bluuebunny/crossref_metadata_2025 huggingface dataset:
Geometry and symmetry presculpt the free-energy landscape of proteins
Authors: Hoang Trinh Xuan , Trovato Antonio , Seno Flavio , Banavar Jayanth R. , Maritan Amos
Published: May 2004

We present a simple physical model that demonstrates that the native-state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by the hydrogen bonds and sterics, and hydrophobicity are sufficient to yield a free-energy landscape with broad minima even for a homopolymer. These minima correspond to marginally compact structures comprising the menu of folds that proteins choose from to house their native states in. Our results provide a general framework for understanding the common characteristics of globular proteins.
The minimal promoter plays a major role in silencing of the galago γ-globin gene in adult erythropoiesis
Authors: Li Qiliang , Fang Xiangdong , Han Hemei , Stamatoyannopoulos George
Published: May 2004

The human γ-globin gene and its orthologous galago γ-globin gene evolved from an ancestral ε-globin gene. In galago, expression of the γ-gene remained restricted to the embryonic stage of development, whereas in humans, expression of the γ-gene was recruited to the fetal stage. To localize the cis-elements responsible for this developmentally distinct regulation, we studied the expression patterns of the human γ-gene driven by either the human or the galago γ-promoters in transgenic mice. γ-gene transcription driven by either promoter reached similar levels in embryonic erythropoiesis. In adult erythropoiesis the γ-gene was silenced when controlled by the galago γ-promoter, but it was expressed at a high level when it was linked to the human γ-promoter. By a series of γ-promoter truncations the sequences required for the down-regulation of the galago γ-globin gene were localized to the minimal promoter. Furthermore, by interchanging the TATA, CCAAT, and CACCC elements between the human and galago minimal promoters we found that whereas each box made a developmentally distinctive contribution to γ-globin gene expression, the CACCC box was largely responsible for the down-regulation of the γ-gene in adult erythropoiesis.
Forebrain degeneration and ventricle enlargement caused by double knockout of Alzheimer's
presenilin-1
and
presenilin-2
Authors: Feng Ruiben , Wang Huimin , Wang Jianlin , Shrom David , Zeng Xuemei , Tsien Joe Z.
Published: May 2004

Early-onset familial Alzheimer's disease is the most aggressive form of Alzheimer's, striking patients as early as their 30s; those patients typically carry mutations in
presenilin-1
and
presenilin-2
. To investigate the coordinated functions of presenilin in the adult brain, we generated double knockout mice, in which both presenilins were deleted in the forebrain. We found that concurrent loss of presenilins in adulthood resulted in massive cortical shrinkage, atrophy of hippocampal molecular layers and corpus callosum, and enlargement of the lateral and third ventricles. We further revealed that deficiency of presenilins caused a series of biochemical alterations, including neuronal atrophy, astrogliosis, caspase-3-mediated apoptosis, and tau hyperphosphorylation. Thus, our study demonstrates that presenilins are essential for the ongoing maintenance of cortical structures and function.
Hypoglycemic Effect of Macrocyclic Binuclear Oxovanadium (IV) Complex on Streptozotocin‐Induced Diabetic Rats
Authors: Ramachandran B. , Sekar D. Sathish , Kandaswamy M. , Narayanan V. , Subramanian S.
Published: May 2004

Though vanadium complexes mimic the action of insulin,
owing to their toxicity, research is still in progress for a new
vanadium complex with maximum efficacy at low concentration
and without any side effects. A novel macrocyclic
binuclear oxovanadium complex was synthesized, its composition
and structure were confirmed by spectral studies
and its efficacy was studied in streptozotocin‐induced diabetic
rats over a period of 30 days. The oral administration
of the complex normalizes the blood glucose level in
the diabetic rats and also maintains normoglycemia after
a glucose load. The biochemical studies revealed that the
complex is not toxic to the system. The nontoxic nature of
this complex may be due to the presence of the vanadyl
ions in an intact form. The study highlights the nontoxic
and hypoglycemic effects of the new macrocyclic binuclear
oxovanadium complex.
Cross‐Linking in Collagen by Nonenzymatic Glycation Increases the Matrix Stiffness in Rabbit Achilles Tendon
Authors: Reddy G. Kesava
Published: May 2004

