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Pathogen research abs 1 || Pathogen research abs 2 || Pathogen research abs 3 || Pathogen research abs 4 || Pathogen research abs 5 || Hormone and endocrine research abs 1 || Hormone and endocrine research abs 2 || Hormone and endocrine research abs 3 || Hormone and endocrine research abs 4 || Hormone and endocrine research abs 5 || Follicle and follicular cells research abs 1 || Interferon research abs 1 || Hemoglobin research abs || Stem cell research abs || Nucleic acid research abs

Nucleic Acids Res. 2000 Oct 1;28(19):3823-9.
Distinct properties of Mycobacterium tuberculosis single-stranded DNA binding protein and its functional characterization in Escherichia coli.

Handa P, Acharya N, Thanedar S, Purnapatre K, Varshney U.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India.

Single-stranded DNA binding proteins (SSBs) play an essential role in various DNA functions. Characterization of SSB from Mycobacterium tuberculosis, which infects nearly one-third of the world's population and kills about 2-3 million people every year, showed that its oligomeric state and various in vitro DNA binding properties were similar to those of the SSB from Escherichia coli. In this study, use of the yeast two-hybrid assay suggests that the ECO:SSB and the MTU:SSB are even capable of heterooligomerization. However, the MTU:SSB failed to complement a Deltassb strain of E. coli. The sequence comparison suggested that MTU:SSB contained a distinct C-terminal domain. The C-terminal domain of ECO:SSB interacts with various cellular proteins. The chimeric constructs between the N- and C-terminal domains of the MTU:SSB and ECO:SSB exist as homotetramers and demonstrate DNA binding properties similar to the wild-type counterparts. Despite similar biochemical properties, the chimeric SSBs also failed to complement the Deltassb strain of E.coli. These data allude to the occurrence of a 'cross talk' between the N- and the C-terminal domains of the SSBs for their in vivo function. Further, compared with those of the ECO:SSB, the secondary/tertiary interactions within MTU:SSB were found to be less susceptible to disruption by guanidinium hydrochloride. Such structural differences could be exploited for utilizing such essential proteins as crucial molecular targets for controlling the growth of the pathogen.

online pharmacy ref. source: www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11000276&dopt=Abstract

Nucleic Acids Res. 2000 Oct 1;28(19):3830-8.
Cloning and characterization of the histone-fold proteins YBL1 and YCL1.

Bolognese F, Imbriano C, Caretti G, Mantovani R.

Dipartimento di Genetica e Biologia dei Microrganismi, Universita di Milano, Via Celoria 26, 20133 Milano, Italy.

Histones are among the most conserved proteins in evolution, sharing a histone fold motif. A number of additional histonic proteins exist and are involved in the process of transcriptional regulation. We describe here the identification, cloning and characterization of two small members of the H2A-H2B sub-family (YBL1 and YCL1) related to the NF-YB and NF-YC subunits of the CCAAT-binding activator NF-Y and to the TATA-binding protein (TBP) binding repressor NC2. Unlike the latters, YBL1 and YCL1 have no intrinsic CCAAT or TATA-binding capacity. In nucleosome reconstitution assays, they can form complexes with histones in solution and on DNA and they are part of relatively large complexes, as determined by glycerol gradient experiments. Our data support the idea that YBL1 and YCL1 are divergent with respect to NF-YB and NF-YC for specific functions, but have coevolved the capacity to interact with nucleosomal structures.

online pharmacy ref. source: www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11000277&dopt=Abstract

Nucleic Acids Res. 2000 Jul 1;28(13):1514-24.
Characterization of an unusual tRNA-like sequence found inserted in a Neurospora retroplasmid[Corrected and republished from Nucleic Acids Res. 2000 Apr 1;28(7);1514-24]

Mohr S, Wanner LA, Bertrand H, Lambowitz AM.

Institute for Cellular and Molecular Biology, School of Biological Sciences, University of Texas at Austin 78712, USA.

