bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence of congenital cardiovascular malformations among relatives of infants with hypoplastic left heart, coarctation of the aorta, and d‐transposition of the great arteries
Authors: Loffredo Christopher A. , Chokkalingam Anand , Sill Anne M. , Boughman Joann A. , Clark Edward B. , Scheel Janet , Brenner Joel I.
Published: January 2004

Cardiovascular malformations (CVM) are the most common birth defects and carry significant and lifelong personal and societal costs. Research into genetic and environmental risk factors is therefore critical in identifying clues to causation and prevention. The purpose of this study was to investigate patterns of familial aggregation in CVM, specifically among infants with left‐sided obstructive heart defects. We ascertained families of probands with hypoplastic left heart (HLH: N = 38), coarctation of the aorta (CoA: N = 46), and d‐transposition of the great arteries (dTGA: N = 22). First degree relatives had clinical examinations and echocardiograms; all other relatives had detailed reviews of medical records. A total of 2,694 relatives were included in the study: 379 1st degree, 986 2nd degree, and 1,329 3rd degree. Mean nuclear family size and sibship size were similar among the groups. CVM were detected more frequently in 1st degree relatives of probands with HLH (19.3%) or CoA (9.4%) than among dTGA families (2.7%). The proportions of affected 2nd degree relatives were similar across groups (≤1%). In 3rd degree relatives, CVM was detected in 1.8% of the HLH families compared to 1.2% in CoA and 0.4% in dTGA families. The predominant types of CVM among relatives of HLH and CoA probands were left‐sided obstructive lesions, in 72% (21 of 29) and 67% (25 of 37) of the affected relatives, respectively. Familial aggregation of these types of CVM is therefore confirmed in this study, potentially facilitating the search for specific genetic and other risk factors in recurrent CVM. © 2003 Wiley‐Liss, Inc.
Complex chromosome re‐arrangement 45,X,t(Y;9) in a girl with sex reversal and mental retardation
Authors: de Ravel T.J.L. , Fryns J.P. , Driessche J. Van , Vermeesch J.R.
Published: January 2004

A girl with mental retardation and multiple minor anomalies was found to have a complex chromosome 9p re‐arrangement comprising a deleted, translocated Y chromosome, a deletion of the sex reversal gene region (DMRT1) at 9p, together with an inverted duplication of the more proximal part of 9p. The karyotype was 45,X,der(Y;9)(Ypter→Yq12::9p21.1→9p22.2::9p22.2→9qter) de novo. The karyotypic male, phenotypic female had a dysgerminoma of the left dysplastic ovary. The patient had typical ‘trisomy 9p’ syndrome, and we propose that the critical region for this phenotype is located between 9p22.1 and 9p22.2. © 2003 Wiley‐Liss, Inc.
Lissencephaly with der(17)t(17;20)(p13.3;p12.2)mat
Authors: Thomas Mary Ann , Duncan Alessandra M.V. , Bardin Claudette , Kaloustian Vazken M. Der
Published: January 2004

The isolated lissencephaly sequence may be caused by point mutations of the LIS1 gene or by FISH‐detectable microdeletions of the 17p13.3 region, which carries the LIS1 gene. These have various patterns of phenotypic presentations, including the Miller–Dieker syndrome (MDS). Approximately 20% of these deletions are associated with a derivative chromosome 17 inherited from a parent who has a balanced reciprocal translocation involving chromosome 17 and another chromosome. We report a case of lissencephaly associated with a maternally inherited unbalanced translocation involving chromosome arms 17p and 20p. This results in partial monosomy of 17p13.3→pter and partial trisomy of 20p12.2→pter. To our knowledge, this is the first report of a reciprocal translocation between 17p and 20p. Our patient has a combination of findings of the MDS and trisomy 20p, along with several unique anomalies not described in either of those two conditions. This report may contribute to the delineation of a phenotype resulting from partial monosomy 17p and partial trisomy of 20p. © 2003 Wiley‐Liss, Inc.
Autosomal recessive frontotemporal pachygyria
Authors: Ramirez Dorian , Lammer Edward J. , Johnson Caroline B. , Peterson Cynthia D.
Published: January 2004

Pachygyria is a cortical malformation that results from the abnormal migration of neurons. Regions of the brain with pachygyria have an abnormally thick cortex that lacks normal folding and has deficient layering. We describe three siblings, born to nonconsanguineous Mexican parents, who have bilateral frontotemporal pachygyria without polymicrogyria. The pachygyria is accompanied by moderate mental retardation, esotropia, and either hypertelorism or telecanthus. They are otherwise morphologically normal and do not have microcephaly. Two experienced a single seizure in infancy. The characteristic phenotype present in this family suggests a new genetic syndrome that is likely inherited as an autosomal recessive trait. © 2003 Wiley‐Liss, Inc.
Subtelomeric deletion of 18p in an adult with paranoid schizophrenia and mental retardation
Authors: Babovic‐Vuksanovic Dusica , Jenkins S.C. , Ensenauer R. , Newman D.C. , Jalal S.M.
Published: January 2004

