1
|
Mathur S, Singh P, Yadava SK, Gupta V, Pradhan AK, Pental D. Genetic mapping of some key plant architecture traits in Brassica juncea using a doubled haploid population derived from a cross between two distinct lines: vegetable type Tumida and oleiferous Varuna. Theor Appl Genet 2023; 136:96. [PMID: 37017803 DOI: 10.1007/s00122-023-04321-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
Genetic mapping of some key plant architectural traits in a vegetable type and an oleiferous B. juncea cross revealed QTL and candidate genes for breeding more productive ideotypes. Brassica juncea (AABB, 2n = 36), commonly called mustard, is an allopolyploid crop of recent origin but contains considerable morphological and genetic variation. An F1-derived doubled haploid population developed from a cross between an Indian oleiferous line, Varuna, and a Chinese stem type vegetable mustard, Tumida showed significant variability for some key plant architectural traits-four stem strength-related traits, stem diameter (Dia), plant height (Plht), branch initiation height (Bih), number of primary branches (Pbr), and days to flowering (Df). Multi-environment QTL analysis identified twenty Stable QTL for the above-mentioned nine plant architectural traits. Though Tumida is ill-adapted to the Indian growing conditions, it was found to contribute favorable alleles in Stable QTL for five architectural traits-press force, Dia, Plht, Bih, and Pbr; these QTL could be used to breed superior ideotypes in the oleiferous mustard lines. A QTL cluster on LG A10 contained Stable QTL for seven architectural traits that included major QTL (phenotypic variance ≥ 10%) for Df and Pbr, with Tumida contributing the trait-enhancing alleles for both. Since early flowering is critical for the cultivation of mustard in the Indian subcontinent, this QTL cannot be used for the improvement of Pbr in the Indian gene pool lines. Conditional QTL analysis for Pbr, however, identified other QTL which could be used for the improvement of Pbr without affecting Df. The Stable QTL intervals were mapped on the genome assemblies of Tumida and Varuna for the identification of candidate genes.
Collapse
Affiliation(s)
- Shikha Mathur
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India
| | - Priyansha Singh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Akshay Kumar Pradhan
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India.
| |
Collapse
|
2
|
Chaudhary G, Pradhan AK, Shah S, Roy S, Singh V, Dwivedi SK, Sethi R, Chandra S, Vishwakarma P, Sharma AK, Bhandari M, Shukla A, Singh A. Unraveling the invisible demon: a study of the oxidative stress markers, antioxidant activities and inflammatory markers in patients admitted with complete heart block. Eur Heart J 2023. [DOI: 10.1093/eurheartj/ehac779.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Abstract
Funding Acknowledgements
Type of funding sources: None.
Introduction
Despite the recent advancements in the management of Complete Heart Block (CHB), the aetiology of CHB is still idiopathic in most of the cases. Our study explores this hitherto untouched aspect of complete heart block.
Purpose
We aimed to assess the aetiological profile of Complete Heart Block patients in our study.
Methods
The study population consisted of 60 patients with complete heart block aged between 30 to 80 years, attending as an inpatient in ER. Oxidative stress was measured by serum MDA, serum GSH, serum Catalase activity and serum SOD activity. Antioxidant activity was obtained by measuring the levels of serum total antioxidant capacity. Inflammatory stress was measured by IL-5 and TNF-alpha levels. These values were compared to 30 healthy controls with no prior history of smoking and diabetes mellitus.
Results
The mean age of the patient was 62.48 ± 7.98 years and the gender distribution was 37 males and 23 females out of 60 patients. The mean value of serum MDA (ng/mL) in cases is 1451.26 ± 206.32, and in controls, the mean value is 1197.98 ± 234.71 (p=<0.001). The mean value of serum GSH (mcg/mL) in cases is 46.982 ± 18.613, and in controls, the mean value is 54.155 ± 10.762 (p=0.027). The mean value of serum Catalase Activity (U/min/mg protein) in cases is 10.763 ± 4.038 and in controls, the mean value is 19.878 ± 7.787 (p=0.003). The mean value of serum SOD Activity (U/g) in cases is 24.950 ± 5.4565, and in controls, the mean value is 46.214 ± 14.6309 (p=0.891). The mean value of serum Total Antioxidant Capacity (U/mL) in cases is 5.546 ± 0.620 and in controls, the mean value is 8.346 ± 2.781 (p=0.025). The mean value of serum IL-5 (pg/mL) in cases is 481.442 ± 28.8995, and in controls, the mean value is 67.347 ± 20.445 (p<0.001). The mean value of serum TNF-ALFA (pg/mL) in cases is 196.741 ± 73.771, and in controls, the mean value is 144.530 ± 42.599 (p= 0.081).
Conclusions
During a complete heart block, SOD (p=0.891), CAT (p=0.003), GSH (p=0.027) and total antioxidant (TAOC) (p=0.025) were significantly decreased in cases, compared to healthy controls, thus suggesting that the elevated levels of oxidative free radicals causes endothelial dysfunctioning. The increase in ROS was observed by a highly significant increase of malondialdehyde (MDA) (p=<0.001) showing high ROS-mediated tissue damage. Besides damage by oxidative stress, our study suggests that there are certain inflammatory markers like TNF-α and IL-5 that actively participate in causing heart block. There was a significant increase in the concentration of IL-5 (p<0.001) in the cases as compared to the controls.
Collapse
Affiliation(s)
- G Chaudhary
- King George's Medical University , Lucknow , India
| | - A K Pradhan
- King George's Medical University , Lucknow , India
| | - S Shah
- King George's Medical University , Lucknow , India
| | - S Roy
- King George's Medical University , Lucknow , India
| | - V Singh
- King George's Medical University , Lucknow , India
| | - S K Dwivedi
- King George's Medical University , Lucknow , India
| | - R Sethi
- King George's Medical University , Lucknow , India
| | - S Chandra
- King George's Medical University , Lucknow , India
| | | | - A K Sharma
- King George's Medical University , Lucknow , India
| | - M Bhandari
- King George's Medical University , Lucknow , India
| | - A Shukla
- King George's Medical University , Lucknow , India
| | - A Singh
- King George's Medical University , Lucknow , India
| |
Collapse
|
3
|
Roy S, Singh V, Ahmed J, Dwivedi SK, Sethi R, Chandra S, Pradhan AK, Vishwakarma P, Sharma AK, Bhandari M, Shukla A, Singh A, Chaudhary G. The surprises in optical coherence tomography (OCT) findings in patients presenting with in-stent restenosis: the road less travelled. Eur Heart J 2023. [DOI: 10.1093/eurheartj/ehac779.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Abstract
Funding Acknowledgements
Type of funding sources: None.
Background
Morphological features of neointimal tissue play a pivotal role in the pathophysiology of In-Stent Restenosis (ISR) after percutaneous coronary intervention, hence understanding these features and patterns is crucial.
Purpose
The present study was designed to qualitatively and quantitatively assess neointimal characteristics of lesions using OCT in patients presenting with ISR.
Methods
This was a single-center, prospective, observational study performed between 1st August 2020 and 30th December 2021 at a tertiary-care center in India. Patients diagnosed with stable angina and acute coronary syndrome with post-procedural angiographically documented restenosis (>50%) were included. Qualitative and quantitative assessment of neointimal hyperplasia patterns was performed using OCT.
Results
A total of 34 patients with ISR were studied. Neointimal hyperplasia was classified as (i) homogenous group (n=18) and (ii) non-homogenous group (n=16). As many as 14 (77.8%) diabetics belonged to the homogenous group. Predominant plaque characteristics such as neoatherosclerosis, cholesterol crystals, and calcium were documented in 14 (77.8%), 12 (66.7%), and 11 (61.1%) patients in the homogenous group and in 10 (62.5%), 10 (62.5%), and 9 (56.2%) patients in the non-homogenous group, respectively. Unexpanded stent struts were identified in 11 (61.1%) and 11 (68.8%) patients in the homogenous and non-homogenous groups, respectively. Mean strut thickness was 93.73 ± 31.03 µm and 83.54 ± 18.0 µm, ISR was 72.50 ± 15.93% and 65.37 ± 21.69%, the neointimal thickness was 588.06 ± 167.82 mm and 666.25 ± 218.05 mm, and neointimal hyperplasia was 54.54 ± 11.23% and 59.26 ± 8.86% in the homogenous and non-homogenous groups, respectively.
Conclusion
Neoatherosclerosis and stent underexpansion was predominantly observed in our study, which was in contrast to most of the existing literature [1,2,3], and only diabetes was found to be significantly associated with homogenous neointimal hyperplasia, irrespective of the generation of the stent.
