bluuebunny/crossref_metadata_2025 huggingface dataset:
Syngap1 regulates the synaptic drive and membrane excitability of Parvalbumin-positive interneurons in mouse auditory cortex
Authors: Francavilla Ruggiero , Chattopadhyaya Bidisha , Damo Kamda Jorelle Linda , Jadhav Vidya , Kourrich Saïd , Michaud Jacques L. , Cristo Graziella Di
Published: May 2024

SYNGAP1 haploinsufficiency-related intellectual disability (SYNGAP1-ID) is characterized by moderate to severe ID, generalized epilepsy, autism spectrum disorder, sensory processing dysfunction and other behavioral abnormalities. While most studies, so far, have focussed on the role of Syngap1 in cortical excitatory neurons, recent studies suggest that Syngap1 plays a role in GABAergic inhibitory neuron development as well. However, the molecular pathways by which Syngap1 acts on GABAergic neurons, and whether they are similar or different from the mechanisms underlying its effects in excitatory neurons, is unknown. Here we examined whether, and how, embryonic-onset
Syngap1
haploinsufficiency restricted to GABAergic interneurons derived from the medial ganglionic eminence (MGE) impacts their synaptic and intrinsic properties in adulthood. We found that
Syngap1
haploinsufficiency affects the intrinsic properties, overall leading to increased firing threshold, and decreased excitatory synaptic drive of Parvalbumin (PV)+ neurons from Layer IV auditory cortex in adult mice, whilst Somatostatin (SST)+ interneurons were mostly resistant to
Syngap1
haploinsufficiency. Further, the AMPA component of thalamocortical evoked-EPSC was decreased in PV+ cells from mutant mice. Finally, we found that targeting the Kv1 family of voltage-gated potassium channels was sufficient to rescue PV+ mutant cell-intrinsic properties to wild-type levels. Together, these data suggest that
Syngap1
plays a specific role in the maturation of PV+ cell intrinsic properties and synaptic drive, and its haploinsufficiency may lead to reduced PV cell recruitment in the adult auditory cortex, which could thus underlie the auditory processing alterations found in SYNGAP1-ID preclinical models and patients.
A direct experimental test of Ohno’s hypothesis
Authors: Mihajlovic Ljiljana , Iyengar Bharat Ravi , Baier Florian , Barbier Içvara , Iwaszkiewicz Justyna , Zoete Vincent , Wagner Andreas , Schaerli Yolanda
Published: May 2024

Gene duplication drives evolution by providing raw material for proteins with novel functions. The oldest and historically most influential hypothesis about the evolutionary fate and potential of duplicated genes has been proposed by Susumu Ohno in 1970. This hypothesis essentially posits that gene duplication can help genes tolerate new mutations and thus facilitates the evolution of new phenotypes. Competing hypotheses argue that deleterious mutations will usually inactivate gene duplicates too rapidly for Ohno’s hypothesis to work. Here, we provide a first direct experimental test of Ohno’s hypothesis. Specifically, we evolved one or exactly two copies of a gene encoding a fluorescent protein in
Escherichia coli
through multiple rounds of mutagenesis and selection. We then analyzed the genotypic and phenotypic evolutionary dynamics of the evolving populations through high-throughput DNA sequencing, biochemical assays, and engineering of selected variants. In support of Ohno’s hypothesis, populations carrying two gene copies displayed higher mutational robustness than those carrying a single gene copy. As a consequence, the double-copy populations experienced relaxed purifying selection, evolved higher phenotypic and genetic diversity, carried more mutations and accumulated combinations of key beneficial mutations earlier. However, their phenotypic evolution was not accelerated, possibly because one gene copy rapidly became inactivated by deleterious mutations. Our work provides an experimental platform to test models of evolution by gene duplication, and it supports alternatives to Ohno’s hypothesis that point to the importance of gene dosage.
Evaluation of Clinical Performance and Colour Match of Single and Multiple Shade Composites in Class-I Restorations: A Randomised Clinical Study
Authors: Porwal Priya , Shah Nimisha Chinmay , Batra Renu , Kotecha Niral , Jain Aishwarya
Published: May 2024

Introduction: Biomimetic dentistry primarily focuses on achieving aesthetics that closely resemble natural enamel and dentin. This approach ensures that dental restorations seamlessly match the appearance of enamel and dentin, rendering them virtually invisible. Additionally, biomimetic dentistry aims to mimic not only the visual characteristics but also the physical properties of enamel and dentin, thereby ensuring functional acceptability. The introduction of new composite materials in the market is a gradual progression aimed at attaining the mentioned objectives. Aim: To compare clinical performance and colour matching of single and multiple shade composites in simple Class-I carious lesions after one year. Materials and Methods: This randomised clinical study included 21 patients with a total of 72 Class-I carious lesions with patients who provided informed consent. Teeth were randomised into two groups: Group-A (n=36) received multishade composite (3M Filtek z350), and Group-B (n=36) received single-shade composite (Omnichroma). Clinical performance was assessed by two blinded evaluators at baseline, six months, and one year using modified United States Public Health Service (USPHS) criteria. Colour matching was evaluated by capturing digital photographs with a DSLR camera, ring flash, and 100 mm macro lens. Colour measurements (L*, a*, b*) were analysed using Adobe Photoshop, and ΔE was calculated immediately after restoration. Statistical analysis was performed using Statistical Package for Social Sciences (SPSS) 21.0 software, employing Chi-square test, Friedman test, and independent t-test. Results: No significant difference was found in clinical outcomes after one year using modified USPHS criteria (p>0.05). However, both Group-A (p=0.002) and Group-B (p=0.007) showed increased marginal discolouration, and decreased colour match (p<0.001) from baseline to one year. There was no statistically significant difference in colour matching potential between the two groups (p=0.056). Conclusion: Single-shade composites effectively treat Class-I carious lesions, demonstrating satisfactory colour matching and clinical performance.
Effective Surgical Management of Femoralhead Affections in Dogs: Review of Ten Cases
Authors: Reddy Puli Vishnu Vardhan , Raj Pushkin , Shafiuzama Mohammed , Simon Shiju , R. Sindhu , S. Saran
Published: May 2024