Chromosome anomalies are responsible for a significant proportion of patients with mental retardation, and congenital anomalies. Development of new molecular cytogenetic techniques has provided a powerful tool for detection of patients with subtle chromosome abnormalities. Particularly, investigation of the gene‐rich subtelomeric regions has generated interest regarding the implications and prevalence of cryptic chromosomal rearrangements. Here we describe an adult with a submicroscopic deletion of 18pter, detected by subtelomeric FISH probe. The patient is a 42‐year‐old man with a history of developmental delay, moderate mental retardation, and symptoms of paranoid schizophrenia since adolescence. His physical examination is remarkable for only a few dysmorphic findings typically seen in 18p− syndrome (round face, hypertelorism, down‐slanted palpebral fissures, temporal narrowing, small hands and feet). He lacks significant short stature, skin changes, and associated anomalies involving internal organs. All known patients with deletions of the short arm of chromosome 18 have either loss of large parts of 18p or of the entire p‐arm, or have complex chromosomal rearrangement involving other chromosomes. To our knowledge, this is the first description of a cryptic subtelomeric deletion of 18p and the first case of such a chromosomal anomaly in a patient with schizophrenia. Small subtelomeric chromosomal deletions would be missed by standard G‐banded karyotyping. Therefore, FISH analysis using subtelomeric probes should be considered for diagnostic evaluation of patients with psychiatric symptoms and mental retardation in whom the karyotype is normal. © 2003 Wiley‐Liss, Inc.
Mosaic trisomy 11p in monozygotic twins with discordant clinical phenotypes
Authors: Marcus‐Soekarman D. , Hamers G. , Velzeboer S. , Nijhuis J. , Loneus W.H. , Herbergs J. , de Die‐Smulders C. , Schrander‐Stumpel C. , Engelen J.
Published: January 2004

We report on monozygotic (MZ) twins with a de novo mos 46,XX,der(15)t(11;15)(p12;p11.2)/46,XX karyotype varying in different tissues. The clinical presentation and findings at the cytogenetic level are described. One of the infants had definite minor anomalies at birth, also found in other cases of trisomy of 11p resembling the Beckwith–Wiedemann syndrome. Theoretical backgrounds regarding the string of events leading to the cytogenetic findings in these twins and the various factors that might have contributed to the dissimilarities in phenotype between these twins are discussed. © 2003 Wiley‐Liss, Inc.
A new mutation in the skeletal ryanodine receptor gene (RYR1) is potentially causative of malignant hyperthermia, central core disease, and severe skeletal malformation
Authors: Rueffert Henrik , Olthoff Derk , Deutrich Christine , Schober Ralf , Froster Ursula G.
Published: January 2004

Malignant hyperthermia susceptibility (MHS) and central core disease (CCD) have been shown to result from missense mutations in the ryanodine receptor gene of the skeletal muscle (RYR1). A 15‐year‐old patient who had spondylocostal dysostosis (SCD) developed an MH crisis during general anesthesia. The patient was characterized phenotypically by block vertebrae, vertebral fusion, short neck and thorax, fused ribs, craniofacial abnormalities, spina bifida occulta, and a diaphragmatic defect closed surgically in early infancy. The diagnosis MH susceptible (MHS) was confirmed by the in vitro contracture test (IVCT) on a muscle biopsy. Surprisingly, the histopathological investigation revealed the presence of CCD too. Molecular genetic investigation of the RYR1 gene was performed to search for known MH‐related mutations. Cluster regions of the RYR1 gene, in which mutations have already been found, were examined by direct automated sequencing. In addition to the diagnosis MHS and CCD we were able to identify a novel RYR1 mutation in exon 46: 7358ATC > ACC, resulting in an Ile2453Thr substitution. This mutation was also present in the mother, in whom MH disposition and CCD were determined by muscle investigations. We suggest that the newly identified RYR1 mutation is closely associated with MH and CCD. A probable causative role of the RYR1 gene in SCD patients should be assessed by further genetic investigations. © 2003 Wiley‐Liss, Inc.
Onset and progression of disease in familial and sporadic Parkinson's disease
Authors: Inzelberg R. , Schecthman E. , Paleacu D. , Zach L. , Bonwitt R. , Carasso R.L. , Nisipeanu P.
Published: January 2004