Collapse
Affiliation(s)
- S Roy
- King George's Medical University , Lucknow , India
| | - V Singh
- King George's Medical University , Lucknow , India
| | - J Ahmed
- King George's Medical University , Lucknow , India
| | - S K Dwivedi
- King George's Medical University , Lucknow , India
| | - R Sethi
- King George's Medical University , Lucknow , India
| | - S Chandra
- King George's Medical University , Lucknow , India
| | - A K Pradhan
- King George's Medical University , Lucknow , India
| | | | - A K Sharma
- King George's Medical University , Lucknow , India
| | - M Bhandari
- King George's Medical University , Lucknow , India
| | - A Shukla
- King George's Medical University , Lucknow , India
| | - A Singh
- King George's Medical University , Lucknow , India
| | - G Chaudhary
- King George's Medical University , Lucknow , India
| |
Collapse
|
4
|
Paritosh K, Yadava SK, Singh P, Bhayana L, Mukhopadhyay A, Gupta V, Bisht NC, Zhang J, Kudrna DA, Copetti D, Wing RA, Reddy Lachagari VB, Pradhan AK, Pental D. A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes. Plant Biotechnol J 2021; 19:602-614. [PMID: 33073461 PMCID: PMC7955877 DOI: 10.1111/pbi.13492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/14/2020] [Accepted: 09/27/2020] [Indexed: 05/19/2023]
Abstract
Brassica juncea (AABB), commonly referred to as mustard, is a natural allopolyploid of two diploid species-B. rapa (AA) and B. nigra (BB). We report a highly contiguous genome assembly of an oleiferous type of B. juncea variety Varuna, an archetypical Indian gene pool line of mustard, with ~100× PacBio single-molecule real-time (SMRT) long reads providing contigs with an N50 value of >5 Mb. Contigs were corrected for the misassemblies and scaffolded with BioNano optical mapping. We also assembled a draft genome of B. nigra (BB) variety Sangam using Illumina short-read sequencing and Oxford Nanopore long reads and used it to validate the assembly of the B genome of B. juncea. Two different linkage maps of B. juncea, containing a large number of genotyping-by-sequencing markers, were developed and used to anchor scaffolds/contigs to the 18 linkage groups of the species. The resulting chromosome-scale assembly of B. juncea Varuna is a significant improvement over the previous draft assembly of B. juncea Tumida, a vegetable type of mustard. The assembled genome was characterized for transposons, centromeric repeats, gene content and gene block associations. In comparison to the A genome, the B genome contains a significantly higher content of LTR/Gypsy retrotransposons, distinct centromeric repeats and a large number of B. nigra specific gene clusters that break the gene collinearity between the A and the B genomes. The B. juncea Varuna assembly will be of major value to the breeding work on oleiferous types of mustard that are grown extensively in south Asia and elsewhere.
Collapse
Affiliation(s)
- Kumar Paritosh
- Centre for Genetic Manipulation of Crop PlantsUniversity of Delhi South CampusNew DelhiIndia
| | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop PlantsUniversity of Delhi South CampusNew DelhiIndia
| | - Priyansha Singh
- Department of GeneticsUniversity of Delhi South CampusNew DelhiIndia
| | - Latika Bhayana
- Department of GeneticsUniversity of Delhi South CampusNew DelhiIndia
| | - Arundhati Mukhopadhyay
- Centre for Genetic Manipulation of Crop PlantsUniversity of Delhi South CampusNew DelhiIndia
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop PlantsUniversity of Delhi South CampusNew DelhiIndia
| | | | - Jianwei Zhang
- Arizona Genomics InstituteSchool of Plant SciencesThe University of ArizonaTucsonAZUSA
| | - David A. Kudrna
- Arizona Genomics InstituteSchool of Plant SciencesThe University of ArizonaTucsonAZUSA
| | - Dario Copetti
- Arizona Genomics InstituteSchool of Plant SciencesThe University of ArizonaTucsonAZUSA
| | - Rod A. Wing
- Arizona Genomics InstituteSchool of Plant SciencesThe University of ArizonaTucsonAZUSA
| | | | - Akshay Kumar Pradhan
- Centre for Genetic Manipulation of Crop PlantsUniversity of Delhi South CampusNew DelhiIndia
- Department of GeneticsUniversity of Delhi South CampusNew DelhiIndia
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop PlantsUniversity of Delhi South CampusNew DelhiIndia
| |
Collapse
|
5
|
Paritosh K, Yadava SK, Singh P, Bhayana L, Mukhopadhyay A, Gupta V, Bisht NC, Zhang J, Kudrna DA, Copetti D, Wing RA, Reddy Lachagari VB, Pradhan AK, Pental D. A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes. Plant Biotechnol J 2021; 19:602-614. [PMID: 33073461 DOI: 10.1101/681080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/14/2020] [Accepted: 09/27/2020] [Indexed: 05/23/2023]
Abstract
Brassica juncea (AABB), commonly referred to as mustard, is a natural allopolyploid of two diploid species-B. rapa (AA) and B. nigra (BB). We report a highly contiguous genome assembly of an oleiferous type of B. juncea variety Varuna, an archetypical Indian gene pool line of mustard, with ~100× PacBio single-molecule real-time (SMRT) long reads providing contigs with an N50 value of >5 Mb. Contigs were corrected for the misassemblies and scaffolded with BioNano optical mapping. We also assembled a draft genome of B. nigra (BB) variety Sangam using Illumina short-read sequencing and Oxford Nanopore long reads and used it to validate the assembly of the B genome of B. juncea. Two different linkage maps of B. juncea, containing a large number of genotyping-by-sequencing markers, were developed and used to anchor scaffolds/contigs to the 18 linkage groups of the species. The resulting chromosome-scale assembly of B. juncea Varuna is a significant improvement over the previous draft assembly of B. juncea Tumida, a vegetable type of mustard. The assembled genome was characterized for transposons, centromeric repeats, gene content and gene block associations. In comparison to the A genome, the B genome contains a significantly higher content of LTR/Gypsy retrotransposons, distinct centromeric repeats and a large number of B. nigra specific gene clusters that break the gene collinearity between the A and the B genomes. The B. juncea Varuna assembly will be of major value to the breeding work on oleiferous types of mustard that are grown extensively in south Asia and elsewhere.
Collapse
Affiliation(s)
- Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Priyansha Singh
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Latika Bhayana
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Arundhati Mukhopadhyay
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | | | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, AZ, USA
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, AZ, USA
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, AZ, USA
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, AZ, USA
| | | | - Akshay Kumar Pradhan
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| |
Collapse
|
6
|
Paritosh K, Pradhan AK, Pental D. A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes. BMC Genomics 2020; 21:887. [PMID: 33308149 PMCID: PMC7731534 DOI: 10.1186/s12864-020-07271-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/23/2020] [Indexed: 01/13/2023] Open
Abstract
Background Brassica nigra (BB), also called black mustard, is grown as a condiment crop in India. B. nigra represents the B genome of U’s triangle and is one of the progenitor species of B. juncea (AABB), an important oilseed crop of the Indian subcontinent. We report the genome assembly of B. nigra variety Sangam. Results The genome assembly was carried out using Oxford Nanopore long-read sequencing and optical mapping. A total of 1549 contigs were assembled, which covered ~ 515.4 Mb of the estimated ~ 522 Mb of the genome. The final assembly consisted of 15 scaffolds that were assigned to eight pseudochromosomes using a high-density genetic map of B. nigra. Around 246 Mb of the genome consisted of the repeat elements; LTR/Gypsy types of retrotransposons being the most predominant. The B genome-specific repeats were identified in the centromeric regions of the B. nigra pseudochromosomes. A total of 57,249 protein-coding genes were identified of which 42,444 genes were found to be expressed in the transcriptome analysis. A comparison of the B genomes of B. nigra and B. juncea revealed high gene colinearity and similar gene block arrangements. A comparison of the structure of the A, B, and C genomes of U’s triangle showed the B genome to be divergent from the A and C genomes for gene block arrangements and centromeric regions. Conclusions A highly contiguous genome assembly of the B. nigra genome reported here is an improvement over the previous short-read assemblies and has allowed a comparative structural analysis of the A, B, and C genomes of the species belonging to the U’s triangle. Based on the comparison, we propose a new nomenclature for B. nigra pseudochromosomes, taking the B. rapa pseudochromosome nomenclature as the reference. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07271-w.
Collapse
Affiliation(s)
- Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Akshay Kumar Pradhan
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India.,Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India.
| |
Collapse
|
7
|
Harper AL, He Z, Langer S, Havlickova L, Wang L, Fellgett A, Gupta V, Kumar Pradhan A, Bancroft I. Validation of an Associative Transcriptomics platform in the polyploid crop species Brassica juncea by dissection of the genetic architecture of agronomic and quality traits. Plant J 2020; 103:1885-1893. [PMID: 32530074 DOI: 10.1111/tpj.14876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/22/2020] [Accepted: 06/01/2020] [Indexed: 05/22/2023]
Abstract
The development of more productive crops will be key to addressing the challenges that climate change, population growth and diminishing resources pose to global food security. Advanced 'omics techniques can help to accelerate breeding by facilitating the identification of genetic markers for use in marker-assisted selection. Here, we present the validation of a new Associative Transcriptomics platform in the important oilseed crop Brassica juncea. To develop this platform, we established a pan-transcriptome reference for B. juncea, to which we mapped transcriptome data from a diverse panel of B. juncea accessions. From this panel, we identified 355 050 single nucleotide polymorphism variants and quantified the abundance of 93 963 transcripts. Subsequent association analysis of functional genotypes against a number of important agronomic and quality traits revealed a promising candidate gene for seed weight, BjA.TTL, as well as additional markers linked to seed colour and vitamin E content. The establishment of the first full-scale Associative Transcriptomics platform for B. juncea enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops.
