Confirmation of linkage and refinement of the RP28 locus for autosomal recessive retinitis pigmentosa on chromosome 2p14-p15 in an Indian family

PURPOSE: To report the linkage analysis of retinitis pigmentosa (RP) in an Indian family. METHODS: Individuals were examined for symptoms of retinitis pigmentosa and their blood samples were withdrawn for genetic analysis. The disorder was tested for linkage to known 14 adRP and 22 arRP loci using microsatellite markers. RESULTS: Seventeen individuals including seven affecteds participated in the study. All affected individuals had typical RP. The age of onset of the disease ranged from 8-18 years. The disorder in this family segregated either as an autosomal recessive trait with pseudodominance or an autosomal dominant trait. Linkage to an autosomal recessive locus RP28 on chromosome 2p14-p15 was positive with a maximum two-point lod score of 3.96 at theta=0 for D2S380. All affected individuals were homozygous for alleles at D2S2320, D2S2397, D2S380, and D2S136. Recombination events placed the minimum critical region (MCR) for the RP28 gene in a 1.06 cM region between D2S2225 and D2S296. CONCLUSIONS : The present data confirmed linkage of arRP to the RP28 locus in a second Indian family. The RP28 locus was previously mapped to a 16 cM region between D2S1337 and D2S286 in a single Indian family. Haplotype analysis in this family has further narrowed the MCR for the RP28 locus to a 1.06 cM region between D2S2225 and D2S296. Of 15 genes reported in the MCR, 14 genes (KIAA0903, OTX1, MDH1, UGP2, VPS54, PELI1, HSPC159, FLJ20080, TRIP-Br2, SLC1A4, KIAA0582, RAB1A, ACTR2, and SPRED2) are either expressed in the eye or retina. Further study needs to be done to test which of these genes is mutated in patients with RP linked to the RP28 locus.

Characterization of two M17 family members in Escherichia coli, Peptidase A and Peptidase B

Escherichia coil encodes two aminopeptidases belonging to the M17 family: Peptidase A (PepA) and Peptidase B (PepB). To gain insights into their substrate specificities, PepA or PepB were overexpressed in Delta pepN, which shows greatly reduced activity against the majority of amino acid substrates. Overexpression of PepA or PepB increases catalytic activity of several aminopeptidase substrates and partially rescues growth of Delta pepN during nutritional downshift and hightemperature stress. Purified PepA and PepB display broad substratespecificity and Leu, Lys, Met and Gly are preferred substrates. However, distinct differences are observed between these two paralogs: PepA is more stable at high temperature whereas PepB displays broader substrate specificity as it cleaves Asp and insulin B chain peptide. Importantly, this strategy, i.e. overexpression of peptidases in Delta pepN and screening a panel of substrates for cleavage, can be used to rapidly identify peptidases with novel substrate specificities encoded in genomes of different organisms. (C) 2010 Elsevier Inc. All rights reserved.

Evolution, Homology Conservation, and Identification of Unique Sequence Signatures in GH19 Family Chitinases

The discovery of GH (Glycoside Hydrolase) 19 chitinases in Streptomyces sp. raises the possibility of the presence of these proteins in other bacterial species, since they were initially thought to be confined to higher plants. The present study mainly concentrates on the phylogenetic distribution and homology conservation in GH19 family chitinases. Extensive database searches are performed to identify the presence of GH19 family chitinases in the three major super kingdoms of life. Multiple sequence alignment of all the identified GH19 chitinase family members resulted in the identification of globally conserved residues. We further identified conserved sequence motifs across the major sub groups within the family. Estimation of evolutionary distance between the various bacterial and plant chitinases are carried out to better understand the pattern of evolution. Our study also supports the horizontal gene transfer theory, which states that GH19 chitinase genes are transferred from higher plants to bacteria. Further, the present study sheds light on the phylogenetic distribution and identifies unique sequence signatures that define GH19 chitinase family of proteins. The identified motifs could be used as markers to delineate uncharacterized GH19 family chitinases. The estimation of evolutionary distance between chitinase identified in plants and bacteria shows that the flowering plants are more related to chitinase in actinobacteria than that of identified in purple bacteria. We propose a model to elucidate the natural history of GH19 family chitinases.