Nonenzymatic glycation of connective tissue matrix proteins
is a major contributor to the pathology of diabetes
and aging. Previously the author and colleagues have shown
that nonenzymatic glycation significantly enhances the matrix
stability in the Achilles tendon (Reddy et al., 2002,
Arch. Biochem. Biophys., 399, 174–180). The present study
was designed to gain further insight into glycation‐induced
collagen cross‐linking and its relationship to matrix stiffness
in the rabbit Achilles tendon. The glycation process
was initiated by incubating the Achilles tendons (n = 6) in
phosphate‐buffered saline containing ribose, whereas control
tendons (n = 6) were incubated in phosphate‐buffered
saline without ribose. Eight weeks following glycation, the
biomechanical attributes as well as the degree of collagen
cross‐linking were determined to examine the potential associations
between matrix stiffness and molecular properties
of collagen. Compared to nonglycated tendons, the
glycated tendons showed increased maximum load, stress,
strain, Young′s modulus of elasticity, and toughness indicating
that glycation increases the matrix stiffness in the
tendons. Glycation of tendons resulted in a considerable decrease
in soluble collagen content and a significant increase
in insoluble collagen and pentosidine. Analysis of potential
associations between the matrix stiffness and degree of collagen
cross‐linking showed that both insoluble collagen and
pentosidine exhibited a significant positive correlation with
the maximum load, stress, and strain, Young′s modulus of
elasticity, and toughness (r values ranging from .61 to .94) in the Achilles tendons. However, the soluble collagen content
present in neutral salt buffer, acetate buffer, and acetate
buffer containing pepsin showed an inverse relation
with the various biomechanical attributes tested (r values
ranging from .22 to .84) in the Achilles tendons. The results
of the study demonstrate that glycation‐induced collagen
cross‐linking is directly associated with the increased matrix
stiffness and other mechanical attributes of the tendon.
Increased Expression of Tissue Factor and Receptor for Advanced Glycation End Products in Peripheral Blood Mononuclear Cells of Patients With Type 2 Diabetes Mellitus with Vascular Complications
Authors: Buchs A. E. , Kornberg A. , Zahavi M. , Aharoni D. , Zarfati C. , Rapoport M. J.
Published: May 2004

The aim of the study was to determine the correlation between
the expression of tissue factor (TF) and the receptor
for advanced glycation end products (RAGEs) and vascular
complications in patients with longstanding uncontrolled
type 2 diabetes (T2D). TF and RAGE mRNAs as well as
TF antigen and activity were investigated in 21 T2D patients
with and without vascular complications. mRNA expression
was assessed by reverse transcriptase–polymerase
chain reaction (RT‐PCR) in nonstimulated and advanced
glycation end product (AGE) albumin–stimulated peripheral
blood mononuclear cells (PBMCs). TF antigen expression
was determined by enzyme‐linked immunosorbent assay
(ELISA) and TF activity by a modified prothrombin
time assay. Basal RAGE mRNA expression was 0.2 ± 0.06
in patients with complications and 0.05 ± 0.06 patients without
complications (P = .004). Stimulation did not cause any
further increase in either group. TF mRNA was 0.58 ± 0.29
in patients with complications and 0.21 ± 0.18 in patients
without complications (P = .003). Stimulation resulted in
a nonsignificant increase in both groups. Basal TF activity
(U/106 PBMCs) was 18.4 ± 13.2 in patients with complications
and 6.96 ± 5.2 in patients without complications (P =
.003). It increased 3‐fold in both groups after stimulation
(P = .001). TF antigen (pg/106 PBMCs) was 33.7 ± 28.6 in
patients with complications, 10.4 ± 7.8 in patients without complications (P = .02). Stimulation tripled TF antigen in
both groups of patients (P = .001). The RAGE/TF axis is
up‐regulated inT2Dpatients with vascular complications as
compared to patients without complications. This suggests
a role for this axis in the pathogenesis of vascular complications
in T2D.
Review: Peroxisome Proliferator‐Activated Receptor‐γ and Its Role in the Development and Treatment of Diabetes
Authors: Leff Todd , Mathews Suresh T. , Camp Heidi S.
Published: May 2004

Since its identification as the receptor for antidiabetic
thiazolidinedione drugs, peroxisome proliferator‐activated
receptor‐γ (PPARγ) has been the focus of pharmaceutical
drug discovery programs directed toward finding better
drugs for the treatment of diabetes, as well as the object
of basic research aimed at understanding its role in
the regulation of metabolism. We now understand a great
deal about the crucial role that PPARγ plays in adipocyte
differentiation and development, and are rapidly gaining
knowledge about the role of the receptor in the regulation
of metabolism. However, many crucial aspects of the molecular
mechanism by which modulation of PPARγ activity
affects insulin resistance and glucose homeostasis are still
not clearly understood. Here the authors review the current
status of PPARγ research, with an emphasis on its role in
the causes and treatment of type 2 diabetes.
Review: Pancreatic β‐Cell Neogenesis Revisited
Authors: Paris Maryline , Tourrel-Cuzin Cécile , Plachot Cédric , Ktorza Alain
Published: May 2004