Collapse
Affiliation(s)
- Andrea L Harper
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Zhesi He
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Swen Langer
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Lenka Havlickova
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Lihong Wang
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Alison Fellgett
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Akshay Kumar Pradhan
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| |
Collapse
|
8
|
Bhayana L, Paritosh K, Arora H, Yadava SK, Singh P, Nandan D, Mukhopadhyay A, Gupta V, Pradhan AK, Pental D. A Mapped Locus on LG A6 of Brassica juncea Line Tumida Conferring Resistance to White Rust Contains a CNL Type R Gene. Front Plant Sci 2020; 10:1690. [PMID: 31998351 PMCID: PMC6960627 DOI: 10.3389/fpls.2019.01690] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/29/2019] [Indexed: 05/26/2023]
Abstract
White rust, causal agent oomycete Albugo candida, is a significant disease of the cultivated Brassica species. The Indian gene pool lines of oilseed mustard, Brassica juncea, are highly susceptible to the pathogen. Resistance to A. candida has been reported in the east European gene pool lines of mustard and mapped to LG A4 in line Heera and LG A5 in line Donskaja-IV. A new resistance-conferring locus to A. candida isolate AcB1 has been mapped to LG A6 of B. juncea line Tumida-a Chinese vegetable type mustard using an F1DH mapping population that has been developed from a Tumida × Varuna (susceptible Indian gene pool line) cross. A molecular map containing 8,303 genic and GBS markers was used to map the resistance trait to an interval of 63.0 cM-70.8 cM on LG A6. Genome assemblies of Tumida and Varuna were used to find the genes present within the flanking markers discerned by genetic mapping. The most likely candidate gene in the mapped interval is BjuA046215, a CC-NBS-LRR (CNL) type R gene that encodes a protein with all the specific subdomains of the proteins encoded by such genes. Alleles of BjuA046215 in Varuna and other lines of the Indian and the east European gene pools encode proteins that have truncated LRR domains. Analysis of the syntenic regions in some of the Brassicaceae genomes and phylogenetic analysis of CNL type R genes showed BjuA046215 to be closely related to a recently described white rust resistance-conferring R gene BjuWRR1 in B. juncea Donskaja-IV, both belonging to the CNL-D group of R genes. Related R genes in Arabidopsis thaliana confer resistance to another oomycete, Peronospora parasitica.
Collapse
Affiliation(s)
- Latika Bhayana
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Heena Arora
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Priyansha Singh
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Divakar Nandan
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Arundhati Mukhopadhyay
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Akshay Kumar Pradhan
- Department of Genetics, University of Delhi South Campus, New Delhi, India
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| |
Collapse
|
9
|
Rajarammohan S, Pradhan AK, Pental D, Kaur J. Genome-wide association mapping in Arabidopsis identifies novel genes underlying quantitative disease resistance to Alternaria brassicae. Mol Plant Pathol 2018; 19:1719-1732. [PMID: 29271603 PMCID: PMC6638106 DOI: 10.1111/mpp.12654] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 05/19/2023]
Abstract
Quantitative disease resistance (QDR) is the predominant form of resistance against necrotrophic pathogens. The genes and mechanisms underlying QDR are not well known. In the current study, the Arabidopsis-Alternaria brassicae pathosystem was used to uncover the genetic architecture underlying resistance to A. brassicae in a set of geographically diverse Arabidopsis accessions. Arabidopsis accessions revealed a rich variation in the host responses to the pathogen, varying from complete resistance to high susceptibility. Genome-wide association (GWA) mapping revealed multiple regions to be associated with disease resistance. A subset of genes prioritized on the basis of gene annotations and evidence of transcriptional regulation in other biotic stresses was analysed using a reverse genetics approach employing T-DNA insertion mutants. The mutants of three genes, namely At1g06990 (GDSL-motif lipase), At3g25180 (CYP82G1) and At5g37500 (GORK), displayed an enhanced susceptibility relative to the wild-type. These genes are involved in the development of morphological phenotypes (stomatal aperture) and secondary metabolite synthesis, thus defining some of the diverse facets of quantitative resistance against A. brassicae.
Collapse
Affiliation(s)
| | - Akshay Kumar Pradhan
- Department of GeneticsUniversity of Delhi South CampusNew Delhi110021India
- Centre for Genetic Manipulation of Crop PlantsUniversity of Delhi South CampusNew Delhi110021India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop PlantsUniversity of Delhi South CampusNew Delhi110021India
| | - Jagreet Kaur
- Department of GeneticsUniversity of Delhi South CampusNew Delhi110021India
| |
Collapse
|
10
|
Roy UN, Mundle RM, Camarda GS, Cui Y, Gul R, Hossain A, Yang G, Pradhan AK, James RB. Novel ZnO:Al contacts to CdZnTe for X- and gamma-ray detectors. Sci Rep 2016; 6:26384. [PMID: 27216387 PMCID: PMC4877641 DOI: 10.1038/srep26384] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/29/2016] [Indexed: 11/09/2022] Open
Abstract
CdZnTe (CZT) has made a significant impact as a material for room-temperature nuclear-radiation detectors due to its potential impact in applications related to nonproliferation, homeland security, medical imaging, and gamma-ray telescopes. In all such applications, common metals, such as gold, platinum and indium, have been used as electrodes for fabricating the detectors. Because of the large mismatch in the thermal-expansion coefficient between the metal contacts and CZT, the contacts can undergo stress and mechanical degradation, which is the main cause for device instability over the long term. Here, we report for the first time on our use of Al-doped ZnO as the preferred electrode for such detectors. The material was selected because of its better contact properties compared to those of the metals commonly used today. Comparisons were conducted for the detector properties using different contacts, and improvements in the performances of ZnO:Al-coated detectors are described in this paper. These studies show that Al:ZnO contacts to CZT radiation detectors offer the potential of becoming a transformative replacement for the common metallic contacts due to the dramatic improvements in the performance of detectors and improved long-term stability.
Collapse
Affiliation(s)
- U N Roy
- Brookhaven National Laboratory, Upton, NY 11973, United States
| | - R M Mundle
- Department of Engineering, Norfolk State University, Norfolk, VA 23504, United States
| | - G S Camarda
- Brookhaven National Laboratory, Upton, NY 11973, United States
| | - Y Cui
- Brookhaven National Laboratory, Upton, NY 11973, United States
| | - R Gul
- Brookhaven National Laboratory, Upton, NY 11973, United States
| | - A Hossain
- Brookhaven National Laboratory, Upton, NY 11973, United States
| | - G Yang
- Brookhaven National Laboratory, Upton, NY 11973, United States
| | - A K Pradhan
- Department of Engineering, Norfolk State University, Norfolk, VA 23504, United States
| | - R B James
- Brookhaven National Laboratory, Upton, NY 11973, United States
| |
Collapse
|
11
|
Smith RL, Gröhn YT, Pradhan AK, Whitlock RH, Van Kessel JS, Smith JM, Wolfgang DR, Schukken YH. The effects of progressing and nonprogressing Mycobacterium avium ssp. paratuberculosis infection on milk production in dairy cows. J Dairy Sci 2015; 99:1383-1390. [PMID: 26686721 DOI: 10.3168/jds.2015-9822] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/29/2015] [Indexed: 01/23/2023]
Abstract
Longitudinal data from 3 commercial dairy herds in the northeast United States, collected from 2004 to 2011, were analyzed to determine the effect of Mycobacterium avium ssp. paratuberculosis (MAP) infection status and progression path on milk production. Disease status, as indicated by MAP test results, was determined through quarterly ELISA serum testing, biannual fecal culture, and culture of tissues and feces at slaughter. Milk production data were collected from the Dairy Herd Information Association. Animals with positive MAP test results were categorized, based on test results over the full course of the study, as high path (at least one high-positive culture) or low path (at least one positive culture or ELISA). The cumulative numbers of positive ELISA and culture results were recorded. The effects of both MAP infection path, status, and number of positive tests on milk production were analyzed using a mixed linear model with an autocorrelation random effect structure. Low- and high-path animals produced more milk before their first positive test than always-negative animals, especially high-path animals. Although mean production decreased after a first positive test, low-path animals were shown to recover some productivity. High-path animals continued to exhibit a decrease in milk production, especially after their first high-positive fecal culture. These results show that not all animals that test positive for MAP will have long-term production losses. Milk production decreased significantly with each additional positive test. Ultimately, production loss appeared to be a function of MAP infection progression.
Collapse
Affiliation(s)
- Rebecca L Smith
- Department of Pathobiology, University of Illinois College of Veterinary Medicine, Urbana 61802.
| | - Y T Gröhn
- Department of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14850
| | - A K Pradhan
- Department of Nutrition and Food Science and Center for Food Safety and Security Systems, College of Agriculture and Natural Resources, University of Maryland, College Park 20742
| | - R H Whitlock
- New Bolton Center, Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348
| | - J S Van Kessel
- Environmental Microbial and Food Safety Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705
| | - J M Smith
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington 05405
| | - D R Wolfgang
- Department of Veterinary and Biomedical Science, Penn State University, University Park 16802
| | - Y H Schukken
- Department of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14850; GD Animal Health, 7400 AA, Deventer, the Netherlands
| |
Collapse
|
12
|
Taylor T, Pradhan AK, Divekar G, Romoser M, Muttart J, Gomez R, Pollatsek A, Fisher DL. The view from the road: the contribution of on-road glance-monitoring technologies to understanding driver behavior. Accid Anal Prev 2013; 58:175-186. [PMID: 23548549 DOI: 10.1016/j.aap.2013.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 02/04/2013] [Accepted: 02/07/2013] [Indexed: 06/02/2023]
Abstract
Using glance-monitoring technologies for on-road studies is an excellent way to investigate driver behaviors in an ecologically valid setting. Recent advances in glance-monitoring technologies have made it possible to conduct on-road studies of drivers' glance behavior that heretofore were simply not possible. Yet it is not always easy to determine which glance-monitoring technology to use for a particular application. Here, we first identify the generic capabilities of the various glance-monitoring technologies. We then describe how particular glance-monitoring technologies have been used in the field to (a) identify the skill deficiencies of novice and older drivers, (b) evaluate the effectiveness of training programs that are designed to reduce deficits in these skills, and (c) address interface issues both inside (e.g., collision warning systems) and outside (e.g., yield markings) the vehicle. The limitations and advantages of on-road eye-tracking and the associated glance-monitoring technologies are identified throughout. A comparison, where possible, is made between the results of on-road eye-tracking studies of drivers' behaviors and the results of those studies conducted in the laboratory. Overall, the use of appropriate on-road glance-monitoring technologies has greatly enhanced our theoretical understanding of why drivers behave the way they do, and this knowledge has paved the way for significant improvements in road user safety.