Ten dogs suffering from various conditions affecting the coxofemoral joint, including hip dysplasia, hip luxation, and femoral capital fractures, were included in the study. Nine of these dogs underwent treatment with femoral head osteotomy, while one case of hip luxation was treated using a toggle technique. All procedures involved a cranio-lateral incision approach and osteotomy performed with an oscillating saw. Following physiotherapy and passive range of motion exercises, all the dogs exhibited pain-free ambulation. The simple Femoral Head Ostectomy surgery effectively manages various femoral head affections, alleviating pain and leading to a significant improvement in the quality of life.
A Study of the Effectiveness of Teachers Training in Sindh Province
Authors: Ali Rubina Usman , Afzal Asma , Fahd Madiha
Published: May 2024

This research study take a look into a study of the effectiveness of teachers training program for private secondary schools in Sindh. Technology integration is far behind in Pakistani Schools as a consequence of ICT deficiency, absence of in-service teachers training. ICT has tremendous potential to prepare students for the workplaces globally and improve educational systems, if it’s integrated wisely into a curriculum. ICT Teacher Training is being sorted out at distinctive levels for the educators to outfit them with essential most recent information and abilities to make them great ICT educators by the Government of Pakistan and Education Department; in this study the relationships between in service ICT teachers training and changes in teaching behavior will be investigated.  This research take a look into a study of the effectiveness of ICT teachers training program for private secondary schools in Sindh to promote Ubiquitous learning among students. The study's main goals were to investigate the impact of in-service teachers' ICT training on subject teachers' teaching methodology based on Ubiquitous Learning. Apricot Education System conducted this study in private schools in Karachi, and 150 teachers were chosen as a target sample using purposive random sampling following three months of teacher training. The investigation was descriptive in nature. A questionnaire with 60 items based on a 5 Likert scale was used to collect data using the survey method. The data was analyzed using the correlation, regression, and reliability tests. The results of the regression test revealed that teacher training had a substantial impact on subject teachers' teaching style based on Ubiquitous Learning. The t- value is 5.079.The data was analyzed using the correlation, regression, and reliability tests. The results of the regression test revealed that teacher training had a substantial impact on subject teachers' teaching style based on Ubiquitous Learning. The t-value is 5.079, and the p-value is.000 less than 0.05. That equals.000. It indicates that H1 is acceptable. Finding administrators should perform maximal ICT Teachers Training to improve teacher competencies, according to the recommendation.
Assessing the Impact of Coated and Prilled Urea Fertilizers on Nitrogen Dynamics and Fodder Maize Yield in Alfisols
Authors: Channavar Vijayakumari Raveendra , K R Ashoka , Fathima P. S. , Sanathkumar V B , T Bhagyalakshmi , S B Yogananda , K N Jakir Hussain , B R Jagadeesh
Published: May 2024

The study investigates the impact of different urea fertilizers on nitrogen mineralization, leaching losses, and growth, yield of fodder maize in Alfisols. Nitrogen is vital for plant growth but deficient in soils. Urea, a widespread nitrogen fertilizer, suffers from significant losses, prompting the development of controlled-release urea (CRU) fertilizers. This study assesses various urea formulations with coated urea and prilled urea. Laboratory incubation studies show that coated urea exhibits slower NH4+-N release, reducing losses and improving efficiency compared to uncoated urea. Nitrate content increases steadily periodically with coated urea, potentially enhancing nitrogen availability to plants. Greenhouse experiments reveal significant differences in plant height, leaf number, and leaf area among treatments. Coated urea formulations, chiefly CSPC @3%, demonstrate superior growth parameters (plant height-169.56cm, number of leaves-10.33 and leaf area-1850.59), yield (green fodder-328.25 gplant-1, dry fodder-198.61 gplant-1 and dry matter percentage-54.52) and quality parameters (crude protein-4.03, total ash content-3.82%) compared to prilled urea growth parameters (plant height-113.38cm, number of leaves-8.07 and leaf area-1670.98), yield (green fodder-246.26 gplant-1, dry fodder-116.35 gplant-1 and dry matter percentage-44.32) and quality parameters (crude protein-2.88, total ash content-2.75%), likely due to sustained nitrogen release. Higher nitrogen availability from coated urea leads to increased forage yield and quality. The findings suggest that coated urea fertilizers, specially CSPC @3% advocate improved nitrogen management, enhancing fodder maize productivity and sustainability.
Modeling human genetic history
Authors: Chikhi Lounès , Beaumont Mark A.
Published: November 2009

