Khuri… – PloS one, 2011 – dx.plos.org
… of Medicine, University of Miami, Miami, Florida, United States of America, 3 Department of
Neurology and Molecular and Cellular Pharmacology, Miller School of Medicine, University of
Miami, Miami, Florida, United States of America, 4 Gene Logic, Gaithersburg, Maryland

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11. [PDF] Pandemic (H1N1) 2009 influenza virus induces weaker host immune responses in vitro: a possible mechanism of high transmissibility

[PDF] from virologyj.comS Mukherjee, VC Vipat, AC Mishra, SD Pawar… – Virology …, 2011 – virologyj.com
 MS EXCEL [15]. Data Analysis Microarray data analysis was carried out with
GENOWIZ Microarray data and pathway analysis tool (Ocimum Biosolutions,
Hyderabad, India).

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12. Genome-Wide Analysis of RNA Extracted from Isolated Mitochondria.

E Eliyahu, D Melamed… – Methods in molecular biology (Clifton, …, 2011 – Springer
 11. Slides Blocking Buffer – 0.5% BSA (A7906 sigma), 5× saline- sodium citrate buffer (SSC),
and 1% SDS. 12. Hybridization Buffer – 2× MWG buffer (Ocimum Biosolutions 1180-000010).

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13.[PDF] Distribution pattern of HCV genotypes & its association with viral load

[PDF] from icmr.nic.inA Chakravarti, G Dogra, V Verma… – Indian J Med Res, 2011 – icmr.nic.in
 out at 42 0C for 1 h. Direct PCR was performed with the cDNA in the reaction mixture containing
PCR buffer (10 X), 2.5 mmol/µl MgCl2, 250 µmol/µl dNTPs, 0.75 U Taq DNA polymerase (MBI
Fermentas, Lithunia), and 20 pmol primers (Ocimum Biosolutions, Hyderabad)

Articles in 2010

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1 . OI-57, a genomic island of Escherichia coli O157, is present in other seropathotypes of Shiga toxin-producing E. coli associated with severe human disease

Lejla Imamovic, Rosangela Tozzoli, Valeria Michelacci, Fabio Minelli,Maria Luisa Marziano, Alfredo Caprioli, and Stefano Morabito*

European Union Reference Laboratory for Escherichia coli, Istituto Superiore di Sanità, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Rome, Italy

Damien B. B. P. Paris A E F, Ewart W. Kuijk B C, Bernard A. J. Roelen A D and Tom A. E. Stout A D

Italian researchers using our extremely popular E-coli chip

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2.  Crucial Role for Insertion Sequence Elements inLactobacillus helveticus Evolution as Revealed by Interstrain Genomic Comparison {triangledown}

Pawel Kaleta,1 John O’Callaghan,1 Gerald F. Fitzgerald,2,3 Thomas P. Beresford,1* and R. Paul Ross1,2

Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, County Cork, Ireland,1 Alimentary Pharmabiotic Centre, Cork, County Cork, Ireland,2Department of Microbiology, University College Cork, Cork, County Cork, Ireland3

And now this one came from Ireland and it uses a custom cDNA chip that they obtained from us. Very nice

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3. Compensations for Diminished Terminal Oxidase Activity in Escherichia coli

CYTOCHROME bd-II-MEDIATED RESPIRATION AND GLUTAMATE METABOLISM*

Mark Shepherd,1Guido Sanguinetti§,Gregory M. Cook and Robert K. Poole

This one also references the E-coli chip used at Sheffield.

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4.  Diabetogenic glucose and insulin concentrations modulate transcriptom and protein levels involved in tumour cell migration, adhesion and proliferation

K Masur1, C Vetter1, A Hinz1, N Tomas1, H Henrich1, B Niggemann1 and K S Zänker1

 

this also uses some of our custom chips.

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5. Comparison of Restriction Fragment Length Polymorphism with the Polymorphic Guanine-Cytosine-Rich Sequence and Spoligotyping for Differentiation ofMycobacterium tuberculosis Isolates with Five or Fewer Copies of IS6110{triangledown}

Laura Flores,1 Leah G. Jarlsberg,1 Elizabeth Y. Kim,1 Dennis Osmond,2Jennifer Grinsdale,3 Masae Kawamura,3 Ed Desmond,4 Philip C. Hopewell,1 and Midori Kato-Maeda1*

Francis J. Curry National Tuberculosis Center, Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, Department of Medicine, University of California, San Francisco, San Francisco, California,1 Department of Epidemiology and Biostatistics University of California, San Francisco, San Francisco, California,2 Tuberculosis Control Section, San Francisco Department of Public Health,3 Microbial Diseases Laboratory, California Department of Public Health, Richmond, California4

this also uses our spoligotyping kits.

