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Anti-HLA-DR/anti-DOTA diabody construction in a modular gene design platform: bispecific antibodies for pretargeted radioimmunotherapy.

Recombinant immunoglobulin libraries of single chain molecules (sc) from the variable domains of antibody light and heavy chains (Fv), have great promise for new approaches to radioimmunotherapy (RIT). However, creating and evaluating scFv from diverse sources is time consuming and differences in molecular format can influence in vitro and in vivo characteristics. Furthermore, scFv do not have optimal characteristics for targeting therapy to tumor because of their small size and univalent binding. Diabody molecules at least twice the size of scFv are better for RIT because bivalent and bispecific molecules can be constructed. A polymerase chain reaction (PCR) based primer system was created to easily convert scFv genes into a diabody gene format, once they have been placed into pCANTAB 5E, a readily available vector. The primer system for this diabody gene platform was developed and tested by constructing an anti-lymphoma/anti-chelate, bispecific diabody (anti-HLA-DR/anti-DOTA). Two mouse scFv libraries were screened for reactive clones using recombinant phage display techniques. Selected mouse anti-HLA-DR and anti-DOTA scFv genes were combined, ligated into the pCANTAB 5E vector that co-expressed these self-assembling scFv in E. coli as two mismatched nonlinked pairs (VHA-link-VLB; VHB-link-VLA). The diabody protein that was purified from periplasm had the expected molecular characteristics when analyzed by sequencing, chromatography, electrophoresis and Western blot. This modular gene design platform provides methodology for easy and rapid creation of diabody molecules from diverse scFv libraries. Diabodies from various scFv can easily be produced, thereby facilitating comparative preclinical studies en route to development of new tumor targeting molecules.

Antibodies, Bispecific↗

Modular tube/plate-based sample management: a business model optimized for scalable storage and processing.

Modular approaches to sample management allow staged implementation and progressive expansion of libraries within existing laboratory space. A completely integrated, inert atmosphere system for the storage and processing of a variety of microplate and microtube formats is currently available as an integrated series of individual modules. Liquid handling for reformatting and replication into microplates, plus high-capacity cherry picking, can be performed within the inert environmental envelope to maximize compound integrity. Complete process automation provides ondemand access to samples and improved process control. Expansion of such a system provides a low-risk tactic for implementing a large-scale storage and processing system.

Automation↗

A highly modular cloning vector for the analysis of eukaryotic genes and gene regulatory elements.

We have developed a highly modular vector, pDSP1, which contains two independent mammalian transcription cassettes. Each cassette contains SV40 early gene regulatory elements controlling the expression of an easily assayable, selectable Escherichia coli marker gene, either galK or xgprt. The regulatory elements of the galK cassette are bounded by multiple unique and nearly unique restriction sites allowing for the easy removal and replacement of either the regulatory sequences or of the galK gene itself. Expression of the marker genes is monitored by transient transfection into mammalian cells followed by filter enzyme assays. Expression of xgprt serves as an internal control and the relative expression of galK/xgprt is used to quantitate modifications made to the vector. We have used this system to analyze many eukaryotic polyadenylation regions as well as several other eukaryotic gene regulatory elements. We have also removed the galK gene and replaced it with other mammalian genes. The entire galK cassette is contained on a Sal I restriction fragment that can be readily removed and placed into a unique Sal I site in one of our Epstein-Barr virus (EBV), bovine papilloma virus (BPV), or BK defective viral stable expression vectors. We believe that pDSP1 is a powerful vector system for studying eukaryotic gene regulation, and in conjunction with our stable expression vectors, it represents a unified system for exploring expression in mammalian cells both transiently and stably.

Animals↗

CINEMA-MX: a modular multiple alignment editor.

UNLABELLED: Analyzing and visualizing multiple sequence alignments is a common task in many areas of molecular biology and bioinformatics. Many tools exist for this purpose, but are not easily customizable for specific in-house uses. Here we report the development of an editor, CINEMA-MX, that addresses these issues. CINEMA-MX is highly modular and configurable, and we present examples to illustrate its extensibility. AVAILABILITY: The program and full source code, which are available from http://www.bioinf.man.ac.uk/dbbrowser/cinema-mx, are being released under a combination of the LGPL and GPL, for Unix or Windows platforms.

