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PubMed2005

UPR-independent dithiothreitol stress-induced genes in Aspergillus niger.

A subtraction library was prepared from cultures of Aspergillus niger that had or had not been exposed to dithiothreitol (DTT), in order to identify genes involved in the unfolded protein response (UPR) or in the response to reductive stress. A large fraction of the clones in the library (40%) encoded two putative methyltransferases (MTs) whose function has yet to be determined. Other stress-responsive genes included a homologue of the Mn2+-containing superoxide dismutase gene (sodB) and a number of genes predicted to code for products that function in protein turnover and in intra- and extracellular transport of molecules. Transcriptional microarray analysis was carried out with a group of 15 genes, comprising 11 from the cDNA library, two genes linked to the putative MT genes but not represented in the library, and two UPR control genes (bipA and pdiA). Eleven of the 15 genes were inducible with DTT. This was either reflected by the presence of transcripts in cells subjected to DTT stress compared to absence under control conditions, or by an induction ratio of between 1.4 and 8.0 in cases where transcripts were already detectable under control conditions. The MT genes were among the four most highly induced. None of the genes, apart from bipA and pdiA, showed significant induction in response to other stresses that are known to induce the UPR in fungi. We conclude that DTT alone does not provide for specific induction of UPR genes and that other stress conditions must also be examined.

Amino Acid Sequence↗
PubMed1986

A cell hybrid and recombinant DNA library that facilitate identification of polymorphic loci in the vicinity of the Huntington disease gene.

Somatic cell hybrids were selected that retain a derivative chromosome 5 from an individual in which the p15.1-pter segment of chromosome 5 is replaced with the p15.1-pter segment of chromosome 4. Hybrids that retain this derivative chromosome exclusively were found to be positive for G8, a DNA marker closely linked to the Huntington disease gene on chromosome 4p. From one such hybrid, a segregant was isolated that had deleted the entire q arm of the derivative chromosome but retained the p arm intact as its only detectable human DNA. A complete recombinant DNA library was prepared from this cell line, and the inserts in approximately 1/3 of the recombinant phage with human DNA were shown to be derived from 4pter-4p15.1, which represents only approximately 1% of the total human genome. The cell hybrid and DNA library represent a rapid and efficient means to identify and isolate many polymorphic DNA markers close to and flanking the Huntington disease gene.

Animals↗
PubMed1996

Identification of a new antifungal target site through a dual biochemical and molecular-genetics approach.

The target site of the antifungal compound LY214352 [8-chloro-4-(2-chloro-4-fluorophenoxy) quinoline] has been identified through a dual biochemical and molecular-genetics approach. In the molecular-genetics approach, a cosmid library was prepared from an Aspergillus nidulans mutant that was resistant to LY214352 because of a dominant mutation in a single gene. A single cosmid (6A6-6) that could transform an LY214352-sensitive strain of A. nidulans to LY214352-resistance was isolated from the library by sib-selection. Restriction fragments from cosmid 6A6-6 containing the functional resistance gene were identified by transformation, and sequenced. The LY214352-resistance gene coded for a protein of 520 amino acids that had a 34% identity and a 57% similarity in a 333 amino-acid overlap to E. coli dihydroorotate dehydrogenase (DHO-DH). The results of a series of biochemical mechanism-of-action studies initiated simultaneously with molecular-genetic experiments also suggested that DHO-DH was the target of LY214352. Assays measuring the inhibition of DHO-DH activity by LY214352 in a wild-type strain (I50=40 ng/ml) and a highly resistant mutant (I50>100 microgram/ml) conclusively demonstrated that DHO-DH is the target site of LY214352 in A. nidulans. Several mutations in the DHO-DH (pyrE) gene that resulted in resistance to LY214352 were identified.

Antifungal Agents↗
PubMed1989

Babesia bovis: gene isolation and characterization using a mung bean nuclease-derived expression library.