Lately different and rare genetic forms of Parkinson's disease (PD) have been described. Complete genomic screening has suggested that still undefined multiple genetic factors might underlie the development of PD. The course of PD patients with and without genetic background might be different. We compared the age at onset and progression of PD with (FH) and without (NFH) family history. Two hundred forty PD patients attending the outpatient Movement Disorders Clinic were evaluated. The age of onset (AO), the duration of disease until stage III of Hoehn and Yahr (YST3), until dementia (YDEM) and family history of PD were determined by interview, examination of medical files and of affected family members. Patients with young onset who reported another PD patient among their siblings were tested for parkin mutations. Statistical analysis used ANOVA, Fisher's Least Significant Difference, log‐rank and Wilcoxon's tests for Kaplan–Meier survival curves taking stage III and dementia as end‐points. Of the 240 patients (age 73.3 ± 10.9 years), 29 (12%) had positive FH. Six of them carried parkin mutations. The AO was 33.5 ± 8.1 (range 19–42) years for parkin carriers, 59.3 ± 11.3 (range 34–76) for FH and 66.5 ± 11.8 (27–91) years for NFH (P < 0.0001). The three groups were significantly different from each other (α = 0.05). Stage III and dementia were reached only in non‐parkin patients. YST3 was 12.6 ± 6.6 years for FH and 6.5 ± 5.0 years for NFH (P < 0.0001). YDEM was 10.1 ± 6.0 years for FH versus 4.7 ± 4.5 years for NFH (P = 0.002). Kaplan–Meier survival analysis revealed faster motor (P = 0.0016) and mental decline (P = 0.02) in NFH versus FH. Our results showed that the AO of PD is younger in patients with FH. Motor and mental deterioration, however, showed a less steep course in familial PD patients. © 2003 Wiley‐Liss, Inc.
FOXC1 gene deletion is associated with eye anomalies in ring chromosome 6
Authors: Zhang Hui Z. , Li Peining , Wang Dongmei , Huff Shannon , Nimmakayalu Manjunath , Qumsiyeh Mazin , Pober Barbara R.
Published: January 2004

We report a case of ring chromosome 6 presenting with growth and mental retardation, cerebral dysgenesis, eye malformations, mixed hearing loss, and abnormal physical features. Fluorescent in situ hybridization (FISH) and microsatellite genotyping demonstrated segmental deletions of less than 6 Mb on 6p and 1–2 Mb on 6q. The primary karyotype is designated as 46,XY,r(6)(p25q27).ish r(6)(p25.1q27)(D6S344−, FOXC1−, D6S1574+, D6S281−, D6S297+). Secondary structural and numerical variants of the ring 6 were observed in 16% of the cells analyzed. Intragenic genotyping revealed deletion of the paternal FOXC1 gene, haploinsufficiency of which has been reported to cause eye anterior chamber developmental defects. Accordingly, we propose that our patient's ophthalmologic abnormalities result from haploinsufficiency of the transcription factor FOXC1. We present clinical and cytogenetic summaries on 23 reported cases of ring 6 and categorize them into mild, moderate, and severely affected groups. Further phenotype comparisons between cases with ring 6 and cases with only 6p or 6q terminal deletions suggest that genes important for hearing, vision, and central nervous system development remain to be identified in chromosome 6 terminal regions. Molecular definition of the fusion points and tissue mosaicism studies are necessary to better understand the genotype–phenotype correlation of ring 6. We recommend ophthalmology, audiology, cardiology, and central nervous system examinations be part of the routine evaluation for children with a ring chromosome 6. © 2003 Wiley‐Liss, Inc.
“Everybody in the world is my friend” hypersociability in young children with Williams syndrome
Authors: Doyle Teresa F. , Bellugi Ursula , Korenberg Julie R. , Graham John
Published: January 2004

Williams syndrome (WS) is a rare genetic disorder involving a characteristic cardiac defect, typical facial appearance, and an uneven profile of cognitive strengths and weaknesses. WS is caused by a hemizygous deletion in chromosome band 7q11.23, including the gene for elastin (ELN). Typically, individuals with WS seem driven to greet and interact with strangers. The goal of the present study was to investigate age‐related changes in the expression of hypersociability in WS. Parents of 64 children with WS, 31 children with Down syndrome (DS), and 27 normal controls (NC) provided data concerning specific aspects of their children's social behavior using the Salk Institute Sociability Questionnaire (SISQ). Children ranged in age from 1 year, 1 month to 12 years, 10 months. Consistent with earlier findings, whole group analyses showed the WS group to be significantly higher on all aspects of sociability studied. Comparisons among the groups at different ages revealed that hypersociability is evident even among very young children with WS, and, significantly, children with WS exceed children with DS with respect to Global Sociability and Approach Strangers in every age group. The findings from children who have the typical deletion for WS are contrasted with data obtained from a young child with WS who has a smaller deletion and many physical features of WS, but who does not demonstrate hypersociability, providing intriguing clues to a genetic basis of social behavior in this syndrome. These data suggest the involvement of a genetic predisposition in the expression of hypersociability in WS. © 2003 Wiley‐Liss, Inc.
Kousseff syndrome: A causally heterogeneous disorder
Authors: Maclean K. , Field M.J. , Colley A.S. , Mowat D.R. , Sparrow D.B. , Dunwoodie S.L. , Kirk E.P.E.
Published: January 2004

The existence of Kousseff syndrome as a distinct entity has been thrown into doubt by a recent study conducted on the family originally reported by Kousseff. In all cases where chromosome 22q11.2 FISH testing has been undertaken, including the original sibship, a chromosome 22q11.2‐microdeletion has been identified. We report two cases of sacral myelomeningocele associated with a conotruncal cardiac anomaly or “Kousseff syndrome.” The first case, a 4‐year‐old girl, had a sacral myelomeningocele, tetralogy of Fallot, microcephaly, hydrocephalus, hypoplasia of the corpus callosum and mild–moderate developmental delay. Chromosome 22q11.2 FISH was normal and the facial phenotype was not that of velocardiofacial syndrome. Sequencing of the entire coding region of CITED2 did not reveal a mutation. The second case, a male infant, was found to have a 22q11.2‐microdeletion. These cases confirm Kousseff syndrome to be a causally heterogeneous disorder. © 2003 Wiley‐Liss, Inc.
Independent de novo 22q11.2 deletions in first cousins with DiGeorge/velocardiofacial syndrome
Authors: Saitta Sulagna C. , Harris Stacy E. , McDonald‐McGinn Donna M. , Emanuel Beverly S. , Tonnesen Melissa K. , Zackai Elaine H. , Seitz Suzanne C. , Driscoll Deborah A.
Published: January 2004