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6.  Sphingosine 1-phosphate receptor 1 and 3 are upregulated in multiple sclerosis lesions

this uses our oligos.

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7. Are adenosquamous lung carcinomas a simple mix of adenocarcinomas andsquamous cell carcinomas, or more complex at the molecular level?

This paper by french researchers uses our oligoset.
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8.  Host gene expression profiling in influenza A virus-infected lung epithelial (A549) cells: a comparative analysis between highly pathogenic and modified H5N1 viruses

Alok K Chakrabarti,corresponding author1 Veena C Vipat,1 Sanjay Mukherjee,1 Rashmi Singh,1Shailesh D Pawar,1 and Akhilesh C Mishra1
1Microbial Containment Complex, National Institute of Virology, Sus Road, Pashan, Pune – 411021 India
This refers to our Genowiz tool for data analysis.
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10. Transcriptional changes associated with ethanol tolerance in Saccharomyces cerevisiaeDragana Stanley, Paul J. Chambers, Grant A. Stanley, Anthony Borneman and Sarah FraserThey used Genowiz for their analysis.

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11. ResearchpARIS-htt: an optimised expression platform to study huntingtin reveals functional domains required for vesicular traffickingRaúl Pardo†1,2,3, Maria Molina-Calavita†1,2,3, Ghislaine Poizat1,2,3, Guy Keryer1,2,3, Sandrine Humbert1,2,3 and Frédéric Saudou*1,2,

very interesting paper found in molecular brain.
pARIS-htt was engineered based on the cDNA of fulllengh human htt using OptGene (Ocimum Biosolutions,Hyderabad, India) gene optimizing tool.

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Alexander T. Fleck1,*, Thandar Nye1, Cornelia Repenning2, Frank Stahl2, Marc Zahn1 and Manfred K. Schenk1

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Andrea von Groll1*, Anandi Martin1, Matthias Stehr2, Mahavir Singh2, Françoise Portaels1, Pedro Eduardo Almeida da Silva3, Juan Carlos Palomino1
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14. Effect of osmotic stress on plant growth promoting Pseudomonas spp.Sandhya VAli SZVenkateswarlu BReddy GGrover M.Department of Microbiology, Central Research Institute for Dryland Agriculture, Santoshnagar, Hyderabad, Andhra Pradesh, India.

Abstract

In this study we isolated and screened drought tolerant Pseudomonas isolates from arid and semi arid crop production systems of India. Five isolates could tolerate osmotic stress up to -0.73 MPa and possessed multiple PGP properties such as P-solubilization, production of phytohormones (IAA, GA and cytokinin), siderophores, ammonia and HCN however under osmotic stress expression of PGP traits was low compared to non-stressed conditions. The strains were identified as Pseudomonas entomophila, Pseudomonas stutzeri, Pseudomonas putida, Pseudomonas syringae and Pseudomonas monteilli respectively on the basis of 16S rRNA gene sequence analysis. Osmotic stress affected growth pattern of all the isolates as indicated by increased mean generation time. An increase level of intracellular free amino acids, proline, total soluble sugars and exopolysaccharides was observed under osmotic stress suggesting bacterial response to applied stress. Further, strains GAP-P45 and GRFHYTP52 showing higher levels of EPS and osmolytes (amino acids and proline) accumulation under stress as compared to non-stress conditions, also exhibited higher expression of PGP traits under stress indicating a relationship between stress response and expression of PGP traits. We conclude that isolation and screening of indigenous, stress adaptable strains possessing PGP traits can be a method for selection of efficient stress tolerant PGPR strains.

Tags

This references our sequencing services.