Identification of Specific DNA Binding Residues in the TCP Family of Transcription Factors in Arabidopsis

The TCP transcription factors control multiple developmental traits in diverse plant species. Members of this family share an similar to 60-residue-long TCP domain that binds to DNA. The TCP domain is predicted to form a basic helix-loop-helix ( bHLH) structure but shares little sequence similarity with canonical bHLH domain. This classifies the TCP domain as a novel class of DNA binding domain specific to the plant kingdom. Little is known about how the TCP domain interacts with its target DNA. We report biochemical characterization and DNA binding properties of a TCP member in Arabidopsis thaliana, TCP4. We have shown that the 58-residue domain of TCP4 is essential and sufficient for binding to DNA and possesses DNA binding parameters comparable to canonical bHLH proteins. Using a yeast-based random mutagenesis screen and site-directed mutants, we identified the residues important for DNA binding and dimer formation. Mutants defective in binding and dimerization failed to rescue the phenotype of an Arabidopsis line lacking the endogenous TCP4 activity. By combining structure prediction, functional characterization of the mutants, and molecular modeling, we suggest a possible DNA binding mechanism for this class of transcription factors.

New family of thallium cuprate superconductors not containing calcium or barium: TlSrn+1−xLnxCunO2n+3+δ (Ln=La, Pr, or Nd)

The first two members of the new TlSrn+1−xLnxCunO2n+3+δ (Ln=La, Pr, or Nd) series of superconducting cuprates possessing 1021 and 1122 type structures are described. The n=1 (1021) members with Tcs around 40 K have electrons or holes as the majority charge carriers depending on x. The n=2 (1122) cuprate (Ln=Pr or Nd) shows a Tc in the 80–90 K range.

The Critical Role of N- and C-Terminal Contact in Protein Stability and Folding of a Family 10 Xylanase under Extreme Conditions

Background: Stabilization strategies adopted by proteins under extreme conditions are very complex and involve various kinds of interactions. Recent studies have shown that a large proportion of proteins have their N- and C-terminal elements in close contact and suggested they play a role in protein folding and stability. However, the biological significance of this contact remains elusive. Methodology: In the present study, we investigate the role of N- and C-terminal residue interaction using a family 10 xylanase (BSX) with a TIM-barrel structure that shows stability under high temperature,alkali pH, and protease and SDS treatment. Based on crystal structure,an aromatic cluster was identified that involves Phe4, Trp6 and Tyr343 holding the Nand C-terminus together; this is a unique and important feature of this protein that might be crucial for folding and stabilityunder poly-extreme conditions. Conclusion: A series of mutants was created to disrupt this aromatic cluster formation and study the loss of stability and function under given conditions. While the deletions of Phe4 resulted in loss of stability, removal of Trp6 and Tyr343 affected in vivo folding and activity. Alanine substitution with Phe4, Trp6 and Tyr343 drastically decreased stability under all parameters studied. Importantly,substitution of Phe4 with Trp increased stability in SDS treatment.Mass spectrometry results of limited proteolysis further demonstrated that the Arg344 residue is highly susceptible to trypsin digestion in sensitive mutants such as DF4, W6A and Y343A, suggesting again that disruption of the Phe4-Trp6-Tyr343 (F-W-Y) cluster destabilizes the N-and C-terminal interaction. Our results underscore the importance of N- and C-terminal contact through aromatic interactions in protein folding and stability under extreme conditions, and these results may be useful to improve the stability of other proteins under suboptimal conditions.