Genomic DNA prepared from erythrocyte cultures of Babesia bovis merozoites was digested with mung bean nuclease and used to construct a lambda gt11 expression library of B. bovis recombinants. Immunoscreening with two polyclonal antibody probes detected multiple recombinants from which two, designated Bb-1 and Bb-3, were chosen for further analysis. Monospecific immunoglobulins isolated from the screening sera using nitrocellulose-bound fusion proteins were employed to determine the native molecular weight and the intracellular location of the babesial proteins encoded by the recombinants. Clone Bb-1 encodes an antigen of 77,000 Da located at the apical end of the intraerythrocytic parasite. A protein of 75,000 Da encoded by clone Bb-3 is associated with the infected red blood cell cytoplasm and/or membrane but not with the merozoite.

Animals↗
PubMed2006

Isolating apparently pure libraries of replication origins from complex genomes.

Because of the complexity of higher eukaryotic genomes and the lack of a reliable autonomously replicating sequence (ARS) assay for isolating potential replicators, the identification of origins has proven to be extremely challenging and time consuming. We have developed a new origin-trapping method based on the partially circular nature of restriction fragments containing replication bubbles and have prepared a library of approximately 1,000 clones from early S phase CHO cells. When 15 randomly selected clones were analyzed by a stringent two-dimensional (2D) gel replicon mapping method, all were shown to correspond to active, early firing origins. Furthermore, most of these appear to derive from broad zones of potential sites, and the five that were analyzed in a time-course study are all inefficient. This bubble-trapping scheme will allow the construction of comprehensive origin libraries from any complex genome so that their natures and distributions vis-a-vis other chromosomal markers can be established.

Animals↗
PubMed1996

Dendrimer-supported combinatorial chemistry.

A new methodology for the construction of combinatorial libraries is described. The approach, termed dendrimer-supported combinatorial chemistry (DCC), centers on the use of dendrimers as soluble supports. Salient features of DCC include solution phase chemistry, homogeneous purification, routine characterization of intermediates, and high support loadings. To demonstrate the feasibility of DCC, single compounds and a small combinatorial library were prepared via the Fischer indole synthesis. Excellent product yields and purities were obtained, and dendrimer-protected intermediates could be routinely analyzed by 1H and 13C NMR and by mass spectrometry. The results indicate that DCC is a general and efficient strategy for the generation of combinatorial libraries.

Journal Article↗
PubMed2001

Infrared analysis of urinary calculi by a single reflection accessory and a neural network interpretation algorithm.

BACKGROUND: Preparation of KBr tablets, used for Fourier transform infrared (FT-IR) analysis of urinary calculus composition, is time-consuming and often hampered by pellet breakage. We developed a new FT-IR method for urinary calculus analysis. This method makes use of a Golden Gate Single Reflection Diamond Attenuated Total Reflection sample holder, a computer library, and an artificial neural network (ANN) for spectral interpretation. METHODS: The library was prepared from 25 pure components and 236 binary and ternary mixtures of the 8 most commonly occurring components. The ANN was trained and validated with 248 similar mixtures and tested with 92 patient samples, respectively. RESULTS: The optimum ANN model yielded root mean square errors of 1.5% and 2.3% for the training and validation sets, respectively. Fourteen simple expert rules were added to correct systematic network inaccuracies. Results of 92 consecutive patient samples were compared with those of a FT-IR method with KBr tablets, based on an initial computerized library search followed by visual inspection. The bias was significantly different from zero for brushite (-0.8%) and the concomitantly occurring whewellite (-2.8%) and weddellite (3.8%), but not for ammonium hydrogen urate (-0.1%), carbonate apatite (0.5%), cystine (0.0%), struvite (0.4%), and uric acid (-0.1%). The 95% level of agreement of all results was 9%. CONCLUSIONS: The new Golden Gate method is superior because of its smaller sample size, user-friendliness, robustness, and speed. Expert knowledge for spectral interpretation is minimized by the combination of a library search and ANN prediction, but visual inspection remains necessary.