Collapse
Affiliation(s)
- T Taylor
- Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, MA 01003, USA.
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Bamiduro O, Chennamadhava G, Bowie C, Robinson B, Dondapati H, Konda RB, Robertson B, Bahoura M, Pradhan AK, Cui Y, Bhattacharya P, Burger A. Self-assembled hierarchical nanostructures composed of novel chalcopyrite nanosheets for photovoltaic properties. J Nanosci Nanotechnol 2013; 13:467-476. [PMID: 23646756 DOI: 10.1166/jnn.2013.6724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Self-assembled nanostructures of CulnGaSe2 (CIGS) comprising of nanosheets with sheet thickness of 20 nm have been developed via one-step electrochemically alloying technique. These self-assembled nanoplates exhibit highly intersecting behavior and transform from CuSe to CIGS as the reduction potential was varied. The morphological analysis indicated that the process resulted in a progression of crystallites to a series of heavy dense intersecting nanoplates. Further analyses revealed that the nanostructures keep their integrity on heat treatment. The structure confirms the inclusion of Indium and Gallium at higher reduction potentials and its transition from pseudoamorphous to polycrystalline structure. A strong correlation between reduction potential, and the composition was established. The spectroscopic and optical spectra clearly prove that the direct band gap for the as-grown and annealed thin films, and appropriate for solar cell applications. These self-assembled dense interweaved nanoplates structure have not been observed previously in CIGS semiconductor system and have potential implications forenergy applications.
Collapse
Affiliation(s)
- O Bamiduro
- Center for Materials Research, Norfolk State University, Norfolk, Virginia VA 23504, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Pradhan AK, Shukla AK, Reddy MVR, Garg N. Assessment of oxidative stress and antioxidant status in age related cataract in a rural population. Indian J Clin Biochem 2012; 19:83-7. [PMID: 23105434 DOI: 10.1007/bf02872397] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Oxidative stress was assesed by estimating lipid peroxidation product (LPO) in the form of thiobarbituric acid reactive substances (TBARS), enzymatic antioxidants in the form of superoxide dismutase (SOD), catalase and nonenzymatic antioxidant vitamins e.g. vitamin C, β carotene and vitamin E in either serum or plasma or erythrocytes in 190 cases of age related cataract in the age group of 50-80 years. 190 cases were grouped into three morphological types namely, 73 cases of cortical, 77 cases of posterior subcapsular and 40 cases of nuclear cataract and values of LPO and antioxidants were compared with 78 cases of age matched healthy control groups. Plasma TBARS levels were cataract cases when compared with control groups. There were no significant differences in the erythrocyte levels of catalase and plasma levels of Vit E between cataract cases and control groups. No significant changes of parameters were seen among three different morphological types of age related cataract. The present study shows that the oxidative stress may play an important role in the age related cataract.
Collapse
Affiliation(s)
- A K Pradhan
- Department of Biochemistry and J.B. Tropical Disease Research Centre, MGIMS, 442 102 Wardha Sevagram India
| | | | | | | |
Collapse
|
15
|
Mundle R, Holloway T, Zhang K, Bahoura M, Pradhan AK. Effects of surface potential on growth of ZnO nanorod arrays investigated by electric force microscopy. J Nanosci Nanotechnol 2012; 12:3938-3942. [PMID: 22852328 DOI: 10.1166/jnn.2012.6158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The electric and Kelvin force probe microscopy were used to investigate the surface potentials on the ZnO seed layer, which shows a remarkable dependence on the annealing temperature. The optimum temperature for the growth of nanorod arrays normal to the surface was found to be at 600 degrees C, which is in the range of right surface potentials and energy measured between 500 degrees C and 700 degrees C. We demonstrated from both electric and Kelvin force probe microscopy studies that surface potential controls the growth of ZnO nanorods, illustrating the fact that this is a promising technique to visualize the control of ZnO nanorod arrays by studying their surface potentials. This study will provide important understanding of growth of other nanostructures.
Collapse
Affiliation(s)
- R Mundle
- Center for Materials Research, Norfolk State University, Norfolk, Virginia, VA 23504, USA
| | | | | | | | | |
Collapse
|
16
|
Jagannath A, Sodhi YS, Gupta V, Mukhopadhyay A, Arumugam N, Singh I, Rohatgi S, Burma PK, Pradhan AK, Pental D. Eliminating expression of erucic acid-encoding loci allows the identification of "hidden" QTL contributing to oil quality fractions and oil content in Brassica juncea (Indian mustard). Theor Appl Genet 2011; 122:1091-103. [PMID: 21188349 DOI: 10.1007/s00122-010-1515-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 12/08/2010] [Indexed: 05/03/2023]
Abstract
Oil content and oil quality fractions (viz., oleic, linoleic and linolenic acid) are strongly influenced by the erucic acid pathway in oilseed Brassicas. Low levels of erucic acid in seed oil increases oleic acid content to nutritionally desirable levels, but also increases the linoleic and linolenic acid fractions and reduces oil content in Indian mustard (Brassica juncea). Analysis of phenotypic variability for oil quality fractions among a high-erucic Indian variety (Varuna), a low-erucic east-European variety (Heera) and a zero-erucic Indian variety (ZE-Varuna) developed by backcross breeding in this study indicated that lower levels of linoleic and linolenic acid in Varuna are due to substrate limitation caused by an active erucic acid pathway and not due to weaker alleles or enzyme limitation. To identify compensatory loci that could be used to increase oil content and maintain desirable levels of oil quality fractions under zero-erucic conditions, we performed Quantitative Trait Loci (QTL) mapping for the above traits on two independent F1 doubled haploid (F1DH) mapping populations developed from a cross between Varuna and Heera. One of the populations comprised plants segregating for erucic acid content (SE) and was used earlier for construction of a linkage map and QTL mapping of several yield-influencing traits in B. juncea. The second population consisted of zero-erucic acid individuals (ZE) for which, an Amplified Fragment Length Polymorphism (AFLP)-based framework linkage map was constructed in the present study. By QTL mapping for oil quality fractions and oil content in the ZE population, we detected novel loci contributing to the above traits. These loci did not co-localize with mapped locations of the fatty acid desaturase 2 (FAD2), fatty acid desaturase 3 (FAD3) or fatty acid elongase (FAE) genes unlike those of the SE population wherein major QTL were found to coincide with mapped locations of the FAE genes. Some of the new loci identified in the ZE population could be detected as 'weak' contributors (with LOD < 2.5) in the SE population in which their contribution to the traits was "masked" due to pleiotropic effects of erucic acid genes. The novel loci identified in this study could now be used to improve oil quality parameters and oil content in B. juncea under zero-erucic conditions.
Collapse
Affiliation(s)
- Arun Jagannath
- University of Delhi South Campus, New Delhi, 110021, India
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Smith RL, Strawderman RL, Schukken YH, Wells SJ, Pradhan AK, Espejo LA, Whitlock RH, Van Kessel JS, Smith JM, Wolfgang DR, Gröhn YT. Effect of Johne's disease status on reproduction and culling in dairy cattle. J Dairy Sci 2010; 93:3513-24. [PMID: 20655419 DOI: 10.3168/jds.2009-2742] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Accepted: 03/30/2010] [Indexed: 11/19/2022]
Abstract
Among the costs attributed to Mycobacterium avium ssp. paratuberculosis (MAP) infection in dairy cattle, the effects on reproduction and culling are the least documented. To estimate the cost of MAP infections and Johne's disease in a dairy herd, the rates of calving and culling were calculated for cows in each stage of MAP infection relative to uninfected cows. Data from 6 commercial dairy herds, consisting of 2,818 cows with 2,754 calvings and 1,483 cullings, were used for analysis. Every cow in each study herd was tested regularly for MAP, and herds were followed for between 4 and 7 yr. An ordinal categorical variable for Johne's disease status [test-negative, low-positive (low-shedding or ELISA-positive only), or high-shedding] was defined as a time-dependent variable for all cows with at least 1 positive test result or 2 negative test results. A Cox regression model, stratified on herd and controlling for the time-dependent infection variable, was used to analyze time to culling. Nonshedding animals were significantly less likely to be culled in comparison with animals in the low-shedding or ELISA-positive category, and high-shedding animals had nonsignificantly higher culling rates than low-shedding or ELISA-positive animals. Time to calving was analyzed using a proportional rates model, an analog to the Andersen-Gill regression model suitable for recurrent event data, stratifying on herd and weighted to adjust for the dependent censoring caused by the culling effects described above. High-shedding animals had lower calving rates in comparison with low-shedding or ELISA-positive animals, which tended to have higher calving rates than test-negative animals.