Bi2−xPbx(Ca, Sr)n+1CunO2n+4+δ (n = 1, 2, 3, and 4) family of superconductors

Superconducting oxides of the Bi1.5Pb0.5(Ca, Sr)n+1CunO2n+4+δ series with n = 1, 2, 3 and 4 have been characterized. The superconducting transition temperature increases markedly with n up to n = 3, but the Tc of the n = 4 member is not much higher than that of the n = 3 member. The Tc does not change significantly in Bi2−xPbxCaSr2Cu2O8+δ with x (0.1 < x ≤ 0.5).

Synthesis, Structure and Optical Studies of a Family of Three-Dimensional Rare-Earth Aminoisophthalates M(mu(2)-OH)(C8H5NO4)] (M = Y3+, La3+, Pr3+, Nd3+, Sm3+, Eu3+, Gd3+, Dy3+, and Er3+)

A hydrothermal reaction of the acetate salts of the rare-earths, 5-aminoisophthalic acid (H(2)AIP), and NaOH at 150 degrees C for 3 days gave rise to a new family of three-dimensional rare-earth aminoisophthalates, M(mu(2)-OH)(C8H5NO4)] M = Y3+ (I), La3+ (II), Pr3+ (III), Nd3+ (IV), Sm3+ (V), Eu3+ (VI), Gd3+ (VII), Dy3+ (VIII), and Er3+ (IX)]. The structures contain M-O(H)-M chains connected by AIP anions. The AIP ions are connected to five metal centers and each metal center is connected with five AIP anions giving rise to a unique (5,5) net. To the best of our knowledge, this is the first observation of a (5,5) net in metal-organic frameworks that involve rare-earth elements. The doping of Eu3+/(3+) ions in place of Y3+/ La3+ in the parent structures gave rise to characteristic metal-centered emission (red = Eu3+, green = Tb3+). Life-time studies indicated that the excited emission states in the case of Eu3+ (4 mol-% doped) are in the range 0.287-0.490 ms and for Tb3+ (4 mol-% doped) are in the range of 1.265-1.702 ms. The Nd3+-containing compound exhibits up-conversion behavior based on two-photon absorption when excited using lambda = 580 nm.

Hierarchy of structures in the family of amine templated open-framework gallium arsenates

Five new gallium arsenate compounds C2N2H10]Ga(H2AsO4)(HAsO4)(2)]center dot H2O, I; C2N2H10]Ga(OH)(AsO4)](2), II; C2N2H10]GaF(AsO4)](2), III; C3N2H12]Ga(OH)(AsO4)](2), IV; Ga2F3(AsO4)(HAsO4)]center dot 2H(3)O, V, have been synthesized under hydrothermal conditions and the structures determined employing single crystal X-ray diffraction studies. All the structures consist of octahedral gallium and tetrahedral arsenate units connected together forming a hierarchy of structures. Thus, one- (I), two- (II and IV) and three-dimensionally (III and V) extended structures have been observed. The Ga-O(H)/F-Ga connectivity in some of the structures suggests the coordination requirements posed by the octahedral gallium in these compounds. The observation of only one type of secondary building unit in the structures of III (SBU-4) and V (spiro-5) is unique and noteworthy. All the compounds have been characterized by a variety of techniques that include powder XRD, IR, and TGA. (C) 2010 Elsevier B. V. All rights reserved.

Structure and superconducting properties of a new family of thallium cuprates, TlSr3−xLnxCu2O7

Cuprates of the formula TlSr3−xLnxCu2O7 (Ln=Pr, NdorY) derived from the hypothetical TlSr3Cu2O7 show superconductivity with Tcs up to 95 K when 0.5less, approximatex≤0.75, the x=1.0 compositions being insulators. Rietveld analysis of X-ray diffraction profiles has been carried out for two superconducting members of this family. The unit cell a-parameter, and hence the in-plane Cu-O distance, increases with increase in x. The Tc value decreases with increase in x or the in-plane Cu-O distance in all the series of cuprates. Superconductivity in the Tl1−yPbySr3−xNdxCu2O7 systems is found with the highest Tc of 95 K when y=0.2 and x=0.5. The in-plane Cu-O distances in all the cuprates studied fall in the range found in the Sr-class of cuprate superconductors.

