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Shifting the limits in wheat research and breeding using a fully annotated reference genome (2018)

American Association for the Advancement of Science (AAAS)

In: Science

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Publication Date: 2018-08-17

Description: An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

Keywords: Botany, Ecology, Online Only

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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Epigenetic upregulation of lncRNAs at 13q14.3 in leukemia is linked to the In Cis downregulation of a gene cluster that targets NF-kB

Garding A ; Bhattacharya N ; Claus R ; [et al.]

PloS Genetics 9 (4), e1003373-

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Keywords: DNA methylation ; FACTOR-KAPPA-B ; CHRONIC LYMPHOCYTIC-LEUKEMIA ; DISEASE PROGRESSION ; CHROMOSOME 13Q14 ; TUMOR-SUPPRESSOR LOCUS ; LONG NONCODING RNAS ; PROMOTER CPG METHYLATION ; PI3K/NF-KAPPA-B PATHWAY ; ANTISENSE TRANSCRIPTS

Abstract: Non-coding RNAs are much more common than previously thought. However, for the vast majority of non-coding RNAs, the cellular function remains enigmatic. The two long non-coding RNA (lncRNA) genes DLEU1 and DLEU2 map to a critical region at chromosomal band 13q14.3 that is recurrently deleted in solid tumors and hematopoietic malignancies like chronic lymphocytic leukemia (CLL). While no point mutations have been found in the protein coding candidate genes at 13q14.3, they are deregulated in malignant cells, suggesting an epigenetic tumor suppressor mechanism. We therefore characterized the epigenetic makeup of 13q14.3 in CLL cells and found histone modifications by chromatin-immunoprecipitation (ChIP) that are associated with activated transcription and significant DNA-demethylation at the transcriptional start sites of DLEU1 and DLEU2 using 5 different semi-quantitative and quantitative methods (aPRIMES, BioCOBRA, MCIp, MassARRAY, and bisulfite sequencing). These epigenetic aberrations were correlated with transcriptional deregulation of the neighboring candidate tumor suppressor genes, suggesting a coregulation in cis of this gene cluster. We found that the 13q14.3 genes in addition to their previously known functions regulate NF-kB activity, which we could show after overexpression, siRNA-mediated knockdown, and dominant-negative mutant genes by using Western blots with previously undescribed antibodies, by a customized ELISA as well as by reporter assays. In addition, we performed an unbiased screen of 810 human miRNAs and identified the miR-15/16 family of genes at 13q14.3 as the strongest inducers of NF-kB activity. In summary, the tumor suppressor mechanism at 13q14.3 is a cluster of genes controlled by two lncRNA genes that are regulated by DNA-methylation and histone modifications and whose members all regulate NF-kB. Therefore, the tumor suppressor mechanism in 13q14.3 underlines the role both of epigenetic aberrations and of lncRNA genes in human tumorigenesis and is an example of colocalization of a functionally related gene cluster.

DOI: 10.1371/journal.pgen.1003373

Type of Publication: Journal article published

PubMed ID: 23593011

Deep Link: http://www.dkfz.de/cgi-bin/sel?http://www.dkfz.de/PublicationManager/Show/ShowJournal.aspx%3fpublishedId=40433

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Ozone distribution over India (1973)

Tiwari, V. S.

Springer

Pure and applied geophysics 106-108 (1973), S. 1010-1017

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ISSN: 1420-9136

Source: Springer Online Journal Archives 1860-2000

Topics: Geosciences , Physics

Notes: Abstract The spatial and temporal distribution of total ozone over India and its vertical distribution in theatmosphere during 1964–1969 was studied using Dobson spectrophotometer data at a network of six stations in India, Srinagar (34°N), New Delhi (28°N), Varanasi (24°N), Ahmedabad (23°N), Dum Dum (22°N), and Kodaikanal (10°N). The annual and seasonal variations show a clear phase-shift in the occurrence of the ozone maxima and minima as one proceeds from higher to lower latitudes in the tropics. In the northern stations (north of 25°N) the increase in total ozone during the course of the annual variation is caused by the fractional increase in all layers from the ground to 28 km, the main contribution coming from 10–24 km. Above 28 km the concentration changes roughly in accordance with photochemical production. In lower latitudes (south of 25°N) an increase in total ozone amount during the annual cycle is caused by a gradual increase in all the layers from the ground to 36 km above which the variation is negligible.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00881053

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Ozone concentration studies and ozone flux measurements near the ground at Poona (1973)

Tiwari, V. S. ; Sreedharan, C. R.

