Specialized hidden markov model databases for microbial genomics

As hidden Markov models (HMMs) become increasingly more important in the analysis of biological sequences, so too have databases of HMMs expanded in size, number and importance. While the standard paradigm a short while ago was the analysis of one or a few sequences at a time, it has now become standard procedure to submit an entire microbial genome. In the future, it will be common to submit large groups of completed genomes to run simultaneously against a dozen public databases and any number of internally developed targets. This paper looks at some of the readily available HMM (or HMM-like) algorithms and several publicly available HMM databases, and outlines methods by which the reader may develop custom HMM targets.     

Dynamic model for sedimentation of supercoiled molecules.

An experimental curve for the sedimentation of SV40 DNA has been fitted by using a three parameter theory. The chain stiffness parameter is evaluated at each point, and the general behavior as a function of the number of loops (superhelix density) has been described. The chain stiffness, like the sedimentation ratio, also depends on the superhelical density in a complicated way.     

History of neurophysiology in Japan.

The progress of the neurophysiological research in Japan during the past 45 years is related. Modern Japanese neurophysiology started immediately after the end of World War 2. The introduction of microelectrode techniques contributed greatly to most fields of Japanese neurophysiology. These techniques were used to study most neurophysiological phenomena: sensory physiology including vision, audition, chemical sensitivity, and other modalities; learning and memory. These techniques plus lesions, transplants, and behavioral physiology were used to study circadian rhythm, posture and motor control, and sex. These and other techniques were used to study neural plasticity, immunity, membrane excitability, pain and other psychophysiological functions. The disciplines advanced quickly into multidiscipline approaches into not only electrophysiological, but biophysical, biochemical and immunological research fields. From the past research results our neurophysiologists can be expected to advance rapidly toward further development in the future of Japanese neurophysiology.     

Behavioral guides for sensory neurophysiology

The study of natural behavior is important for understanding the coding schemes of sensory systems. The jamming avoidance response of the weakly electric fish Eigenmannia is an excellent example of a bottom–up approach, in which behavioral analyses guided neurophysiological studies. These studies started from the electroreceptive sense organs to the motor output consisting of pacemaker neurons. Going in the opposite direction, from the central nervous system to lower centers, is the characteristic of the top–down approach. Although this approach is perhaps more difficult than the bottom–up approach, it was successfully employed in the neuroethological analysis of sound localization in the barn owl. In the latter studies, high-order neurons selective for complex natural stimuli led to the discovery of neural pathways and networks responsible for the genesis of the stimulus selectivity. Comparison of Eigenmannia and barn owls, and their neural systems, has revealed similarities in network designs, such as parallel pathways and their convergence to produce stimulus selectivity necessary for detection of natural stimuli.     

Ocular tracking: behavior and neurophysiology.

'Ocular tracking' refers to visually driven, slow eye movements that stabilize moving images on the retina, thereby facilitating high acuity vision. Recent behavioral studies have shown that the primate brain produces several kinds of ocular tracking responses that operate precisely and consistently, with ultra-short latencies. Electrophysiological studies indicate that these tracking responses are mediated by a pathway that includes the medial superior temporal area of the cerebral cortex. Responses of neurons in this pathway are consistent with the short latencies and complex visual properties observed in behavioral studies of the tracking response.     

The PIR-International databases.

PIR-International is an association of macromolecular sequence data collection centers dedicated to fostering international cooperation as an essential element in the development of scientific databases. PIR-International is most noted for the Protein Sequence Database. This database originated in the early 1960's with the pioneering work of the late Margaret Dayhoff as a research tool for the study of protein evolution and intersequence relationships; it is maintained as a scientific resource, organized by biological concepts, using sequence homology as a guiding principle. PIR-International also maintains a number of other genomic, protein sequence, and sequence-related databases. The databases of PIR-International are made widely available. This paper briefly describes the architecture of the Protein Sequence Database, a number of other PIR-International databases, and mechanisms for providing access to and for distribution of these databases.     

Global guidance principles for life cycle assessment databases: development of training material and other implementation activities on the publication

Purpose

The paper introduces the publication on “Global Guidance Principles for Life Cycle Assessment Databases”; it focuses on the development of training material and other implementation activities on the publication.

Methods

The document is the output of the “Shonan Guidance Principles” workshop. The publication provides guidance principles for life cycle assessment (LCA) databases; this includes how to collect raw data, how to develop datasets, and how to manage databases. The publication also addresses questions concerning data documentation and review, coordination among databases, capacity building, and future scenarios. As a next step, the publication is used to prepare training material and other implementation activities.

