Finding module-based gene networks with state-space models - Mining high-dimensional and short time-course gene expression data

This study explores some problems to analyze time-course gene expression data by state-space models (SSMs). One problem is regarding the methods of parameter estimation and determination of the dimension of the internal state variable. Although several methods have been applied, there are few literature studies which with to compare them. Thus, this paper gives a brief review of the existing literature that use the SSM to analyze the gene expression time-course data. Another problem is the identifiability of the model. If the parameters of SSMs are simply estimated without any constraints for parameter space, they lack identifiability. To identify a system uniquely, it requires a specific algorithm to estimate the parameters with some constraints. For that purpose, an identifiable form of SSMs and an algorithm for estimating parameters are derived. The last problem is the extraction of biological information by interpreting the estimated parameters, such as mechanism of gene regulations at the module level. For that one, this paper explores methods to extract further information using the estimated parameters, that is, reconstruction of a module network from time-course gene expression data     

Relationship between local structure and stability in hen egg white lysozyme mutant with alanine substituted for glycine

We prepared five mutant lysozymes in which glycines whose dihedralangles are located in the region of the left-handed helix, Gly49,Gly67, Gly71, Gly102 and Gly117, were mutated to an alanineresidue. From analyses of their thermal stabilities using differentialscanning calorimetry, most of them were more destabilized thanthe native lysozyme, except for the G102A mutant, which hasa stability similar to that of the native lysozyme at pH 2.7.As for the destabilized mutant lysozymes, their X-ray crystallographicanalyses showed that their global structures did not changebut that the local structures changed slightly. By examiningthe dihedral angles at the mutation sites based on X-ray crystallographicresults, it was found that the dihedral angles at these mutationsites tended to adopt favorable values in a Ramachandran plotand that the extent and direction of their shifts from the originalvalue had similar tendencies. Therefore, the change in dihedralangles may be the cause of the slight local structural changesaround the mutation site. On the other hand, regarding the mutationof G102A, the global structure was almost identical with thatof the native structure but the local structure was drasticallychanged. Therefore, it was suggested that the drastic localconformational change might be effective in releasing the unfavorableinteraction of the native state at the mutation site.     

A Single Mutation at the Ferredoxin Binding Site of P450 Vdh Enables Efficient Biocatalytic Production of 25‐Hydroxyvitamin D3

Vitamin D₃ hydroxylase (Vdh) from Pseudonocardia autotrophica is a cytochrome P450 monooxygenase that catalyzes the two‐step hydroxylation of vitamin D₃ (VD₃) to produce 25‐hydroxyvitamin D₃ (25(OH)VD₃) and 1α,25‐dihydroxyvitamin D₃ (1α,25(OH)₂VD₃). These hydroxylated forms of VD₃ are useful as pharmaceuticals for the treatment of conditions associated with VD₃ deficiency and VD₃ metabolic disorder. Herein, we describe the creation of a highly active T107A mutant of Vdh by engineering the putative ferredoxin‐binding site. Crystallographic and kinetic analyses indicate that the T107A mutation results in conformational change from an open to a closed state, thereby increasing the binding affinity with ferredoxin. We also report the efficient biocatalytic synthesis of 25(OH)VD₃, a promising intermediate for the synthesis of various hydroxylated VD₃ derivatives, by using nisin‐treated Rhodococcus erythropolis cells containing Vdh_T107A. The gene‐expression cassette encoding Bacillus megaterium glucose dehydrogenase‐IV was inserted into the R. erythropolis chromosome and expressed to avoid exhaustion of NADH in a cytoplasm during bioconversion. As a result, approximately 573 μg mL^?1 25(OH)VD₃ was successfully produced by a 2 h bioconversion.     

