Abstract TS1-2: Proteogenomic Landscape of Prospectively Collected Breast Cancer

A persistent central deficiency in our knowledge of cancer concerns how genomic changes drive the proteome and phosphoproteome to execute phenotypic characteristics. Furthermore increasing evidence implicating epigenetic and post-translational changes in cancer biology reinforce the notion that molecular profiles based on nucleic acids are incomplete and are critically complemented by analyses of proteins and their post-translational modifications. We present the first integrated proteogenomic study on a prospectively collected breast cancer cohort, and provide new insights including on taxonomy, metabolic dependencies, and immune milieu. 122 invasive ductal breast cancer samples were collected under the auspices of the National Cancer Institute’s Clinical Proteomics Tumor Analysis Consortium using rigorous protocols to minimize ischemic time and other pre-analytical variability. Samples underwent comprehensive genomic and proteomic characterization, providing whole exome, whole genome, copy number, RNAseq, global proteome, phosphoproteome, and acetylome data. Multi-omics clustering by nonnegative matrix factorization revealed basal-, luminal A-, and HER2-enriched clusters, as well as a combined luminal A/B cluster. Luminal A and A/B clusters were distinguished by differential expression of cytoskeletal signatures possibly driven by YAP1 overexpression and hyper-phosphorylation in the luminal A subset. Kinase outlier analysis revealed luminal A enrichment of PEAK1, an atypical kinase that regulates YAP1 expression. PTPN2, recently shown to synergize with anti-PD1 therapy, was an outlier in basal tumors, suggesting therapeutic opportunities in that difficult-to-treat subtype. Acetylation plays a dominant role in mitochondrial metabolism, and downregulation of deacetylase SIRT3 in basal and HER2-enriched samples was associated with upregulation of TCA cycle- and amino acid metabolism-related proteins suggesting metabolic dependencies that could be exploited. Immunological subtyping of the breast cohort identified immune-cold, immune-hot, immune-excluded and interferon-independent clusters associated with distinct patterns of tumor-infiltrating lymphocytes. Basal tumors generally overexpressed PDL1 relative to other subtypes, whereas the newly described immuno-oncology target SIGLEC15 was overexpressed in luminal tumors. While these and other analyses are intended to provide new insights into breast cancer biology and facilitate testable therapeutic hypotheses, the larger purpose of the program is to provide a resource to the breast cancer and broader scientific communities. To facilitate this, these and previously published data will be integrated to provide a sample set of 199 proteogenomically characterized breast cancers for further exploration.

Citation Format: M Gillette, K Krug, S Satpathy, E Jaehnig, A Karpova, K Clauser, L Tang, L Blumenberg, R Kothadia, K Ruggles, B Zhang, L Ding, P Mertins, DR Mani, M Ellis, S Carr. Proteogenomic Landscape of Prospectively Collected Breast Cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr TS1-2.

Two dimensional electron gas in the [Formula: see text]-doped iridates with strong spin-orbit coupling: La[Formula: see text]Sr2IrO4

Iridates are of considerable current interest because of the strong spin-orbit coupling that leads to a variety of new phenomena. Using density-functional studies, we predict the formation of a spin-orbital entangled two dimensional electron gas (2DEG) in the [Formula: see text]-doped iridate La[Formula: see text]Sr₂IrO₄, where a single SrO layer is replaced by a LaO layer. The extra La electron resides close to the [Formula: see text]-doped layer, partially occupying the [Formula: see text] upper Hubbard band and thereby making the interface metallic. The magnetic structure of the bulk is destroyed near the interface, with the Ir₀ layer closest to the interface becoming non-magnetic, while the next layer (Ir₁) continues to maintain the AFM structure of the bulk, but with a reduced magnetic moment. The Fermi surface consists of a hole pocket and an electron pocket, located in two different Ir layers (Ir₀ and Ir₁), with both carriers derived from the [Formula: see text] upper Hubbard band. The presence of both electrons and holes at the [Formula: see text]-doped interface suggests unusual transport properties, leading to possible device applications.