Recent years have seen the development of new ways of handling genetic data and making inferences on specific types of demographic events such as population expansions, bottlenecks, or admixture events. Indeed, simulations have shown that ancient demographic events can leave specific signatures in genetic data extracted from present‐day populations. How specific these signatures are is the focus of ongoing research. In this article, we present some of the principles underlying demographic inference based on genetic data. We discuss some results from the coalescent theory, which has been the backbone of population genetic modeling for the last 15–20 years. We also describe some of the recent methodological developments including the introduction of Bayesian and the so‐called approximate Bayesian computational methods. Genetic data provide unique and very powerful means of inferring or understanding the patterns of sometimes very ancient demographic events. However, we also emphasize the huge uncertainty in our ability to reconstruct past events from genetic data in general, and from mtDNA or Y chromosome haplotypes in particular. We conclude by discussing a number of problems associated with the use of network‐based methods, and briefly highlight some promising avenues of research for the future.
Human cytogenetics and human chromosome abnormalities
Authors: Hassold Terry
Published: November 2009

Human cytogenetics is a relatively new field of scientific investigation, with the identification of the first chromosome abnormalities occurring less than 50 years ago. In this section, we review the technical advances that have driven the field, and summarize the different types of chromosome disorders that have been identified in our species.
Imprinting and epigenetic inheritance in human disease
Authors: Polychronakos Constantin
Published: November 2009

The silencing of either the paternal or the maternal copy of the few human genes that are subject to parental imprinting may contribute to genetic disease or modify its inheritance pattern. Disruption of the normal process of imprinting may result in double gene dosage if both copies are expressed or in a null phenotype if neither is. When normally imposed, imprinting can play a role in disease by leaving only one of the two copies to be inactivated by mutation. This introductory review explains the various mechanisms and gives examples of the best‐understood diseases where imprinting plays an important role.
Evolution of genomic imprinting in mammals
Authors: Spencer Hamish G.
Published: November 2009

Genomic imprinting is an evolutionary paradox because it seems at first glance to be disadvantageous: the monoallelic expression it entails means that recessive deleterious mutations cannot be masked. Several hypotheses seek to resolve the paradox, and the strengths and weaknesses of the most plausible of these – ovarian time bomb, genomic conflict, differential selection on males and females – are discussed.
Bioinformatics and the identification of imprinted genes in mammals
Authors: Fazzari Melissa J. , Greally John M.
Published: November 2009

With the identification of DNA sequence features that are unusually distributed in regions undergoing genomic imprinting, the basis is created for the bioinformatic prediction of the remaining imprinted genes in mammalian genomes, believed to number several hundreds. It is technically challenging to prove that a gene is imprinted, so any technique that narrows down the candidates for analysis is of obvious value. Genome sequence annotations can be mined to create large datasets for analysis, introducing a number of statistical challenges. We discuss how these challenges can be addressed, allowing every gene in the genome to be assigned a relative likelihood of imprinting on the basis of their similarity to known imprinted genes in terms of their most discriminatory sequence characteristics.
Genetics of complex diseases: lessons from type 2 diabetes
Authors: Groop Leif , Almgren Peter
Published: November 2009

While the genetic causes of monogenic disorders have been successfully identified in the past, the success in dissecting the genetics of complex polygenic diseases has been limited. There are several reasons for these shortcomings. For many complex diseases, variants in several genes increase the susceptibility to the disease but the individual risk may be too low to be detected by current methods. In addition, the genetic variants almost always require environmental triggers, which need to be taken into account in the search for the underlying genetic causes. The rapid development of high‐throughput tools for genotyping and improved understanding of basic concepts of complex diseases may open up for some future success.
Hematopoietic stem cell gene therapy
Authors: Thrasher Adrian J. , Candotti Fabio
Published: November 2009

Hematopoiesis is sustained throughout fetal and adult life by hematopoietic stem cells (HSCs) that are defined by their self‐renewal capacity, pluripotentiality, and their ability to repopulate myeloablated recipients. HSCs have therefore become important targets for transplantation and somatic gene therapy. Models of HSC gene therapy in mice and large animals have reproducibly demonstrated that a significant proportion of cells participating in long‐term engraftment can be stably transduced by integrating vectors based on mammalian retroviruses. Several clinical studies have also shown that conventional gene transfer technology can produce major beneficial therapeutic effects in human patients.
Linkage disequilibrium and whole‐genome association studies
Authors: Novik Karen L. , Brooks‐Wilson Angela R.
Published: November 2009

Complex diseases affect a substantial proportion of the human population and are caused by multiple genetic and environmental effects. The association study is a means of identifying genetic variation that may be involved in complex disease etiology. The existence of linkage disequilibrium (nonrandom association of alleles) across the human genome can be used to reduce the number of variants needed to successfully correlate with phenotypic traits. We discuss the current status and problems inherent in performing whole genome association studies to analyze complex diseases.
Fingerprint mapping
Authors: Schein Jacqueline E. , Krzywinski Martin I.
Published: November 2009

Restriction fingerprint maps have played a significant role in genomics research over the past 35 years. Representing the size and order of restriction endonuclease fragments along the genome, these maps provided a physical framework on which to locate known features and functions in genomes of early scientific interest. Over the last 20 years, large‐insert, clone‐based fingerprint maps have been critical components in genome mapping and sequencing projects, including those for
Caenorhabditis elegans
,
Saccharomyces cervisiae
,
Mus musculus
, and
Homo sapiens
. In this review, we provide a summary of the evolution of fingerprint mapping, and an overview of the current methodologies used and technical considerations for the generation of ordered‐clone fingerprint maps.
Alternative splicing: conservation and function
Authors: Gelfand Mikhail S. , Kriventseva Evgenia V.
Published: November 2009