Collapse
Affiliation(s)
- R L Smith
- Section of Epidemiology, Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Latorre AA, Van Kessel JS, Karns JS, Zurakowski MJ, Pradhan AK, Boor KJ, Jayarao BM, Houser BA, Daugherty CS, Schukken YH. Biofilm in milking equipment on a dairy farm as a potential source of bulk tank milk contamination with Listeria monocytogenes. J Dairy Sci 2010; 93:2792-802. [PMID: 20494189 DOI: 10.3168/jds.2009-2717] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 03/08/2010] [Indexed: 11/19/2022]
Abstract
The objective of this study was to assess the presence of a Listeria monocytogenes-containing biofilm in milking equipment as a potential source of bulk tank milk contamination on a dairy farm where milk contamination had been previously documented. Samples were collected from milking equipment and milking parlor premises on 4 occasions and analyzed for the presence of L. monocytogenes. Pulsed-field gel electrophoresis (PFGE) typing was conducted on L. monocytogenes isolates from the milking equipment, parlor and storage room floors, bulk tank milk, and in-line milk filters. Pieces from milk meters and rubber liners were obtained to visually assess the presence of a biofilm using scanning electron microscopy. A total of 6 (15%), 4 (25%), and 1 (6%) samples were culture-positive for L. monocytogenes in the first, second, and third sample collection, respectively. Two samples were L. monocytogenes hly PCR-positive but were culture-negative in the fourth sample collection. Combined AscI and ApaI restriction analysis yielded 6 PFGE types for 15 L. monocytogenes isolates obtained from milking equipment, parlor, bulk tank milk, and milk filters. A predominant and persistent PFGE type (PFGE type T) was observed among these L. monocytogenes isolates (9/15 isolates). Scanning electron microscopy of samples from the bottom cover of 2 milk meters showed the presence of individual and clusters of bacteria, mainly associated with surface scratches. The presence of a bacterial biofilm was observed on the bottom covers of the 2 milk meters. Prevention of the establishment of biofilms in milking equipment is a crucial step in fulfilling the requirement of safe, high-quality milk.
Collapse
Affiliation(s)
- A A Latorre
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Zhang K, Holloway T, Pradhan J, Bahoura M, Bah R, Rakhimov RR, Pradhan AK, Prabakaran R, Ramesh GT. Synthesis and magnetic characterizations of La(1-x)Sr(x)MnO3 nanoparticles for biomedical applications. J Nanosci Nanotechnol 2010; 10:5520-5526. [PMID: 21133070 DOI: 10.1166/jnn.2010.2437] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The La(1-x)Sr(x)MnO3 (LSMO) nanoparticles have been synthesized by citric gel process followed by ball milling method. These nanoparticles demonstrated high crystalline quality. Nanoparticle size was further decreased by ball milling technique as observed by the field-emission scanning electron microscopic studies. The ball milled and silica coated LSMO nanoparticles show magnetic transition at about 370 K with a superparamagnetic properties. The ferromagnetic resonance (FMR) spectra analysis of LSMO nanoparticles shows large FMR linewidth due to the surface strain of the nanoparticles. Both magnetization and FMR studies demonstrate that the LSMO nanoparticles are highly anisotropic. The toxicity of the nanoparticles was studied for safe biomedical applications. Measurement of intracellular reactive oxygen species (ROS) and MTT assay results show that LSMO nanoparticles are relatively nontoxic and the toxicity is further reduced by SiO2 coating. These results are very important for applications in the field of biotechnology.
Collapse
Affiliation(s)
- K Zhang
- Center for Materials Research, Norfolk State University, 700 ParkAvenue, Norfolk, VA 23504, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Pradhan AK, Pollatsek A, Knodler M, Fisher DL. Can younger drivers be trained to scan for information that will reduce their risk in roadway traffic scenarios that are hard to identify as hazardous? Ergonomics 2009; 52:657-73. [PMID: 19296315 PMCID: PMC2707454 DOI: 10.1080/00140130802550232] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Younger drivers (18-21 years) are over-involved in crashes. Research suggests that one of the reasons for this over-involvement is their failure to scan areas of the roadway for information about potential risks in situations that are hazardous, but not obviously so. The primary objective of the present study is to develop and evaluate a training program that addresses this failure. It was hypothesised that PC-based hazard anticipation training would increase the likelihood that younger drivers would scan for potential hazards on the open road. In order to test this hypothesis, 12 trained and 12 untrained drivers' eye movements were measured as they drove a vehicle on local residential, feeder and arterial roads. Overall, the trained drivers were significantly more likely to gaze at areas of the roadway that contained information relevant to the reduction of risks (64.4%) than were the untrained drivers (37.4%). Significant training effects were observed even in situations on the road that were quite different from those shown in training. These findings have clear implications for the type of training of teen drivers that is necessary in order to increase their anticipation of hazards.
Collapse
Affiliation(s)
- A K Pradhan
- Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, MA 01003, USA.
| | | | | | | |
Collapse
|
21
|
Roul BK, Mishra DK, Ray M, Sahu DR, Mishra PK, Srinivasu VV, Pradhan AK. Magnetic characterization of radio frequency heat affected micron size Fe3O4 powders: a bio-application perspective. J Nanosci Nanotechnol 2009; 9:3204-3209. [PMID: 19452992 DOI: 10.1166/jnn.2009.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Micron size Fe3O4 powders were chemically prepared and processed by radio frequency (13.56 MHz) oxygen plasma irradiation technique at different elevated temperatures using low radio frequency (RF) power level. Low magnetic field RF superconducting quantum interference device (SQUID) magnetization studies were performed up to a maximum magnetic field of 100 Oe, which was well below the magnetic field tolerance factor of human beings and at different temperatures (down to 5 K). Heat-treated powders in RF oxygen plasma showed significant changes in blocking temperature, magnetization and susceptibility, which are important parameters for bio-applications. It is observed that blocking temperature is decreased under identical RF heat treatment in oxygen plasma and noted to be dependent on average particle size. Microscopic rise in electron temperature during RF heating may likely to enhance the electron-hopping rate between Fe(+2) and Fe(+3) in the octahedral site of Fe3O4 molecular crystal structure, which in turn exhibit changes in blocking temperature including low field magnetization and susceptibility. These properties of Fe3O4 fine powder are likely to play important role in generating and processing biocompatible Ferro-fluid down to nanoscopic size for biomaterials applications.
Collapse
Affiliation(s)
- B K Roul
- Institute of Materials Science, Planetarium Building, Bhubaneswar 751013, Orissa, India. 2
| | | | | | | | | | | | | |
Collapse
|
22
|
Pradhan AK, Van Kessel JS, Karns JS, Wolfgang DR, Hovingh E, Nelen KA, Smith JM, Whitlock RH, Fyock T, Ladely S, Fedorka-Cray PJ, Schukken YH. Dynamics of endemic infectious diseases of animal and human importance on three dairy herds in the northeastern United States. J Dairy Sci 2009; 92:1811-25. [PMID: 19307664 DOI: 10.3168/jds.2008-1486] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Endemic infectious diseases in dairy cattle are of significant concern to the industry as well as for public health because of their potential impact on animal and human health, milk and meat production, food safety, and economics. We sought to provide insight into the dynamics of important endemic infectious diseases in 3 northeastern US dairy herds. Fecal samples from individual cows and various environmental samples from these farms were tested for the presence of major zoonotic pathogens (i.e., Salmonella, Campylobacter, and Listeria) as well as commensal bacteria Escherichia coli and enterococci. Additionally, the presence of Mycobacterium avium ssp. paratuberculosis was tested in fecal and serum samples from individual cows. Test results and health and reproductive records were maintained in a database, and fecal, plasma, DNA, and tissue samples were kept in a biobank. All bacteria of interest were detected on these farms and their presence was variable both within and between farms. The prevalence of Listeria spp. and L. monocytogenes in individual fecal samples within farm A ranged from 0 to 68.2% and 0 to 25.5%, respectively, over a period of 3 yr. Within farm B, continuous fecal shedding of Salmonella spp. was observed with a prevalence ranging from 8 to 88%; Salmonella Cerro was the predominant serotype. Farm C appeared less contaminated with Salmonella and Listeria, although in the summer of 2005, 50 and 19.2% of fecal samples were positive for Listeria and L. monocytogenes, respectively. The high prevalence of E. coli (89 to 100%), Enterococcus (75 to 100%), and Campylobacter (0 to 81%) in feces suggested they were ubiquitous throughout the farm environment. Fecal culture and ELISA results indicated a low prevalence of Mycobacterium avium ssp. paratuberculosis infection in these farms (0 to 13.6% and 0 to 4.9% for culture-positive and ELISA-positive, respectively), although the occasional presence of high shedders was observed. Results have major implications for food safety and epidemiology by providing a better understanding of infectious disease dynamics on dairy farms. Comprehensive understanding of these infections may lead to better farm management practices and pathogen reduction programs to control and reduce the on-farm contamination of these pathogens and to prevent their further entry into the food-chain.