Field-specific nutrient management using Rice Crop Manager decision support tool in Odisha, India

The requirement of rice (Oryza sativa L.) for fertilizer can depend on crop and soil management practices, which can vary among fields within a rice-growing area. A web-based decision support tool named Rice Crop Manager (RCM) was developed previously to calculate field-specific rates of fertilizer N, P, and K for rice in Odisha State in eastern India. We compared field-specific nutrient management calculated by RCM with farmers' fertilizer practice (FFP) and a blanket fertilizer recommendation (BFR), which used a uniform 80 kg N ha-1, 17 kg P ha-1, and 33 kg K ha-1. A total of 209 field trials were conducted in two seasons (kharif and rabi) for two years across ten districts in six agro-climatic zones. Grain yield was consistently higher with fertilization recommended by RCM than with FFP. Higher yield with RCM was attributed to a combination of applying more of the total fertilizer N at the critical growth stage of panicle initiation, applying more fertilizer N in kharif, and applying zinc. The RCM recommendation frequently increased yield compared to BFR as a result of improved N management, which included the adjustment of N rate for a target yield set slightly higher than historical yield reported by a farmer. Fertilization based on RCM rather than BFR reduced the risk of financial loss. The effectiveness of an RCM recommendation relative to BFR and FFP was consistent across rice varieties with different growth duration, irrigated and rainfed rice, and three categories of soil clay content. The RCM recommendation failed to increase yield relative to BFR in one of the six agro-climatic zones, where a higher rate of fertilizer P and/or K was apparently required. The nutrient management calculations used by RCM can be improved as new information and research findings become available. Experiences with RCM in Odisha can help guide the development of comparable nutrient management decision tools in other rice-growing areas.

Unit Cost Analysis of PET-CT at an Apex Public Sector Health Care Institute in India

Context:

PET/CT scan service is one of the capital intensive and revenue-generating centres of a tertiary care hospital. The cost associated with the provisioning of PET services is dependent upon the unit costs of the resources consumed.

Aims:

The study aims to determine the cost of providing PET/CT Scan services in a hospital.

Methods and Material:

This descriptive and observational study was conducted in the Department of Nuclear Medicine at a tertiary apex teaching hospital in New Delhi, India in the year 2014-15. Traditional costing methodology was used for calculating the unit cost of PET/CT scan service. The cost was calculated under two heads that is capital and operating cost. Annualized cost of capital assets was calculated using methodology prescribed by WHO and operating costs was taken on an actual basis.

Results:

Average number of PET/CT scan performed in a day is 30. The annual cost of providing PET/CT scan services was calculated to be 65,311,719 Indian Rupees (INR) (US$ 1,020,496), while the unit cost of PET scan was calculated to be 9625.92 INR (US$ 150). 3/4th cost was spent on machinery and equipment (75.3%) followed by healthcare personnel (11.37%), electricity (5%), consumables and supplies (4%) engineering maintenance (3.24%), building, furniture and HVAC capital cost (0.76%), and manifold cost (0.05%). Of the total cost, 76% was capital cost while the remaining was operating cost.

Conclusions:

Total cost for establishing PET/CT scan facility with cyclotron and chemistry module and PET/CT scan without cyclotron and chemistry module was calculated to be INR 610,873,517 (US$9944899) and 226,745,158 (US$3542893), respectively. (US$ 1=INR 64)

Toxicity and bioefficacy of individual and combination of diversified insecticides against jute hairy caterpillar, Spilarctia obliqua

Toxicity of conventional (profenofos 50 EC and λ-cyhalothrin 5 EC) and non-conventional (flubendiamide 480 SC, chlorantraniliprole 18.5 SC, emamectin benzoate 5 SG) insecticides was determined on the basis of median lethal concentration (LC50) values on third instar larvae of jute hairy caterpillar, Spilarctia obliqua under laboratory conditions. Further, the promising binary insecticides combinations with lesser LC50 values and adequate synergistic activity were evaluated under field conditions. The LC50 values calculated for insecticides viz., chlorantraniliprole, flubendiamide emamectin benzoate, λ-cyhalothrin and profenophos were 0.212, 0.232, 0.511, 0.985 and 3.263 ppm, respectively. Likewise, the LC50 values for flubendiamide with λ-cyhalothrin in 3:1 proportion was most toxic (0.103 ppm) amongst all the other binary combinations with λ-cyhalothrin. Chlorantraniliprole in combination with λ-cyhalothrin at 1:1 proportion (0.209 ppm) was most toxic followed by 3:1 proportion (0.345 ppm). Similarly, emamectin benzoate in combination with λ-cyhalothrin at 1:1 proportion was more toxic (0.271 ppm) than 3:1 ratio (0.333 ppm). Toxicity index of flubendiamide + λ-cyhalothrin (3:1 ratio) was highest (970.87). Bioefficacy of synergistic binary combinations along with individual insecticides established the superiority of profenophos + λ-cyhalothrin (3:1) with 89.12% reduction in infestation and recorded maximum fibre yield 38.67qha' under field condition. Moreover, combination of diverse insecticides group might sustain toxicity against the target insect for longer period with least probability of resistance development.

