CiteULike: Author Konieczny

Polyelectrolyte-Compression Forces between Spherical DNA Brushes

Kati Kegler — 2008-05-07T21:14:58-00:00

Physical Review Letters, Vol. 100, No. 11. (2008)

Optical tweezers are employed to measure the forces of interaction within a single pair of DNA-grafted colloids, dependent on the molecular weight of the DNA chains, and the concentration and valence of the surrounding ionic medium. The resulting forces are short range and set in as the surface-to-surface distance between the colloidal cores reaches the value of the brush height. The measured force-distance relation is analyzed by means of a theoretical treatment that quantitatively describes the effects of compression of the chains on the surface of the opposite-lying colloid. Quantitative agreement with the experiment is obtained for all parameter combinations.

An internal regulatory element controls troponin I gene expression.

KE Yutzey — 2008-03-18T13:10:36-00:00

Mol Cell Biol, Vol. 9, No. 4. (April 1989), pp. 1397-1405.

During skeletal myogenesis, approximately 20 contractile proteins and related gene products temporally accumulate as the cells fuse to form multinucleated muscle fibers. In most instances, the contractile protein genes are regulated transcriptionally, which suggests that a common molecular mechanism may coordinate the expression of this diverse and evolutionarily unrelated gene set. Recent studies have examined the muscle-specific cis-acting elements associated with numerous contractile protein genes. All of the identified regulatory elements are positioned in the 5'-flanking regions, usually within 1,500 base pairs of the transcription start site. Surprisingly, a DNA consensus sequence that is common to each contractile protein gene has not been identified. In contrast to the results of these earlier studies, we have found that the 5'-flanking region of the quail troponin I (TnI) gene is not sufficient to permit the normal myofiber transcriptional activation of the gene. Instead, the TnI gene utilizes a unique internal regulatory element that is responsible for the correct myofiber-specific expression pattern associated with the TnI gene. This is the first example in which a contractile protein gene has been shown to rely primarily on an internal regulatory element to elicit transcriptional activation during myogenesis. The diversity of regulatory elements associated with the contractile protein genes suggests that the temporal expression of the genes may involve individual cis-trans regulatory components specific for each gene.

A coagulation-MF system for water treatment using ceramic membranes

Krystyna Konieczny — 2008-02-27T19:07:05-00:00

Desalination, Vol. 198, No. 1-3. (30 October 2006), pp. 92-101.

The results of studies are presented on the treatment of natural waters with a high content of organic compounds. The research involved unit processes of coagulation, microfiltration, and the hybrid process coagulation-sedimentation-microfiltration. In the membrane filtration process 19-channnel ceramic membranes manufactured by Orelis (France) were used. Simulated water containing humic acids in an amount of 20 and 30 mg/l was also used. Four coagulants were tested for which optimal process parameters were determined experimentally. The effectiveness of coagulation and microfiltration and that of the hybrid system coagulation-membrane filtration was tested, based on measurements of the membrane yield (permeate flux) and physicochemical analysis of raw water and permeates. The application of the hybrid system combining coagulation and microfiltration offers better removal of organic pollution (100% for TOC).

Complement C5 mediates experimental tubulointerstitial fibrosis.

P Boor — 2008-01-21T12:48:37-00:00

J Am Soc Nephrol, Vol. 18, No. 5. (May 2007), pp. 1508-1515.

Renal fibrosis is the final common pathway of most progressive renal diseases. C5 was recently identified as a risk factor for liver fibrosis. This study investigated the role of C5 in the development of renal tubulointerstitial fibrosis by (1) induction of renal fibrosis in wild-type and C5(-/-) mice by unilateral ureteral ligation (UUO) and (2) investigation of the effects of a C5a receptor antagonist (C5aRA) in UUO. In C5(-/-) mice, when compared with wild-type controls, markers of renal fibrosis (Sirius Red, type I collagen, fibronectin, alpha-smooth muscle actin, vimentin, and infiltrating macrophages) were significantly reduced on day 5 of UUO. On day 10, fibronectin mRNA and protein expression were still reduced in the C5(-/-) mice. Cortical mRNA of all PDGF isoforms and of TGF-beta(1) (i.e., central mediators of renal disease) were significantly reduced in C5(-/-) mice when compared with controls. Renal tubular cell expression of the C5aR was sparse in normal cortex but markedly upregulated after UUO. Treatment of wild-type UUO mice with C5aRA also led to a significant reduction of cortical Sirius Red staining, fibronectin protein expression, and PDGF-B mRNA expression on day 5. Neither genetic C5 deficiency nor C5aRA treatment caused any histologic changes in the nonobstructed kidneys. In cultured murine cortical tubular cells, C5a stimulated production of TGF-beta(1), and this was inhibited by C5aRA. Using a combined genetic and pharmacologic approach, C5, in particular C5a, is identified as a novel profibrotic factor in renal disease and as a potential new therapeutic target.