Adolescent↗
PubMed2004

Complexes of 5,5'-aminoacido-substituted 2,2'-bipyridyl ligands: control of diastereoselectivity with a pH switch and a chloride-responsive combinatorial library.

The synthesis and coordination chemistry of a new chiral ligand, 2,2'-bipyridine substituted at the 5 and 5' positions by N-methyl-L-valine methyl ester (5), is presented. The ligand readily forms complexes [M(5)3]2+ where M = Co(II) and Fe(II) in CH3CN, and the complexation reaction is slightly diastereoselective (d.e. =ca. 20%) in favour of the Delta diastereomer. The addition of six equivalents of HCl to these complexes [M(II)(5)3]2+ leads to formation of Delta-[M(II)(5H2)3]8+ with a d.e. of 100%. This high diastereoselectivity can be reversed by the addition of base i.e. the diastereoselectivity can be controlled by the pH. Delta-[Fe(5H2)3]8+ was found to bind chloride ions in CD3OD-CD3CN (6:1) with a binding constant of 260 M(-1). [Co(II)(5)3]2+ can be oxidised to Delta-[Co(III)(5H2)3]9+. Formation constants for both [Co(II)(5)3]2+ and [Co(II)(5H2)3]8+ in acetonitrile were obtained by spectrophotometric titrations. In the former case, the stability constant, log beta3 = 19.5(8), is very similar to that measured for [Co(II)(bipy)3]2+ (log beta3 = 19.3(7)) but this drops significantly when the amine groups of are protonated (log beta3 = 16.5(2)). A dynamic combinatorial library was prepared by mixing three equivalents of, three equivalents of bipy, and two equivalents of Co(II) in CD3CN. The presence of all possible Delta- and Lambda-[Co(II)(5)x(bipy)(3-x)]2+ complexes was inferred from 1H NMR and ES-MS spectra. Addition of protons to this library reduced the number of components by inducing diastereoselectivity, and presence of chloride further simplified the 1H NMR spectrum, indicating that [Cl2 ligand Delta-[Co(II)(5H2)3]]6+ and [Co(II)(bipy)3]2+ were the dominant products.

Journal Article↗
PubMed2004

BAC resources for the rat genome project.

Two 11-fold redundant bacterial artificial chromosome (BAC) libraries (RPCI-32 and CHORI-230) have been constructed to support the rat genome project. The first library was constructed using a male Brown Norway (BN/SsNHsd) rat as a DNA source long before plans for rat genome sequencing had been launched. The second library was prepared from a highly inbred female (BN/SsNHsd/MCW) rat in support of the rat genome sequencing project. The use of an inbred rat strain is essential to avoid problems with genome assembly resulting from the difficulty of distinguishing haplotype variation from variation among duplicons. We have demonstrated the suitability of the library by using a detailed quality assessment of large insert sizes, narrow size distribution, consistent redundancy for many markers, and long-range continuity of BAC contig maps. The widespread use of the two libraries as an integral part of the rat genome project has led to the database annotations for many clones, providing rat researchers with a rich resource of BAC clones that can be screened in silico for genes of interest.

Animals↗
PubMed2007

The influence of grafted polymer architecture and fluid hydrodynamics on protein separation by entropic interaction chromatography.