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15. Nitrile-metabolizing potential of Amycolatopsis sp. IITR215

Vikash Babua, Shilpia and Bijan ChoudhuryCorresponding Author Contact InformationaE-mail The Corresponding Author

a Department of Biotechnology, Indian Institute of Technology, IIT Roorkee, Roorkee-247667, Uttarakhand, India

Abstract

Strain Amycolatopsis sp. IITR215 was isolated from a sewage sample using polyacrylonitrile powder as the sole nitrogen source. Identification was performed by 16S rDNA analysis. The isolated strain harbored multiple nitrile-metabolizing enzymes having a wide range of substrate specificities. It metabolized nitrile and amide compounds with constitutive enzymes. Studies using an amidase inhibitor showed that hydrolysis of acrylonitrile and acrylamide occurred due to nitrile hydratase and amidase, respectively, while hydrolysis of hexanenitrile was due to the action of either nitrilase or a second nitrile hydratase/amidase system. The inhibitory effects of N-bromosuccinimide and N-ethylmaleimide on enzymes of this culture were also studied and this further indicated the involvement of either a nitrilase or a second nitrile hydratase/amidase system for hydrolysis of hexanenitrile. Interestingly, hexanenitrile hydrolysis exhibited an optimum temperature of 55 °C, whereas acrylonitrile and acrylamide hydrolysis showed an optimum temperature of 45 °C. The optimum pH was 5.8 for hexanenitrile hydrolysis and 7.0 for acrylonitrile and acrylamide hydrolysis. Hexanenitrile hydrolysis by enzymes of this strain showed better organic solvent tolerance in the presence of alcohols. The maximum enzyme activity of nitrile-metabolizing enzymes was found using media containing isobutyramide as the nitrogen source. This is the first report on constitutive multiple enzymes from the Amycolatopsis genus.

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This references our sequencing services

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16. Characterization of Pseudomonas aeruginosa RM-3 as a Potential Biocontrol Agent

Authors: Minaxi1; Saxena, Jyoti2

Source: Mycopathologia, Volume 170, Number 3, September 2010 , pp. 181-193(13)

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This references our sequencing services.

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Articles in 2009

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Kazuhiro Daino, Nicolas Ugolin, Sandrine Altmeyer-Morel, Marie-Noëlle Guilly, Sylvie Chevillard,

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2. TLR2 polymorphisms, Arg753Gln and Arg677Trp, are not associated with increased burden of tuberculosis in Indian patients Debasis Biswas1, Shailendra K Gupta2, Girish Sindhwani3and Abhishek Patras1

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3. Indian Biotech Sector Paving for Strong Growth

Deepak Ranjan , Shuchi Jaiswal

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4.Vitamin D: bringing light to the issue

Stiff, Lynn,Miller, Sharon M.

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Alison I. Graham, Stuart Hunt, Sarah L. Stokes§, Neil Bramall§, Josephine Bunch§,1, Alan G. Cox§, Cameron W. McLeod§ and Robert K. Poole‡,2

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Michael Berger1, Anca Farcas1, Marcel Geertz1, Petya Zhelyazkova1, Klaudia Brix1, Andrew Travers2 & Georgi Muskhelishvili1

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7.A conserved small RNA promotes silencing of the outer membrane protein YbfM

Anders Aamann Rasmussen,Jesper Johansen, Jesper S. Nielsen, Martin Overgaard, Birgitte Kallipolitis, Poul Valentin-Hansen
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S Natesh, MK Bhan

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Mahatsangy Raharijaona1,2#, Soazig Le Pennec3,4#, Julie Poirier3,4, Delphine Mirebeau-Prunier3,4,5, Clothilde Rouxel3,4, Caroline Jacques3,4, Jean-Fred Fontaine3,4, Yves Malthiery3,4,5, Rémi Houlgatte1,2, Frédérique Savagner1,3,4,5*

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9. LIMS IMPLEMENTATION IN A GENOTYPING STUDY

[PDF] from iupui.eduD Kennedy – 2009 – scholarworks.iupui.edu

 The LIMS application used was Biotracker TM (Ocimum Biosolutions), and its modular

design led users through each step  Informatics), Biotracker (Ocimum Biosolutions

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10. Interstrain genomic comparison reveals a crucial role for IS elements in the evolution of Lactobacillus helveticus.
P Kaleta, J O’Callaghan, GF Fitzgerald… – Applied and …, 2009 – Am Soc Microbiol
 147 148 Array design. cDNA microarrays were obtained from the Ocimum Biosolutions Ltd. 149 
prepared by mixing 40 µl of purified labelled DNA with 10 µl of salmon sperm DNA 193 (1 µg/
µl) and 120 µl of salt-based hybridization buffer (Ocimum Biosolutions Ltd.)

