Use of Genomic Estimated Breeding Values Results in Rapid Genetic Gains for Drought Tolerance in Maize.

More than 80% of the 19 million ha of maize ( L.) in tropical Asia is rainfed and prone to drought. The breeding methods for improving drought tolerance (DT), including genomic selection (GS), are geared to increase the frequency of favorable alleles. Two biparental populations (CIMMYT-Asia Population 1 [CAP1] and CAP2) were generated by crossing elite Asian-adapted yellow inbreds (CML470 and VL1012767) with an African white drought-tolerant line, CML444. Marker effects of polymorphic single-nucleotide polymorphisms (SNPs) were determined from testcross (TC) performance of F families under drought and optimal conditions. Cycle 1 (C1) was formed by recombining the top 10% of the F families based on TC data. Subsequently, (i) C2[PerSe_PS] was derived by recombining those C1 plants that exhibited superior per se phenotypes (phenotype-only selection), and (ii) C2[TC-GS] was derived by recombining a second set of C1 plants with high genomic estimated breeding values (GEBVs) derived from TC phenotypes of F families (marker-only selection). All the generations and their top crosses to testers were evaluated under drought and optimal conditions. Per se grain yields (GYs) of C2[PerSe_PS] and that of C2[TC-GS] were 23 to 39 and 31 to 53% better, respectively, than that of the corresponding F population. The C2[TC-GS] populations showed superiority of 10 to 20% over C2[PerSe-PS] of respective populations. Top crosses of C2[TC-GS] showed 4 to 43% superiority of GY over that of C2[PerSe_PS] of respective populations. Thus, GEBV-enabled selection of superior phenotypes (without the target stress) resulted in rapid genetic gains for DT.

MMP-9 as a potential biomarker for carcinoma of oral cavity: a study in eastern India.

Carcinoma of oral cavity have a high risk of recurrence after initial treatment with surgery, radiotherapy, surgery with adjuvant radiotherapy, or radio-chemotherapy.The present study investigated the changes in expression, activity and regulation of matrix metalloproteinases (MMP) -2 and -9 in oral squamous cell carcinoma (OSCC) which might help to ascertain the invasive potential of the tumor . Tumor tissues and adjacent normal tissues of OSCC patients [N,37; either sex; 20-70 yrs] were subjected to clinico-pathology, histopathology and TNM grading. The enzyme activity and associated signalling was observed with gelatin zymography, immunohistochemistry, ELISA, western blot and semi quantitative reverse transcriptase PCR. OSCC tissues were observed with elevated MMP-9 activity, enhanced expression of fibronectin (FN), phosphorylated focal adhesion kinase (FAK Try 397), phosphatidyl inositol 3­kinase (PI3K), protein kinase B (AKT) and reduced expression of tissue inhibitor of metalloproteinase- 1(TIMP-1) than the control tissues.OSCC patients elicited a predominance of MMP-9 activity via up regulated FAK/PI3K/AKT pathway. A routine MMP-9 analysis may ascertain the invasiveness of the tumor and therefore may be professed as a suitable biomarker for metastatic potential of oral cancer.

Histone methylase MLL1 has critical roles in tumor growth and angiogenesis and its knockdown suppresses tumor growth in vivo.

Mixed lineage leukemias (MLLs) are human histone H3 lysine-4-specific methyl transferases that have critical roles in gene expression, epigenetics and cancer. Herein, we demonstrated that antisense-mediated knockdown of MLL1 induced cell-cycle arrest and apoptosis in cultured cells. Intriguingly, application of MLL1 antisense specifically knocked down MLL1 in vivo and suppressed the growth of xenografted cervical tumor implanted in nude mouse. MLL1 knockdown downregulated various growth and angiogenic factors, such as HIF1α, VEGF and CD31, in tumor tissue affecting tumor growth. MLL1 is overexpressed along the line of vascular network and localized adjacent to endothelial cell layer expressing CD31, indicating potential roles of MLL1 in vasculogenesis. MLL1 is also overexpressed in the hypoxic regions along with HIF1α. Overall, our studies demonstrated that MLL1 is a key factor in hypoxia signaling, vasculogenesis and tumor growth, and its depletion suppresses tumor growth in vivo, indicating its potential in novel cancer therapy.