First Report of Potato leaf roll virus (PLRV) Naturally Occurring on Jute (Corchorus olitorius) in India

Jute (Corchorus olitorius L.) is an important bast fiber crop that is mainly grown in the Southeast Asian countries like India, Bangladesh, Nepal, China, Indonesia, Thailand, Myanmar, and a few South American countries. In June 2013, symptoms suggestive of a viral disease were noticed on jute (cv. JRO524) in an experimental field of the CRIJAF research farm, Barrackpore, India, and the incidence of the disease was less than 2%. The infected plants showed stunted growth and short height. Mostly the upper leaves elongated with curling and coiling of lamina. Puckering and shoe string effect were also noticed. Petioles and stipules of the affected leaves were exceptionally longer. Although initially the incidence was low, it may spread to larger areas in subsequent years. Because the jute fiber is extracted from the stem, stunted growth and short height would badly affect the fiber yield and quality. Ten symptomatic and ten asymptomatic healthy looking samples were collected from the field. Corchorus golden mosaic begomovirus is common in jute; therefore, all the samples were tested by PCR using JMFL-AF/JMFL-AR, DNA-A component specific primer pair and JMFL-BF/JMFL-BR, DNA-B component specific primer pairs (1). However, there was no amplification. Because the aphid Aphis gossypii was often noticed in the jute field, all the samples were tested by double-antibody sandwich (DAS)-ELISA for common aphid transmitted viruses, e.g., Cucumber mosaic virus, Bean common mosaic virus, Cowpea mosaic virus, Papaya ring spot virus, Potato leaf roll virus (PLRV), Potato virus Y, and Watermelon mosaic virus using commercial diagnostic kits (Agdia). The symptomatic samples showed positive reaction only for PLRV. Five ELISA-positive samples and five asymptomatic healthy samples were used for RNA extraction. Total RNA was extracted by using QIAGEN RNeasy mini kit. RT-PCR was carried out with PLRV CP gene specific primer pair (3) which generated a cDNA amplicon of 627 bp in all ELISA-positive symptomatic samples. PLRV was not detected in symptomless samples. The five purified cDNA products were cloned in a pGEM-T Easy vector (Promega) and were sequenced. One of the five identical sequences was deposited in GenBank (Accession No. KF233880). The consensus sequence was analyzed by NCBI BLAST and found to share 99% similarity with the coat protein sequence of PLRV reference strain (S77421). Nucleotide span and ORF finder (NCBI) analysis indicated the 627-bp PCR amplicon coded part of a coat protein gene that had 100% identity with translated gene product (Protein ID AAB33483). PLRV is a small isometric RNA virus with worldwide distribution belonging to the family Luteoviridae whose natural host range is mainly restricted to solanaceous plants and few plants of other families (2,4). To the best of our knowledge, this is the first report of PLRV naturally occurring on jute (C. olitorius). References: (1) R. Ghosh et al. J. Virol. Methods 159:34, 2009. (2) S. Guyader and D. G. Ducray. J. Gen. Virol. 83:1799, 2002. (3) M. A. Mayo et al. J. Gen. Virol. 70:1037, 1989. (4) K. Mukherjee et al. Virus Genes 26:247, 2003.

First Report of a 16Sr I-B Phytoplasma Associated with Phyllody and Stem Fasciation of Flax (Linum usitatissimum) in India

