Ocimum Sequencing and Oligos mentioned in papers, journals etc


This is an attempt to separate our publications by product type. This is a list for our sequencing services and where they have been mentioned. As always this is wip and I hope to continue to complete this.

2012 

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S Dalal, DP Panigrahi, GS Randhawa, RC Dubey – 2012 – Taylor & Francis
 out. The amplified products were analysed using 2% w/v agarose gel. The desired
band was cut and eluted. The products were sequenced through the sequencing
service provided by Ocimum Biosolutions, Hyderabad, India. 

Enzymatic degradation of textile dye Reactive Orange 13 by newly isolated bacterial strain< i> Alcaligenes faecalis</i> PMS-1

PD Shah, SR Dave, MS Rao – International Biodeterioration & …, 2012 – Elsevier
 photolytic activity etc. and based on these results the isolate was identified as
Alcaligenes species. 16S rDNA sequencing of isolated bacteria was carried out at
Ocimum Biosolutions, Hyderabad, India. The nucleotide sequence 

[PDF] Sphingosine 1-phosphate receptor 5 mediates the immune quiescence of the human brain endothelial barrier

R van Doorn, MAL Pinheiro, G Kooij… – Journal of …, 2012 – jneuroinflammation.com
 All oligonucleotides were synthesized by Ocimum Biosolutions (Ocimum Biosolutions, Ijsselstein,
The Netherlands) (Table 2), RNA was isolated using the  qPCR reactions were performed in an
ABI7900HT sequence detection system with the SYBR Green method (Applied 

[HTML] Cloning, Sequencing and In Silico Analysis of Omp C of Salmonella Typhimurium

R Jha, A Kumar, A Saxena, S Tamuly… – ISRN Veterinary Science, 2012 – isrn.com
 The recombinant clones were screened to obtain insert of desired size verified by
colony PCR amplification. The cloned product was sequenced by Ocimum Biosolutions
Ltd., Hyderabad. The sequence was submitted to NCBI. 2.3. 

[CITATION] Quantitative competitive PCR for the detection and quantification of genetically modified cotton event MON-531

D Narra, V Srivatsava – 2012

Simultaneous adsorption and bioaccumulation: A study on continuous mass transfer in column reactor

V Mishra, C Balomajumder… – … Progress & Sustainable …, 2012 – Wiley Online Library
 The same was sent to Ocimum biosolutions, Hyderabad, India for sequencing. The nucleotide
sequence similarity searches were conducted using BLAST program of NCBI and the phylogenetic
analysis was carried out using the MEGA package version 4. Carrier Preparation. 

[PDF] In vitro characterization of Saccharomyces cerevisiae HM535662 obtained from an indigenous fermented food “Bhaturu” of Western Himalayas

A Sourabh, SS Kanwar… – African Journal of …, 2012 – academicjournals.org
 3730xl automated sequencer) by using same upstream and downstream primers
(Life Technologies India, Pvt. Ltd), by a commercial sequencing facility (Ocimum
biosolutions, Pvt. Ltd. Hyderabad, India). The corrected sequence 

Optimization of physical parameters for batch mode Zn (II) ion removal from liquid phase: A potential biosorption study

V Mishra, S Dalal, C Balomajumder – Environmental Progress & … – Wiley Online Library
 Amplification was confirmed by running the PCR products on 1% agarose gel. A desired length
was cut from the gel and purified using Bangalore Genei PCR purification kit, and after elution
the product was sent to Ocimum biosolutions for sequencing

[PDF] Journal of Chemical, Biological and Physical Sciences

JA Johnson, T Citarasu, PAM Helen – jcbsc.org
 Fr. Prem Kumar, Correspondent and Secretary, Malankara Catholic College, Mariagiri for his
constant encouragement and support. We are also grateful to CEPC Laboratory, Kollam for the
GC-MS analysis and Ocimum Biosolutions, Hyderabad for Sequencing work. 
P Yang – cdn.intechopen.com
 (47) SHR and BNR for the control Kidney Affymetrix U34A-C microarrays, validation by RT-PCR,
DNA sequencing and RFLP analyses.  Affymetrix Scanner 428, Imagene and Genowiz softwares
by Ocimum Biosolutions (India) and subjected to arsinh transformation 

Cold-active extracellular α-amylase production from novel bacteria< i> Microbacterium foliorum</i> GA2 and< i> Bacillus cereus</i> GA6 isolated from Gangotri …

M Kuddus, IZ Ahmad – Journal of Genetic Engineering and Biotechnology, 2012 – Elsevier
 processed for sequencingSequencing was carried out using the same set of primers
in both the directions to check the validity of the sequenceSequencing was done by
Ocimum Biosolutions, India. 2.5.3. Antibiotic susceptibility test. 