β‐cell neogenesis triggers the generation of new β‐cells
from precursor cells. Neogenesis from duct epithelium is the
most currently described and the best documented process
of differentiation of precursor cells into β‐cells. It is contributes
not only to β‐cell mass expansion during fetal and
nonatal life but it is also involved in the maintenance of the
β‐cell mass in adults. It is also required for the increase in
β‐cell mass in situations of increase insulin demand (obesity,
pregnancy). A large number of factors controlling the differentiation
of β‐cells has been identified. They are classified
into the following main categories: growth factors, cytokine
and inflamatory factors, and hormones such as PTHrP and
GLP‐1. The fact that intestinal incretin hormone GLP‐1
exerts a major trophic role on pancreatic β‐cells provides
insights into the possibility to pharmacologically stimulate
β‐cell neogenesis. This could have important implications
for the of treatment of type 1 and type 2 diabetes. Transdifferentiation,
that is, the differentiation of already differentiated
cells into β‐cells, remains controversial.However, more
and more studies support this concept. The cells, which can
potentially “transdifferentiate” into β‐cells, can belong to
the pancreas (acinar cells) and even islets, or originate from
extra‐pancreatic tissues such as the liver. Neogenesis from intra‐islet precursors also have been proposed and subpopulations
of cell precursors inside islets have been described
by some authors. Nestin positive cells, which have been considered
as the main candidates, appear rather as progenitors
of endothelial cells rather than β‐cells and contribute to
angiogenesis rather than neogenesis. To take advantage of
the different differentiation processes may be a direction for
future cellular therapies. Ultimately, a better understanding
of the molecular mechanisms involved in β‐cell neogenesis
will allow us to use any type of differentiated and/or undifferentiated
cells as a source of potential cell precursors.
Carbohydrate–carbohydrate interaction provides adhesion force and specificity for cellular recognition
Authors: Bucior Iwona , Scheuring Simon , Engel Andreas , Burger Max M.
Published: May 2004

The adhesion force and specificity in the first experimental evidence for cell–cell recognition in the animal kingdom were assigned to marine sponge cell surface proteoglycans. However, the question whether the specificity resided in a protein or carbohydrate moiety could not yet be resolved. Here, the strength and species specificity of cell–cell recognition could be assigned to a direct carbohydrate–carbohydrate interaction. Atomic force microscopy measurements revealed equally strong adhesion forces between glycan molecules (190–310 piconewtons) as between proteins in antibody–antigen interactions (244 piconewtons). Quantitative measurements of adhesion forces between glycans from identical species versus glycans from different species confirmed the species specificity of the interaction. Glycan-coated beads aggregated according to their species of origin, i.e., the same way as live sponge cells did. Live cells also demonstrated species selective binding to glycans coated on surfaces. These findings confirm for the first time the existence of relatively strong and species-specific recognition between surface glycans, a process that may have significant implications in cellular recognition.
Incomplete Incorporation of Tandem Subunits in Recombinant Neuronal Nicotinic Receptors
Authors: Groot-Kormelink Paul J. , Broadbent Steven D. , Boorman James P. , Sivilotti Lucia G.
Published: May 2004

Tandem constructs are increasingly being used to restrict the composition of recombinant multimeric channels. It is therefore important to assess not only whether such approaches give functional channels, but also whether such channels completely incorporate the subunit tandems. We have addressed this question for neuronal nicotinic acetylcholine receptors, using a channel mutation as a reporter for subunit incorporation. We prepared tandem constructs of nicotinic receptors by linking α (α2–α4, α6) and β (β2, β4) subunits by a short linker of eight glutamine residues. Robust functional expression in oocytes was observed for several tandems (β4_α2, β4_α3, β4_α4, and β2_α4) when coexpressed with the corresponding β monomer subunit. All tandems expressed when injected alone, except for β4_α3, which produced functional channels only together with β4 monomer and was chosen for further characterization. These channels produced from β4_α3 tandem constructs plus β4 monomer were identical with receptors expressed from monomer α3 and β4 constructs in acetylcholine sensitivity and in the number of α and β subunits incorporated in the channel gate. However, separately mutating the β subunit in either the monomer or the tandem revealed that tandem-expressed channels are heterogeneous. Only a proportion of these channels contained as expected two copies of β subunits from the tandem and one from the β monomer construct, whereas the rest incorporated two or three β monomers. Such inaccuracies in concatameric receptor assembly would not have been apparent with a standard functional characterization of the receptor. Extensive validation is needed for tandem-expressed receptors in the nicotinic superfamily.
Transmembrane Peptides as Inhibitors of ErbB Receptor Signaling
Authors: Bennasroune Amar , Fickova Maria , Gardin Anne , Dirrig-Grosch Sylvie , Aunis Dominique , Crémel Gérard , Hubert Pierre
Published: May 2004

Receptor tyrosine kinases have a single transmembrane (TM) segment that is usually assumed to play a passive role in ligand-induced dimerization and activation of the receptor. However, mutations within some of these receptors, and recent studies with the epidermal growth factor (EGF) and ErbB2 receptors have indicated that interactions between TM domains do contribute to stabilization of ligand-independent and/or ligand-induced receptor dimerization and activation. One consequence of the importance of these interactions is that short hydrophobic peptides corresponding to these domains should act as specific inhibitors. To test this hypothesis, we constructed expression vectors encoding short fusion peptides encompassing native or mutated TM domains of the EGF, ErbB2, and insulin receptors. In human cell lines overexpressing the wild-type EGF receptor or ErbB2, we observed that the peptides are expressed at the cell surface and that they inhibit specifically the autophosphorylation and signaling pathway of their cognate receptor. Identical results were obtained with peptides chemically synthesized. Mechanism of action involves inhibition of dimerization of the receptors as shown by the lack of effects of mutant nondimerizing sequences, completed by density centrifugation and covalent cross-linking experiments. Our findings stress the role of TM domain interactions in ErbB receptor function, and possibly for other single-spanning membrane proteins.
Mitosis-specific Anchoring of γ Tubulin Complexes by Pericentrin Controls Spindle Organization and Mitotic Entry
Authors: Zimmerman Wendy C. , Sillibourne James , Rosa Jack , Doxsey Stephen J.
Published: May 2004