A major role in the analysis of alternative splicing belongs to the large‐scale computational examination of available EST and genome data. At least half of human genes are alternatively spliced, and many of them have isoforms not conserved in mouse. Alternative splicing tends to shuffle protein domains and frequently affects signal peptides and functional sites within domains. Thus, alternative splicing is a major mechanism generating functional and evolutional diversity of proteins. On the other hand, unlike simple gene duplication, this mechanism allows for the production of absolutely identical, in some parts, proteins.
History of genetic mapping
Authors: Morton Newton E.
Published: November 2009

Unlike physical maps, genetic maps are not directly derived from the DNA sequence. There are two types of genetic maps based on linkage and allelic association (linkage disequilibrium), respectively. Linkage maps are a century old and their use is stable, performing well in assigning a gene of unknown structure and function to a broad candidate region. Association maps were impossible until a trustworthy physical map became available and the block structure of linkage disequilibrium became known. Their use is in rapid evolution because (like functional tests) they are more efficient than linkage in identifying a causal locus within a candidate region. The questions raised by association mapping, although too new to be found in textbooks, are being pursued by many investigators.
Pharmacogenetics and the future of medicine
Authors: McCarthy Alun D. , Kennedy James L. , Middleton Lefkos T.
Published: November 2009

The efforts over the last 20 years to identify polymorphisms that influence human diseases are beginning to have a clear impact on medical care. The promise of the “new genetics” lies in its ability to provide information on an individual's susceptibility to disease, the exact nature of that disease, and the best therapeutic choice. During most of the history of pharmacogenetics (PGx – the use of genetic information to impact drug choice), it has been limited to simple phenotypes such as drug concentrations in plasma. Key developments in genetics technology have now made a wider range of efficacy and safety PGx studies possible, with a likely impact on a wide range of drug discovery and development activities. Existing PGx data show the ability of this approach to generate information relevant to dose selection, efficacy determination, and safety issues. This in turn will lead to significant impacts on both the design of clinical development programs and on the probability of success of those programs – the latter being a key issue for pharmaceutical companies today as well as for patients who will benefit from these novel medicines.
2‐DDifferenceGelElectrophoresis – an accurate quantitative method for protein analysis
Authors: Hawkins Edward , David Stephen O.
Published: November 2009

2‐D Difference Gel Electrophoresis (DIGE) is a novel technique that enables multiple protein extracts to be labeled with different fluorescent dyes. The labeled samples are then separated on the same 2‐D gel. The dyes known as CyDyeTMDIGE Fluors are spectrally resolvable as well as size‐ and charge‐matched.

The ability to add more than one sample to a 2‐D electrophoresis (2‐DE) gel enables the introduction of an internal standard that adds the quantitative advantages of a reference sample commonly seen in DNA microarray studies.

Measurement of protein abundance as a “Standardized Ratio” instead of an “Absolute volume” greatly reduces the influence of experimental variation commonly associated with conventional 2‐DE.
Probing cellular function with bioluminescence imaging
Authors: Rutter Guy A. , da Silva Xavier Gabriela , Tsuboi Takashi , Mitchell Kathryn J. , Hanrahan John W.
Published: November 2009

Bioluminescence is widely used by lower organisms as a means for communication. In recent years, gene transfer technologies have allowed this potential to be harnessed by cell biologists interested in intracellular signaling and other cellular processes. Here, we focus on the use of bioluminescence to image ATP, Ca
2+
, and gene expression in single mammalian cells.
What use is a protein structure?
Authors: Phillips Simon E. V.
Published: November 2009

The revolution generated by the pioneering protein crystallographers in the second half of the twentieth century has created a huge database of known protein structures. These are increasingly being used to design new drugs and therapies, as well as provide novel engineered reagents for industrial processes. While the three‐dimensional structures of proteins are often beautiful in themselves, our ability to use and manipulate them is becoming increasingly valuable.
Modeling membrane protein structures
Authors: Arinaminpathy Yalini , Sansom Mark S.P.
Published: November 2009

Integral membrane proteins play a central role in many biological activities of cells. Only a small number of structures are known at high resolution, in contrast to the relatively large fraction (∼25%) of genes encoding membrane proteins. It is somewhat easier to model the structure of a transmembrane protein than that of a globular protein as a consequence of the constraints imposed by the transmembrane environment. Modeling of membrane proteins plays an important role as the majority of experimentally determined structures are bacterial homologs of human proteins. The first stage of membrane protein modeling is to predict the location and extent of the transmembrane α‐helices. A number of sequence‐based methods are available for this, and the consensus accuracy of prediction is ∼80%. If a three‐dimensional structure is available for a homolog of the target membrane protein, this structure may be used as a template for homology modeling of the target protein. Secondary structure prediction and experimentally derived restraints may be used to aid the process of homology modeling. Once generated, a model may be evaluated in terms of general principles of membrane protein structure, such as the presence of bands of tryptophan and tyrosine side chains on the membrane protein surface positioned so as to interact with lipid bilayer headgroups. The stability and dynamic behavior of the membrane protein model may be investigated via molecular dynamics simulations. As an example of the overall process, generation of a model of the transmembrane domain of a prokaryotic glutamate receptor (GluR0) using a bacterial potassium channel (KcsA) as a template is described.
Data collection and analysis in systems biology
Authors: Ideker Trey
Published: November 2009