Flax or linseed is grown as a fiber or oilseed crop in tropical and temperate regions. It is commercially cultivated in many countries of the world including Canada, China, India, the United States, Ethiopia, Pakistan, Russia, Poland, and Argentina (1). In December 2013, symptoms suggestive of phytoplasma infection were noticed on flax in different experimental fields of Central Research Institute for Jute and Allied Fibres (CRIJAF) research farm, Barrackpore, India, and the incidence was less than 2%. Because incidence of phytoplasma diseases are increasing worldwide, occurrence of a phytoplasma in a new geographical area poses an imminent threat. The infected plants showed floral virescence, phyllody, and stem fasciation (flattened stem). Floral malformation was very conspicuous with abnormal structures replacing normal flowers. All the floral parts, including petals, turned into green leaves. Total DNA was extracted from leaf mid veins of three symptomatic and three asymptomatic plants using a DNeasy Plant Mini Kit (Qiagen). PCR was carried out with the phytoplasma-specific universal P1/P7 primer set followed by nested primer pair R16F2n/R16R2 (2), resulting in DNA amplicons that were 1.8 kb and 1.2 kb, respectively, in all symptomatic samples tested. No amplification was observed with DNA from symptomless samples. This suggested association of a phytoplasma with the disease. The five purified nested PCR products were cloned in a pGEM-T Easy vector (Promega) and sequenced. One of the sequences that proved to be identical to the others was deposited in GenBank (Accession No. KJ417660). The consensus sequence was analyzed by NCBI BLAST and found to share 99% similarity with the 16Sr DNA sequence of the 'Candidatus Phytoplasma asteris' reference strain (GenBank HQ828108), which belongs to 16SrI group. The phylogenetic tree based on 16SrDNA sequence of phytoplasmas belonging to group 16SrI and other distinct phytoplasma groups also showed that the phytoplasma clustered with members of group 16SrI (3). The nested PCR product of R16F2n/R16R2 was digested using restriction enzymes AluI, BfaI, BstU, HhaI, HpaI, KpnI, MseI, and RsaI. The RFLP patterns were compared with those of known phytoplasma strains (2) and they matched the patterns for aster yellows subgroup B (16Sr I-B). Subsequently, the iPhyClassifier 16Sr group/subgroup classification based on similarity (4) analyses showed that the studied strain had 16SrDNA sequences in the 16SrI-B group with a similarity coefficient of 1.00. To the best of our knowledge, this is the first report of 16SrI-B phytoplasma associated with flax in India. References: (1) K. P. Akhtar et al. Phytoparasitica 41:383, 2013. (2) I. M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004. (3) N. Saitou and M. Nei. Mol. Biol. Evol. 4:406, 1987. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.

First Report of a 16SrV-C Phytoplasma Causing Little Leaf and Bunchy Top of Tossa Jute (Corchorus olitorius) in India

Jute is the most important phloem fiber crop of the world, and is mainly grown in the South East Asian countries of India, Bangladesh, Nepal, China, Indonesia, Thailand, and Myanmar, and few South American countries. The fiber is used in making sacks, ropes, bags, carpets, shoes, geo-textiles, and home decorations. There are two kinds of jute: tossa jute (Corchorus olitorius L.) and white jute (C. capsularis). In June 2012, symptoms suggestive of phytoplasma infection (little leaf and bunchy top) were noticed on tossa jute in different experimental fields of the CRIJAF research farm, Barrackpore, India, and the incidence of the disease varied from 5 to 20%. The infected plants showed profuse lateral branching with a bushy appearance. In many plants, branching at the apical portion developed a bunchy top symptom with tufts of smaller leaves. Leafy stem was also common in many plants with main stems covered with numerous little leaves. Total DNA was extracted from leaf midveins of 15 symptomatic and 5 asymptomatic plants by using an improved salt concentration and simple sodium acetate CTAB method (1). PCR was carried out with universal P1/P7 primer set followed by nested primer pair R16F2n/R16R2 (3), resulting in DNA amplicons that were 1.8 kb and 1.2 kb, respectively, in all symptomatic samples tested. Phytoplasma was not detected in symptomless samples. The five purified nested products were cloned in a pGEM-T Easy vector (Promega) and sequenced. One of the sequences that proved to be identical was deposited in GenBank (Accession No. KF501045). The consensus sequence was analyzed by NCBI BLAST and found to share 99% similarity with the 16Sr DNA sequence of the alder yellows phytoplasma reference strain (GenBank Accession No. AY028789), which belongs to the 16SrV group. The phylogenetic tree based on the 16SrDNA sequence of phytoplasmas belonging to group 16SrV and other distinct phytoplasma groups also showed that the phytoplasma clustered with members of subgroup 16SrV (4). Subsequently, in silico RFLP analysis of the nested PCR product with the pDRAW32 program using AluI and TruI restriction site used for 16SrV subgroups A, B, C, D, and E indicated that the 16SrV Corchorus strain belonged to subgroup C. RFLP patterns from all symptomatic C. olitorius samples were identical to the 16SrV-C pattern (2). The vector species transmitting the concerned phytoplasma in C. olitorius still needs to be identified. The leaf hopper, Amrasca biguttula biguttula, may be a potential vector as it is often noticed in jute fields. To the best of our knowledge, this is the first report of 16SrV-C phytoplasma associated with tossa jute (C. olitorius) in India. Initiative has to be taken to manage this disease; otherwise, branching of the main stems would badly affect the fiber quality as well as yield. References: (1) C. Biswas et al. Lett. Appl. Microbiol. 56:105, 2012. (2) B. Duduk et al. J. Phytopathology 152:575, 2004. (3) I. M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004. (4) N. Saitou and M. Nei. Mol. Biol. Evol. 4:406, 1987.