We characterized an unusual tRNA-like sequence that had been found inserted in suppressive variants of the mitochondrial retroplasmid of Neurospora intermedia strain Varkud. We previously identified two forms of the tRNA-like sequence, one of 64 nt (TRL-64)and the other of 78 nt (TRL-78) containing a 14-nt internal insertion in the anticodon stem at a position expected for a nuclear tRNA intron. Here, we show that TRL-78 is encoded in Varkud mitochondrial (mt)DNA within a 7 kb sequence that is not present in Neurospora crassa wild-type 74A mtDNA. This 7-kb insertion also contains a perfectly duplicated tRNA(Trp)gene, segments of several mitochondrial plasmids and numerous GC-rich pallindromic sequences that are repeated elsewhere in the mtDNA. The mtDNA-encoded copy of TRL-78 is transcribed and apparently undergoes 5'- and 3'-end processing and 3' nucleotide addition by tRNA nucleotidyl transferase to yield a discrete tRNA-sized molecule. However, the 14 nt intron-like sequence in TRL-78, which is missing in the TRL-64 form, is not spliced detectably in vivo or in vitro. Our results show that TRL-78 is an unusual tRNA-like species that could be incorporated into suppressive retroplasmids by the same reverse transcription mechanism used to incorporate mt tRNAs. The tRNA-like sequence may have been derived from an intron-containing nuclear tRNA gene or it may serve some function, like tmRNA. Our results suggest that mtRNAs or tRNA-like species may be integrated into mtDNA via reverse transcription, analogous to SINE elements in animal cells.

online pharmacy ref. source: www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11001704&dopt=Abstract

J Magn Reson. 2000 Oct;146(2):249-54.
Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force.

Kuszewski J, Clore GM.

Laboratory of Chemical Physics, National Institutes of Health, Building 5, Bethesda, Maryland 20892-0510, USA.

It is often the case that a substantial number of torsion angles (both backbone and sidechain) in structures of proteins and nucleic acids determined by NMR are found in physically unlikely and energetically unfavorable conformations. We have previously proposed a database-derived potential of mean force comprising one-, two-, three-, and four-dimensional potential surfaces which describe the likelihood of various torsion angle combinations to bias conformational sampling during simulated annealing refinement toward those regions that are populated in very high resolution (< or =1.75 A) crystal structures. We now note a shortcoming of our original implementation of this approach: namely, the forces it places on atoms are very rough. When the density of experimental restraints is low, this roughness can both hinder convergence to commonly populated regions of torsion angle space and reduce overall conformational sampling. In this paper we describe a modification that completely eliminates these problems by replacing the original potential surfaces by a sum of multidimensional Gaussian functions. Structures refined with the new Gaussian implementation now simultaneously enjoy excellent global sampling and excellent local choices of torsion angles.

online pharmacy ref. source: www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11001840&dopt=Abstract

Nucleic Acids Res. 2002 Nov 15;30(22):5004-14.
Comparison of whole genome assemblies of the human genome.

Rouchka EC, Gish W, States DJ.

Department of Computer Science, Washington University, Washington University School of Medicine, St Louis, MO 63110, USA.

A fundamental problem in the human genome project is uncovering the correct assembly of the human genome. Many studies, including transcriptional analysis, SNP detection and characterization, gene finding and EST clustering, use genome assemblies as templates so it is important to determine the consistency among the various whole genome assemblies. A comparison of the order and orientation of the GenBank entries used to construct the NCBI and UCSC Goldenpath assemblies was made. In addition, a sequence level comparison was performed using MULTI, an efficient database search tool developed to make whole genome comparisons possible. The resulting comparisons show significant discrepancies in the sequence as well as in the order and orientation of GenBank entries used in constructing the NCBI and UCSC assemblies.

online pharmacy ref. source: www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12434005&dopt=Abstract

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