Computer Graphics↗

Analysing microarray data using modular regulation analysis.

MOTIVATION: Microarray experiments measure complex changes in the abundance of many mRNAs under different conditions. Current analysis methods cannot distinguish between direct and indirect effects on expression, or calculate the relative importance of mRNAs in effecting responses. RESULTS: Application of modular regulation analysis to microarray data reveals and quantifies which mRNA changes are important for cellular responses. The mRNAs are clustered, and then we calculate how perturbations alter each cluster and how strongly those clusters affect an output response. The product of these values quantifies how an input changes a response through each cluster. Two published datasets are analysed. Two mRNA clusters transmit most of the response of yeast doubling time to galactose; one contains mainly galactose metabolic genes, and the other a regulatory gene. Analysis of the response of yeast relative fitness to 2-deoxy-D-glucose reveals that control is distributed between several mRNA clusters, but experimental error limits statistical significance.

Algorithms↗

Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting.

UNLABELLED: A set of new algorithms and software tools for automatic protein identification using peptide mass fingerprinting is presented. The software is automatic, fast and modular to suit different laboratory needs, and it can be operated either via a Java user interface or called from within scripts. The software modules do peak extraction, peak filtering and protein database matching, and communicate via XML. Individual modules can therefore easily be replaced with other software if desired, and all intermediate results are available to the user. The algorithms are designed to operate without human intervention and contain several novel approaches. The performance and capabilities of the software is illustrated on spectra from different mass spectrometer manufacturers, and the factors influencing successful identification are discussed and quantified. MOTIVATION: Protein identification with mass spectrometric methods is a key step in modern proteomics studies. Some tools are available today for doing different steps in the analysis. Only a few commercial systems integrate all the steps in the analysis, often for only one vendor's hardware, and the details of these systems are not public. RESULTS: A complete system for doing protein identification with peptide mass fingerprints is presented, including everything from peak picking to matching the database protein. The details of the different algorithms are disclosed so that academic researchers can have full control of their tools. AVAILABILITY: The described software tools are available from the Halmstad University website www.hh.se/staff/bioinf/ SUPPLEMENTARY INFORMATION: Details of the algorithms are described in supporting information available from the Halmstad University website www.hh.se/staff/bioinf/

Algorithms↗

SNPbox: a modular software package for large-scale primer design.

UNLABELLED: We developed a modular software package SNPbox that automates and standardizes the generation of PCR primers and is used in the strategy for constructing single nucleotide polymorphisms (SNPs) maps. In this strategy, the focus of primer design can be either on the validation of annotated public SNPs or on the SNP discovery in exon regions or extended genomic regions, both by resequencing. SNPbox relies on Primer3 for the primer design and combines this program with other publicly available software tools such as BLAST, Spidey and RepeatMasker, and newly developed algorithms. Primer conditions were chosen such that PCR amplifications are uniform for each PCR amplicon facilitating the use of high-throughput genetic platforms. SNPbox can also be used for the design of primer sets for mutation analysis, STR marker genotyping and microarray oligo design. Of the 2500 primer sets designed by SNPbox, 95% successfully amplified genomic DNA under uniform PCR conditions. AVAILABILITY: The software is available from the authors upon request. SUPPLEMENTARY INFORMATION: SNPbox_supplement.

Algorithms↗

Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering.

MOTIVATION: A holistic approach to the study of cellular processes is identifying both gene-expression changes and regulatory elements promoting such changes. Cellular regulatory processes can be viewed as transcriptional modules (TMs), groups of coexpressed genes regulated by groups of transcription factors (TFs). We set out to devise a method that would identify TMs while avoiding arbitrary thresholds on TM sizes and number. METHOD: Assuming that gene expression is determined by TFs that bind to the gene's promoter, clustering of genes based on TF binding sites (cis-elements) should create gene groups similar to those obtained by gene expression clustering. Intersections between the expression and cis-element-based gene clusters reveal TMs. Statistical significance assigned to each TM allows identification of regulatory units of any size. RESULTS: Our method correctly identifies the number and sizes of TMs on simulated datasets. We demonstrate that yeast experimental TMs are biologically relevant by comparing them with MIPS and GO categories. Our modules are in statistically significant agreement with TMs from other research groups. This work suggests that there is no preferential division of biological processes into regulatory units; each degree of partitioning exhibits a slice of biological network revealing hierarchical modular organization of transcriptional regulation.