Soluble network polymers based on trifluoropropyl-substituted open-cage silsesquioxane: Synthesis,properties, and application for surface modifiers

Fluorinated completely condensed polyhedral oligomeric silsesquioxanes (F-CC-POSSs) are widely utilized as surface modifiers for polymeric materials because of their polyhedral and fluorine-rich structures, which generate polymers with lower surface energies under molecular-level control. In contrast, their derivatives, fluorinated incompletely condensed or open-cage POSSs (F-IC-POSSs), have similarly intriguing structures, but their utilization for polymer synthesis remains undeveloped. Herein, fluorinated network polymers were prepared based on a 3,3,3-trifluoropropyl-substituted IC-POSSs via hydrosilylation polymerization with isobutyl- and phenyl-substituted IC-POSS under optimized conditions. In addition to their good thermal stability and tunable refractive indices, these polymers exhibited solution processability and their casting films showed excellent optical transparency, indicating their potential for constructing fluorinated polymers. Their utilization as surface modifiers was examined by addition to poly(methylmethacrylate) (PMMA) films. Intriguingly, modified PMMA films with 2.0 and 0.5 wt% addition showed similar hydrophobicity and surface energies to the films prepared with only fluorinated network polymers.     

Effect of additives on the renaturation of reduced lysozyme in the presence of 4 M urea

Reduced lysozyme was renatured by sulfhydryl-disuffide interchangereactions at pH 8.0 in the presence of 4 M urea, with or withoutadditives at 40°C. In the absence of additives, the finalfolding yield of reduced lysozyme was 40%. In the presence ofsarcosine, glycerol, ammonium sulfate, N-acetyl glucosamineand glucose, its folding yields increased in all cases. In particular,yields increased up to 90% in the presence of 4 M sarcosine.On the other hand, the melting temperatures of lysozyme withor without additives in 0.02 M citrate buffer (pH 6.0) wereevaluated using differential scanning calorimetry. In the absenceof additive, the melting temperature of lysozyme was 73.8°C.In the presence of additives, all melting temperatures werehigher than that of lysozyme in the absence of additives. Moreover,there was a good correlation on addition of additives betweenan increase in the folding yield of reduced lysozyme with 4M urea and an increase in the melting temperature without 4M urea. Therefore, we conclude that additives, which stabilizenative lysozyme, are effective at increasing the folding yieldof reduced lysozyme in 4 M urea.     

A control method with pheromone information for a transport system

Since the control methods of a transport system between processing machines are specialized for each layout of the system, it is difficult to design prompt schedules and control logic for new complicated systems, especially in cases of machine faults or restructuring the system to modify the layout. In this article, we describe a multiagent transport control system which utilizes pheromone information. Each element of the system acts as an agent and estimates the appropriate path and time to drive out the products using information obtained by communication with other elements as well as pheromone information deposited on the tracks of the products.     

Abnormal myelination in a patient with ring chromosome 18

BACKGROUND: Most adult anatomical texts state that the deep inguinal ring is situated midway between the anterior superior iliac spine and the pubic tubercle. The aim of this study was to determine if this was true in prepubescent children. METHODS: A total of 107 inguinal ligaments and canals were measured during inguinal operations in 80 children (68 boys, age range 1-118 months). RESULTS: The length of the inguinal ligament increased from a median of 4.3 cm (range 3.6-6.8) at less than 1 year of age to 7.5 cm (range 6.7-10.1) at over 4 years of age. The internal ring was situated medial to the midpoint of the inguinal ligament throughout childhood. The ratio of internal ring to public tubercle over inguinal ligament length was 42% (range 27-58) at less than 2 years; and 34% (range 25-46) at over 4 years. The inguinal canal remained short (median 1 cm (range 0.7-1.1) at less than 2 years, and median 1.1 cm (range 0.7-2.3) at over 4 years) suggesting that growth of the inguinal region in this age group occurs outside the canal. CONCLUSIONS: These results have implications for the siting of incisions, and question the necessity of opening the inguinal canal in children.     

Novel method for centre wavelength tuning of silica waveguide type Mach-Zehnder multi/demultiplexers

A novel method for tuning the centre wavelength of silica waveguide type Mach-Zehnder multi/demultiplexers (MUX/DEMUXs) has been devised. This tuning is achieved by irradiating a CO/sub 2/ laser beam onto either arm of the Mach-Zehnder interferometer. In a MUX/DEMUX for channel spacing of 20 nm, the centre wavelength is tuned about 3 nm and the results closely agree with the calculation.<>