Mixed lineage leukaemia-4 regulates cell-cycle progression and cell viability and its depletion suppresses growth of xenografted tumour in vivo.

BACKGROUND: Mixed lineage leukaemia-4 (MLL4) is one of the MLL family of histone H3 lysine-4 (H3K4)-specific methyl transferases that have critical roles in gene expression and epigenetics in human. Though MLLs are well recognised as crucial players in histone methylation and gene regulation; little is known about the biochemical functions of MLL4 and its roles in cancer. METHODS: Herein, we have investigated the roles of MLL4 in cell viability, cell-cycle progression and explored its potential roles in tumour growth using antisense-mediated knockdown experiments, flow-cytometry analysis, chromatin immunoprecipitation, immunofluorescence staining and animal models. RESULTS: Our studies demonstrated that knockdown of MLL4 severely affects cell-cycle progression and induces apoptotic cell death in cultured tumour cells. Knockdown of MLL4 induced nuclear condensation, fragmentation, cytochrome-c release from mitochondria to cytosol and activated caspase-3/7 indicating apoptotic cell death. The MLL4 regulates expression of various critical cell-cycle regulatory genes such as cyclin D, cyclin E, p27, HOXA5 and HOXB7 via histone H3K4 trimethylation and recruitment of RNA polymerase II. Interestingly, application of MLL4 antisense suppressed tumour growth in vivo in colon cancer xenograft implanted in nude mouse. The MLL4 antisense specifically knocked down MLL4 in tumour tissue and also downregulated the expression of various growth and angiogenic factors resulting in tumour suppression. CONCLUSION: Our results demonstrated that MLL4 is a crucial player in cell viability, cell-cycle progression and is critical for tumour growth in vivo.

Observation of nonconventional spin waves in composite-fermion ferromagnets.

We find unexpected low energy excitations of fully spin-polarized composite-fermion ferromagnets in the fractional quantum Hall liquid, resulting from a complex interplay between a topological order manifesting through new energy levels and a magnetic order due to spin polarization. The lowest energy modes, which involve spin reversal, are remarkable in displaying unconventional negative dispersion at small momenta followed by a deep roton minimum at larger momenta. This behavior results from a nontrivial mixing of spin-wave and spin-flip modes creating a spin-flip excitonic state of composite-fermion particle-hole pairs. The striking properties of spin-flip excitons imply highly tunable mode couplings that enable fine control of topological states of itinerant two-dimensional ferromagnets.

Inhibition of a protein tyrosine phosphatase using mesoporous oxides.

The feasibility of utilizing mesoporous matrices of alumina and silica for the inhibition of enzymatic activity is presented here. These studies were performed on a protein tyrosine phosphatase by the name chick retinal tyrosine phosphotase-2 (CRYP-2), a protein that is identical in sequence to the human glomerular epithelial protein-1 and involved in hepatic carcinoma. The inhibition of CRYP-2 is of tremendous therapeutic importance. Inhibition of catalytic activity was examined using the sustained delivery of p-nitrocatechol sulfate (pNCS) from bare and amine functionalized mesoporous silica (MCM-48) and mesoporous alumina (Al(2)O(3)). Among the various mesoporous matrices employed, amine functionalized MCM-48 exhibited the best release of pNCS and also inhibition of CRYP-2. The maximum speed of reaction v(max) (=160 +/- 10 micromol/mnt/mg) and inhibition constant K(i) (=85.0 +/- 5.0 micromol) estimated using a competitive inhibition model were found to be very similar to inhibition activities of protein tyrosine phosphatases using other methods.

Mutational and pH studies of the 3' --> 5' exonuclease activity of bacteriophage T4 DNA polymerase.