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11. Parkinson’s disease-associated parkin colocalizes with Alzheimer’s disease and multiple sclerosis brain lesions
ME Witte, JGJM Bol, WH Gerritsen, P Valk… – Neurobiology of …, 2009 – Elsevier
 All oligonucleotides were synthesized by Ocimum Biosolutions (Ocimum Biosolutions, IJsselstein,
the Netherlands). Statistical analysis was performed using one-way ANOVA followed by Students’
t-test (analyzed by GraphPad Prism, version 4.03)

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Articles in 2008

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Susana L. Rebelo, Mohammad R. Amel-Kashipaz, Paul M. Radford, Susan E. Bainbridge, Roel Fiets, Johnny Fang, Elizabeth M. McDermott, Richard J. Powell, Ian Todd, Patrick J. Tighe

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2. ROLE OF SPECIFIC SIGNALLING MOLECULES DURING PROLIFERATION OF CD4+ T CELLS IN RESPONSE TO DIFFERENT STIMULI

D .Sharma ,S.K.Sandur,R.Checker,R.Raghuand K.B.Sainis RadiationBiology & Health Sciences Division and S. Khanam Tata Institute of Fundamental Research , Mumbai

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3. Three Consecutive Arginines Are Important for the Mycobacterial Peptide Deformylase Enzyme Activity

Rahul Saxena 1, Pavitra Kanudia, Manish Datt, Haider Hussain Dar, ubramanian Karthikeyan, Balvinder Singh and             Pradip K. Chakraborti 2

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4.Differential Gene Expression in Danio rerio during Optic Nerve Regeneration

Katherine E. Saul

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5. Serial changes in expression of functionally clustered genes in progression of liver fibrosis in hepatitis C patients

Yoshiyuki Takahara, Mitsuo Takahashi, Qing-Wei Zhang, Hirotaka Wagatsuma, Maiko Mori, Akihiro Tamori, Susumu Shiomi, and Shuhei Nishiguchi

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Karl T. Butterworth1, Helen O. McCarthy1, Andrea Devlin2, Louise Ming2, Tracy Robson1, Stephanie R. McKeown2,

Jenny Worthington2,*,†

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6.Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling

Chandran Vijayendran1,2*, Aiko Barsch3, Karl Friehs2, Karsten Niehaus3, Anke Becker3 and Erwin Flaschel2

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7. Nonvirally Modified Autologous Primary Hepatocytes Correct Diabetes and Prevent Target Organ Injury in a Large Preclinical Model

Nelson K. F. Chen1, Jen San Wong1,2, Irene H. C. Kee3, Siang Hui Lai4, Choon Hua Thng5, Wai Har Ng1, Robert T. H. Ng3, Soo Yong Tan6, Shu Yen Lee7, Mark E. H. Tan1, Jaichandran Sivalingam1, Pierce K. H. Chow2,3*, Oi Lian Kon1*

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8. Nonvirally Modified Autologous Primary Hepatocytes Correct Diabetes and Prevent Target Organ Injury in a Large Preclinical Model

Nelson K. F. Chen1, Jen San Wong1,2, Irene H. C. Kee3, Siang Hui Lai4, Choon Hua Thng5, Wai Har Ng1, Robert T. H. Ng3, Soo Yong Tan6, Shu Yen Lee7, Mark E. H. Tan1, Jaichandran Sivalingam1, Pierce K. H. Chow2,3*, Oi Lian Kon1*

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9. A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes

Young-Su Seo1* , Malinee Sriariyanun1*, Li Wang2,6, Janice Pfeiff3, Jirapa Phetsom1, Ye Lin4, Ki-Hong Jung1, Hui Hsien Chou4,5, Adam Bogdanove2 and Pamela Ronald1

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10. Key Role of Mfd in the Development of Fluoroquinolone Resistance in Campylobacter jejuni

Jing Han, Orhan Sahin, Yi-Wen Barton, Qijing Zhang*

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11. METHOD AND SYSTEM FOR PREPARING A MICROARRAY FOR A DISEASE ASSOCIATION GENE TRANSCRIPT TEST

Sproles, Dean Iverson (Seattle, WA, US)

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Han, Jing ; Sahin, Orhan ; Barton, Yi-Wen ; Zhang, Qijing *