Entropic interaction chromatography (EIC) provides efficient size-based separation of protein mixtures through the entropy change associated with solute partitioning into a layer of hydrophilic homopolymer that has been end-grafted within the pores of a macroporous chromatography support. In this work, surface-initiated atom-transfer radical polymerization (ATRP) is used to prepare a library of EIC stationary phases covering a wide range of grafted-chain densities and molecular weights. Exhaustive chain cleavage and analysis by saponification and GPC-MALLS, respectively, show that the new ATRP synthesis procedure allows for excellent control over graft molecular weight and polydispersity. The method is used to prepare high-density grafts (up to 0.164 +/- 0.005 chains/nm(2)) that extend the range of EIC applications to include efficient buffer-exchange and desalting of protein preparations. Reducing the graft density allows for greater partitioning of high molecular weight solutes, extending the linear range of the selectivity curve. Increasing graft molecular weight also alters selectivity, but more directly affects column capacity by increasing the volume of the grafted layer. Protein partitioning in high-density EIC columns is found to decrease with mobile-phase velocity (u). Although solute mass transfer resistances leading to an increase in plate height can explain this effect, pressure drop data across the column are indicative of weak convective flow through at least a fraction of the grafted architecture. Modeling of the grafted brush properties in the presence of solvent flow by subjecting a self-consistent-field theory representation of the brush to a viscous shear force predicts that the grafted chains will tilt and elongate in the direction of flow. The shear force may therefore act to reduce the number of conformations available to chains, increasing their rigidity without significantly altering the thickness of the grafted layer. A reduction in protein partitioning is then predicted when the dependence on u of the solute entropy loss is stronger than that of the grafted polymer, a condition met at high graft densities.

Chromatography, Gel↗
PubMed2006

Towards developing surface eroding poly(alpha-hydroxy acids).

We have prepared a library of biodegradable polyesters derived from poly(alpha-hydroxy acids) (PHAs) that appear to primarily exhibit surface erosion behavior. This was achieved by increasing the hydrophobicity of the polymers in two distinct steps, namely: macromer formation and a coupling step. In the first step, macromerdiols (MDs) with varying lipophilicities were prepared by polymerization of L-lactide or mixture of L-lactide and glycolide (3/1 by mole) to various lengths (n = 10, 20, 30, and 40) using alkanediols of increasing C-chain length (C6, C8, and C12) as initiators in the presence of Tin(II) catalyst. In the second step, the macromer diols were linked together with diacid dichlorides of varying C-chain lengths (C6, C8, C10, and C12) to yield polyesters ranging in molecular weight (Mw) from 20 to 130 KDa and polydispersity of 1.5-6. These polyesters exhibited different thermal behavior from pure PHAs that can be tuned by changing the initiator core, the lactide/glycolide chain length, and diacid dichloride type. In addition, all these polymers showed solubility in tetrahydrofuran unlike poly(L-lactic acid) (PLLA) and poly(lactide-co-glycolide) (PLGA). In contrast to PLLA and PLGA, the degradation behavior of these novel polyesters exhibited linear profiles consistent with a surface erosion behavior. Release studies using Congo red as a model drug from microspheres prepared from these polyesters showed linear release profiles with correlation constants of least-square fits approaching a value of unity. Degradable polyesters with tunable thermal and degradation behavior may find applications in drug delivery and tissue engineering, where control over these parameters is critical to ensure predictable outcomes.

Absorbable Implants↗
PubMed2004

Privileged scaffolds for blocking protein-protein interactions: 1,4-disubstituted naphthalene antagonists of transcription factor complex HOX-PBX/DNA.

Structure-based-design studies, with the crystal structure of the HOXB1-PBX1/DNA transcription factor complex, were used to identify 1,4-disubstituted naphthalenes as potential antagonists. An initial library of 32 analogs was synthesized, two of which were found to be more potent than the reported activity for a 12 amino acid peptide antagonist. Antagonists were also identified of the related BRN1/DNA and BRN2/DNA transcription factor complexes indicating that a 1,4-disubstituted naphthalene may be a privileged scaffold for preparing screening libraries targeting this family of transcription factor complexes.

Crystallography, X-Ray↗
PubMed2006

Discovery of galectin ligands in fully randomized combinatorial one-bead-one-compound (glyco)peptide libraries.

The involvement of human lectins (galectins) in disease progression accounts for the interest to design potent inhibitors. Three fully randomized hexa(glyco)peptide libraries were prepared using the portion mixing method combined with ladder synthesis. On-bead screening with fluorescently labelled galectin-1 and -3 yielded a series of lead structures, whose inhibitory activity on carbohydrate-dependent galectin binding was tested in solution by solid-phase and cell assays. The various data obtained define the library approach as a facile route for the discovery of selective (glyco)peptide-based galectin inhibitors.