PDGF-D inhibition by CR002 ameliorates tubulointerstitial fibrosis following experimental glomerulonephritis

Boor — 2007-05-02T13:42:51-00:00

Nephrology Dialysis Transplantation, Vol. 22, No. 5. (May 2007), pp. 1323-1331.

DA2 merging operators

S Konieczny — 2007-11-12T20:23:26-00:00

Artificial Intelligence, Vol. 157, No. 1-2. (August 2004), pp. 49-79.

A new framework for propositional merging is presented. DA2 merging operators, parameterized by a distance between interpretations and two aggregation functions, are introduced. Many distances and aggregation functions can be used and many merging operators already defined in the literature (including both model-based ones and syntax-based ones) can be encoded as specific DA2 operators. Both logical and complexity properties of those operators are studied. An important result is that (under very weak assumptions) query entailment from merged bases is "only" at the first level of the polynomial hierarchy when any of the DA2 operators is used. As a by-product, complexity results for several existing merging operators are derived as well.

A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers

Andrzej Konieczny — 2007-09-28T12:51:54-00:00

The Plant Journal, Vol. 4, No. 2. (1993), pp. 403-410.

A set of mapping markers have been designed for Arabidopsis thaliana that correspond to DNA fragments amplifed by the polymerase chain reaction (PCR). The ecotype of origin of these amplified fragments can be determined by cleavage with a restriction endo-nuclease. Specifically, 18 sets of PCR primers were synthesized, each of which amplifies a single mapped DNA sequence from the Columbia and Landsberg erecta ecotypes. Also identifed was at least one restriction endonuclease for each of these PCR products that generates ecotype-specific digestion patterns. Using these co-dominant cleaved amplified polymorphic sequences (CAPS), an Arabidopsis gene can be unambiguously mapped to one of the 10 Arabidopsis chromosome arms in a single cross using a limited number of F2 progeny.

Merging with Integrity Constraints

Sébastien Konieczny — 2007-08-24T18:16:11-00:00

(1999), pp. 233-244.

PDGF-D inhibition by CR002 ameliorates tubulointerstitial fibrosis following experimental glomerulonephritis.

P Boor — 2007-07-15T14:51:58-00:00

Nephrol Dial Transplant, Vol. 22, No. 5. (May 2007), pp. 1323-1331.

BACKGROUND: Arresting or regressing kidney scarring is of major clinical relevance. Platelet-derived growth factor D (PDGF-D) is widely expressed in fibrotic kidneys. Administration of the PDGF-D neutralizing fully human monoclonal antibody CR002 in the acute phase of progressive anti-Thy 1.1 glomerulonephritis reduced glomerular and secondary tubulointerstitial damage. METHODS: Using this model, we now assessed the effects of CR002 (n=15) vs irrelevant control IgG (n=17) administered on days 17, 28 and 35 after disease induction, i.e. after acute glomerular damage had subsided. RESULTS: In vitro, CR002 inhibited the PDGF-D- but not the PDGF-B-induced proliferation of rat renal fibroblasts. Following the first CR002 injection on day 17, exposure to therapeutic levels was maintained until day 49. Proteinuria in the CR002-treated group was transiently reduced between days 49 and 77 (-19 to -23% in comparison with the controls; P<0.05). On day 100, CR002 treatment reduced the number of rats that had doubled their serum creatinine (CR002: 40 vs controls: 71%; P<0.05). Compared with controls, the CR002 animals, on day 100, significantly lowered glomerular expression of vimentin and collagens as well as tubulointerstitial damage scores, interstitial fibrosis, vimentin and cortical PDGF-D mRNA levels. CONCLUSIONS: PDGF-D antagonism, even after the phase of acute glomerular damage, exerts beneficial effects on the course of tubulointerstitial damage, i.e. the final common pathway of most renal diseases.

A framework for iterated revision

S Konieczny — 2007-07-07T13:35:16-00:00

(2000)

We consider in this work the problem of iterated belief revision. We propose a family of belief revision operators called revision with memory operators and we give a logical characterization of these operators. They obey what we call the principle of strong primacy of update, i.e. when one revises his beliefs by a new evidence, then all possible worlds that satisfy that new evidence become more reliable than those that do not. Keywords. Belief revision, Iteration 1 Introduction...