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13. Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues

Tatiana Popova, Detlev Mennerich, Andreas Weith and Karsten Quast

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Thad Koontz 1, Marina Bralic 4, Jelena Tomac 4, Ester Pernjak-Pugel , Glen Bantug 3, Stipan Jonjic 4, and William J. Britt 1,2,3

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Articles in 2007

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Jonathan D. Partridge ‡ , Guido Sanguinetti § , David P. Dibden ‡ ,Ruth E. Roberts ‡ ,Robert K. Poole ‡ and Jeffrey              Green ‡ 1

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2.  Optimal encoding rules for synthetic genes: the need for a community effort

Gang Wu1, Laura Dress2&Stephen J Freeland3

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3. Modulation of Host Gene Expression by the K15 Protein of Kaposi’s Sarcoma-Associated Herpesvirus

Melanie M. Brinkmann,1, Marcel Pietrek,1 Oliver Dittrich-Breiholz,2 Michael Kracht,2 and Thomas F. Schulz1*

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4. A Comparative Analysis of Perturbations Caused by a Gene Knock-out, a Dominant Negative Allele, and a Set of Peptide Aptamers

Nadia Abed‡§, Marc Bickle, Bernard Mari, Matthieu Schapira, Raquel Sanjuan-España, Karine Robbe Sermesant, Olivier Moncorgé, Sandrine Mouradian-Garcia, Pascal Barbry, Brian B. Rudkin, Marie-Odile Fauvarque**, Isabelle Michaud-Soret§‡‡ and Pierre Colas‡¶§§

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5. Polymorphism and regulation of the spxB (pyruvate oxidase) virulence factor gene by a CBS-HotDog domain protein (SpxR) in serotype 2 Streptococcus pneumoniae

Smirla Ramos-Montañez1,†, Ho-Ching Tiffany Tsui1,†, Kyle J. Wayne1, Jordan L. Morris1, Lindsey E. Peters1, Faming Zhang2, Krystyna M. Kazmierczak1, Lok-To Sham1, Malcolm E. Winkler1,*

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Articles in 2006

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Jonathan D. Partridge, Colin Scott, Yue Tang, Robert K. Poole and Jeffrey Green 1

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2. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies

 

 

Winston Patrick Kuo1,2,3,18, Fang Liu4,18, Jeff Trimarchi2, Claudio Punzo2, Michael Lombardi5, Jasjit Sarang5, Mark E Whipple6, Malini Maysuria7, Kyle Serikawa7, Sun Young Lee8, Donald McCrann9, Jason Kang10, Jeffrey R Shearstone11, Jocelyn Burke2,12, Daniel J Park2,12, Xiaowei Wang1,12, Trent L Rector2, Paola Ricciardi-Castagnoli13, Steven Perrin11, Sangdun Choi14, Roger Bumgarner7, Ju Han Kim15, Glenn F Short, III2,12, Mason W Freeman2,12, Brian Seed2,12, Roderick Jensen5, George M Church2, Eivind Hovig4, Connie L Cepko2, Peter Park16, Lucila Ohno-Machado3 & Tor-Kristian Jenssen17

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Patrick J. Ginty *,†, Daniel Howard *, Felicity R. A. J. Rose *, Martin J. Whitaker * , † , John J. A. Barry * , †, Patrick Tighe , Stacey R. Mutch, Gulay Serhatkulu  , Richard O. C. Oreffo §, Steven M. Howdle †,¶,and Kevin M. Shakesheff*, ¶

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Articles in 2005

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1. The stability of the Arabidopsis transcriptome in transgenic plants expressing the marker genes nptII and uidASouad El Ouakfaoui, Brian Miki

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Articles in 2004

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Tara Acharya1, Nandini K Kumar2,Vasantha Muthuswamy2,Abdallah S Daar1 and Peter A Singer1

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Articles in 2002

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D.Raje, V. Krishnan, S. Bundela and M.S. Rekha Rao

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4. Data Integration and Analysis: P.falciparum Microarray Data as a Case Study

Rekha Rao,Ashwin Sivakumar,Govind Rao

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Doctoral Dissertations

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Mechanisms of Antimicrobial Peptide Resistancein Campylobacter-
Ky Van HoangThe University of Tennessee

I found one of the doctoral dissertation papers online that uses a lot of our chips, buffers etc.

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