Deletions of chromosome 22q11.2 are found in the vast majority of patients with DiGeorge/velocardiofacial syndrome (DGS/VCFS). This most frequent microdeletion syndrome is estimated to occur in 1 in 4,000 live births. The majority of deletions are de novo, with 10% or less inherited from an affected parent. Here, we report two separate families with recurrence of a 22q11.2 deletion in first cousins. In each family, unaffected siblings (brother and sister) had an affected child. Fluorescence in situ hybridization (FISH) studies of the parents of each affected child were normal and hence, relatives were not considered at an increased risk for recurrence in another pregnancy. We used highly polymorphic microsatellite repeat markers from within 22q11.2 to determine the parental origin of each cousin's deletion and to assess whether parental germline mosaicism for the 22q11.2 deletion might be a factor in these cases. This analysis confirmed that in each case, the deletion occurred on a chromosome 22 derived from unrelated parents, consistent with independent de novo deletion events. Thus, we concluded that germline mosaicism as the underlying mechanism for affected cousins in these families was unlikely. Our findings underscore the high frequency with which the 22q11.2 deletion occurs in the general population and demonstrate the important role that PCR‐based parental origin determination can have in recurrence risk counselling. Furthermore, relatives of affected individuals may benefit from genetic counselling and consider prenatal testing for the 22q11.2 deletion in future pregnancies, despite a low recurrence risk. © 2003 Wiley‐Liss, Inc.
Mosaic paternal uniparental (iso)disomy for chromosome 20 associated with multiple anomalies
Authors: Venditti Charles P. , Hunt Piper , Donnenfeld Alan , Zackai Elaine , Spinner Nancy B.
Published: January 2004

Uniparental disomy for a number of human chromosomes is associated with clinical abnormalities. We report a child with a complex chromosomal rearrangement involving chromosome 20 (45,XY,psu dic (20;20)(p13;p13)) and paternal uniparental isodisomy for chromosome 20 in peripheral blood and bone marrow. This patient had multiple congenital abnormalities including microtia/anotia, micrencephaly, congenital heart disease, neuronal subependymal heterotopias, and colonic agangliosis. Molecular studies on DNA from peripheral blood demonstrated paternal uniparental inheritance of chromosome 20. However, fibroblasts demonstrated a mosaic karyotype, with one cell line having 45 chromosomes, including the pseudodicentric chromosome 20 (75% of cells), and a second cell line having 46 chromosomes, including the pseudodicentric chromosome 20, and a normal chromosome 20 (trisomy 20) (25% of cells). FISH experiments using a sub‐telomeric probe that maps ∼120 kb from the 20p telomere, showed that both copies of these sequences were present on the rearranged chromosome, consistent with deletion of a very small interval. This leads us to suggest that in addition to trisomy 20 mosaicism, paternal uniparental disomy for chromosome 20 could contribute to his clinical phenotype. © 2003 Wiley‐Liss, Inc.
Insights into the relation between mrna and protein expression patterns: ii. Experimental observations in Escherichia coli1
Authors: Lee Pat S. , Shaw Leah B. , Choe Leila H. , Mehra Amit , Hatzimanikatis Vassily , Lee Kelvin H.
Published: January 2004

There is a need for improved appreciation of the importance of genome‐wide mRNA and protein expression measurements and their role in understanding translation and in relation to genome‐wide mathematical frameworks for gene expression regulation. We investigated the use of a high‐density microarray technique for mRNA expression analysis and a two‐dimensional protein electrophoresis–tandem mass spectrometry method for protein analysis to monitor changes in gene expression. We applied these analytical tools in the context of an environmental perturbation of Escherichia coli cells—the addition of varying amounts of IPTG. We also tested the application of these tools to the study of a genetic perturbation of Escherichia coli cells—the ability of certain strains to hypersecrete the hemolysin protein. We observed a lack of correspondence between mRNA and protein expression profiles. Although our data do not include measurements on all expressed genes (because the ability to measure protein expression profiles is limiting), we observed that the qualitative and quantitative behavior of the measurements of a subset of expressed genes is similar to the behavior of the entire system. The change in observed average mRNA and protein amplification factors for 77 and 52 genes coincided with the observed change in mRNA amplification factor for the entire system. Furthermore, we found that the use of relative changes in expression could be used to elucidate mechanisms of gene expression regulation for the system studied, even when measurements were made on a small subset of the system. © 2003 Wiley Periodicals, Inc.
The complexity of complexes in signal transduction
Authors: Hlavacek William S. , Faeder James R. , Blinov Michael L. , Perelson Alan S. , Goldstein Byron
Published: January 2004