[PDF] Full length cDNA synthesis of differentially displayed ESTs during lactation in the Indian buffalo (Bubalus bubalis)

AK TRIPATHI, KM SINGH, MN VAZE… – Turk. J. Vet. Anim …, 2012 – journals.tubitak.gov.tr
 Sequence analysis Analysis of the 5′ RACE amplified products of the respective ESTs was carried
out using Megablast  Seven sense primers were designed and commercially synthesized (OCIMUM
BIOSOLUTIONS, Hyderabad) from the 5′ RACE sequences (Table 2) using 

[PDF] Transcription of gD and gI gene in BHV-1 infected cells

S Chowdhury, B Sharma – ias.ac.in
 RLM product was cloned into Pgemt easy TA vector and was sequenced through vendors
(Ocimum Biosolutions, Hyderabad). The sequence was aligned with BHV-1 sequence and the
TSS identified from the aligned sequence. Results: Computational analysis: 

Fingolimod attenuates ceramide-induced blood–brain barrier dysfunction in multiple sclerosis by targeting reactive astrocytes

R van Doorn, PG Nijland, N Dekker, ME Witte… – Acta …, 2012 – Springer
 Oligonucleotides were synthesized by Ocimum Biosolu- tions (Ocimum Biosolutions, IJsselstein,
The Netherlands).  Quantitative PCR (qPCR) reactions were performed in an ABI7900HT sequence
detection system using the SYBR Green method (Applied Biosys- tems, New York 

Differential expression of silent polyketide biosynthesis gene clusters in chemostat cultures of< i> Aspergillus nidulans</i>

A Sarkar, AN Funk, K Scherlach, F Horn… – Journal of …, 2012 – Elsevier
 Mining the A. nidulans full genome sequence revealed the existence of nearly 50 gene loci
encoding polyketide synthases (PKSs) or nonribosomal peptide synthetases  Custom made A.
nidulans full genome microarrays (Ocimum Biosolutions) were used in these studies. 

Superparamagnetic Nanoparticles Based Immunomagnetic SeparationMultiplex Polymerase Chain Reaction Assay for Detection of Salmonella

B Padmavathy, A Patel, RV Kumar… – Science of Advanced …, 2012 – ingentaconnect.com
 Four pairs of oligonucleotide primers based on the sequence of invA, prt, fliC, viaB genes are
used for detec- tion of the presence of Salmonella Typhi and Salmonella  All the oligonucleotide
primers were custom synthesized from Ocimum Biosolutions Pvt Ltd., Netherlands. 

Identification and distribution of putative virulence genes in clinical strains of Yersinia enterocolitica biovar 1A by suppression subtractive hybridization

P Kumar, JS Virdi – Journal of Applied Microbiology, 2012 – Wiley Online Library
 sequenced directly using appropriate primers in either one or both directions. The commercial
facilities provided by M/s Link Biotech (Ocimum Biosolutions, Delhi) and M/S Lab India (Gurgaon,
India) were used for sequencing of the samples. The sequences obtained were 

[PDF] Non structural protein of avian influenza A (H11N1) virus is a weaker suppressor of immune responses but capable of inducing apoptosis in host cells

S Mukherjee, S Majumdar, VC Vipat, AC Mishra… – Virology …, 2012 – virologyj.com
 Amplicons cloned into pcDNA 3.0(-) expression vector (Invitrogen, Carlsbad, CA) were
screened by sequencing Data was analyzed using GENOWIZ Microarray and Pathway
analysis tool (Ocimum Biosolutions, Hyderabad, India). 

Polymorphism in RD1 locus and its effect on down stream genes among South Indian clinical isolates of M. tuberculosis

AK Refaya, SS Kumar, S Balaji… – Journal of Medical …, 2012 – Soc General Microbiol
 earlier (Baess 1974). Spoligotyping was performed with a commercially available
kit 111 (Ocimum biosolutions, Hyderabad, India) according to the instructions of the
112 manufacturer.  134 135 Automated DNA sequencing 136 

A novel mechanism of gall midge resistance in the rice variety Kavya revealed by microarray analysis

N Rawat, N Chiruvuri Naga… – Functional & integrative …, 2012 – Springer
 RNA, target hybridization, as well as washing, staining, and scanning of the arrays were carried
out by Ocimum Biosolutions (Hyderabad, India  The data were analyzed using the 7500 Sequence
Detection Software (Applied Biosystems, USA) with default baseline and threshold. 