Systems biology studies biological systems by systematically perturbing them (biologically, genetically, or chemically); monitoring the global biological response at the gene, protein, and informational pathway level; integrating these data; and ultimately, formulating mathematical models that describe the structure of the system and its response to individual perturbations. The key technologies that enable systems biology are reviewed with a focus on high‐throughput measurement technologies and computational modeling approaches for integrating the resulting large‐scale data.
Graphs and metrics
Authors: Dress Andreas
Published: November 2009

Graphs and metrics are mathematical concepts that are widely used in bioinformatics. The article introduces the basic notions and discusses important relationships between them, for example, that between trees and tree metrics
Contextual inference of protein function
Authors: Narain Seshasayee Aswin Sai , Babu M. Madan
Published: November 2009

The objective of this article is to provide an overview of various contextual, homology‐independent methods for inferring protein function. The article is divided into two parts; the first part discusses methods used to infer function from genome sequence data, while the second part deals with the application of large‐scale experimental data to infer function. Genome sequence–based methods fundamentally rely on identifying orthologs of the protein of interest across multiple genomes. On the other hand, the second class is closer to experimental studies, as the underlying data, namely, protein–protein or protein–DNA interaction or gene‐expression data, are essentially obtained from high‐throughput functional genomics experiments. This article tries to put experimental and computational methods in the right perspective, giving each of them the right emphasis, so that their usefulness is appreciated by the readers.
Large‐scale, classification‐driven, rule‐based functional annotation of proteins
Authors: Natale Darren A. , Vinayaka C. R. , Wu Cathy H.
Published: November 2009

Experimentally verified information on protein function lags far behind the rapid accumulation of protein sequences. The simple approach to propagating information from characterized proteins to unknown proteins – namely, by sequence similarity search against databases of individual proteins – may fail to produce accurate results, and typically is used to transfer only protein name information. A more accurate, consistent, and comprehensive approach for large‐scale automated annotation makes use of protein family classification‐driven rules. Unannotated proteins that satisfy a set of conditions for a particular rule can be annotated with the information appropriate for that rule. The approach leads to facile, accurate prediction and functional inference for uncharacterized proteins, allows systematic detection of genome annotation errors, and provides sensible propagation and standardization of protein annotation, including position‐specific sequence features, protein names and synonyms, and Gene Ontology terms. Rule‐based annotation will be discussed in the context of the PIRSF protein classification system, PIRNR Name Rule system, and the PIRSR Site Rule system.
Signal peptides and protein localization prediction
Authors: Nielsen Henrik
Published: November 2009

Proteins have signals that direct their localization in the cell. The best known of these signals is the secretory signal peptide. Prediction of protein localization from the amino acid sequence is done by two approaches: either by recognizing the signals themselves or by using global properties, such as amino acid composition, of the protein. A number of machine‐learning methods using both these approaches are implemented as publicly available servers, and a brief presentation of these methods is given here.
Phylogenomics for studies of microbial evolution
Authors: Andersson Siv G. E. , Fuxelius Hans‐Henrik
Published: November 2009

The classification of microorganisms represents a major challenge, the basis of which has been an issue of debate for the past 100 years. Phylogenetic inference based on rRNA sequences is currently the gold standard for studies related to microbial evolution and classification. As more and more microbial genomes are added to the rapidly expanding pool of sequence data, automatic systems are being developed to meet the growing demand for large‐scale phylogenetic analyses. However, the development of such tools and their application to biological problems has raised more questions than have been solved, and the debate about the extent to which microorganisms are related by vertical descent versus horizontal transmission is more heated than ever before. Here, we describe the recent development of methods and tools for phylogenomic studies and their application in microbiological research.
Connecting genes by comparative genomics
Authors: Yanai Itai
Published: November 2009

Comparative genomics provides at least three methods beyond traditional sequence similarity for identifying functional links between genes: the examination of common phylogenetic distributions, the analysis of conserved proximity along the chromosomes of multiple genomes, and observations of fusions of genes into a multidomain gene in another organism.
Statistical methods for gene expression analysis
Authors: Deng Shibing , Chu Tzu‐Ming , Truong Young K. , Wolfinger Russ D.
Published: November 2009

Microarray technology makes it possible to simultaneously study the expression levels from thousands of genes and is widely used in functional genomics research. The analysis of microarray data provides a challenge to researchers because of its high dimensionality and complexity. Extensive research has been devoted recently to address the statistical issues raised from the analysis of the microarray data, and a comprehensive review is not possible here given space limitations and the proliferation of new papers. Instead, this chapter reviews some of the more basic statistical methods used for microarray gene expression data analysis. We divide the methods into three major areas: differential expression, classification, and clustering.
Complexity in biological structures and systems
Authors: Lesk Arthur M.
Published: November 2009

Complexity and related concepts are important for understanding life processes as revealed in the new high‐throughput data streams. Formal analysis of complexity is less advanced in biology than in certain other fields, including mathematics, physics, and computer science. This article offers an introduction to complexity for biologists, with emphasis on explaining the concepts and results from other fields applicable to understanding living systems at the molecular level. Many of the questions raised are subjects of current research.
Perl in bioinformatics
Authors: Niedner R. Hannes , Nair T. Murlidharan , Gribskov Michael
Published: November 2009

Bioinformatics evolved as a discipline that applies techniques from math, computer science, and statistics to make sense of the vast amounts of data produced by high‐throughput experiments in biology. These data are frequently output as experiment‐specific text files, which need to be parsed from and to a variety of formats to be amenable to further computational analyses. This process often involves accessing of additional information from on‐line repositories, reading and writing to and from files and databases, and ultimately the presentation of results on the World Wide Web.