Microtubule nucleation is the best known function of centrosomes. Centrosomal microtubule nucleation is mediated primarily by γ tubulin ring complexes (γ TuRCs). However, little is known about the molecules that anchor these complexes to centrosomes. In this study, we show that the centrosomal coiled-coil protein pericentrin anchors γ TuRCs at spindle poles through an interaction with γ tubulin complex proteins 2 and 3 (GCP2/3). Pericentrin silencing by small interfering RNAs in somatic cells disrupted γ tubulin localization and spindle organization in mitosis but had no effect on γ tubulin localization or microtubule organization in interphase cells. Similarly, overexpression of the GCP2/3 binding domain of pericentrin disrupted the endogenous pericentrin–γ TuRC interaction and perturbed astral microtubules and spindle bipolarity. When added to Xenopus mitotic extracts, this domain uncoupled γ TuRCs from centrosomes, inhibited microtubule aster assembly, and induced rapid disassembly of preassembled asters. All phenotypes were significantly reduced in a pericentrin mutant with diminished GCP2/3 binding and were specific for mitotic centrosomal asters as we observed little effect on interphase asters or on asters assembled by the Ran-mediated centrosome-independent pathway. Additionally, pericentrin silencing or overexpression induced G2/antephase arrest followed by apoptosis in many but not all cell types. We conclude that pericentrin anchoring of γ tubulin complexes at centrosomes in mitotic cells is required for proper spindle organization and that loss of this anchoring mechanism elicits a checkpoint response that prevents mitotic entry and triggers apoptotic cell death.
Rho Kinase Regulates the Intracellular Micromechanical Response of Adherent Cells to Rho Activation
Authors: Kole Thomas P. , Tseng Yiider , Huang Lawrence , Katz Joseph L. , Wirtz Denis
Published: May 2004

Local sol-gel transitions of the cytoskeleton modulate cell shape changes, which are required for essential cellular functions, including motility and adhesion. In vitro studies using purified cytoskeletal proteins have suggested molecular mechanisms of regulation of cytoskeleton mechanics; however, the mechanical behavior of living cells and the signaling pathways by which it is regulated remains largely unknown. To address this issue, we used a nanoscale sensing method, intracellular microrheology, to examine the mechanical response of the cell to activation of the small GTPase Rho. We observe that the cytoplasmic stiffness and viscosity of serum-starved Swiss 3T3 cells transiently and locally enhances upon treatment with lysophosphatidic acid, and this mechanical behavior follows a trend similar to Rho activity. Furthermore, the time-dependent activation of Rho decreases the degree of microheterogeneity of the cytoplasm. Our results reveal fundamental differences between intracellular elasticity and cellular tension and suggest a critical role for Rho kinase in the regulation of intracellular mechanics.
Spatial and Temporal Regulation of Condensins I and II in Mitotic Chromosome Assembly in Human Cells
Authors: Ono Takao , Fang Yuda , Spector David L. , Hirano Tatsuya
Published: May 2004

Two different condensin complexes make distinct contributions to metaphase chromosome architecture in vertebrate cells. We show here that the spatial and temporal distributions of condensins I and II are differentially regulated during the cell cycle in HeLa cells. Condensin II is predominantly nuclear during interphase and contributes to early stages of chromosome assembly in prophase. In contrast, condensin I is sequestered in the cytoplasm from interphase through prophase and gains access to chromosomes only after the nuclear envelope breaks down in prometaphase. The two complexes alternate along the axis of metaphase chromatids, but they are arranged into a unique geometry at the centromere/kinetochore region, with condensin II enriched near the inner kinetochore plate. This region-specific distribution of condensins I and II is severely disrupted upon depletion of Aurora B, although their association with the chromosome arm is not. Depletion of condensin subunits causes defects in kinetochore structure and function, leading to aberrant chromosome alignment and segregation. Our results suggest that the two condensin complexes act sequentially to initiate the assembly of mitotic chromosomes and that their specialized distribution at the centromere/kinetochore region may play a crucial role in placing sister kinetochores into the back-to-back orientation.
Disruption of Astral Microtubule Contact with the Cell Cortex Activates a Bub1, Bub3, and Mad3-dependent Checkpoint in Fission Yeast
Authors: Tournier Sylvie , Gachet Yannick , Buck Vicky , Hyams Jeremy S. , Millar Jonathan B.A.
Published: May 2004