Algorithms↗

Modularized learning of genetic interaction networks from biological annotations and mRNA expression data.

MOTIVATION: Inferring the genetic interaction mechanism using Bayesian networks has recently drawn increasing attention due to its well-established theoretical foundation and statistical robustness. However, the relative insufficiency of experiments with respect to the number of genes leads to many false positive inferences. RESULTS: We propose a novel method to infer genetic networks by alleviating the shortage of available mRNA expression data with prior knowledge. We call the proposed method 'modularized network learning' (MONET). Firstly, the proposed method divides a whole gene set to overlapped modules considering biological annotations and expression data together. Secondly, it infers a Bayesian network for each module, and integrates the learned subnetworks to a global network. An algorithm that measures a similarity between genes based on hierarchy, specificity and multiplicity of biological annotations is presented. The proposed method draws a global picture of inter-module relationships as well as a detailed look of intra-module interactions. We applied the proposed method to analyze Saccharomyces cerevisiae stress data, and found several hypotheses to suggest putative functions of unclassified genes. We also compared the proposed method with a whole-set-based approach and two expression-based clustering approaches.

Algorithms↗

Distributed modular architectures linking basal ganglia, cerebellum, and cerebral cortex: their role in planning and controlling action.

The motor system includes structures distributed widely through the CNS, and in this feature article we present a scheme for how they might cooperate in the control of action. Distributed modules, which constitute the basic building blocks of our model, include recurrent loops connecting distant brain structures, as well as local circuitry that modulates loop activity. We consider interconnections among the basal ganglia, cerebellum, and cerebral cortex and the specialized properties of certain cell types within each of those structures, namely, striatal spiny neurons, cerebellar Purkinje cells, and neocortical pyramidal cells. In our model, striatal spiny neurons of the basal ganglia function in contextual pattern recognition under the training influence of reinforcement signals transmitted in dopamine fibers. Cerebellar Purkinje cells also function in pattern recognition, in their case to select and execute actions through training supervised by climbing fibers, which signal discoordination. Neocortical pyramidal cells perform collective computations learned through a local training mechanism and also function as information stores for other modular operations. We discuss how distributed modules might function in a parallel, cooperative manner to plan, modulate, and execute action.

Action Potentials↗

Solution structure of the Mu end DNA-binding ibeta subdomain of phage Mu transposase: modular DNA recognition by two tethered domains.

The phage Mu transposase (MuA) binds to the ends of the Mu genome during the assembly of higher order nucleoprotein complexes. We investigate the structure and function of the MuA end-binding domain (Ibetagamma). The three-dimensional solution structure of the Ibeta subdomain (residues 77-174) has been determined using multidimensional NMR spectroscopy. It comprises five alpha-helices, including a helix-turn-helix (HTH) DNA-binding motif formed by helices 3 and 4, and can be subdivided into two interacting structural elements. The structure has an elongated disc-like appearance from which protrudes the recognition helix of the HTH motif. The topology of helices 2-4 is very similar to that of helices 1-3 of the previously determined solution structure of the MuA Igamma subdomain and to that of the homeodomain family of HTH DNA-binding proteins. We show that each of the two subdomains binds to one half of the 22 bp recognition sequence, Ibeta to the more conserved Mu end distal half (beta subsite) and Igamma to the Mu end proximal half (gamma subsite) of the consensus Mu end-binding site. The complete Ibetagamma domain binds the recognition sequence with a 100- to 1000-fold higher affinity than the two subdomains independently, indicating a cooperative effect. Our results show that the Mu end DNA-binding domain of MuA has a modular organization, with each module acting on a specific part of the 22 bp binding site. Based on the present binding data and the structures of the Ibeta and Igamma subdomains, a model for the interaction of the complete Ibetagamma domain with DNA is proposed.

Amino Acid Sequence↗

Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.

DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. Despite the difference in cofactor specificity and limited overall sequence similarity, the two classes of DNA ligase share basically the same catalytic mechanism. In this study, the crystal structure of an NAD(+)-dependent DNA ligase from Thermus filiformis, a 667 residue multidomain protein, has been determined by the multiwavelength anomalous diffraction (MAD) method. It reveals highly modular architecture and a unique circular arrangement of its four distinct domains. It also provides clues for protein flexibility and DNA-binding sites. A model for the multidomain ligase action involving large conformational changes is proposed.