Perl stands for Practical Extraction and Report Language, and was developed as a UNIX glue language by Larry Wall in the mid‐1980s. It has proven to be a powerful tool for the tasks outlined above. Since its inception, Perl has grown far beyond its original use as a text‐parsing tool into a fully featured high‐level programming language. In this article, we give an overview on how this versatile language can be used to tackle a wide variety of frequent problems in bioinformatics.
Co‐Oxidation by Cyclooxygenases
Authors: Szewczuk Lawrence M. , Penning Trevor M.
Published: November 2009

Cyclooxygenases (COXs; prostaglandin H2synthases) catalyze the bis‐dioxygenation of arachidonic acid (AA) to generate prostaglandin (PG) G2followed by the peroxidative cleavage of PGG2to yield PGH2, the precursor to all of the vasoactive PGs. These enzymes utilize a Fe‐protoporhyrin IX (heme) co‐factor to catalyze peroxide bond cleavage, which puts the Fe at a higher oxidation state (Fe3+→︀ Fe5+). The heme Fe requires two electrons (e−) to return to its resting state (Fe3+) for the next round of catalysis. Peroxide bond cleavage thus occurs via compound I and compound II, observed for horseradish peroxidase. To return to Fe3+, electrons come from “co‐reductants” and their subsequent oxidation by the enzyme is known as “co‐oxidation”. The protocols in this unit are aimed at characterizing this side reaction of COXs.Curr. Protoc. Toxicol. 42:4.30.1‐4.30.14. © 2009 by John Wiley & Sons, Inc.
Acrylamide Polymers
Authors: Kozakiewicz Joseph , Lipp David
Published: November 2009

Physical Properties

Chemical Properties

Uses

Safety and Health
Adsorption
Authors: Ruthven Douglas M.
Published: November 2009

Fundamental Principles

Practical Adsorbents

Adsorption Equilibrium

Adsorption Kinetics

Adsorption Column Dynamics

Applications

Notation
Adsorption: Liquid Separation
Authors: Gembicki Stanley A. , Oroskar Anil R. , Johnson James A.
Published: November 2009

Adsorbate–Adsorbent Interactions

Practical Adsorbents

Commercial Processes

Continuous Countercurrent Processes

Cyclic‐Batch Processes

Liquid Chromatography

Outlook
Aluminum
Authors: Sansonetti S. J.
Published: November 2009

Uses

Discovery and Early Production

Contemporary Production Methods

Thermal Reduction Process

Continuing Research and Development

Aluminum and Space

Aluminum Chemistry and Chemicals
Amino Acids
Authors: Oeda Hauromi
Published: November 2009

Chemical Nature of Amino Acids
Anesthetics
Authors: Lenz George R. , Schoepke Hollis G. , Spaulding Theodore C.
Published: November 2009

Theories of General Anesthesia

Anesthetic Agents
Antibiotics: β‐Lactamase Inhibitors
Authors: Stam J. G.
Published: November 2009

Mechanistic Aspects of β‐Lactamase Inhibition

β‐Lactam‐Based Inhibitors

Economic Aspects
Antibiotics: Cephalosporins
Authors: Roberts John
Published: November 2009

Nomenclature and Stereochemistry

Biogenesis

Physical Properties

Chemical Properties

Biological Properties

Manufacture and Chemical Synthesis

Nuclear Analogues of Cephalosporins

Cephalosporins With Special Properties

Uses

Toxicity
Antibiotics: Oligosaccharides
Authors: Girijavallabhan V. M. , Ganguly Ashit K.
Published: November 2009

Properties

Everninomicins

Flambamycin, Curamycin, and Avilamycins

Other Oligosaccharides and Relevant Work
Antibiotics: Penicillins and Others
Authors: Ponsford R. J.
Published: November 2009

Physical Properties

Chemical Properties

Synthesis

Biological Properties

Production, Manufacture, and Processing
Antibiotics: Tetracyclines
Authors: Hlavka Joseph J. , Ellestad George A. , Chopra Ian
Published: November 2009

Physical Properties

Semisynthetic Modifications

Structure–Activity Correlations

Manufacture

Economic Aspects

Biological Aspects

Uses
Antiviral Agents
Authors: Revankar Ganapathi R. , Robins Roland K.
Published: November 2009

Agents Active Against
DNA
Viruses

Agents Active Against Persistent Viral Infections
Batteries: Lead‐Acid
Authors: R. Bullock Kathryn , R. Pierson John
Published: November 2009

Cell Thermodynamics

Lead Grid Corrosion

Charge–Discharge Processes

Material Fabrication and Manufacturing Processes

Economic Aspects
Batteries: Primary Cells
Authors: Blomgren George , Hunter James
Published: November 2009

Carbon–Zinc Cells

Cylindrical Alkaline Cells

Miniature Alkaline Cells

Lithium Cells

Reserve Batteries
Beryllium
Authors: Walsh Kenneth A.
Published: November 2009

Background

Occurrence

Extractive and Process Metallurgy

Important Commercial Properties

Commercial and Aerospace Applications

Chemical Properties

Compounds of Beryllium

Biology and Toxicology
Biosensors
Authors: Pietro William
Published: November 2009

Basic Components

Factors Affecting Biosensor Detection Limits
Bleaching Agents
Authors: P. Farr James , L. Smith William , S. Steichen Dale
Published: November 2009