In animal and yeast cells, the mitotic spindle is aligned perpendicularly to the axis of cell division. This ensures that sister chromatids are separated to opposite sides of the cytokinetic actomyosin ring. In fission yeast, spindle rotation is dependent upon the interaction of astral microtubules with the cortical actin cytoskeleton. In this article, we show that addition of Latrunculin A, which prevents spindle rotation, delays the separation of sister chromatids and anaphase promoting complex-mediated destruction of spindle-associated Securin and Cyclin B. Moreover, we find that whereas sister kinetochore pairs normally congress to the spindle midzone before anaphase onset, this congression is disrupted when astral microtubule contact with the actin cytoskeleton is disturbed. By analyzing the timing of kinetochore separation, we find that this anaphase delay requires the Bub3, Mad3, and Bub1 but not the Mad1 or Mad2 spindle assembly checkpoint proteins. In agreement with this, we find that Bub1 remains associated with kinetochores when spindles are mispositioned. These data indicate that, in fission yeast, astral microtubule contact with the medial cell cortex is monitored by a subset of spindle assembly checkpoint proteins. We propose that this checkpoint ensures spindles are properly oriented before anaphase takes place.
Cholera Toxin Toxicity Does Not Require Functional Arf6- and Dynamin-dependent Endocytic Pathways
Authors: Massol Ramiro H. , Larsen Jakob E. , Fujinaga Yukako , Lencer Wayne I. , Kirchhausen Tomas
Published: May 2004

Cholera toxin (CT) and related AB5toxins bind to glycolipids at the plasma membrane and are then transported in a retrograde manner, first to the Golgi and then to the endoplasmic reticulum (ER). In the ER, the catalytic subunit of CT is translocated into the cytosol, resulting in toxicity. Using fluorescence microscopy, we found that CT is internalized by multiple endocytic pathways. Inhibition of the clathrin-, caveolin-, or Arf6-dependent pathways by overexpression of appropriate dominant mutants had no effect on retrograde traffic of CT to the Golgi and ER, and it did not affect CT toxicity. Unexpectedly, when we blocked all three endocytic pathways at once, although fluorescent CT in the Golgi and ER became undetectable, CT-induced toxicity was largely unaffected. These results are consistent with the existence of an additional retrograde pathway used by CT to reach the ER.
An object model and database for functional genomics
Authors: Jones Andrew , Hunt Ela , Wastling Jonathan M. , Pizarro Angel , Stoeckert Christian J.
Published: May 2004

Motivation: Large-scale functional genomics analysis is now feasible and presents significant challenges in data analysis, storage and querying. Data standards are required to enable the development of public data repositories and to improve data sharing. There is an established data format for microarrays (microarray gene expression markup language, MAGE-ML) and a draft standard for proteomics (PEDRo). We believe that all types of functional genomics experiments should be annotated in a consistent manner, and we hope to open up new ways of comparing multiple datasets used in functional genomics.

Results: We have created a functional genomics experiment object model (FGE-OM), developed from the microarray model, MAGE-OM and two models for proteomics, PEDRo and our own model (Gla-PSI—Glasgow Proposal for the Proteomics Standards Initiative). FGE-OM comprises three namespaces representing (i) the parts of the model common to all functional genomics experiments; (ii) microarray-specific components; and (iii) proteomics-specific components. We believe that FGE-OM should initiate discussion about the contents and structure of the next version of MAGE and the future of proteomics standards. A prototype database called RNA And Protein Abundance Database (RAPAD), based on FGE-OM, has been implemented and populated with data from microbial pathogenesis.

Availability: FGE-OM and the RAPAD schema are available from http://www.gusdb.org/fge.html, along with a set of more detailed diagrams. RAPAD can be accessed by registration at the site.
Dblox: a genome-wide test for ancient segmental duplication
Authors: Friedman Robert , Ekollu Vikram , Rose John R. , Hughes Austin L.
Published: May 2004

Summary: Dblox and RDblox provide a simple statistical test for duplicated genomic structure; the same programs can also be used to identify putatively duplicated regions. The method focuses on ancient duplication events involving protein-coding genes.

Availability:  http://www.biol.sc.edu/~austin/
An efficient algorithm for optimizing whole genome alignment with noise
Authors: Wong Prudence W. H. , Lam T. W. , Lu N. , Ting H. F. , Yiu S. M.
Published: May 2004

Motivation: This paper is concerned with algorithms for aligning two whole genomes so as to identify regions that possibly contain conserved genes. Motivated by existing heuristic-based software tools, we initiate the study of an optimization problem that attempts to uncover conserved genes with a global concern. Another interesting feature in our formulation is the tolerance of noise, which also complicates the optimization problem. A brute-force approach takes time exponential in the noise level.

Results: We show how an insight into the optimization structure can lead to a drastic improvement in the time and space requirement [precisely, to O(k2n2) and O(k2n), respectively, where n is the size of the input and k is the noise level]. The reduced space requirement allows us to implement the new algorithm, called MaxMinCluster, on a PC. It is exciting to see that when tested with different real data sets, MaxMinCluster consistently uncovers a high percentage of conserved genes that have been published by GenBank. Its performance is indeed favorably compared to MUMmer (perhaps the most popular software tool for uncovering conserved genes in a whole-genome scale).