Springer

Pure and applied geophysics 106-108 (1973), S. 1124-1138

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ISSN: 1420-9136

Source: Springer Online Journal Archives 1860-2000

Topics: Geosciences , Physics

Notes: Abstract Using a modified Brewer bubbler ozone sensor, continuous measurements of the ozone concentration near the ground were made at Poona (18°N, 73°E) for one year 1969–1970. The surface ozone concentration shows a pronounced seasonal variation, with a minimum during the monsoon months and a maximum during the pre-monsoon summer months. There is also a marked diurnal variation in surface ozone concentration which clearly follows the diurnal variation of temperature and is again a maximum during the summer months and a minimum during the monsoon. A secondary maximum in ozone concentration occurs in the forenoon during the winter months, associated with the temperature inversions that occur near the ground in this season. Both ozone and radioactive tracers, such as Cs-137 both in air and in precipitation show variations indicating that they have identical source regions and sinks. The latitudinal anomaly of surface ozone and Cs-137 observed in the low latitudes over India is explained as arising from the reduction in the rate of transfer of these tracers from the stratosphere to the troposphere, as a result of the reversed circulation at the upper levels in this season. From continuous measurements of surface ozone made with three electrochemical sensors exposed at three levels, 0, 15 and 35 m above the ground, the ozone flux has been directly calculated for the first time in the tropics. The ozone flux was calculated using both the rate of decay method used by Kroening and Ney and Regener's profile method. The profile method gives values of the order of 1.71 to 7.04×1011 mol/cm2/sec and that obtained by the rate of decay method is found to be 4.2 to 5.6×1011 mol/cm2/sec and are in good agreement with the flux values reported by other investigators.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00881066

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Short-term ground ozone fluctuations at Poona (1973)

Sreedharan, C. R. ; Tiwari, V. S.

Springer

Pure and applied geophysics 106-108 (1973), S. 1097-1105

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ISSN: 1420-9136

Source: Springer Online Journal Archives 1860-2000

Topics: Geosciences , Physics

Notes: Abstract Short-term fluctuations superimposed on the diurnal variations of surface ozone recorded at Poona during 1969–1970 are discussed. While there is a net production of ozone during electrical discharges in a thunder cloud, the surface ozone recorder often registered a decrease in surface ozone concentration. This decrease coincided with updraughts generated during the formation of a thunderstorm. Similar sharp increases in ozone were observed with downdraughts. In cases of lightning without the development of a thunderstorm over the station, an increase in ozone density was observed just after the first lightning discharge. Apart from the fluctuations associated with thunderstorms in summer, sharp fluctuations in density were also noticed during winter, in the mornings. Abrupt falls in ozone occur with the formation of a stable layer near the ground at night and a sudden surge after the breaking up of the layers in the morning. The changes in ozone are, however, much more pronounced than those in temperature and wind and this striking correlation between surface ozone, surface air temperature and wind provides a unique tool for the study of low-level temperature inversions, their establishment and destruction.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00881063

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Electronic Resource

Allergenic nature of Parthenium hysterophorus (1979)

Sohi, A. S. ; Tiwari, V. D. ; Lonkar, A. ; [et al.]

Oxford, UK : Blackwell Publishing Ltd

Contact dermatitis 5 (1979), S. 0

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ISSN: 1600-0536

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Medicine

Notes: Parthenin has been reported as the active allergen in Parthenium hysterophorus contact sensitivity. A study was carried out to test various chemical fractions of the plant for isolating and identifying the exact allergens. Two additional sesquiterpene lactones apart from parthenin have been shown to be allergenically active. Structures of these sesquiterpenoids are presented. Photopatch tests do not indicate a photosensitizing capacity for these compounds.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1600-0536.1979.tb04823.x

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Identification and characterization of a gene encoding a 35-kDa protein from Mycobacterium avium subspecies paratuberculosis (2001)

Banasure, K.D. ; Basagoudanavar, S.H. ; Chaudhury, P. ; [et al.]

Oxford, UK : Blackwell Publishing Ltd

FEMS microbiology letters 196 (2001), S. 0

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ISSN: 1574-6968

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: Mycobacterium avium subspecies paratuberculosis is the causative agent of Johne's disease, a chronic enteritis in ruminants. A gene homologous to that of 35-kDa antigen of Mycobacterium leprae was cloned and sequenced from Mycobacterium paratuberculosis. The database searches revealed 82.79% and 95.67% similarities of its nucleotide sequence, with those of immunodominant 35-kDa protein of M. leprae and M. avium, respectively.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1574-6968.2001.tb10564.x

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Effect of powder synthesis procedure on calcium site occupancies in barium calcium titanate: A Rietveld analysis (1993)

Krishna, P. S. R. ; Pandey, Dhananjai ; Tiwari, V. S. ; [et al.]