Erratum: ING1 induces apoptosis through direct effects at the mitochondria

The ING family of tumor suppressors acts as readers and writers of the histone epigenetic code, affecting DNA repair, chromatin remodeling, cellular senescence, cell cycle regulation and apoptosis. The best characterized member of the ING family, ING1, interacts with the proliferating cell nuclear antigen (PCNA) in a UV-inducible manner. ING1 also interacts with members of the 14-3-3 family leading to its cytoplasmic relocalization. Overexpression of ING1 enhances expression of the Bax gene and was reported to alter mitochondrial membrane potential in a p53-dependent manner. Here we show that ING1 translocates to the mitochondria of primary fibroblasts and established epithelial cell lines in response to apoptosis inducing stimuli, independent of the cellular p53 status. The ability of ING1 to induce apoptosis in various breast cancer cell lines correlates well with its degree of translocation to the mitochondria after UV treatment. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX, and colocalizes with BAX in a UV-inducible manner. Ectopic expression of a mitochondria-targeted ING1 construct is more proficient in inducing apoptosis than the wild type ING1 protein. Bioinformatic analysis of the yeast interactome indicates that yeast ING proteins interact with 64 mitochondrial proteins. Also, sequence analysis of ING1 reveals the presence of a BH3-like domain. These data suggest a model in which stress-induced cytoplasmic relocalization of ING1 by 14-3-3 induces ING1-BAX interaction to promote mitochondrial membrane permeability and represent a paradigm shift in our understanding of ING1 function in the cytoplasm and its contribution to apoptosis.

ING1 induces apoptosis through direct effects at the mitochondria

The ING family of tumor suppressors acts as readers and writers of the histone epigenetic code, affecting DNA repair, chromatin remodeling, cellular senescence, cell cycle regulation and apoptosis. The best characterized member of the ING family, ING1,interacts with the proliferating cell nuclear antigen (PCNA) in a UV-inducible manner. ING1 also interacts with members of the14-3-3 family leading to its cytoplasmic relocalization. Overexpression of ING1 enhances expression of the Bax gene and was reported to alter mitochondrial membrane potential in a p53-dependent manner. Here we show that ING1 translocates to the mitochondria of primary fibroblasts and established epithelial cell lines in response to apoptosis inducing stimuli, independent of the cellular p53 status. The ability of ING1 to induce apoptosis in various breast cancer cell lines correlates well with its degree of translocation to the mitochondria after UV treatment. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX, and colocalizes with BAX in a UV-inducible manner. Ectopic expression of a mitochondria-targeted ING1 construct is more proficient in inducing apoptosis than the wild type ING1 protein. Bioinformatic analysis of the yeast interactome indicates that yeast ING proteins interact with 64 mitochondrial proteins. Also, sequence analysis of ING1 reveals the presence of a BH3-like domain. These data suggest a model in which stress-induced cytoplasmic relocalization of ING1 by14-3-3 induces ING1-BAX interaction to promote mitochondrial membrane permeability and represent a paradigm shift in our understanding of ING1 function in the cytoplasm and its contribution to apoptosis [corrected].

First Report of Bacterial Leaf Spot Caused by Xanthomonas campestris pv. olitorii on Jute Grown for Seed in India