Availability: The source code is available from the website http://www.csis.hku.hk/~colly/maxmincluster/. Detailed proof of the propositions can also be found there.
Correcting log ratios for signal saturation in cDNA microarrays
Authors: Dodd Lori E. , Korn Edward L. , McShane Lisa M. , Chandramouli G.V.R. , Chuang Eric Y.
Published: May 2004

Motivation: Pixel saturation occurs when the pixel intensity exceeds a threshold and the recorded pixel intensity is truncated. Microarray experiments are commonly afflicted with saturated pixels. As a result, estimators of gene expression are biased, with the amount of bias increasing as a function of the proportion of pixels saturated. Saturation is directly related to the photomultiplier tube (PMT) voltage settings and RNA abundance and is not necessarily associated with poor array or poor spot quality. When choosing PMT settings, higher PMT settings are desired because of improved signal-to-noise ratios of low-intensity spots. This improved signal is somewhat offset by saturation of high-intensity spots. In practice, spots with saturated pixels are discarded or the biased value is used. Neither of these approaches is appealing, particularly the former approach when a highly expressed gene is discarded because of saturation.

Results: We present a method to correct for saturation using pixel-level data. The method is based on a censored regression model. Evaluations on several arrays indicate that the method performs well. Simulation studies suggest that the method is robust under certain model violations.

Supplementary material: Supplementary tables and figures can be found at http://linus.nci.nih.gov/Data/doddl/saturation/extras.pdf
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
Authors: Majoros W. H. , Pertea M. , Salzberg S. L.
Published: May 2004

Summary: We describe two new Generalized Hidden Markov Model implementations for ab initio eukaryotic gene prediction. The C/C++ source code for both is available as open source and is highly reusable due to their modular and extensible architectures. Unlike most of the currently available gene-finders, the programs are re-trainable by the end user. They are also re-configurable and include several types of probabilistic submodels which can be independently combined, such as Maximal Dependence Decomposition trees and interpolated Markov models. Both programs have been used at TIGR for the annotation of the Aspergillus fumigatus and Toxoplasma gondii genomes.

Availability: Source code and documentation are available under the open source Artistic License from http://www.tigr.org/software/pirate.
FigSearch: a figure legend indexing and classification system
Authors: Liu Fang , Jenssen Tor-Kristian , Nygaard Vegard , Sack John , Hovig Eivind
Published: May 2004

Summary: FigSearch is a prototype text-mining and classification system for figures from any corpus of full-text biological papers. The system allows users to search for figures that contain genes of interest and illustrate protein interactions. The retrieved figures are ranked by a score representing the likelihood to be of a certain type, in this case, schematic illustrations of protein interactions and signaling events. The system contains a Web interface for search, a module for classification of figures based on vector representations of figure legends and a module for indexing gene names. In a preliminary validation, the FigSearch system showed satisfactory performance according to domain experts in providing the most relevant graphical representations. This strategy may be easily extended to other figure types. Moreover, as more full-text data become available, such a system will find increased usefulness in identifying and presenting compressed biological knowledge.

Availability: A searchable Web interface, FigSearch, is accessible via http://pubgeneserver.uio.no/figsearch/ for all figures from the available corpus.
Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication
Authors: Omont Nicolas , Képès François
Published: May 2004

Motivation: The costs of head-on versus codirectional collisions between the replication complex and the much slower transcription complex on the circular bacterial chromosomes are much debated. Although it is established that the number of genes on the leading strand is higher than on the lagging strand of replication, the consequences of collisions on the length of transcription units are unknown.

Results: Here, we show that transcription units are generally longer on the leading strand, in rough proportion to the bias in number of units between the two strands. We propose a statistical physics model, based on the assumption that the proportion of interrupted transcripts for each unit is the major factor contributing to these biases. Its main prediction is that a large replication/transcription speed ratio implies a low leading/lagging bias for transcription unit length and number. This model is validated by an analysis of proven and predicted units in Escherichia coli and Bacillus subtilis. The results are consistent with an equal cost of head-on versus codirectional collisions.
A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks
Authors: Zhou Xiaobo , Wang Xiaodong , Pal Ranadip , Ivanov Ivan , Bittner Michael , Dougherty Edward R.
Published: May 2004

Motivation: We have hypothesized that the construction of transcriptional regulatory networks using a method that optimizes connectivity would lead to regulation consistent with biological expectations. A key expectation is that the hypothetical networks should produce a few, very strong attractors, highly similar to the original observations, mimicking biological state stability and determinism. Another central expectation is that, since it is expected that the biological control is distributed and mutually reinforcing, interpretation of the observations should lead to a very small number of connection schemes.

Results: We propose a fully Bayesian approach to constructing probabilistic gene regulatory networks (PGRNs) that emphasizes network topology. The method computes the possible parent sets of each gene, the corresponding predictors and the associated probabilities based on a nonlinear perceptron model, using a reversible jump Markov chain Monte Carlo (MCMC) technique, and an MCMC method is employed to search the network configurations to find those with the highest Bayesian scores to construct the PGRN. The Bayesian method has been used to construct a PGRN based on the observed behavior of a set of genes whose expression patterns vary across a set of melanoma samples exhibiting two very different phenotypes with respect to cell motility and invasiveness. Key biological features have been faithfully reflected in the model. Its steady-state distribution contains attractors that are either identical or very similar to the states observed in the data, and many of the attractors are singletons, which mimics the biological propensity to stably occupy a given state. Most interestingly, the connectivity rules for the most optimal generated networks constituting the PGRN are remarkably similar, as would be expected for a network operating on a distributed basis, with strong interactions between the components.

Availability: The appendix is available at http://gspsnap.tamu.edu/gspweb/pgrn/bayes.html username: gspweb password: gsplab.