Many activities of cells are controlled by cell‐surface receptors, which in response to ligands, trigger intracellular signaling reactions that elicit cellular responses. A hallmark of these signaling reactions is the reversible nucleation of multicomponent complexes, which typically begin to assemble when ligand‐receptor binding allows an enzyme, often a kinase, to create docking sites for signaling molecules through chemical modifications, such as tyrosine phosphorylation. One function of such docking sites is the co‐localization of enzymes with their substrates, which can enhance both enzyme activity and specificity. The directed assembly of complexes can also influence the sensitivity of cellular responses to ligand‐receptor binding kinetics and determine whether a cellular response is up‐ or downregulated in response to a ligand stimulus. The full functional implications of ligand‐stimulated complex formation are difficult to discern intuitively. Complex formation is governed by conditional interactions among multivalent signaling molecules and influenced by quantitative properties of both the components in a system and the system itself. Even a simple list of the complexes that can potentially form in response to a ligand stimulus is problematic because of the number of ways signaling molecules can be modified and combined. Here, we review the role of multicomponent complexes in signal transduction and advocate the use of mathematical models that incorporate detail at the level of molecular domains to study this important aspect of cellular signaling. © 2003 Wiley Periodicals, Inc.
Prediction of transcriptional profiles of Synechocystis PCC6803 by dynamic autoregressive modeling of DNA microarray data
Authors: Schmitt William A. , Stephanopoulos Gregory
Published: January 2004

Time‐series profiles of gene expression generated by DNA microarrays possess sufficient information for building dynamic models of transcriptional behavior. This, however, requires properly designed experiments and sufficient independent data to validate such models. Here we report the use of AutoRegressive with eXogenous input (ARX) models to fit dynamic gene expression data obtained by subjecting cultures of the photosynthetic bacterium Synechocystis PCC6803 to consecutive light‐to‐dark transitions. Autoregressive with exogenous input models of appropriate complexity were selected by applying Akaike's information criterion (AIC) such as to maximize agreement between model predictions with experimental data without overfitting. These models were subsequently used to design the experimental profile of an optimal validating data set. Predictions from these models were tested in a second experiment and were found to match well with the validation data. Additionally, the models with the least error in predicting the expression profiles of the validation data set exactly match the model complexity predicted by AIC. Such models offer insights into cellular responses to environmental conditions and form the basis for hypothesizing and quantifying relationships that are presently poorly understood at the level of fundamental mechanisms. © 2003 Wiley Periodicals, Inc.
Theoretical and computational studies of the glucose signaling pathways in yeast using global gene expression data
Authors: Lin Xiaoxia , Floudas Christodoulos A. , Wang Ying , Broach James R.
Published: January 2004

We have combined DNA microarray experiments with novel computational methods as a means of defining the topology of a biological signal transduction pathway. By DNA microarray techniques, we previously acquired data on expression over time of all genes in the yeast Saccharomyces following addition of glucose to wild‐type cells and to cells mutated in one or more components of the Ras signaling network. In addition, we examined the time course of expression following activation of components of the Ras signaling network in the absence of glucose addition. In this current study, we have applied a novel theoretical and computational framework to these data to identify the network topology of the glucose signaling pathway in yeast and the role of Ras components in that network. The computational approach involves clustering genes by expression pattern, postulating a signaling network topology superstructure that includes all possible component interconnections and then evaluating the feasibility of the superstructure interconnections by optimization methods using Mixed Integer Linear Programming techniques. This approach is the first rigorous mathematical framework for addressing the biological network topology issue, and the novel formulation features the introduction of discrete variables for the connectivity and logical expressions that connect the experimental observations to the network structure. This analysis yields a topology for the glucose signaling pathway that is consistent with, and an extension of, known biological interactions in glucose signaling. © 2003 Wiley Periodicals, Inc.
A perspective of metabolic engineering strategies: moving up the systems hierarchy
Authors: Bulter Thomas , Bernstein Jeffrey R. , Liao James C.
Published: January 2004

Metabolic engineering has been established as an important field in biotechnology. It involves the analysis, design, and alteration of the stoichiometric network using sophisticated mathematical and molecular biology techniques. It allows for improvement of pathway kinetics by removing flux bottlenecks, balancing precursors, and recycling cofactors used to increase product formation. The next step in the systems hierarchy is the constructive manipulation of regulatory networks. As our understanding of regulation continues to expand rapidly, engineering of intracellular regulation will become an integral aspect of metabolic engineering. © 2003 Wiley Periodicals, Inc.
Environmental conditions and transcriptional regulation in Escherichia coli: a physiological integrative approach
Authors: Martínez‐Antonio Agustino , Salgado Heladia , Gama‐Castro Socorro , Gutiérrez‐Ríos Rosa María , Jiménez‐Jacinto Verónica , Collado‐Vides Julio
Published: January 2004