Jute (Corchorus olitorius L.) is the second most important fiber crop after cotton in terms of global production (3). In November 2011, symptoms suggestive of bacterial infection were observed on a seed crop of jute at the CRIJAF research farm, Barrackpore, West Bengal, India. The disease appeared as small, brown, circular spots, usually less than 5 mm in diameter on the leaves and some of the spots were surrounded by a yellow halo. The lesions on the stems were elongated and in some cases were found to girdle the stem. In the later stages of disease, brown sunken spots were found on the green capsules. Disease incidence varied from about 20% to 90% of the total plants in different affected fields at the CRIJAF research farm. Bacterial leaf spot of jute with similar symptoms was reported in 1957 from Sudan (4). Five symptomatic and three asymptomatic leaf samples were collected from different jute fields. Bacterial colonies isolated on nutrient agar medium from infected young leaves were Xanthomonas-like and pale yellow cream in color. Total DNA was extracted from symptomatic as well as asymptomatic leaf samples by using an improved salt concentration and simple sodium acetate CTAB method (2). Single bacterial colonies were transferred to nutrient agar (NA) medium plates and incubated at 28°C for 48 h. Pure colonies from plates were used directly for DNA extraction using the QIAGEN DNeasy Blood and Tissue kit. PCR was carried out with Xanthomonas campestris specific primers NZ8F3/NZ85R3 (1), which generated an amplicon of 530 bp from all the symptomatic leaf samples as well as pure cultures of the isolated bacteria. No amplification was obtained from asymptomatic leaves. The amplicons from the five symptomatic samples collected from the field were sequenced and showed 100% identity with one another, and one sequence (strain JB-CO-13) was deposited in GenBank (Accession No. KC342185). The BLASTn analysis revealed that bacterial strain JB-CO-13 had 100% identity with X. campestris pv. olitorii (EU285213). Nucleotide span and ORF finder (NCBI) analysis indicated the 530-bp PCR amplicon coded part of a gyrase B gene that had 100% identity with a translated gene product (Protein ID: ABX84334). Three leaves of five 1-month-old jute plants (cv. JRO 204) in pot culture were infiltrated each with a separate bacterial strain using suspensions (1 × 10⁵ CFU/ml) in distilled water. The negative control consisted of leaves infiltrated with sterile distilled water. The plants were kept in a greenhouse with mean maximum and minimum temperatures of 28.96 and 21.8°C, respectively. The plants were covered with plastic bags to maintain high relative humidity (>80%). Typical bacterial lesions were recorded on all the inoculated plants after 1 week. No lesions were seen on the negative control. To the best of our knowledge, this is the first report of bacterial leaf spot on C. olitorius caused by X. campestris pv. olitorii from India. References: (1) J. Adriko et al. Plant Pathol. 61:489, 2012. (2) C. Biswas, et al. Lett. Appl. Microbiol. 56:105, 2013. (3) Food and Agriculture Organization of the United Nations. Agricultural Commodities: Profiles and Relevant WTO Negotiating Issues. Online: http://www.fao.org/docrep/006/Y4343E/y4343e03.htm , 2003. (4) K. A. Sabet. Ann. Appl. Biol. 45:516, 1957.

A multiplex nested PCR assay for simultaneous detection of Corchorus golden mosaic virus and a phytoplasma in white jute (Corchorus capsularis L.)

A multiplex nested PCR assay was developed by optimizing reaction components and reaction cycling parameters for simultaneous detection of Corchorus golden mosaic virus (CoGMV) and a phytoplasma (Group 16Sr V-C) causing little leaf and bunchy top in white jute (Corchorus capsularis). Three sets of specific primers viz. a CoGMV specific (DNA-A region) primer, a 16S rDNA universal primer pair P1/P7 and nested primer pair R16F2n/R2 for phytoplasmas were used. The concentrations of the PCR components such as primers, MgCl2 , Taq DNA polymerase, dNTPs and PCR conditions including annealing temperature and amplification cycles were examined and optimized. Expected fragments of 1 kb (CoGMV), 674 bp (phytoplasma) and 370 bp (nested R16F2n/R2) were successfully amplified by this multiplex nested PCR system ensuring simultaneous, sensitive and specific detection of the phytoplasma and the virus. The multiplex nested PCR provides a sensitive, rapid and low-cost method for simultaneous detection of jute little leaf phytoplasma and CoGMV. Based on BLASTn analyses, the phytoplasma was found to belong to the Group 16Sr V-C.

A simple method of DNA isolation from jute (Corchorus olitorius) seed suitable for PCR-based detection of the pathogen Macrophomina phaseolina (Tassi) Goid

A simple method was developed for isolating DNA from jute seed, which contains high amounts of mucilage and secondary metabolites, and a PCR protocol was standardized for detecting the seedborne pathogen Macrophomina phaseolina. The cetyl trimethyl ammonium bromide method was modified with increased salt concentration and a simple sodium acetate treatment to extract genomic as well as fungal DNA directly from infected jute seed. The Miniprep was evaluated along with five other methods of DNA isolation in terms of yield and quality of DNA and number of PCR positive samples. The Miniprep consistently recovered high amounts of DNA with good spectral qualities at A260/A280. The DNA isolated from jute seed was found suitable for PCR amplification. Macrophomina phaseolina could be detected by PCR from artificially inoculated as well as naturally infected jute seeds. The limit of PCR-based detection of M. phaseolina in jute seed was determined to be 0·62 × 10(-7) CFU g(-1) seed.