Chlorine‐Containing Bleaching Agents

Peroxygen Compounds

Reducing Bleaches

The Mechanism of Bleaching

Applications of Bleaching Compounds
Butylenes
Authors: Calamur Narasimhan , Carrera Martin E. , Wilsak Richard A.
Published: November 2009

Physical Properties

Chemical Properties

Manufacture

Handling and Analysis

Health and Safety

Commercial Utilization
Cellulose Ester Plastics (Organic)
Authors: Rich R. P.
Published: November 2009

Esterification

Hydrolysis

Precipitation, Washing, and Drying

Cellulose Esters

Cellulose Triacetate

Cellulose Acetate

Cellulose Acetate Butyrate and Cellulose Acetate Propionate

Organic Cellulose Ester Plastics

Commercial Production

Properties

Processing
Conversion Coatings
Authors: Hall Wilbur S.
Published: November 2009

Phosphating of Steel

Iron Phosphate Coatings

Crystalline Zinc Phosphate Coatings

Phosphating Chemistry

Phosphating of Zinc

Aluminum Pretreatment

Amorphous Phosphate Coatings for Aluminium
Cyclohexanol‐Cyclohexanone
Authors: Fisher William B. , VanPeppen Jan F.
Published: November 2009

Physical Properties

Reactions

Economic Aspects

Health and Safety Factors
Diuretic Agents
Authors: Cervoni Peter , Chan Peter S.
Published: November 2009

Pharmacology and Mechanism of Action

Economic Aspects
Dyes: Reactive
Authors: Smith Roy E.
Published: November 2009

Reactive Dye Structure

Properties

Reactivity in the Dyebath

Methods of Synthesis

Economic Aspects
Extraction (Liquid–Solid)
Authors: Wakeman Richard J.
Published: November 2009

Mechanisms of Extraction

Process Design

Equilibrium Relationships and Mass Balances

Extractors

Safety and Environmental Considerations
Fiber Glass
Authors: Dow Moore L.
Published: November 2009

Continuous‐Fiber Products
Fibers: Acetate
Authors: Schappel Joseph W.
Published: November 2009

Chemistry

Properties

Manufacture of Acetate Fibers
Fibers: Acrylic
Authors: Knorr Raymond S.
Published: November 2009

Physical Properties

Chemical Properties

Flammability

Fiber Identification

Fiber Characterization

Acrylonitrile Polymerization

Copolymerization

Solution Spinning

Commercial Products

Economic Aspects
Fibers: Cellulose Esters
Authors: Serad George A.
Published: November 2009

Polymer Characteristics

Fiber Properties

Manufacture

Anisotropic Solutions

Products

Economic Aspects
Fibers: Vegetable
Authors: Young Raymond A.
Published: November 2009

General Properties

Processing and Fiber Characteristics

Economic Aspects

Uses
Forensic Chemistry
Authors: Fisher Barry A.J.
Published: November 2009

Physical Evidence

Forensic Testing
Herbicides
Authors: Bradow Judith M. , Dionigi Christopher P. , Johnson Richard M. , Wojkowski Suhad
Published: November 2009

Herbicide Classes and Databases

Herbicide Development

Modes of Herbicide Action

Environmental Fate of Herbicides

Herbicide Groups

Economic Aspects

Innovative Weed Management Agents
High Temperature Alloys
Authors: Stoloff Norman S.
Published: November 2009

Mechanical Behavior

Surface Stability

Specific Alloy Systems
Hydroxy Dicarboxylic Acids
Authors: Blair Gary T. , Defraties Jeffrey J.
Published: November 2009

Malic Acid

Thiomalic Acid

Tartaric Acid
Kinetic Measurements
Authors: Magde Douglas
Published: November 2009

Macroscopic Behavior and the Rate Law

Experimental Verification of a Rate Law

Experimental Variation of Chemical Rates with Temperature andPressure

Microscopic Models in Kinetics
Lubricating Agents
Authors: Mahncke Henry E. , Gunderson Reigh C. , Bondi A. A.
Published: November 2009

Synthetic Lubricants

Lubrication
Manganese
Authors: Welsh J. Y. , De Craene D. F.
Published: November 2009

Processing

Chemistry of Manganese

Health and Safety Factors
Mineral Nutrients
Authors: Enig Mary G.
Published: November 2009

The Principal Elements

Trace Elements and Ultratrace Elements

Health and Safety Factors
Molecular Recognition
Authors: Weber Edwin
Published: November 2009

Principles of Receptor Design

Simple Modes of Molecular Recognition

Multiple and Multisite, Coreceptor‐ and Coupled‐System Substrate Recognition

Chiral Recognition

Artificial Receptors for Particular Substrate Recognition

Molecular Recognition in Polymers and Solids

Molecular Recognition at Interfaces and Surface Monolayers

Self‐Recognition
Molybdenum
Authors: Barr Robert Q.
Published: November 2009

Uses

Chemistry and Compounds
Nitrides
Authors: Markel Eric J. , Leaphart II M. E.
Published: November 2009

Properties

Preparation

Manufacture and Processing

Health and Safety Factors

Uses
Ozone
Authors: Wojtowicz J. A.
Published: November 2009

Properties

Thermal Decomposition

Photochemical Decomposition

Chemistry of Ozone

Ozone Generation

Uses

Health and Safety
Perchloric Acid and Perchlorates
Authors: Mendiratta Sudhir K. , Dotson Ronald L. , Brooker Robert T.
Published: November 2009