Bacteria develop a number of devices for sensing, responding, and adapting to different environmental conditions. Understanding within a genomic perspective how the transcriptional machinery of bacteria is modulated, as a response for changing conditions, is a major challenge for biologists. Knowledge of which genes are turned on or turned off under specific conditions is essential for our understanding of cell behavior. In this study we describe how the information pertaining to gene expression and associated growth conditions (even with very little knowledge of the associated regulatory mechanisms) is gathered from the literature and incorporated into RegulonDB, a database on transcriptional regulation and operon organization in E. coli. The link between growth conditions, signal transduction, and transcriptional regulation is modeled in the database in a simple format that highlights biological relevant information. As far as we know, there is no other database that explicitly clarifies the effect of environmental conditions on gene transcription. We discuss how this knowledge constitutes a benchmark that will impact future research aimed at integration of regulatory responses in the cell; for instance, analysis of microarrays, predicting culture behavior in biotechnological processes, and comprehension of dynamics of regulatory networks. This integrated knowledge will contribute to the future goal of modeling the behavior of E. coli as an entire cell. The RegulonDB database can be accessed on the web at the URL: http://www.cifn.unam.mx/Computational_Biology/regulondb/. © 2003 Wiley Periodicals, Inc.
Maintaining data integrity in microarray data management
Authors: Grant G. R. , Manduchi E. , Pizarro A. , Stoeckert C. J.
Published: January 2004

Gene expression microarrays are a relatively new technology, dating back just a few years, yet they have already become a very widely used tool in biology, and have evolved to a wide range of applications well beyond their original design intent. However, while the use of microarrays has expanded, and the issues of performance optimization have been intensively studied, the fundamental issue of data integrity management has largely been ignored. Now that performance has improved so greatly, the shortcomings of data integrity control methods constitute a greater percent of the stumbling blocks for investigators. Microarray data are cumbersome, and the rule up to this point has mostly been one of hands‐on transformations, leading to human errors which often have dramatic consequences. We show in this review that the time lost on such mistakes is enormous and dramatically affects results; therefore, mistakes should be mitigated in any way possible. We outline the scope of the data integrity issue, to survey some of the most common and dangerous data transformations, and their shortcomings. To illustrate, we review some case studies. We then look at the work done by the research community on this issue (which admittedly is meager up to this point). Some data integrity issues are always going to be difficult, while others will become easier—one of our goals is to expedite the use of integrity control methods. Finally, we present some preliminary guidelines and some specific approaches that we believe should be the focus of future research. © 2003 Wiley Periodicals, Inc.
Escherichia coli—a model system that benefits from and contributes to the evolution of proteomics
Authors: Lee Pat S. , Lee Kelvin H.
Published: January 2004

The large body of knowledge about Escherichia coli makes it a useful model organism for the expression of heterologous proteins. Proteomic studies have helped to elucidate the complex cellular responses of E. coli and facilitated its use in a variety of biotechnology applications. Knowledge of basic cellular processes provides the means for better control of heterologous protein expression. Beyond such important applications, E. coli is an ideal organism for testing new analytical technologies because of the extensive knowledge base available about the organism. For example, improved technology for characterization of unknown proteins using mass spectrometry has made two‐dimensional electrophoresis (2DE) studies more useful and more rewarding, and much of the initial testing of novel protocols is based on well‐studied samples derived from E. coli. These techniques have facilitated the construction of more accurate 2DE maps. In this review, we present work that led to the 2DE databases, including a new map based on tandem time‐of‐flight (TOF) mass spectrometry (MS); describe cellular responses relevant to biotechnology applications; and discuss some emerging proteomic techniques. © 2003 Wiley Periodicals, Inc.
Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?
Authors: Covert Markus W. , Famili Iman , Palsson Bernhard O.
Published: January 2004

Cells must abide by a number of constraints. The environmental constrains of cellular behavior and physicochemical limitations affect cellular processes. To regulate and adapt their functions, cells impose constraints on themselves. Enumerating, understanding, and applying these constraints leads to a constraints‐based modeling formalism that has been helpful in converting conceptual models to computational models in biology. The continued success of the constraints‐based approach depends upon identification and incorporation of new constraints to more accurately define cellular capabilities. This review considers constraints in terms of environmental, physicochemical, and self‐imposed regulatory and evolutionary constraints with the purpose of refining current constraints‐based models of cell phenotype. © 2003 Wiley Periodicals, Inc.
Exploiting evolutionary relationships for predicting protein structures
Authors: Tramontano Anna , Morea Veronica
Published: January 2004

In the last few years there have been many developments in computational biology, particularly with regard to novel, imaginative exploitation of genomic data. Disappointingly, there has been a lack of progress in the methodology for prediction of protein structures. In the last several years, however, promising new methods have finally begun to emerge. These methods are increasing the power and scope of the methodology, but, most importantly, they are generating new areas of investigation that we believe will accelerate progress in the field. In this review we describe recent developments and highlight the implications of their success as well as areas where efforts should be focused. © 2003 Wiley Periodicals, Inc.
Transcriptional analysis of product‐concentration driven changes in cellular programs of recombinant Clostridium acetobutylicumstrains
Authors: Tummala Seshu B. , Junne Stefan G. , Paredes Carlos J. , Papoutsakis Eleftherios T.
Published: January 2004