Amino Acid Sequence↗

Novel modular domain PB1 recognizes PC motif to mediate functional protein-protein interactions.

Modular domains mediating specific protein-protein interactions play central roles in the formation of complex regulatory networks to execute various cellular activities. Here we identify a novel domain PB1 in the budding yeast protein Bem1p, which functions in polarity establishment, and mammalian p67(phox), which activates the microbicidal phagocyte NADPH oxidase. Each of these specifically recognizes an evolutionarily conserved PC motif to interact directly with Cdc24p (an essential protein for cell polarization) and p40(phox) (a component of the signaling complex for the oxidase), respectively. Swapping the PB1 domain of Bem1p with that of p67(phox), which abolishes its interaction with Cdc24p, confers on cells temperature- sensitive growth and a bilateral mating defect. These phenotypes are suppressed by a mutant Cdc24p harboring the PC motif-containing region of p40(phox), which restores the interaction with the altered Bem1p. This domain-swapping experiment demonstrates that Bem1p function requires interaction with Cdc24p, in which the PB1 domain and the PC motif participate as responsible modules.

Adaptor Proteins, Signal Transducing↗

KG-Microbe: Building modular and scalable knowledge graphs for microbiome and microbial sciences.

BACKGROUND: The integration of many disparate forms of data is essential for understanding the microbial world and its interaction with the environment and human health. Doing so is particularly challenging in the context of microbe-host and microbe-microbe interactions that contribute to health or environmental outcomes. There are thousands of relevant microbial species, and millions of interactions among those microbes and with their environment or host. Integrated information (e.g., about host and microbial physiology, genetics, and metabolism) facilitates deeper understanding of complex mechanisms and helps interpret correlative results. RESULTS: The KG-Microbe construction framework is a novel approach to harmonizing bacterial and archaeal data in the form of a findable, accessible, interoperable, reusable and AI-ready knowledge graph (KG). Starting from a core KG with organismal traits, environments, and growth preferences and the integration of established ontologies, the framework generates a hierarchy of related KGs targeting specific use cases, including the human microbiome in the context of disease, or environmental microbiomes. The framework supports customizable taxa subsets representing communities or clades of interest. Evaluations of the KG-Microbe KGs through a series of competency questions demonstrate the accuracy and effectiveness of the data harmonization, and the utility of the resulting KGs in studies of inflammatory bowel disease and Parkinson's disease. Finally, the predictive and environmental capabilities of the KGs are demonstrated by predicting growth preferences using graph features. CONCLUSIONS: The KG-Microbe framework unifies microbial contexts in a single resource to support integrative analyses across biomedical, host, and environmental domains. KG-Microbe is a flexible, modular enabling technology for humans and machine learning methods to uncover candidate mechanistic explanations of microbial associations.

Microbiota↗

A modular system for the assay of transcription regulatory signals: the sequence TAATGARAT is required for herpes simplex virus immediate early gene activation.

A modular system for assaying the activity of transcriptional regulatory signals based on herpes simplex virus (HSV) promoter and terminator sequences linked to the bacterial chloramphenicol acetyltransferase (CAT) gene has been used to study activation of HSV immediate early (IE) gene expression. Insertion of the SV40 72 base pair (bp) repeat increased mRNA levels by 15-fold thus demonstrating the ability of the HSV IE promoter to respond to a heterologous enhancer. A fragment containing part of the intergenic region located between HSV-2 immediate early (IE) genes-3 and -4/-5 increased mRNA levels by 5-fold in response to transactivation by an HSV virion structural polypeptide. The HSV activator fragment increased mRNA levels by 2-fold in the absence of transactivation indicating that cellular proteins are involved in IE gene expression. From HSV-1/HSV-2 DNA sequence comparisons we previously proposed that a DNA sequence, consensus TAATGARAT, present upstream of all HSV-1 and HSV-2 IE genes was required for the co-ordinate induction of IE genes. We show here that a synthetic oligonucleotide containing TAATGARAT conferred the ability to stimulate CAT activity only on transactivation: two copies of TAATGARAT stimulated expression by 2-fold while six copies gave an 8-fold increase. This activation, which was not dependent on orientation of the TAATGARAT sequence, directly demonstrates that TAATGARAT is a component of the IE gene activation sequence.