Boson Inverse Operators and a New Family of Two-photon Annihilation Operators

We introduce the inverse of the Hermitian operator (acircacirc†) and express the Boson inverse operators acirc-1 and acirc†-1 in terms of the operators acirc, acirc† and (acircacirc†)-1. We show that these Boson inverse operators may be realized by Susskind-Glogower phase operators. In this way, we find a new two-photon annihilation operator and denote it as acirc2(acircacirc†)-1. We show that the eigenstates of this operator have interesting non-classical properties. We find that the eigenstates of the operators (acircacirc†)-1 acirc2, acirc(acircacirc†)-1 acirc and acirc2(acircacirc†)-1 have many similar properties and thus they constitute a family of two-photon annihilation operators.

Magnetic properties of rare earth nickelates of the Ln(2)BaNiO(5) family

Rare-earth nickelates Ln(2)BaNi(1-x)Cu(2)O(5), Ln = Nd and Dy, and Dy2-xYxBaNiO5 have been synthesized in order to investigate the effect of substitution of Ni by Cu and Dy by nonmagnetic Y on the magnetic properties of the nickelates. In Ln(2)BaNi(1-x)Cu(x)O(5), the nickelate structure (x=0.0) changes to the cuprate structure (x=1.0) at a specific composition (x=0.3). The Neel temperature of Nd2BaNi1-xCuxO5 decreases continuously with increase in x upto x=0.3 (T-N = 18K); when x > 0.3, the materials are paramagnetic down to 20K. The mu(eff) in Nd2BaNi1-xCxO5 essentially corresponds to the contribution of the Nd ions. In Dy2-xYxBaNiO5, the Neel temperature decreases from 40K when x=0.0 to 24K when x=1.5. The compositions with 1.5 less than or equal to x less than or equal to 2 (including the x=1.95 composition) are paramagnetic down to 20K, unlike Y2BaNiO5 (x=2.0) which exhibits a T-N of 370K. Even the smallest concentration of paramagnetic Dy seems to destroy the antiferromagnetic Ni-O-Ni chains in Y2BaNiO5.

Combustion synthesis and properties of the NASICON family of materials

The fine-particle NASICON family of materials, MZr2P3O12(where M = Na, K, ½Ca and ¼Zr) and NbZrP3O12, have been prepared by the combustion of aqueous heterogeneous mixtures of stoichiometric amounts of metal nitrate, zirconyl nitrate, niobium phosphate, diammonium hydrogen phosphate, ammonium perchlorate and carbohydrazide (CH) at 400 °C. The formation of NASICON materials was confirmed by powder X-ray diffraction (XRD), IR, solid-state (31P) NMR spectroscopy and thermal expansion coefficient measurements. The combustion-synthesized NASICON powders have an average agglomerate size of 9�13 µm with a specific surface area varying from 8 to 28 m2 g�1. The powders pelletized and sintered in the range 1100�1200 °C for 5 h achieved 95�97% theoretical density and showed fine-grain microstructure. The coefficient of thermal expansion of a sintered compact was measured up to 500 °C and ranged from �1.5 × 10�6°C�1 to 1.0 × 10�6°C�1 depending on the composition.

A Combinatorial Family of Near Regular LDPC Codes

An elementary combinatorial Tanner graph construction for a family of near-regular low density parity check (LDPC) codes achieving high girth is presented. These codes are near regular in the sense that the degree of a left/right vertex is allowed to differ by at most one from the average. The construction yields in quadratic time complexity an asymptotic code family with provable lower bounds on the rate and the girth for a given choice of block length and average degree. The construction gives flexibility in the choice of design parameters of the code like rate, girth and average degree. Performance simulations of iterative decoding algorithm for the AWGN channel on codes designed using the method demonstrate that these codes perform better than regular PEG codes and MacKay codes of similar length for all values of Signal to noise ratio.