Antisense RNA (asRNA) downregulation alters protein expression without changing the regulation of gene expression. Downregulation of primary metabolic enzymes possibly combined with overexpression of other metabolic enzymes may result in profound changes in product formation, and this may alter the large‐scale transcriptional program of the cells. DNA‐array based large‐scale transcriptional analysis has the potential to elucidate factors that control cellular fluxes even in the absence of proteome data. These themes are explored in the study of large‐scale transcriptional analysis programs and the in vivo primary‐metabolism fluxes of several related recombinant C. acetobutylicum strains: C. acetobutylicum ATCC 824(pSOS95del) (plasmid control; produces high levels of butanol snd acetone), 824(pCTFB1AS) (expresses antisense RNA against CoA transferase (ctfb1‐asRNA); produces very low levels of butanol and acetone), and 824(pAADB1) (expresses ctfb1‐asRNA and the alcohol‐aldehyde dahydrogenase gene (aad); produce high alcohol and low acetone levels). DNA‐array based transcriptional analysis revealed that the large changes in product concentrations (snd notably butanol concentration) due to ctfb1‐asRNA expression alone and in combination with aad overexpression resulted in dramatic changes of the cellular transcriptome. Cluster analysis and gene expression patterns of established and putative operons involved in stress response, motility, sporulation, and fatty‐acid biosynthesis indicate that these simple genetic changes dramatically alter the cellular programs of C. acetobutylicum. Comparison of gene expression and flux analysis data may point to possible flux‐controling steps and suggest unknown regulatory mechanisms. © 2003; Wiley Periodicals, Inc.
Dynamical and integrative cell signaling: challenges for the new biology
Authors: Levchenko Andre
Published: January 2004

Years of careful experimental analysis have revealed that signaling molecules are organized into complex networks of biochemical reactions exquisitely regulated in time and space to provide a cell with high‐fidelity information about an extremely noisy and volatile environment. A new view of signaling networks as systems consisting of multiple complex elements interacting in a multifarious fashion is emerging, a view that conflicts with the single‐gene or protein‐centric approach common in biological research. The postgenomic era has brought about a different, network‐centric methodology of analysis, suddenly forcing researchers toward the opposite extreme of complexity, where the networks being explored are, to a certain extent, intractable and uninterpretable. Both the cartoons of simple pathways and the very large “hair‐ball” diagrams of large intracellular networks are also representations of static worlds, superficially devoid of dynamics and chemistry. These representations are often viewed as being analogous to stably linked computer and neural networks rather than dynamically changing networks of chemical interactions, where the notions of concentration, compartmentalization, and diffusion may be the primary determinants of connectivity. Arguably, the systems biology approach, relying on computational modeling coupled with various experimental techniques and methodologies, will be an essential component of analysis of the behavior of signal transduction pathways. Combining the dynamical view of rapidly evolving responses and the structural view arising from high‐throughput analyses of the interacting species will be the best approach toward efforts toward greater understanding of intracellular signaling processes. © 2003 Wiley Periodicals, Inc.
Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock
Authors: Pharkya Priti , Burgard Anthony P. , Maranas Costas D.
Published: January 2004

In this study, we modify and extend the bilevel optimization framework OptKnock for identifying gene knockout strategies in the Escherichia coli metabolic network, leading to the overproduction of representative amino acids and key precursors for all five families. These strategies span not only the central metabolic network genes but also the amino acid biosynthetic and degradation pathways. In addition to gene deletions, the transport rates of carbon dioxide, ammonia, and oxygen, as well as the secretion pathways for key metabolites, are introduced as optimization variables in the framework. Computational results demonstrate the importance of manipulating energy‐producing/consuming pathways, controlling the uptake of nitrogen and oxygen, and blocking the secretion pathways of key competing metabolites. The identified pathway modifications include not only straightforward elimination of competing reactions but also a number of nonintuitive knockouts quite distant from the amino acid‐producing pathways. Specifically, OptKnock suggests three reactions (i.e., pyruvate kinase, phosphotransacetylase, and ATPase) for deletion, in addition to the straightforward elimination of 2‐ketoglutarate dehydrogenase, to generate a glutamate‐overproducing mutant. Similarly, phosphofructokinase and ATPase are identified as promising knockout targets to complement the removal of pyruvate formate lyase and pyruvate dehydrogenase for enhancing the yield of alanine. Although OptKnock in its present form does not consider regulatory constraints, it does provide useful suggestions largely in agreement with existing practices and, more importantly, introduces a framework for incorporating additional modeling refinements as they become available. © 2003 Wiley Periodicals, Inc.
The quest for the mechanisms of life
Authors: Klapa Maria I. , Quackenbush John
Published: January 2004

The genomic revolution, manifested by the sequencing of the complete genome of many organisms, along with technological advances, such as DNA microarrays and developments in high‐throughput analysis of proteins, metabolites, and isotopic tracer distribution patterns, challenged the conventional ways in which questions are approached in the biological sciences: (a) rather than examining a small number of genes and/or reactions at any one time;, we can now analyze gene expression and protein activity in the context of systems of interacting genes and gene products; (b) comprehensive analysis of biological systems requires the integration of all cellular fingerprints: genome sequence, maps of gene expression, protein expression, metabolic output, and in vivo enzymatic activity; and (c) collecting, managing, and analyzing comparable data from various cellular profiles requires expertise from several fields that transcend traditional discipline boundaries. While researchers in systems biology have still to address difficult challenges in both experimental and computational arenas, they possess, for the first time, the opportunity to unravel the mechanisms of life. The enormous impact of these discoveries in diverse areas, such as metabolic engineering, strain selection, drug screening and development, bioprocess development, disease prognosis and diagnosis, gene and other medical therapies, is an obvious motivation for pursuing integrated analyses of cellular systems. © 2003 Wiley Periodicals, Inc.
Insights into the relation between mRNA and protein expression patterns: I. theoretical considerations
Authors: Mehra Amit , Lee Kelvin H. , Hatzimanikatis Vassily
Published: January 2004