Supplementary Information:  http://gspsnap.tamu.edu/gspweb/pgrn/bayes.html
The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data
Authors: Mansourian Robert , Mutch David M. , Antille Nicolas , Aubert Jerome , Fogel Paul , Le Goff Jean-Marc , Moulin Julie , Petrov Anton , Rytz Andreas , Voegel Johannes J. , Roberts Matthew-Alan
Published: May 2004

Motivation: Microarray technology has become a powerful research tool in many fields of study; however, the cost of microarrays often results in the use of a low number of replicates (k). Under circumstances where k is low, it becomes difficult to perform standard statistical tests to extract the most biologically significant experimental results. Other more advanced statistical tests have been developed; however, their use and interpretation often remain difficult to implement in routine biological research. The present work outlines a method that achieves sufficient statistical power for selecting differentially expressed genes under conditions of low k, while remaining as an intuitive and computationally efficient procedure.

Results: The present study describes a Global Error Assessment (GEA) methodology to select differentially expressed genes in microarray datasets, and was developed using an in vitro experiment that compared control and interferon-γ treated skin cells. In this experiment, up to nine replicates were used to confidently estimate error, thereby enabling methods of different statistical power to be compared. Gene expression results of a similar absolute expression are binned, so as to enable a highly accurate local estimate of the mean squared error within conditions. The model then relates variability of gene expression in each bin to absolute expression levels and uses this in a test derived from the classical ANOVA. The GEA selection method is compared with both the classical and permutational ANOVA tests, and demonstrates an increased stability, robustness and confidence in gene selection. A subset of the selected genes were validated by real-time reverse transcription–polymerase chain reaction (RT–PCR). All these results suggest that GEA methodology is (i) suitable for selection of differentially expressed genes in microarray data, (ii) intuitive and computationally efficient and (iii) especially advantageous under conditions of low k.

Availability: The GEA code for R software is freely available upon request to authors.
Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura
Authors: Grad Yonatan H. , Roth Frederick P. , Halfon Marc S. , Church George M.
Published: May 2004

Motivation: To date, computational searches for cis-regulatory modules (CRMs) have relied on two methods. The first, phylogenetic footprinting, has been used to find CRMs in non-coding sequence, but does not directly link DNA sequence with spatio-temporal patterns of expression. The second, based on searches for combinations of transcription factor (TF) binding motifs, has been employed in genome-wide discovery of similarly acting enhancers, but requires prior knowledge of the set of TFs acting at the CRM and the TFs' binding motifs.

Results: We propose a method for CRM discovery that combines aspects of both approaches in an effort to overcome their individual limitations. By treating phylogenetically footprinted non-coding regions (PFRs) as proxies for CRMs, we endeavor to find PFRs near co-regulated genes that are comprised of similar short, conserved sequences. Using Markov chains as a convenient formulation to assess similarity, we develop a sampling algorithm to search a large group of PFRs for the most similar subset. When starting with a set of genes involved in Drosophila early blastoderm development and using phylogenetic comparisons of Drosophila melanogaster and D.pseudoobscura genomes, we show here that our algorithm successfully detects known CRMs. Further, we use our similarity metric, based on Markov chain discrimination, in a genome-wide search, and uncover additional known and many candidate early blastoderm CRMs.

Availability: Software is available via http://arep.med.harvard.edu/enhancers

Supplementary information: Can be accessed at http://arep.med.harvard.edu/enhancers
A neural network method for prediction of β-turn types in proteins using evolutionary information
Authors: Kaur Harpreet , Raghava G. P. S.
Published: May 2004

Motivation: The prediction of β-turns is an important element of protein secondary structure prediction. Recently, a highly accurate neural network based method Betatpred2 has been developed for predicting β-turns in proteins using position-specific scoring matrices (PSSM) generated by PSI-BLAST and secondary structure information predicted by PSIPRED. However, the major limitation of Betatpred2 is that it predicts only β-turn and non-β-turn residues and does not provide any information of different β-turn types. Thus, there is a need to predict β-turn types using an approach based on multiple sequence alignment, which will be useful in overall tertiary structure prediction.

Results: In the present work, a method has been developed for the prediction of β-turn types I, II, IV and VIII. For each turn type, two consecutive feed-forward back-propagation networks with a single hidden layer have been used where the first sequence-to-structure network has been trained on single sequences as well as on PSI-BLAST PSSM. The output from the first network along with PSIPRED predicted secondary structure has been used as input for the second-level structure-to-structure network. The networks have been trained and tested on a non-homologous dataset of 426 proteins chains by 7-fold cross-validation. It has been observed that the prediction performance for each turn type is improved significantly by using multiple sequence alignment. The performance has been further improved by using a second level structure-to-structure network and PSIPRED predicted secondary structure information. It has been observed that Type I and II β-turns have better prediction performance than Type IV and VIII β-turns. The final network yields an overall accuracy of 74.5, 93.5, 67.9 and 96.5% with MCC values of 0.29, 0.29, 0.23 and 0.02 for Type I, II, IV and VIII β-turns, respectively, and is better than random prediction.