The 3' --> 5' exonuclease activity of proofreading DNA polymerases requires two divalent metal ions, metal ions A and B. Mutational studies of the 3' --> 5' exonuclease active center of the bacteriophage T4 DNA polymerase indicate that residue Asp-324, which binds metal ion A, is the single most important residue for the hydrolysis reaction. In the absence of a nonenzymatic source of hydroxide ions, an alanine substitution for residue Asp-324 reduced exonuclease activity 10-100-fold more than alanine substitutions for the other metal-binding residues, Asp-112 and Asp-219. Thus, exonuclease activity is reduced 10(5)-fold for the D324A-DNA polymerase compared with the wild-type enzyme, while decreases of 10(3)- to 10(4)-fold are detected for the D219A- and D112A/E114A-DNA polymerases, respectively. Our results are consistent with the proposal that a water molecule, coordinated by metal ion A, forms a metal-hydroxide ion that is oriented to attack the phosphodiester bond at the site of cleavage. Residues Glu-114 and Lys-299 may assist the reaction by lowering the pK(a) of the metal ion-A coordinated water molecule, whereas residue Tyr-320 may help to reorient the DNA from the binding conformation to the catalytically active conformation.

Evidence of interlipidic ion-pairing in anion-induced DNA release from cationic amphiphile-DNA complexes. Mechanistic implications in transfection.

Complex formation of DNA with a number of cationic amphiphiles has been examined using fluorescence, gel electrophoresis, and chemical nuclease digestion. Here we have addressed the status of both DNA and lipid upon complexation with each other. DNA upon binding with cationic amphiphiles changes its structure in such a way that it loses the ability to intercalate and becomes resistant to nuclease digestion. Fluorescence anisotropy measurements due to 1, 6-diphenylhexatriene (DPH) doped in cationic liposomes demonstrated that upon complexation with DNA, the resulting complexes still retain lamellar organizations with modest enhancement in thermal stabilities. The lipid-DNA complexation is most effective only when the complexation was carried out at or around the phase transition temperatures of the cationic lipid employed in the complexation with DNA. The release of DNA from cationic lipid-DNA complexes could be induced by several anionic additives. Determination of fluorescence anisotropies (due to DPH) as a function of temperature clearly demonstrates that the addition of equivalent amounts of anionic amphiphile into cationic lipid-DNA complexes leads to the ion-pairing of the amphiphiles, the melting profiles of which are virtually the same as those obtained in the absence of DNA. In this process DNA gets released from its complexes with cationic lipids and regains its natural intercalation ability, movement, and staining ability on agarose gel and also the sensitivities toward nuclease digestion. This clearly suggests that combination of ion-pairing and hydrophobic interactions between cationic and anionic amphiphiles is stronger than the electrostatic forces involved in the cationic lipid-DNA complexation. It is further revealed that the DNA release by anions is most efficient from the cationic lipid-DNA complexes at or around the Tm of the cationic lipid used in DNA complexation. This explains why more effective DNA delivery is achieved with cationic lipids that bear unsaturated hydrocarbon chains than with their saturated hydrocarbon counterparts.

Role of the central metal ion and ligand charge in the DNA binding and modification by metallosalen complexes.

Several metal complexes of three different functionalized salen derivatives have been synthesized. The salens differ in terms of the electrostatic character and the location of the charges. The interactions of such complexes with DNA were first investigated in detail by UV-vis absorption titrimetry. It appears that the DNA binding by most of these compounds is primarily due to a combination of electrostatic and other modes of interactions. The melting temperatures of DNA in the presence of various metal complexes were higher than that of the pure DNA. The presence of additional charge on the central metal ion core in the complex, however, alters the nature of binding. Bis-cationic salen complexes containing central Ni(II) or Mn(III) were found to induce DNA strand scission, especially in the presence of co-oxidant as revealed by plasmid DNA cleavage assay and also on the basis of the autoradiogram obtained from their respective high-resolution sequencing gels. Modest base selectivity was observed in the DNA cleavage reactions. Comparisons of the linearized and supercoiled forms of DNA in the metal complex-mediated cleavage reactions reveal that the supercoiled forms are more susceptible to DNA scission. Under suitable conditions, the DNA cleavage reactions can be induced either by preformed metal complexes or by in situ complexation of the ligand in the presence of the appropriate metal ion. Also revealed was the fact that the analogous complexes containing Cu(II) or Cr(III) did not effect any DNA strand scission under comparable conditions. Salens with pendant negative charges on either side of the precursor salicylaldehyde or ethylenediamine fragments did not bind with DNA. Similarly, metallosalen complexes with net anionic character also failed to induce any DNA modification activities.