Translation is a central cellular process in every organism and understanding translation from the systems (genome‐wide) perspective is very important for medical and biochemical engineering applications. Moreover, recent advances in cell‐wide monitoring tools for both mRNA and protein levels have necessitated the development of such a model to identify parameters and conditions that influence the mapping between mRNA and protein expression. Experimental studies show a lack of correspondence between mRNA and protein expression profiles. In this study, we describe a mechanistic genome‐wide model for translation that provides mapping between changes in mRNA levels and changes in protein levels. We use our model to study the system in detail and identify the key parameters that affect this mapping. Our results show that the correlation between mRNA and protein levels is a function of both the kinetic parameters and concentration of ribosomes at the reference state. In particular, changes in concentration of free and total ribosomes in response to a perturbation; changes in initiation and elongation kinetics due to competition for aminoacyl tRNAs; changes in termination kinetics; average changes in mRNA levels in response to the perturbation; and changes in protein stability are all important determinants of the mapping between mRNA and protein expression. © 2003 Wiley Periodicals, Inc.
Metabolic database systems for the analysis of genome‐wide function
Authors: Tsoka Sophia , Ouzounis Christos A.
Published: January 2004

Genome sequencing projects provide an inventory of molecular components for a wide variety of organisms. Metabolic databases integrate these functional descriptions of individual modules into a higher‐level characterization of cellular metabolism. This article reviews efforts related to the development of metabolic databases and discusses how such systems have aided the delineation of genome properties. We illustrate the design features of metabolic databases and discuss the challenges facing metabolic as well as databases of other functional type. © 2003; Wiley Periodicals, Inc.
Surgical site infection after groin hernia repair
Authors: Taylor E W , Duffy K , Lee K , Hill R , Noone A , Macintyre I , King P M , O'Dwyer P J
Published: January 2004

Background

Post-discharge surveillance for 30 days is needed to determine the true incidence of surgical site infection (SSI). This study was undertaken to determine the incidence of, and risk factors for, SSI after hernia repair.

Methods

A total of 3150 patients who had undergone groin hernia repair in 32 Scottish hospitals were telephoned 10, 20 and 30 days after operation to screen for SSI. Patients who believed the wound to be infected were seen by a healthcare worker to confirm the diagnosis. Details of operations and risk factors were obtained by case-note review.

Results

One hundred and four patients (3·3 per cent) declined to give a contact telephone number, leaving 3046 patients who agreed to take part in the study. Some 108 patients (3·4 per cent) could not be contacted at any point, giving a response rate of 93·3 per cent. Complete data were available for 2665 patients (87·5 per cent); 140 (5·3 per cent) developed SSI and 57 (2·1 per cent) thought the wound infected but this was not confirmed by the healthcare worker. Patients given a prophylactic antibiotic had a lower incidence of SSI (P = 0·002), but neither increase in the American Society of Anesthesiologists grade of fitness for operation nor prolonged duration of operation was a significant risk factor for infection.

Conclusion

SSI after hernia repair is common and large clinical trials are required to determine whether the use of prophylactic antibiotics reduces the incidence of infection.
An intraductal papillary component is associated with prolonged survival after hepatic resection for intrahepatic cholangiocarcinoma
Authors: Tajima Y , Kuroki T , Fukuda K , Tsuneoka N , Furui J , Kanematsu T
Published: January 2004

Background

The outcome after surgery for intrahepatic cholangiocarcinoma (ICC) is dismal and data on long-term survival are not available. This study evaluated prognostic indicators and characteristic features of long-term survivors after hepatic resection for ICC.

Methods

Thirty-one patients who had undergone hepatic resection for ICC were studied. Univariate and multivariate survival analyses of clinicopathological data included an intraductal papillary carcinoma component (IDPCC) in the tumour, which was defined as the histological demonstration of cancer cells growing in a papillary fashion into the lumen of the large bile duct.

Results

The overall cumulative survival rate after hepatic resection for ICC was 51·2 per cent at 1 year and 24·5 per cent at 5 years, with a mean(s.d.) survival time of 11(4) months. The presence of IDPCC (P = 0·003), curative resection (P = 0·009) and the absence of perineural invasion (P = 0·040) were identified as favourable independent prognostic factors in multivariate analysis. Eight patients with IDPCC had a 5-year survival rate of 87·5 per cent and a mean(s.d.) survival time of 69(13) months. All seven patients who survived for more than 5 years after surgery had IDPCC, regardless of the gross appearance of the tumour.

Conclusion

An IDPCC in the tumour resulted in long-term survival after hepatic resection for ICC.