Results

The publication was launched at the LCM 2011 Conference. Since then outreach activities have been organized in particular in emerging economies. Further developments with regard to the guidance principles are foreseen as part of a flagship project within phase 3 of the Life Cycle Initiative. Training material is being developed that will include how to set up databases and develop datasets. The topic has been taken up by United Nations Environment Programme (UNEP) in its Rio?+?20 Voluntary Commitments: UNEP and Society of Environmental Toxicology and Chemistry (SETAC) through the UNEP/SETAC Life Cycle Initiative commit to facilitate improved access to good quality life cycle data and databases as well as expanded use of key environmental indicators that allows the measurement and monitoring of progress towards the environmental sustainability of selected product chains.

Conclusions

The adoption of the “Global Guidance Principles” publication as a de facto global standard is expected to facilitate the work of database teams, especially, in developing countries, and the collaboration in regional networks. These efforts are supported by the development of training material and other implementation activities.     

Dynamic model for enzyme action

Background: Protein thermodynamic structure theory is an integrated approach to the study of protein dynamics and the mechanisms of enzyme catalysis. In this paper, a hypothesis arising from this theory is examined. The timescale of an enzymatic reaction (TER) gives a key to characterizing enzyme conformational changes. The aspects of timescale important in our approach are: (i) it is logically related to internal motions of the main chain of a protein; (ii) it sets the upper limit on the size or scope of protein conformational changes. Feature (i) is linked to the dynamic properties of enzyme-reactant complexes. Feature (ii) is linked to the dynamic sites of the main chain (promoting motion) involved in enzyme activity. Conclusion: Our analysis shows that a comprehensive understanding of enzymology can be established on the basis of protein thermodynamic structure theory.     

Automated preparation of DNA sequences for publication.

A computer program which draws DNA sequences is described. A simple method is used which enables the user to highlight or annotate specific parts of a sequence. The sizes of the characters in the sequence to be drawn are specified by the user. In addition, vertical spacing between lines and horizontal spacing between characters can be specified. Sequences can be prepared and high quality output produced on a plotter in a short period of time, making the program advantageous to use over typing, computer printing, or preparation by a graphics department.     

Comparison of methods for searching protein sequence databases.

We have compared commonly used sequence comparison algorithms, scoring matrices, and gap penalties using a method that identifies statistically significant differences in performance. Search sensitivity with either the Smith-Waterman algorithm or FASTA is significantly improved by using modern scoring matrices, such as BLOSUM45-55, and optimized gap penalties instead of the conventional PAM250 matrix. More dramatic improvement can be obtained by scaling similarity scores by the logarithm of the length of the library sequence (In()-scaling). With the best modern scoring matrix (BLOSUM55 or JO93) and optimal gap penalties (-12 for the first residue in the gap and -2 for additional residues), Smith-Waterman and FASTA performed significantly better than BLASTP. With In()-scaling and optimal scoring matrices (BLOSUM45 or Gonnet92) and gap penalties (-12, -1), the rigorous Smith-Waterman algorithm performs better than either BLASTP and FASTA, although with the Gonnet92 matrix the difference with FASTA was not significant. Ln()-scaling performed better than normalization based on other simple functions of library sequence length. Ln()-scaling also performed better than scores based on normalized variance, but the differences were not statistically significant for the BLOSUM50 and Gonnet92 matrices. Optimal scoring matrices and gap penalties are reported for Smith-Waterman and FASTA, using conventional or In()-scaled similarity scores. Searches with no penalty for gap extension, or no penalty for gap opening, or an infinite penalty for gaps performed significantly worse than the best methods. Differences in performance between FASTA and Smith-Waterman were not significant when partial query sequences were used. However, the best performance with complete query sequences was obtained with the Smith-Waterman algorithm and In()-scaling.     

Dynamic model for CHO cell engineering

Industrial CHO cell fed-batch processes have progressed significantly over the past decade, with recombinant protein titer consistently reaching the gram per liter level. Such improvements have largely resulted from separate advances in process and cell line development. Model-based selection of targets for metabolic engineering in CHO cells is confounded by the dynamic nature of the fed-batch process. In this work, we use a dynamic model of CHO cell metabolism to simultaneously identify both process and cell modifications that improve antibody production. Model simulations explored ca. 9200 combinations of process variables (shift temperature, shift day, seed density, and harvest day) and knockdowns (8 metabolic enzymes). A comprehensive examination of a simulated solution space showed that optimal gene knockdown clearly depends on the process parameters such as temperature shift day, shift temperature, and seed density. Knockdown of enzymes related to lactate production were the most beneficial; however, depending on the process conditions, modulating such enzymes yielded varying productivities, ranging from a reduction in final titer to greater than 2-fold improvement.