Prediction of Functional Sites Based on the Fuzzy Oil Drop Model

Michał Bryliński — 2007-05-26T04:06:50-00:00

PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e94.

A description of many biological processes requires knowledge of the 3-D structure of proteins and, in particular, the defined active site responsible for biological function. Many proteins, the genes of which have been identified as the result of human genome sequencing, and which were synthesized experimentally, await identification of their biological activity. Currently used methods do not always yield satisfactory results, and new algorithms need to be developed to recognize the localization of active sites in proteins. This paper describes a computational model that can be used to identify potential areas that are able to interact with other molecules (ligands, substrates, inhibitors, etc.). The model for active site recognition is based on the analysis of hydrophobicity distribution in protein molecules. It is shown, based on the analyses of proteins with known biological activity and of proteins of unknown function, that the region of significantly irregular hydrophobicity distribution in proteins appears to be function related.

Prediction of ligand binding site and functionally important residues based on fuzzy-oil-drop model

Michal Brylinski — 2007-04-13T17:52:09-00:00

PLoS Computational Biology, Vol. preprint, No. 2007. (1 April 2007), e94.eor.

The recognition of a ligand binding site in a protein molecule is important for identifying its biological activity. The model for in silico recognition of binding site is applied to 33 proteins of known biological activity and 33 proteins of unknown biological activity (related to genomic project). The hydrophobic core, which stabilizes the protein structure, is assumed to be represented by a three-dimensional Gaussian function, the value of which represents the hydrophobicity density distribution in a protein molecule. The experimentally observed distribution of hydrophobicity compared with the theoretically expected one reveals differences within the molecule. Fully automatic method for preliminary active site recognition in silico. The irregularities between idealized and observed hydrophobicity distribution were found to be localized exactly in the ligation site. Functionally important residues were recognized in the proteins with unknown function on the basis of this finding. The localization of the ligation site according to the presented model can be easily carried out for any protein structure with a free prediction server available from http://bioinformatics.cm-uj.krakow.pl/activesite.

Distance-based merging: a general framework and some complexity results

S Konieczny — 2007-02-11T17:45:50-00:00

(2001)

The importance of belief merging is reflected by the abundance of the literature about it for the last years. In the following, a model for belief merging based on distances is introduced; many merging operators already pointed out so far can be recovered as specific instances of this model. We investigate the computational aspects of such distance-based operators and give two general results showing that the complexity of inference for them is at the first level of the polynomial hierarchy...

Identification and characterization of rain, a novel Ras-interacting protein with a unique subcellular localization.

NY Mitin — 2006-02-19T14:31:26-00:00

J Biol Chem, Vol. 279, No. 21. (21 May 2004), pp. 22353-22361.

The Ras small GTPase functions as a signaling node and is activated by extracellular stimuli. Upon activation, Ras interacts with a spectrum of functionally diverse downstream effectors and stimulates multiple cytoplasmic signaling cascades that regulate cellular proliferation, differentiation, and apoptosis. In addition to the association of Ras with the plasma membrane, recent studies have established an association of Ras with Golgi membranes. Whereas the effectors of signal transduction by activated, plasma membrane-localized Ras are well characterized, very little is known about the effectors used by Golgi-localized Ras. In this study, we report the identification of a novel Ras-interacting protein, Rain, that may serve as an effector for endomembrane-associated Ras. Rain does not share significant sequence similarity with any known mammalian proteins, but contains a Ras-associating domain that is found in RalGDS, AF-6, and other characterized Ras effectors. Rain interacts with Ras in a GTP-dependent manner in vitro and in vivo, requires an intact Ras core effector-binding domain for this interaction, and thus fits the definition of a Ras effector. Unlike other Ras effectors, however, Rain is localized to perinuclear, juxta-Golgi vesicles in intact cells and is recruited to the Golgi by activated Ras. Finally, we found that Rain cooperates with activated Raf and causes synergistic transformation of NIH3T3 cells. Taken together, these observations support a role for Rain as a novel protein that can serve as an effector of endomembrane-localized Ras.

Locality and parsing complexity.

L Konieczny — 2005-09-27T19:07:05-00:00

J Psycholinguist Res, Vol. 29, No. 6. (November 2000), pp. 627-645.

Two experiments, an off-line acceptability judgment study and an on-line self-paced reading experiment, were conducted to tackle the question of locality-based preferences in sentence processing. The material consisted of German verb-final sentences containing a relative clause that was either host adjacent or extraposed. While the off-line data seem to reflect locality based integration cost, the on-line data revealed a highly different picture. It is argued that, in the present constructions at least, locality is relevant for production rather than perception. In perception, heads can be anticipated through incremental integration of their arguments.