Cell Line, Tumor↗
PubMed1998

Phylogenetic diversity of ultraplankton plastid small-subunit rRNA genes recovered in environmental nucleic acid samples from the Pacific and Atlantic coasts of the United States.

The scope of marine phytoplankton diversity is uncertain in many respects because, like bacteria, these organisms sometimes lack defining morphological characteristics and can be a challenge to grow in culture. Here, we report the recovery of phylogenetically diverse plastid small-subunit (SSU) rRNA gene (rDNA) clones from natural plankton populations collected in the Pacific Ocean off the mouth of Yaquina Bay, Oreg. (OCS clones), and from the eastern continental shelf of the United States off Cape Hatteras, N.C. (OM clones). SSU rRNA gene clone libraries were prepared by amplifying rDNAs from nucleic acids isolated from plankton samples and cloning them into plasmid vectors. The PCR primers used for amplification reactions were designed to be specific for bacterial SSU rRNA genes; however, plastid genes have a common phylogenetic origin with bacteria and were common in both SSU rRNA gene clone libraries. A combination of restriction fragment length polymorphism analyses, nucleic acid sequencing, and taxon-specific oligonucleotide probe hybridizations revealed that 54 of the 116 OCS gene clones were of plastid origin. Collectively, clones from the OCS and OM libraries formed at least eight unique lineages within the plastid radiation, including gene lineages related to the classes Bacillariophyceae, Cryptophyceae, Prymnesiophyceae, Chrysophyceae, and Prasinophyceae; for a number of unique clones, no close phylogenetic neighbors could be identified with confidence. Only a group of two OCS rRNA gene clones showed close identity to the plastid SSU rRNA gene sequence of a cultured organism [Emiliania huxleyi (Lohmann) Hay and Mohler; 99.8% similar]. The remaining clones could not be identified to the genus or species level. Although cryptic species are not as prevalent among phytoplankton as they are among their bacterial counterparts, this genetic survey nonetheless uncovered significant new information about phytoplankton diversity.

Animals↗
PubMed1992

The early genetic response to light in the green unicellular alga Chlamydomonas eugametos grown under light/dark cycles involves genes that represent direct responses to light and photosynthesis.

In the green unicellular alga Chlamydomonas eugametos, cellular division is readily synchronized by light/dark cycles. Under these conditions, light initiates photosynthetic growth in daughter cells and begins the G1 phase. Genes whose expression is regulated upon illumination are likely to be important mechanisms controlling cell proliferation. To identify some of those genes, two cDNA libraries were prepared with poly(A)+ extracted from cells either stimulated with light for 1 h or held in darkness (quiescent cells) during the same period. To restrict our analysis to those genes that are part of the primary response, cells were incubated in presence of cycloheximide. Differential screening of approximately 40,000 clones in each library revealed 44 clones which hybridize preferentially with a [32P] cDNA probe derived from RNA of light-stimulated cells and 15 clones which react selectively with a [32P] cDNA probe synthesized from poly(A)+ RNA of quiescent cells. Cross-hybridization of these clones identified 4 independent sequences in the light-induced (LI) collection and 2 in the uninduced (LR) library. Four of these cDNAs correspond to mRNAs that are positively or negatively regulated upon activation of photosynthesis. One clone represents a mRNA that accumulates transitorily at both transitions. Finally, LI818 cDNA identifies a new chlorophyll a/b-binding (cab) gene family whose mRNA accumulation is controlled by light and a circadian oscillator. The endogenous timing system controls LI818 mRNA accumulation so that it precedes the onset of illumination by a few hours. On the other hand, light affects LI818 mRNA levels independently of active photosynthesis.

Amino Acid Sequence↗
PubMed2002

Putative protein digestion in a sap-sucking homopteran plant pest (rice brown plant hopper; Nilaparvata lugens: Delphacidae)--identification of trypsin-like and cathepsin B-like proteases.