Collapse
Affiliation(s)
- A K Pradhan
- Quality Milk Production Services, Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Bisht NC, Gupta V, Ramchiary N, Sodhi YS, Mukhopadhyay A, Arumugam N, Pental D, Pradhan AK. Fine mapping of loci involved with glucosinolate biosynthesis in oilseed mustard (Brassica juncea) using genomic information from allied species. Theor Appl Genet 2009; 118:413-421. [PMID: 18979082 DOI: 10.1007/s00122-008-0907-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 09/27/2008] [Indexed: 05/27/2023]
Abstract
Fine mapping of six seed glucosinolate QTL (J2Gsl1, J3Gsl2, J9Gsl3, J16Gsl4, J17Gsl5 and J3Gsl6) (Ramchiary et al. in Theor Appl Genet 116:77-85, 2007a) was undertaken by the candidate gene approach. Based on the DNA sequences from Arabidopsis and Brassica oleracea for the different genes involved in the aliphatic glucosinolate biosynthesis, candidate genes were amplified and sequenced from high to low glucosinolate Brassica juncea lines Varuna and Heera, respectively. Of the 20 paralogues identified, 17 paralogues belonging to six gene families were mapped to 12 of the 18 linkage groups of B. juncea genome. Co-mapping of candidate genes with glucosinolate QTL revealed that the candidate gene BjuA.GSL-ELONG.a mapped to the QTL interval of J2Gsl1, BjuA.GSL-ELONG.c, BjuA.GSL-ELONG.d and BjuA.Myb28.a mapped to the QTL interval of J3Gsl2, BjuA.GSL-ALK.a mapped to the QTL interval of J3Gsl6 and BjuB.Myb28.a mapped to the QTL interval of J17Gsl5. The QTL J9Gsl3 and J16Gsl4 did not correspond to any of the mapped candidate genes. The functionality and contribution of different candidate genes/QTL was assessed by allelic variation study using phenotypic data of 785 BC(4)DH lines. It was observed that BjuA.Myb28.a and J9Gsl3 contributed significantly to the base level glucosinolate production while J16Gsl4, probably GSL-PRO, BjuA.GSL-ELONG.a and BjuA.GSL-ELONG.c contributed to the C3, C4 and C5 elongation pathways, respectively. Three A genome QTL: J2Gsl1harbouring BjuA.GSL-ELONG.a, J3Gsl2 harbouring both BjuA.GSL-ELONG.c and BjuA.Myb28.a and J9Gsl3, possibly the 'Bronowski genes', were identified as most important loci for breeding low glucosinolate B. juncea. We observed two-step genetic control of seed glucosinolate in B. juncea mainly effected by these three A genome QTL. This study, therefore, provides clues to the genetic mechanism of 'Bronowski genes' controlling the glucosinolate trait and also provides efficient markers for marker-assisted introgression of low glucosinolate trait in B. juncea.
Collapse
Affiliation(s)
- N C Bisht
- Centre for Genetic Manipulation of Crop Plants, Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021, India
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Pradhan AK, Konda RB, Mustafa H, Mundle R, Bamiduro O, Roy UN, Cui Y, Burger A. Surface plasmon resonance in CdSe semiconductor coated with gold nanoparticles. Opt Express 2008; 16:6202-6208. [PMID: 18545322 DOI: 10.1364/oe.16.006202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We have grown CdSe semiconductor films on glass substrates and the films were coated with Au nanoparticles of 10 nm in size by the pulsed-laser deposition technique. The films demonstrate a large enhancement of Raman intensity and photoluminescence of CdSe semiconductor via excitation of surface plasmon resonances in proximate gold metal nanoparticles deposited on the surface of CdSe film. These observations suggest a variety of approaches for improving the performance of devices such as photodetectors, photovoltaics, and related devices, including biosensors.
Collapse
Affiliation(s)
- A K Pradhan
- Center for Materials Research, Norfolk State University, 700 Park Avenue, Norfolk, VA 23504, USA.
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Douglas L, Mundle R, Konda R, Bonner CE, Pradhan AK, Sahu DR, Huang JL. Influence of doping rate in Er3+:ZnO films on emission characteristics. Opt Lett 2008; 33:815-817. [PMID: 18414542 DOI: 10.1364/ol.33.000815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
High-quality Er(3+):ZnO films were grown by the pulsed-laser deposition technique for 0.5 and 2 wt. % Er doping. Two peaks were observed at approximately 1.54 microm in the photoluminescence spectra of samples with 2 wt. % doping contrary to only one peak in the 0.5 wt. % doped sample. Both peaks were found to be strongly temperature dependent. The microscopic studies clearly illustrate that the appearance of the additional peak is attributed to the environment of Er(3+) ions in the form of ErO(6) clusters, which are optically active centers in the ZnO matrix. These results are very important for designing waveguides for telecommunications.
Collapse
Affiliation(s)
- L Douglas
- Center for Materials Research, Norfolk State University, 700 Park Avenue, Norfolk, Virginia 23504, USA
| | | | | | | | | | | | | |
Collapse
|
26
|
Ramchiary N, Bisht NC, Gupta V, Mukhopadhyay A, Arumugam N, Sodhi YS, Pental D, Pradhan AK. QTL analysis reveals context-dependent loci for seed glucosinolate trait in the oilseed Brassica juncea: importance of recurrent selection backcross scheme for the identification of 'true' QTL. Theor Appl Genet 2007; 116:77-85. [PMID: 17898985 DOI: 10.1007/s00122-007-0648-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Accepted: 09/09/2007] [Indexed: 05/17/2023]
Abstract
Seed glucosinolate content in Brassica juncea is a complex quantitative trait. A recurrent selection backcross (RSB) method with a doubled haploid (DH) generation interspersing backcross generations was used for the introgression of low glucosinolate alleles from an east European gene pool B. juncea line, Heera into an Indian gene pool variety, Varuna. Phenotypic comparisons among the DH populations derived from early to advanced backcrosses revealed a shift in the mean values for various glucosinolates with the advancement of backcrossing, indicating a change in the selective values of the alleles with change in the genetic background due to the existence of epistasis and context dependencies. QTL mapping for various seed glucosinolates from early (F(1)DH) and advanced generation (BC(4)DH) populations confirmed the presence of epistasis and context dependency. The common QTL detected in both F(1)DH and BC(4)DH changed their R (2) values from the former to the later generation. Some of the QTL detected in the F(1)DH became irrelevant in the BC(4)DH population. Further, new QTL were detected in the BC(4)DH population for various glucosinolates. A validation study on a population of low glucosinolate DH lines derived from all the backcross generations of the RSB breeding programme revealed that the QTL detected in BC(4)DH were the 'true' QTL. Using glucosinolate as an example, the study provides strong evidence for the importance of the RSB method for the identification of the 'true' QTL which would be significant for marker assisted introgression of a complex quantitative trait whose expression is influenced by epistatic interactions.
Collapse
Affiliation(s)
- N Ramchiary
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Ramchiary N, Padmaja KL, Sharma S, Gupta V, Sodhi YS, Mukhopadhyay A, Arumugam N, Pental D, Pradhan AK. Mapping of yield influencing QTL in Brassica juncea: implications for breeding of a major oilseed crop of dryland areas. Theor Appl Genet 2007; 115:807-17. [PMID: 17646960 DOI: 10.1007/s00122-007-0610-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Accepted: 07/07/2007] [Indexed: 05/16/2023]
Abstract
Quantitative trait loci (QTL) analysis of yield influencing traits was carried out in Brassica juncea (AABB) using a doubled haploid (DH) mapping population of 123 lines derived from a cross between Varuna (a line representing the Indian gene pool) and Heera (representing the east European gene pool) to identify potentially useful alleles from both the parents. The existing AFLP based map of B. juncea was further saturated with RFLP and SSR markers which led to the identification of the linkage groups belonging to the A (B. rapa) and B (B. nigra) genome components of B. juncea. For QTL dissection, the DH lines were evaluated at three different environments and phenotyped for 12 quantitative traits. A total of 65 QTL spread over 13 linkage groups (LG) were identified from the three environments. QTL analysis showed that the A genome has contributed more than the B genome to productivity (68% of the total QTL detected) suggesting a more prominent role of the A genome towards domestication of this crop. The east European line, Heera, carried favorable alleles for 42% of the detected QTL and the remaining 58% were in the Indian gene pool line, Varuna. We observed clustering of major QTL in a few linkage groups, particularly in J7 and J10 of the A genome, with QTL of different traits having agronomically antagonistic allelic effects co-mapping to the same genetic interval. QTL analysis also identified some well-separated QTL which could be readily transferred between the two pools. Based on the QTL analysis, we propose that improvement in yield could be achieved more readily by heterosis breeding rather than by pure line breeding.
Collapse
Affiliation(s)
- N Ramchiary
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Sodhi YS, Chandra A, Verma JK, Arumugam N, Mukhopadhyay A, Gupta V, Pental D, Pradhan AK. A new cytoplasmic male sterility system for hybrid seed production in Indian oilseed mustard Brassica juncea. Theor Appl Genet 2006; 114:93-9. [PMID: 17036218 DOI: 10.1007/s00122-006-0413-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2005] [Accepted: 09/08/2006] [Indexed: 05/12/2023]
Abstract
We report a novel cytoplasmic male sterility (CMS) system in Brassica juncea (oilseed mustard) which could be used for production of hybrid seed in the crop. A male sterile plant identified in a microspore derived doubled haploid population of re-synthesized B. napus line ISN 706 was found to be a CMS as the trait was inherited from the female parent. This CMS, designated '126-1', was subsequently transferred to ten different B. juncea varieties and lines through inter-specific crosses followed by recurrent backcrossing. The F(1)s of inter-specific crosses were invariably partially fertile, but irrespective of the variety/line used, the recipient lines became progressively male sterile over five to seven generations and could be maintained by crossing the male sterile lines with their normal counterparts. The male sterile lines were found to be stable for the trait under both long and short day conditions. CMS lines when crossed with lines other than the respective maintainer line were restored for fertility, implying that any variety could act as a restorer for '126-1' cytoplasm in B. juncea. These unique features in maintenance and restoration of CMS lines coupled with near normal floral morphology of the CMS lines have allowed the use of '126-1' cytoplasm for hybrid seed production. The uniqueness of '126-1' has been further established by Southern hybridization with mitochondrial DNA probes and by a histological study of the development of male sterile anthers.
Collapse
Affiliation(s)
- Y S Sodhi
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, 110021, New Delhi, India.