[PDF] Inhibition of HIV-1 Integrase gene expression by 10-23 DNAzyme

N Singh, A Ranjan, S Sur, R Chandra, V Tandon – Journal of biosciences, 2012 – ias.ac.in
 The sequence GGCTAGCTACAACGA was a specific catalytic domain of 10-23 DNAzyme
molecule, which was flanked by two substrate recognition arm of seven to nine deoxynucleo-
tides. All the DNAzymes were synthesized by Ocimum Biosolutions, Hyderabad, India. 

GenoType MTBDRsl performance on clinical samples with diverse genetic background

P Miotto, AM Cabibbe, P Mantegani… – European …, 2012 – Eur Respiratory Soc
 Sequencing. Genomic regions harbouring drug-resistance mutations were amplified and  The
amplified direct repeat locus of clinical isolates was investigated using the Spoligotyping kit
(Ocimum Biosolutions, Hyderabad, India) following the manufacturer’s instructions. 

A promising strain of Streptomyces sp. with agricultural traits for growth promotion and disease management

M Alam, S Dharni, SKS Abdul-Khaliq… – Indian Journal of …, 2012 – nopr.niscair.res.in
 Primers were procured from Ocimum Biosolutions, India.  The recombinants were selected by
blue/white screening and recombinant plasmid DNA was isolated for further restriction analysis
and sequencing of the insert on a 3130XL Genetic analyzer (Applied Biosystems, USA 

Rapid and Sensitive Detection of Major Uropathogens in a Single-Pot Multiplex PCR Assay

B Padmavathy, R Vinoth Kumar, A Patel… – Current …, 2012 – Springer
 Comparison with closely related species was found to predict no homology or less homology
with the primer sequence used in the mPCR assay.  All the primers were synthesized on
custom-order from Ocimum Biosolutions, Netherlands. Optimization of Uniplex and mPCR 

Performance comparison of multiple microarray platforms for gene expression profiling.

F Liu, WP Kuo, TK Jenssen, E Hovig – Methods in molecular biology ( …, 2012 – Springer
 Following recent studies (17–19), we used probe sequence information to map probes both on
levels of genes and  Biosystems (ABI), Amersham (now GE Healthcare), Compugen (now
Sigma-Genosys), Mergen, MWG BioTech (now Ocimum Biosolutions), Operon, “academic 
G Jeyasekaran, KT Raj, RJ Shakila, AJ Thangarani… – Annals of …, 2012 – Springer
 1992), while fimA, coding for the fimbrial gene, demonstrates a high degree of sequence
conservation among Salmonella serovars (Cohen et al. 1996; Townsend et al. 2001).  All primer
sequences were synthe- sized by Ocimum Biosolutions (Indianapolis, IN). 

Antagonism of microRNA Function in Zebrafish Embryos by Using Locked Nucleic Acid Enzymes (LNAzymes)

H Suryawanshi, MK Lalwani, S Ramasamy… – …, 2012 – Wiley Online Library
 was exactly as previously described.18 All DNA and LNA oligonucleotides used in this study
were purchased from Ocimum Biosolutions (Hyderabad, India  RT products were then used for
real-time PCR with mature miRNA sequence as the forward primer and the universal 

Demonstration of sequential adaptation strategy for developing salt tolerance in bacteria for wastewater treatment: A study using< i> Escherichia coli</i> as model

S Puranik, S Shaligram, V Paliwal, DV Raje… – Bioresource …, 2012 – Elsevier
 The expression data for each sample was obtained on OciChip E.coli K-12 gene chip (M/s Ocimum
Biosolutions, Hyderabad); the gene probe details with chip have been described in Supplementary
Table 1. The  Term and GO ID, Primer Sequence(5′-3′), Product length (bp). 

Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae

MK Yadav, SK Kwon, CG Cho, SW Park… – Microbiology and …, 2012 – Wiley Online Library
 Microarray data analysis was carried out by Genowiz 4.0TM (Ocimum Biosolutions, Hyderabad,
India). Global lowess was used for data analysis with normalization.  Primers were designed by
standard procedures from nucleotide sequence of S. pneumoniae R6 strain 
Z Hou, RC Fink, E Black, M Sugawara… – Journal of Applied …, 2012 – Wiley Online Library
 2007). 2.4 Microarray expression analysis. Triplicate E. coli O157 microarrays (6 slides)
(OciChip™,Ocimum Biosolutions Inc., Indianapolis, IN) were used in this study.  primers listed
in Table 2, using an ABI 7500 real-time PCR system with sequence detection 

The Effect of Secretory Factors of Adipose-Derived Stem Cells on Human Keratinocytes

KM Moon, YH Park, JS Lee, YB Chae, MM Kim… – International journal of …, 2012 – mdpi.com
 Trypsin spot Protein name Accession # Protein score Pep. count Position Sequence coverage
303 Type VI collagen, alpha-2, isoform 2C2a’ NP_478055 86 9 96–393 12%  Trypsin spot Protein
name Accession # Protein score Pep. count Position Sequence coverage 
K Isshiki, RC Ray, D Montet – downloads.hindawi.com
 1, no. 4, pp. 323– 333, 1999. [7] X. Wang, Y. Li, H. Jing et al., “Complete genome sequence of
a Yersinia enterocolitica “old world” (3/O:9) strain and comparison with the “new world”
(1B/O:8) strain,” Journal of Clinical Microbiology, vol. 49, no. 4, pp.  2.1.1. Sequence Retrieval. 

[HTML] Functional Genomic Analysis of Candida glabrata-Macrophage Interaction: Role of Chromatin Remodeling in Virulence

MN Rai, S Balusu, N Gorityala, L Dandu, R Kaur – PLoS Pathogens, 2012 – dx.plos.org
 the screen. Tn7 insertion in the identified mutants was mapped, by transposon rescue
and sequencing analyses, to 56 C. glabrata ORFs and 20 intergenic regions
(http://www.genolevures.org) (Tables S1 and S2). Using the 

2011

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Molecular cloning, overexpression, purification, crystallization and preliminary X-ray diffraction studies of histidinol phosphate aminotransferase (HisC2) from …

N Nasir, R Vyas, C Chugh… – … Section F: Structural …, 2011 – scripts.iucr.org
 positive clones using the same restriction enzymes. The sequence and the directionality
of the clone were confirmed by DNA sequencing (Ocimum Biosolutions, India). A
construct with the following expression sequence, consisting 
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[PDF] Potential of Alkaline Protease Isolated from Thermoactinomyces sp. RM4 as an Alternative to Conventional Chemicals in Leather Industry Dehairing Process

A Verma, HS Pal, R Singh… – International Journal of …, 2011 – ndpublisher.in
 Bergey’s manual (Pillai and Archana, 2008). Approximately 1,500- bp-sequence
information of amplified fragment was obtained through the sequencing services
provided by Ocimum Biosolutions Pvt. Ltd., Hyderabad, India. 
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Roohi, M. Kuddus, IZ Ahmad and JM Arif

ISI Thomson – Asian Journal of Biotechnology, 2011 – scialert.net
 The PCR amplicon for the partial 16S rRNA gene was further processed for sequencing.
Sequencing was carried out using the same set of primers in both the directions to check the
validity of the sequenceSequencing was done by Ocimum Biosolutions, India. 
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[PDF] Production of Cold-active Extracellular a-Amylase by Newly Isolated Microbacterium foliorum GA2 from Gangotri glacier, Western Himalaya, India

MK Roohi, IZ Ahmad… – Asian Journal of Biotechnology, 2011 – docsdrive.com
 Sequencing was done by Ocimum Biosolutions, lndia. Antibiotic susceptibility and
plasmid curing: The antibiotic susceptibility of the isolate was studied on Muller-Hinton
agar media by disc diffusion methods (Bauer elf al., 1966). 
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HisB from Mycobacterium tuberculosis: cloning, overexpression in Mycobacterium smegmatis, purification, crystallization and preliminary X-ray crystallographic …

MS Ahangar, Y Khandokar, N Nasir… – … Section F: Structural …, 2011 – scripts.iucr.org
 using T4 DNA ligase. Successful integration of the insert into the expression vector
and its directionality were confirmed by DNA sequencing (Ocimum Biosolutions,
Hyderabad, India). Table 1 Primers used for PCR amplification. 

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2010

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2009

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2008

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2007

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Genome sequence of Avery’s virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6

JA Lanie, WL Ng, KM Kazmierczak… – Journal of …, 2007 – Am Soc Microbiol
 As was done previously (48), we inserted a placeholder sequence containing the
five repeats reported previously for R6 into this region of the D39 genome sequence
(see the text).  (now available from Ocimum Biosolutions). 

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