Woodbury, NY : American Institute of Physics (AIP)

Applied Physics Letters 62 (1993), S. 231-233

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ISSN: 1077-3118

Source: AIP Digital Archive

Topics: Physics

Notes: (Ba,Ca)TiO3 samples with the ratio of (Ba+Ca) to Ti as unity but prepared by (i) a semiwet route involving (Ba,Ca)CO3 solid solution precursors and TiO2 and (ii) the conventional dry route involving BaCO3, CaCO3, and TiO2 powders, exhibit diffuse and BaTiO3-type sharp ferroelectric phase transitions, respectively. Rietveld analysis of neutron powder diffraction data from the two types of samples shows that, whereas in the samples prepared by the semiwet route, Ca2+ exclusively occupies the Ba2+ site, nearly half of the substituted Ca2+ occupies the Ti4+ site in the case of samples prepared by the dry route. We show that Ca replacement at the Ba site leads to diffuseness whereas Ca introduction at the Ti site leads to sharpening of the transition. To our knowledge, this is the first clear demonstration of the powder synthesis procedure affecting the substitutional sites in multicomponent ceramics and this, in turn, influencing their physical behavior drastically.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1063/1.108974

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Shoot regeneration and somatic embryogenesis from different explants of Brahmi [Bacopa monniera (L.) Wettst.] (1998)

Tiwari, V. ; Deo Singh, B. ; Nath Tiwari, K.

Springer

Plant cell reports 17 (1998), S. 538-543

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ISSN: 1432-203X

Keywords: Key wordsBacopa monniera ; Brahmi ; Shoot regeneration ; Somatic embryogenesis

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract The morphogenetic potential of node, internode and leaf explants of Brahmi [Bacopa monniera (L.) Wettst.] was investigated to develop reliable protocols for shoot regeneration and somatic embryogenesis. The explants were excised from shoots raised from axillary buds of nodal explants cultured on Murashige and Skoog (MS) basal medium. Presence of 6-benzylaminopurine (BA) or kinetin influenced the degree of callus formation, from which a large number of shoot buds regenerated. Leaf explants gave the largest number of shoot buds followed by node and internode explants. BA was superior to kinetin; BA at 1.5 – 2.0 mg/l appeared to be optimum for inducing the maximum number of shoot buds. MS + 0.1 mg/l BA + 0.2 mg/l indole-3-acetic acid was the most suitable for shoot elongation. Elongated shoots were rooted on full- or half-strength MS medium with or without 0.5 – 1.0 mg/l indole-3-butyric acid or 0.5 – 1.0 mg/l α-naphthaleneacetic acid. The rooted plants were successfully established in soil. Calli derived from nodal explants cultured on MS medium containing 0.5 mg/l 2,4-dichlorophenoxyacetic acid (2,4-D), when subcultured on MS medium containing 0.1 or 0.5 mg/l BA or 0.2 mg/l 2,4-D + 0.1 or 0.5 mg/l kinetin, developed somatic embryos. The somatic embryos germinated either on the same media or on MS basal medium, and the resulting plantlets were successfully transplanted to soil.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s002990050438

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Parameters influencing transient and stable transformation of barley (Hordeum vulgare L.) protoplasts (1995)

Zhang, J. ; Tiwari, V. K. ; Golds, T. J. ; [et al.]

Springer

Plant cell, tissue and organ culture 41 (1995), S. 125-138

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ISSN: 1573-5044

Keywords: Hordeum vulgare ; plasmid uptake ; polyethylene glycol (PEG) ; protoplasts ; transient gene expression ; stable transformation

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract Cat gene expression has been investigated following PEG-mediated plasmid uptake into barley protoplasts. The uptake conditions optimised for transient expression were employed for stable transformation. Transformed protoplast-derived calli of the cvs. Dissa and Igri, were selected on medium containing G418 at 40 μg ml−1 or kanamycin sulphate at 250 μg ml−1. Absolute transformation frequencies of 28.9×10−5 and 21.3×10−5 were recorded for Dissa with kanamycin sulphate and G418 selection, respectively. The frequency for Igri was 11.5×10−5 with G418 selection. Antibiotic resistant protoplast-derived colonies expressed NPTII activity; Southern hybridisation confirmed integration of the nptII gene into barley genomic DNA.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00051581

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