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Pradhan AK, Williams TM, Zhang K, Hunter D, Dadson JB, Lord K, Roy UN, Cui Y, Burger A. Growth of aligned ZnO nanorods. J Nanosci Nanotechnol 2006; 6:1985-9. [PMID: 17025113 DOI: 10.1166/jnn.2006.318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Growth of high-density and aligned ZnO nanorods on ZnO film substrate has been demonstrated using vapor-transport of thermally evaporated Zn metal powders followed by condensation. Morphological studies show that the nanorods grow preferentially from a hexagonal ZnO base with a uniform hexagonal structure following three-dimensional island-like growth mechanism. Structural and spectroscopic properties clearly indicate that the nanorods are relatively good and defect-free in quality. These nanorods have potential for technological implications.
Collapse
Affiliation(s)
- A K Pradhan
- Center for Materials Research, Norfolk State University, VA 23504, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Pradhan AK, Li Y, Swem BL, Mauromoustakos A. Predictive model for the survival, death, and growth of Salmonella typhimurium in broiler hatchery. Poult Sci 2005; 84:1959-66. [PMID: 16479956 DOI: 10.1093/ps/84.12.1959] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Contamination and penetration of salmonellae into hatching eggs may comprise an important link in the transmission of these bacteria to growing birds, processed carcasses, and eventually to the consumer. In this study, a predictive model for Salmonella typhimurium as a function of initial cell number and storage or incubation time at a nearly constant temperature and humidity was developed and evaluated to compute the bacterial load after 1 d (holding), 10 d (candling), 17 d (incubation), and 21 d (chick processing). Experiments were conducted for S. typhimurium with both high initial bacterial load (HIBL) and low initial bacterial load (LIBL) of 6.0 and 3.5 log cfu/egg, respectively. Eggs with HIBL experienced 2.0 log reduction in the bacterial load after holding at 4 degrees C for 24 h and 3.0 log increase in the bacterial load during incubation and hatch at approximately 37 degrees C between 17 d and 21 d. Experimental data showed that bacterial load of S. typhimurium from holding to chick processing changed from 3.7 to 6.6 log cfu/egg and from 3.7 to 2.7 log cfu/egg in HIBL and LIBL eggs, respectively. The developed model was able to predict bacterial load of S. typhimurium from 3.6 to 6.6 log cfu/egg in HIBL eggs and from 3.4 to 2.7 log cfu/egg in LIBL eggs from holding to chick processing. Root mean square errors and plot of predicted compared with observed bacterial load of S. typhimurium in contaminated eggs yielded a good fit and prediction. The predicted and experimental results indicated that incubated broiler eggs have an increase in internal bacterial loads between incubation and hatch. This model can be used as a tool to predict bacterial load of S. typhimurium in contaminated eggs as well as help predict the behavior of S. typhimurium during hatch.
Collapse
Affiliation(s)
- A K Pradhan
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | | | | | | |
Collapse
|
31
|
Padmaja KL, Arumugam N, Gupta V, Mukhopadhyay A, Sodhi YS, Pental D, Pradhan AK. Mapping and tagging of seed coat colour and the identification of microsatellite markers for marker-assisted manipulation of the trait in Brassica juncea. Theor Appl Genet 2005; 111:8-14. [PMID: 15902399 DOI: 10.1007/s00122-005-1933-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2004] [Accepted: 01/14/2005] [Indexed: 05/02/2023]
Abstract
Microsatellite marker technology in combination with three doubled haploid mapping populations of Brassica juncea were used to map and tag two independent loci controlling seed coat colour in B. juncea. One of the populations, derived from a cross between a brown-seeded Indian cultivar, Varuna, and a Canadian yellow-seeded line, Heera, segregated for two genes coding for seed coat colour; the other two populations segregated for one gene each. Microsatellite markers were obtained from related Brassica species. Three microsatellite markers (Ra2-A11, Na10-A08 and Ni4-F11) showing strong association with seed coat colour were identified through bulk segregant analysis. Subsequent mapping placed Ra2-A11 and Na10-A08 on linkage group (LG) 1 at an interval of 0.6 cM from each other and marker Ni4-F11 on LG 2 of the linkage map of B. juncea published previously (Pradhan et al., Theor Appl Genet 106:607-614, 2003). The two seed coat colour genes were placed with markers Ra2-A11 and Na10-A08 on LG 1 and Ni4-F11 on LG 2 based on marker genotyping data derived from the two mapping populations segregating for one gene each. One of the genes (BjSC1) co-segregated with marker Na10-A08 in LG 1 and the other gene (BjSC2) with Ni4-F11 in LG 2, without any recombination in the respective mapping populations of 130 and 103 segregating plants. The identified microsatellite markers were studied for their length polymorphism in a number of yellow-seeded eastern European and brown-seeded Indian germplasm of B. juncea and were found to be useful for the diversification of yellow seed coat colour from a variety of sources into Indian germplasm.
Collapse
Affiliation(s)
- K Lakshmi Padmaja
- Department of Genetics and Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | | | | | | | | | | | | |
Collapse
|
32
|
Gupta V, Mukhopadhyay A, Arumugam N, Sodhi YS, Pental D, Pradhan AK. Molecular tagging of erucic acid trait in oilseed mustard (Brassica juncea) by QTL mapping and single nucleotide polymorphisms in FAE1 gene. Theor Appl Genet 2004; 108:743-749. [PMID: 14564400 DOI: 10.1007/s00122-003-1481-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2003] [Accepted: 09/17/2003] [Indexed: 05/24/2023]
Abstract
Molecular mapping and tagging of the erucic acid trait (C22:1) in Brassica juncea was done by a candidate gene approach. Two QTLs underlying the variation of seed erucic acid content were assigned to two linkage groups of a B. juncea map using a doubled haploid (DH) mapping population derived from high x low erucic acid F(1) hybrid. Two consensus primers corresponding to the full-length Fatty Acid Elongase 1 ( FAE1) gene, reported to be involved in the elongation of C18:1 to C22:1, were designed. PCR amplification and subsequent cloning and sequencing identified two FAE1 genes ( FAE1.1 and FAE1.2) in both high and low erucic acid mustard lines. Sequence alignment of corresponding FAE1 genes between high and low erucic acid mustard lines identified four substitution type single nucleotide polymorphisms (SNPs) in FAE1.1 and three in FAE1.2. Using the SNuPE method of SNP genotyping, these two genes were mapped to two independent loci that co-segregated with the two QTLs governing the erucic acid trait. Association of wild ( E1E2) and mutant ( e1e2) haplotypes of two FAE1 genes with erucic acid variation in two segregating populations revealed that the e1e1e2e2 genotype identified low erucic acid individuals (<2%) and E1E1E2E2 identified individuals with highest erucic acid content (>40%). The E1e1E2e2 heterozygote was found to be intermediate in phenotype. The applicability of these SNPs in marker-assisted manipulation of the erucic acid trait was verified by genotyping a set of contrasting germplasm of B. juncea belonging to two distinct gene pools (Indian and east European) and other oil-yielding Brassica species.
Collapse
Affiliation(s)
- V Gupta
- Centre for Genetic Manipulation of Crop Plants and Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | | | | | | | | | | |
Collapse
|
33
|
Pradhan AK, Gupta V, Mukhopadhyay A, Arumugam N, Sodhi YS, Pental D. A high-density linkage map in Brassica juncea (Indian mustard) using AFLP and RFLP markers. Theor Appl Genet 2003; 106:607-614. [PMID: 12595988 DOI: 10.1007/s00122-002-1083-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2002] [Accepted: 06/07/2002] [Indexed: 05/24/2023]
Abstract
A high-density genetic linkage map of Brassica juncea (2n = 36) was constructed with 996 AFLP (amplified fragment length polymorphism) and 33 RFLP (restriction fragment length polymorphism) markers using a F1-derived doubled-haploid (DH) population of 123 individuals. This mapping population was developed by crossing a well-adapted, extensively grown Indian variety Varuna and a canola quality line Heera. The two lines are highly divergent and contain a number of contrasting qualitative and quantitative traits of high agronomic value. AFLPs were generated by the use of restriction enzymes EcoRI or PstI in combination with either MseI or TaqI. Using 91 primer pairs, a total of 1,576 parental polymorphic bands were detected of which 996 were used for mapping. In addition, 33 RFLP markers, developed from genomic clones of B. napus, were added to the map. The segregation of each marker and linkage analysis was performed using the program JoinMap version 2.0. The 1,029 mapped-markers were aligned in 18 linkage groups, which is the haploid chromosome number of the species, at LOD values ranging from 5 to 8. The total map length was 1,629 cM with an average marker interval of 3.5 cM. AFLP markers generated by EcoRI were more clustered, whereas PstI markers showed more extensive distribution. A set of 26 primer pairs (9 EcoRI/ MseI, 6 EcoRI/ TaqI, 6 PstI/ MseI and 5 PstI/ TaqI) generating 385 markers were identified for AFLP-based whole-genome selection as these markers covered 96% of the genome mapped with the 91 primer pairs. The map developed in the present study could be used for dissection and the transfer of agronomically important traits and favourable QTLs from ill-adapted exotic germplasm to cultivated Indian varieties.