Acetyltransferases↗

Modular sequence elements associated with origin regions in eukaryotic chromosomal DNA.

We have postulated that chromosomal replication origin regions in eukaryotes have in common clusters of certain modular sequence elements (Benbow, Zhao, and Larson, BioEssays 14, 661-670, 1992). In this study, computer analyses of DNA sequences from six origin regions showed that each contained one or more potential initiation regions consisting of a putative DUE (DNA unwinding element) aligned with clusters of SAR (scaffold associated region), and ARS (autonomously replicating sequence) consensus sequences, and pyrimidine tracts. The replication origins analyzed were from the following loci: Tetrahymena thermophila macronuclear rDNA gene, Chinese hamster ovary dihydrofolate reductase amplicon, human c-myc proto-oncogene, chicken histone H5 gene, Drosophila melanogaster chorion gene cluster on the third chromosome, and Chinese hamster ovary rhodopsin gene. The locations of putative initiation regions identified by the computer analyses were compared with published data obtained using diverse methods to map initiation sites. For at least four loci, the potential initiation regions identified by sequence analysis aligned with previously mapped initiation events. A consensus DNA sequence, WAWTTDDWWWDHWGWHMAWTT, was found within the potential initiation regions in every case. An additional 35 kb of combined flanking sequences from the six loci were also analyzed, but no additional copies of this consensus sequence were found.

Amino Acid Sequence↗

TectoRNA: modular assembly units for the construction of RNA nano-objects.

Structural information on complex biological RNA molecules can be exploited to design tectoRNAs or artificial modular RNA units that can self-assemble through tertiary interactions thereby forming nanoscale RNA objects. The selective interactions of hairpin tetraloops with their receptors can be used to mediate tectoRNA assembly. Here we report on the modulation of the specificity and the strength of tectoRNA assembly (in the nanomolar to micromolar range) by variation of the length of the RNA subunits, the nature of their interacting motifs and the degree of flexibility of linker regions incorporated into the molecules. The association is also dependent on the concentration of magnesium. Monitoring of tectoRNA assembly by lead(II) cleavage protection indicates that some degree of structural flexibility is required for optimal binding. With tectoRNAs one can compare the binding affinities of different tertiary motifs and quantify the strength of individual interactions. Furthermore, in analogy to the synthons used in organic chemistry to synthesize more complex organic compounds, tectoRNAs form the basic assembly units for constructing complex RNA structures on the nanometer scale. Thus, tectoRNA provides a means for constructing molecular scaffoldings that organize functional modules in three-dimensional space for a wide range of applications.

Base Composition↗

Modular construction for function of a ribonucleoprotein enzyme: the catalytic domain of Bacillus subtilis RNase P complexed with B. subtilis RNase P protein.

The bacterial RNase P holoenzyme catalyzes the formation of the mature 5'-end of tRNAs and is composed of an RNA and a protein subunit. Among the two folding domains of the RNase P RNA, the catalytic domain (C-domain) contains the active site of this ribozyme. We investigated specific binding of the Bacillus subtilis C-domain with the B.subtilis RNase P protein and examined the catalytic activity of this C-domain-P protein complex. The C-domain forms a specific complex with the P protein with a binding constant of approximately 0.1 microM. The C-domain-P protein complex and the holoenzyme are equally efficient in cleaving single-stranded RNA (approximately 0.9 min(-1) at pH 7.8) and substrates with a hairpin-loop 3' to the cleavage site (approximately 40 min(-1)). The holoenzyme reaction is much more efficient with a pre-tRNA substrate, binding at least 100-fold better and cleaving 10-500 times more efficiently. These results demonstrate that the RNase P holoenzyme is functionally constructed in three parts. The catalytic domain alone contains the active site, but has little specificity and affinity for most substrates. The specificity and affinity for the substrate is generated by either the specificity domain of RNase P RNA binding to a T stem-loop-like hairpin or RNase P protein binding to a single-stranded RNA. This modular construction may be exploited to obtain RNase P-based ribonucleoprotein complexes with altered substrate specificity.

Bacillus subtilis↗