Properties

Manufacture

Shipping and Handling

Economic Aspects

Uses
Phenolic Resins
Authors: Waitkus Phillip A.
Published: November 2009

Chemistry of Phenolics

Novolacs

Resols
Pigment Dispersions
Authors: Loebbert Gerd , Sharangpani Anand S. G.
Published: November 2009

Dispersion

Flushing

Equipment

Uses
Platinum and Platinum Group
Authors: Libby Linton
Published: November 2009

Occurrence

Refining Processes

Uses

Platinum Compounds

Health and Safety Factors
Polycarbonates
Authors: Brunelle Daniel J.
Published: November 2009

Properties and Characterization

Preparation

Health and Safety Factors

Uses

Other Polycarbonates, Blends, and Copolymers
Polymerization (Radical)
Authors: Bevington J. C.
Published: November 2009

Initiation

Propagation

Termination

Transfer

Inhibitors and Retarders

Copolymerization
Pyrazoles, Pyrazolines, and Pyrazolones
Authors: Kornis Gabe I.
Published: November 2009

Theoretical Methods

Structural Elucidation

Physical Properties

Chemical Reactivity

Synthesis

Health Factors

Applications
Revegetation
Authors: Plass W. T.
Published: November 2009

Spoil Evaluation

Preparation of the Site

Seeding and Planting

Costs of Refuse Disposal and Land Reclamation
Solutions
Authors: Hildebrand Joel H.
Published: November 2009

Regular Solutions

Gases

Solid Solutions

Metallic Solutions

Salt Solutions
Sonochemistry
Authors: Suslick Kenneth S.
Published: November 2009

Acoustic Cavitation

Two‐Site Model of Sonochemical Reactivity

Microjet Formation during Cavitation at Liquid–Solid Interfaces

Sonoluminescence

Sonochemistry
Thallium
Authors: Carapella S. C.
Published: November 2009

Uses

Toxicity

Chemistry and Compounds
Toluene
Authors: Ozokwelu E. Dickson
Published: November 2009

Properties

Manufacture and Processing

Specifications, Standards, and Quality Control

Health and Safety Factors

Uses

Derivatives

Acknowledgment
Tungsten
Authors: Schussler Fansteel M.
Published: November 2009

Uses

Chemistry and Compounds
Vaccine Technology
Authors: Hsieh Chia‐Lung , Ritchey Mary B.
Published: November 2009

Commercial Vaccines

Vaccines for the General Population

Vaccines for Special Populations

Vaccines Being Developed

Other Vaccines

Future Technology

Process Technology

Economic Aspects
Vanillin
Authors: Esposito Lawrence J. , Formanek K. , Kientz G. , Mauger F. , Maureaux V. , Robert G. , Truchet F.
Published: November 2009

Production

Specifications

Chemical Properties

Applications

Health and Safety Factors
Time‐Lapse Live Imaging of Stem Cells inDrosophilaTestis
Authors: Cheng Jun , Hunt Alan J.
Published: November 2009

This unit describes a protocol for time‐lapse live‐imaging of stem cells inDrosophilatestis. Testis tips are dissected fromDrosophila, sliced, and transferred to glass‐bottom chambers where the stem cells residing in their native microenvironment can be monitored in real time. This protocol, facilitated with various fluorescence‐labeled markers, allows dynamic cellular processes in stem cells to be characterized throughout the cell cycle.Curr. Protoc. Stem Cell Biol. 11:2E.2.1‐2E.2.8. © 2009 by John Wiley & Sons, Inc.
Culturing, Storage, and Quantification of Rotaviruses
Authors: Arnold Michelle , Patton John T. , McDonald Sarah M.
Published: November 2009

Group A rotaviruses (RVs) infect the young of numerous animal species and cause acute gastroenteritis. Cultivation of animal and human RVs in cells requires proteolytic activation of the viral attachment protein using trypsin. Continuous cell lines, such as rhesus monkey kidney cells, as well as primary monkey kidney cells, are routinely used for the growth and characterization of RVs. Isolation and cultivation of human RVs from clinical fecal specimens is difficult and adaptation to growth in vitro requires multiple rounds of passage in primary cells. Following growth, RV stocks can be purified by centrifugation, if required, and quantified using plaque assay or fluorescence focus assay. This unit describes easily applicable procedures for the culturing, storage, and quantification of RVs. Curr. Protoc. Microbiol. 15:15C.3.1‐15C.3.24. © 2009 by John Wiley & Sons, Inc.
A new framework for data reconciliation and measurement bias identification in generalized linear dynamic systems
Authors: Xu Hua , Rong Gang
Published: November 2009

This article describes a new framework for data reconciliation in generalized linear dynamic systems, in which the well‐known Kalman filter (KF) is inadequate for filtering. In contrast to the classical formulation, the proposed framework is in a more concise form but still remains the same filtering accuracy. This comes from the properties of linear dynamic systems and the features of the linear equality constrained least squares solution. Meanwhile, the statistical properties of the framework offer new potentials for dynamic measurement bias detection and identification techniques. On the basis of this new framework, a filtering formula is rederived directly and the generalized likelihood ratio method is modified for generalized linear dynamic systems. Simulation studies of a material network present the effects of both the techniques and emphatically demonstrate the characteristics of the identification approach. Moreover, the new framework provides some insights about the connections between linear dynamic data reconciliation, linear steady state data reconciliation, and KF. © 2009 American Institute of Chemical Engineers AIChE J, 2010