Collapse
Affiliation(s)
- A K Pradhan
- Centre for Genetic Manipulation of Crop Plants and Department of Genetics, University of Delhi South Campus, Benito Juarez Road, India.
| | | | | | | | | | | |
Collapse
|
34
|
|
35
|
|
36
|
|
37
|
|
38
|
|
39
|
Pradhan AK, Seaton MJ. Dielectric recombination. II. Effects on cross sections for inelastic collisions between electrons and atomic ions. ACTA ACUST UNITED AC 1999. [DOI: 10.1088/0022-3700/18/8/017] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
40
|
Arumugam N, Mukhopadhyay A, Gupta V, Pental D, Pradhan AK. Synthesis of hexaploid (AABBCC) somatic hybrids: a bridging material for transfer of 'tour' cytoplasmic male sterility to different Brassica species. Theor Appl Genet 1996; 92:762-768. [PMID: 24166401 DOI: 10.1007/bf00226099] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/1995] [Accepted: 09/08/1995] [Indexed: 06/02/2023]
Abstract
Most of the alloplasmic cytoplasmic male sterility (CMS) systems are known to be associated with a number of floral abnormalities that result from nuclear-cytoplasmic incompatibilities. One such system, 'tour', which is derived from Brassica tournefortii, induces additional floral abnormalities and causes chlorosis in Brassica spp. While the restorer for this CMS has been reported to be present in B. napus, in B. juncea, where the abnormalities are more pronounced, no restorer has yet been identified. Rectification of these floral abnormalities through mitochondrial recombinations and chloroplast replacement might result in the improvement of this CMS system. As organelle recombinations can possibly be achieved only by somatic cell hybridization, fusion experiments were carried out between hygromycin-resistant B. juncea AABB carrying 'tour' cytoplasm and phosphinotricin-resistant, normal B. oleracea CC to generate AABBCC hexaploid somatic hybrids. The presence of selectable marker genes facilitated the selection of hybrids in large numbers. The resulting hybrids showed wide variation in floral morphology and organelle composition. Regenerants with normal, male-sterile flowers having recombinant 'tour'-or 'oleracea'-type mitochondria and 'oleracea'-type chloroplasts were obtained. Hybrids with male-fertile flowers were also obtained that had recombined 'tour' mitochondria. The AABBCC hexaploid hybrids synthesized in the present study were successfully utilized as a bridging material for transferring variability in the organelle genome simultaneously to all the digenomic Brassica species, and all of these hybrids are now being stabilized through repeated backcrosses to the allopolyploid crop brassicas.
Collapse
Affiliation(s)
- N Arumugam
- Tata Energy Research Institute, Darbari Seth Block, Habitat Place, Lodhi Road, 110 003, New Delhi, India
| | | | | | | | | |
Collapse
|
41
|
Nagpal R, Raina SN, Sodhi YS, Mukhopadhyay A, Arumugam N, Pradhan AK, Pental D. Transfer of Brassica tournefartii (TT) genes to allotetraploid oilseed Brassica species (B. juncea AABB, B. napus AACC, B. carinata BBCC): homoeologous pairing is more pronounced in the three-genome hybrids (TACC, TBAA, TCAA, TCBB) as compared to allodiploids (TA, TB, TC). Theor Appl Genet 1996; 92:566-71. [PMID: 24166324 DOI: 10.1007/bf00224559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/1995] [Accepted: 10/20/1995] [Indexed: 05/14/2023]
Abstract
For the transfer of genes from B. tournefortii (TT) to the allotetraploid oilseed brassicas, B. juncea AABB, B. carinata BBCC and B. napus AACC, B. tournefortii was first crossed with the three basic diploid species, B. campestris (AA), B. nigra (BE) and B. oleracea (CC), to produce the allodiploids TA, TB and TC. These were tetraploidized by colchicine treatment to produce the allotetraploids TTAA, TTBB and TTCC, which were further crossed with B. juncea and B. napus to produce three-genome hybrids with substitution-type genomic configurations: TACC, TBAA and TCAA. These hybrids along with another hybrid TCBB produced earlier, the three allodiploids, their allotetraploids and the four diploid parent species were studied for their male meiotic behaviour. The diploid parent and the allotetraploids (TTAA, TTBB and TTCC) showed regular meiosis although the pollen viability was generally low in the allotetraploids. In the allodiploids (TA, TB and TC) only some end-to-end associations were observed without any clearly discernible chiasmata or exchange points. Chromosomes involved in end-to-end associations were randomly distributed at the metaphase/anaphase-I stages. In contrast, the three-genome hybrids (TACC, TBAA, TCAA and TCBB) showed normal bivalents whose number exceeded the expected bivalent values. Bivalents arising out of homoeologous pairing were indistinguishable from normal pairs by their disjunction pattern but could be distinguished on the basis of the heteromorphy of the homoeologous chromosomes. The three-genome hybrids could be backcrossed to allotetraploid oilseed brassicas as they had some fertility. In contrast, the allodiploids could neither be selfed nor back-crossed. On the basis of their meiotic stability, in terms of more pronounced homoeologous pairing and fertility for backcrossing, the three-genome configurations provide the best possible situation for the introgression of alien genes from the secondary gene pool to the allotetraploid oilseed crops B. juncea, B. napus and B. carinata.
Collapse
Affiliation(s)
- R Nagpal
- Laboratory of Cellular and Molecular Cytogenetics, Department of Botany, University of Delhi, 110007, Delhi, India
| | | | | | | | | | | | | |
Collapse
|
42
|
Pradhan AK, Roy SB, Chaddah P, Kanjilal D, Chen C, Wanklyn BM. Effects of 200-MeV Ag-ion irradiation on magnetization in a Bi2Sr2CaCu2O8+y single crystal. Phys Rev B Condens Matter 1996; 53:2269-2272. [PMID: 9983727 DOI: 10.1103/physrevb.53.2269] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
43
|
Roy SB, Pradhan AK, Chaddah P. Magnetic anomaly and the peak effect in superconducting CeRu2. Phys Rev B Condens Matter 1995; 52:R9847-R9850. [PMID: 9980129 DOI: 10.1103/physrevb.52.r9847] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
44
|
Zhang HL, Pradhan AK. Electron-impact excitation of heliumlike titanium. Phys Rev A 1995; 52:3366-3369. [PMID: 9912626 DOI: 10.1103/physreva.52.3366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
45
|
Pradhan AK, Roy SB, Chaddah P, Chen C, Wanklyn BM. Anomalous magnetic behavior in Bi2Sr2CaCu2O8+y single crystals near the superconducting-transition regime. Phys Rev B Condens Matter 1995; 52:6215-6218. [PMID: 9981847 DOI: 10.1103/physrevb.52.6215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
46
|
Zhang HL, Pradhan AK. Electron-impact excitation along an isoelectronic sequence: B-like ions. Phys Rev A 1994; 50:3105-3116. [PMID: 9911251 DOI: 10.1103/physreva.50.3105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
47
|
Pradhan AK, Roy SB, Chaddah P, Chen C, Wanklyn BM. Fluctuation phenomena in excess conductivity and magnetization of single-crystal Bi2Sr2CaCu2O8+y. Phys Rev B Condens Matter 1994; 50:7180-7183. [PMID: 9974683 DOI: 10.1103/physrevb.50.7180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
48
|
Mukhopadhyay A, Arumugam N, Pradhan AK, Murthy HN, Yadav BS, Sodhi YS, Pental D. Somatic hybrids with substitution type genomic configuration TCBB for the transfer of nuclear and organelle genes from Brassica tournefortii TT to allotetraploid oilseed crop B. carinata BBCC. Theor Appl Genet 1994; 89:19-25. [PMID: 24177764 DOI: 10.1007/bf00226977] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/1993] [Accepted: 01/12/1994] [Indexed: 06/02/2023]
Abstract
Oilseed crop Brassica carinata BBCC is a natural allotetraploid of diploid species B. nigra BB and B. oleracea CC. To transfer the nuclear and organelle genes in a concerted manner from an alien species, B. tournefortii TT, to B. carinata, we produced somatic hybrids with genomic configuration TCBB using B. nigra and B. oleracea stocks that carried selectable marker genes. B. tournefortii TT was sexually crossed with hygromycin-resistant B. oleracea CC. Protoplasts isolated from shoot cultures of hygromycin-resistant F1 hybrids of B. tournefortiixB. oleracea TC were fused with protoplasts of kanamycin-resistant B. nigra BB. In two different fusion experiments 80 colonies were obtained through selection on media containing both hygromycin and kanamycin. Of these, 39 colonies regenerated into plants. Analysis of 15 regenerants by random amplified polymorphic DNA (RAPD) markers showed the presence of all three genomes, thereby confirming these to be true hybrids. Restriction fragment length polymorphism (RFLP) analysis of organelle genomes with heterologous chloroplast (cp)and mitochondrial (mt) DNA probes showed that the chloroplast genome was inherited from either of the two parents while mitochondrial genomes predominantly showed novel configurations due to either rearrangements or intergenomic recombinations. We anticipate that the TCBB genomic configuration will provide a more conducive situation for recombination between the T and C genomes during meiosis than the TTCCBB or TCCBB type configurations that are usually produced for alien gene transfer. The agronomic aim of producing TCBB hybrids is to transfer mitochondrial genes conferring cytoplasmic male sterility and nuclear genes for fertility restoration from B. tournefortii to B. carinata.
Collapse
Affiliation(s)
- A Mukhopadhyay
- Tata Energy Research Institute, 90 Jor Bagh, 110 003, New Delhi, India
| | | | | | | | | | | | | |
Collapse
|
49
|
Pradhan AK, Roy SB, Chaddah P, Chen C, Wanklyn BM. Magnetic properties of single-crystal Bi2Sr2CaCu2O8+y: Experimental evidence for a dimensional crossover. Phys Rev B Condens Matter 1994; 49:12984-12989. [PMID: 10010210 DOI: 10.1103/physrevb.49.12984] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
50
|
Nahar SN, Pradhan AK. Unified treatment of electron-ion recombination in the close-coupling approximation. Phys Rev A 1994; 49:1816-1835. [PMID: 9910433 DOI: 10.1103/physreva.49.1816] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|