Sap-sucking phytophagous insect species of the order Hemiptera have been assumed not to carry out digestive proteolysis, but instead to rely on free amino acids in the phloem and xylem saps for their nutritional requirements. Extracts prepared from isolated guts of rice brown planthopper (Nilaparvata lugens), a homopteran crop pest, were shown to contain protease activity, with hydrolysis of both protein and synthetic peptide substrates being observed. Assays with specific inhibitors suggested that a trypsin-like serine protease was responsible for most of hydrolytic activity against synthetic substrates. A cDNA library was prepared from RNA extracted from N. lugens gut tissue, and screened for protease-encoding sequences. cDNAs for a cathepsin B-like protease and a trypsin-like protease were isolated and fully characterised; the latter exhibits a novel C-terminal region and an unusual activation mechanism, and represents a small gene family. Soya bean Kunitz trypsin inhibitor (SKTI) is an effective inhibitor of protein hydrolysis by N. lugens gut extracts in vitro, explaining why transgenic rice plants expressing this protein are partially resistant to the insect (Mol. Breed. 5 (1999) 1). It is suggested that digestive proteolysis may be widespread in sap-sucking homoptera, and can make a significant contribution to nutrition.

Amino Acid Sequence↗
PubMed1985

Molecular cloning of a DNA fragment from human chromosome 14(14q11) involved in T-cell malignancies.

To isolate DNA segments specific to chromosome band 14q11, which has been implicated in a number of human T-cell malignancies, a genomic DNA library was prepared from a variant cell subline of the human lymphoblastic KE37 cell line. This subline (KE37-R) bears a t(8;14) (q24;q11) translocation, and the breakpoint on the resulting chromosome 8q+ has been located at the 3' end of the third c-myc exon. Three molecular clones were isolated by screening the library with a c-myc exon 3 probe, and one of them (lambda K40) was analyzed in detail. It contains a 15-kb insert consisting of 4.5 kb of sequence from chromosome 8 (e.g., downstream of c-myc exon 3) and sequences from chromosome 14. The origin of these latter sequences was established by hybridizing DNA from chromosomes sorted by flow cytometry to a lambda K40 subclone containing only chromosome 14 presumptive sequences and by Southern blot analysis of rodent X human somatic hybrid cell DNA with the same probe. No cross-hybridization was found between the lambda K40 clone and a cDNA clone for the alpha chain T-cell receptor gene which is also located in 14q11. A preliminary survey of DNAs from human T-cell malignancies with a probe corresponding to chromosome 14 sequences of lambda K40 clone revealed for some of them restriction patterns different from those of the germ line DNA. The fact that the rearrangement observed in a leukemic patient was not found in DNA from lymphocytes obtained during remission excluded any polymorphism.(ABSTRACT TRUNCATED AT 250 WORDS)

Chromosomes, Human, 13-15↗
PubMed2003

Gene expression in autumn leaves.

Two cDNA libraries were prepared, one from leaves of a field-grown aspen (Populus tremula) tree, harvested just before any visible sign of leaf senescence in the autumn, and one from young but fully expanded leaves of greenhouse-grown aspen (Populus tremula x tremuloides). Expressed sequence tags (ESTs; 5,128 and 4,841, respectively) were obtained from the two libraries. A semiautomatic method of annotation and functional classification of the ESTs, according to a modified Munich Institute of Protein Sequences classification scheme, was developed, utilizing information from three different databases. The patterns of gene expression in the two libraries were strikingly different. In the autumn leaf library, ESTs encoding metallothionein, early light-inducible proteins, and cysteine proteases were most abundant. Clones encoding other proteases and proteins involved in respiration and breakdown of lipids and pigments, as well as stress-related genes, were also well represented. We identified homologs to many known senescence-associated genes, as well as seven different genes encoding cysteine proteases, two encoding aspartic proteases, five encoding metallothioneins, and 35 additional genes that were up-regulated in autumn leaves. We also indirectly estimated the rate of plastid protein synthesis in the autumn leaves to be less that 10% of that in young leaves.

Arabidopsis Proteins↗