Role of hydrophobic effect and surface charge in surfactant-DNA association.

Ethidium bromide is one of the best known DNA intercalator. Upon intercalation inside DNA, the fluorescence due to ethidium bromide gets enhanced by many orders of magnitude. In this paper, we employed ethidium bromide as a probe for studying surfactant-DNA complexation using fluorescence spectroscopy and agarose gel electrophoresis. Surfactants of different charge types and chain lengths were used and the results were compared with that of the related small organic cations or salts under comparable conditions. The cationic surfactants induced destabilization of the ethidium bromide-DNA complex at concentrations in orders of magnitude lower than that of the small organic cations or salts. In contrast however, the anionic surfactants failed to promote any such destabilization of probe-DNA complex. DNA loses its ethidium bromide stainability in the presence of high concentration of cationic surfactant aggregates as revealed from agarose gel electrophoresis experiments. Inclusion of surfactants and other additives into the DNA generally enhanced the DNA double-strand to single strand transition melting temperatures by a few degrees, in a concentration-dependent manner and at high surfactant concentration melting profiles got broadened.

Interaction of surfactants with DNA. Role of hydrophobicity and surface charge on intercalation and DNA melting.

A probe, 9-(anthrylmethyl)trimethylammonium chloride, 1. was prepared, 1 binds to caF-thymus DNA or Escherichia coli genomic DNA with high affinity, as evidenced from the absorption titration. Strong hypochromism, spectral broadening and red-shifts in the absorption spectra were observed. Half-reciprocal plot constructed from this experiment gave binding constant of 5 +/- 0.5 x 10(4) M-1 in base molarity. We employed this anthryl probe-DNA complex for studying the effects of addition of various surfactant to DNA. Surfactants of different charge types and chain lengths were used in this study and the effects of surfactant addition to such probe-DNA complex were compared with that of small organic cations or salts. Addition of either salts or cationic surfactants led to structural changes in DNA and under these conditions, the probe from the DNA-bound complex appeared to get released. However, the cationic surfactants could induce such release of the probe from the probe-DNA complex at a much lower concentration than that of the small organic cations or salts. In contrast the anionic surfactants failed to promote any destabilization of such probe-DNA complexes. The effects of additives on the probe-DNA complexes were also examined by using a different technique (fluorescence spectroscopy) using a different probe ethidium bromide. The association complexes formed between the cationic surfactants and the plasmid DNA pTZ19R, were further examined under agarose gel electrophoresis and could not be visualized by ethidium bromide staining presumably due to cationic surfactant-induced condensation of DNA. Most of the DNA from such association complexes can be recovered by extraction of surfactants with phenol-chloroform. Inclusion of surfactants and other additives into the DNA generally enhanced the DNA melting temperatures by a few degrees C and at high [surfactant], the corresponding melting profiles got broadened.

Metal-ion-dependent oxidative DNA cleavage by transition metal complexes of a new water-soluble salen derivative.

A new water-soluble, salen [salen = bis(salicylidene) ethylenediamine]-based ligand, 3 was developed. Two of the metal complexes of this ligand, i.e., 3a, [Mn(III)] and 3b, [Ni(II)], in the presence of cooxidant magnesium monoperoxyphthalate (MMPP) cleaved plasmid DNA pTZ19R efficiently and rapidly at a concentration approximately 1 microM. In contrast, under comparable conditions, other metal complexes 3c, [Cu(II)] or 3d, [Cr(III)] could not induce any significant DNA nicking. The findings with Ni(II) complex suggest that the DNA cleavage processes can be modulated by the disposition of charges around the ligand.