Spin-polarized two-dimensional electron gas at oxide interfaces

The possibility of formation of a fully spin-polarized 2D electron gas at the SrMnO_3/(LaMnO_3)_1/SrMnO_3 heterostructure is predicted from density-functional calculations. The La(d) electrons become confined in the direction normal to the interface in the electrostatic potential well of the positively charged layer of La atoms, acting as electron donors. These electrons mediate a ferromagnetic alignment of the Mn t_2g spins near the interface via Zener double exchange and become, in turn, spin-polarized due to the internal magnetic fields of the Mn moments.

Electron leakage and double-exchange ferromagnetism at the interface between a metal and an antiferromagnetic insulator: CaRuO3/CaMnO3

Density-functional electronic structure studies of a prototype interface between a paramagnetic metal and an antiferromagnetic (AFM) insulator (CaRuO(3)/CaMnO(3)) reveal the exponential leakage of the metallic electrons into the insulator side. The leaked electrons in turn control the magnetism at the interface via the ferromagnetic (FM) Anderson-Hasegawa double exchange, which competes with the AFM superexchange of the bulk CaMnO3. The competition produces a FM interfacial CaMnO3 layer (possibly canted); but beyond this layer, the electron penetration is insufficient to alter the bulk magnetism.

Wedge-shaped potential and Airy-function electron localization in oxide superlattices

Oxide superlattices and microstructures hold the promise for creating a new class of devices with unprecedented functionalities. Density-functional studies of the recently fabricated, lattice-matched perovskite titanates (SrTiO3)n/(LaTiO3)m reveal a classic wedge-shaped potential well for the monolayer (m = 1) structure, originating from the Coulomb potential of a two-dimensional charged La sheet. The potential in turn confines the electrons in the Airy-function-localized states. Magnetism is suppressed for the monolayer structure, while in structures with a thicker LaTiO3 part, bulk antiferromagnetism is recovered, with a narrow transition region separating the magnetic LaTiO3 and the nonmagnetic SrTiO3.

Does the self-trapped magnetic polaron exist in electron-doped manganites?

We show from ab initio density-functional calculations and model studies that, in the electron-doped manganite LaxCa1-xMnO3 (x<<1), unbound electrons are introduced into the conduction band, which then trap themselves in the exchange-induced magnetic potential wells forming the self-trapped magnetic polarons (STMP). Hopping beyond the nearest neighbors drastically reduces the binding energy, while the Jahn-Teller coupling increases it somewhat, resulting in a net binding of about 100+/-20 meV. The electron is self-trapped in a seven-site ferromagnetic region, beyond which the lattice is essentially antiferromagnetic. In light of the recent experiments of Neumeier and Cohn, our results suggest that the STMP may be present in the lightly electron-doped manganites.

Origin of charge-orbital order in the half-doped manganites

The microscopic origin of the charge and orbital order in the half-doped manganites is examined from ab initio density-functional calculations and exact diagonalization studies. It is shown that the dominant mechanism responsible for the charge order is the Jahn-Teller coupling, with a lesser but significant contribution from the on-site Coulomb interaction. The band structure shows a sizable interchain coupling between the zigzag chains, leading to a considerable band dispersion normal to the chains, in sharp contrast with the zigzag chain physics.

Cooperative jahn-teller coupling in the manganites

The cooperative Jahn-Teller coupling between the Mn e(g) electrons and the oxygen octahedral distortions in LaMnO3 is studied using ab initio density-functional calculations and tight-binding models. The linear and quadratic vibronic coupling parameters are calculated using density-functional methods. It is shown that the cooperative Jahn-Teller coupling, primarily due to the interoctahedral electron hopping (band structure term), leads to the ordering of the octahedral distortion and simultaneously to orbital ordering. The coupling results in a two-minima adiabatic potential surface in the solid, instead of the three-minima "Mexican-hat" surface for the isolated octahedron.

Hospital staff do not know how much drugs cost

Images