Availability: A web server for prediction of β-turn types I, II, IV and VIII based on above approach is available at http://www.imtech.res.in/raghava/betaturns/ and http://bioinformatics.uams.edu/mirror/betaturns/ (mirror site).
Alkylating DNA damage stimulates a regulated form of necrotic cell death
Authors: Zong Wei-Xing , Ditsworth Dara , Bauer Daniel E. , Wang Zhao-Qi , Thompson Craig B.
Published: May 2004

Necrosis has been considered a passive form of cell death in which the cell dies as a result of a bioenergetic catastrophe imposed by external conditions. However, in response to alkylating DNA damage, cells undergo necrosis as a self-determined cell fate. This form of death does not require the central apoptotic mediators p53, Bax/Bak, or caspases and actively induces an inflammatory response. Necrosis in response to DNA damage requires activation of the DNA repair protein poly(ADP-ribose) polymerase (PARP), but PARP activation is not sufficient to determine cell fate. Cell death is determined by the effect of PARP-mediated β-nicotinamide adenine dinucleotide (NAD) consumption on cellular metabolism. Cells using aerobic glycolysis to support their bioenergetics undergo rapid ATP depletion and death in response to PARP activation. In contrast, cells catabolizing nonglucose substrates to maintain oxidative phosphorylation are resistant to ATP depletion and death in response to PARP activation. Because most cancer cells maintain their ATP production through aerobic glycolysis, these data may explain the molecular basis by which DNA-damaging agents can selectively induce tumor cell death independent of p53 or Bcl-2 family proteins.
A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin
Authors: Schotta Gunnar , Lachner Monika , Sarma Kavitha , Ebert Anja , Sengupta Roopsha , Reuter Gunter , Reinberg Danny , Jenuwein Thomas
Published: May 2004

Histone lysine methylation is a central modification to mark functionally distinct chromatin regions. In particular, H3-K9 trimethylation has emerged as a hallmark of pericentric heterochromatin in mammals. Here we show that H4-K20 trimethylation is also focally enriched at pericentric heterochromatin. Intriguingly, H3-K9 trimethylation by the Suv39h HMTases is required for the induction of H4-K20 trimethylation, although the H4 Lys 20 position is not an intrinsic substrate for these enzymes. By using a candidate approach, we identified Suv4-20h1 and Suv4-20h2 as two novel SET domain HMTases that localize to pericentric heterochromatin and specifically act as nucleosomal H4-K20 trimethylating enzymes. Interaction of the Suv4-20h enzymes with HP1 isoforms suggests a sequential mechanism to establish H3-K9 and H4-K20 trimethylation at pericentric heterochromatin. Heterochromatic H4-K20 trimethylation is evolutionarily conserved, and in Drosophila, the Suv4-20 homolog is a novel PEV modifier to regulate position-effect variegation. Together, our data indicate a function for H4-K20 trimethylation in gene silencing and further suggest H3-K9 and H4-K20 trimethylation as important components of a repressive pathway that can index pericentric heterochromatin.
Large-Scale Integration of Human Genetic and Physical Maps
Authors: Nievergelt Caroline M. , Smith Douglas W. , Kohlenberg J. Bradley , Schork Nicholas J.
Published: May 2004

Genetic maps are used routinely in family-based linkage studies to identify the rough location of genes that influence human traits and diseases. Unlike physical maps, genetic maps are based on the amount of recombination occurring between adjacent loci rather than the actual number of bases separating them. Genetic maps are constructed by statistically characterizing the number of crossovers observed in parental meioses leading to the transmission of alleles to their offspring. Considerations such as the number of meioses observed, the heterozygosity and physical distance between the loci studied, and the statistical methods used can impact the construction and reliability of a genetic map. As is well known, poorly constructed genetic maps can have adverse effects on linkage mapping studies. With the availability of sequence-based maps, as well as genetic maps generated by different researchers (such as those generated by the Marshfield and deCODE groups), one can investigate the compatibility and properties of different maps. We have integrated information from the most current human genome sequence data (UCSC genome assembly Human July 2003) as well as 8399 microsatellite markers used in the Marshfield and deCODE maps to reconcile the these maps. Our efforts resulted in updated sex-specific genetic maps.
Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
Authors: Chevreux Bastien , Pfisterer Thomas , Drescher Bernd , Driesel Albert J. , Müller Werner E.G. , Wetter Thomas , Suhai Sándor
Published: May 2004

We present an EST sequence assembler that specializes in reconstruction of pristine mRNA transcripts, while at the same time detecting and classifying single nucleotide polymorphisms (SNPs) occuring in different variations thereof. The assembler uses iterative multipass strategies centered on high-confidence regions within sequences and has a fallback strategy for using low-confidence regions when needed. It features special functions to assemble high numbers of highly similar sequences without prior masking, an automatic editor that edits and analyzes alignments by inspecting the underlying traces, and detection and classification of sequence properties like SNPs with a high specificity and a sensitivity down to one mutation per sequence. In addition, it includes possibilities to use incorrectly preprocessed sequences, routines to make use of additional sequencing information such as base-error probabilities, template insert sizes, strain information, etc., and functions to detect and resolve possible misassemblies. The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments.