Relationship between noise characteristics in protein expressions and regulatory structures of amino acid biosynthesis pathways

Gene regulatory dynamics involves several stochastic chemical reactions. As a consequence, the copy number of given protein varies greatly among cells even in the case of isogeneic cells. Recently, the characteristics of noise in gene expressions were studied by using simple artificial gene networks. However, the noise characteristics in natural regulatory networks having complex interactions still remain unclear. In this study, we have focused on the noise in natural regulatory networks to understand the relationship between the characteristics of the noise and the structures of regulatory interactions. We targeted the expressions of genes related to amino acid biosynthesis (AAB) because of their well known regulatory structures. By measuring the noise of AAB genes in isogeneic Escherichia coli cells using flow cytometry, we found the noise amplitude in AAB genes to depend on the structure of the regulatory network. We categorised the regulatory networks with feedback regulation into two cases. In one case, the gene expression is negatively regulated by the final products of the AAB pathway known as feedback repression, whereas in another case, the gene expression is negatively regulated as a result of depletion of the substrate that is located upstream of the AAB pathway and activates the expression of the corresponding gene. Our data revealed that the noise amplitude of AAB genes in the former case is significantly smaller than the noise amplitude in the latter case. Furthermore, we found that the response time as a result of environmental changes is generally longer in the former case. This result provides a basis for understanding the role of natural regulatory networks better.     

Histological Contribution of Collagen Architecture to Beef Toughness

ABSTRACT:  The relationship between shear-force value and collagen architecture of connective tissue of the  longissimus thoracis  (LT) muscle of Japanese Black ( n  = 10) and Brown (Kumamoto) ( n  = 5) steers (body weight: 688.4 ± 8.6 kg as average and standard error) was investigated. There were negative correlations between the shear-force value and lipid content ( n  = 15,  R ²= 0.3709,  P  < 0.01) and protein content and lipid content ( n  = 15,  R ²= 0.6748,  P  < 0.01). Shear-force value and collagen content ( n  = 15,  R ²= 0.4344,  P  < 0.01) were positively correlated. In scanning electron microscopic photographs of the macerated preparation, the perimysium of the high-lipid LT muscle was broken down compared with the low-lipid LT muscle. The endomysium in all LT muscle fibers showed similar architecture. The fine surface cover of reticular collagen fibers around an adipocyte was observed in the high-lipid LT muscle perimysium. These results suggested that the shear-force value of the LT muscle was related to change in collagen architecture and of the perimysium in particular.     

A parallel iterative partitioned coupling analysis system for large-scale acoustic fluid–structure interactions

In many engineering fields, dynamic response in fluid–structure interaction (FSI) is important, and some of the FSI phenomena are treated as acoustic FSI (AFSI) problems. Dynamic interactions between fluids and structures may change dynamic characteristics of the structure and its response to external excitation parameters such as seismic loading. This paper describes a parallel coupling analysis system for large-scale AFSI problems using iterative partitioned coupling techniques. We employ an open source parallel finite element analysis system called ADVENTURE, which adopts an efficient preconditioned iterative linear algebraic solver. In addition, we have recently developed a parallel coupling tool called ADVENTURE_Coupler to efficiently handle interface variables in various parallel computing environments. We also employ the Broyden method for updating interface variables to attain robust and fast convergence of fixed-point iterations. This paper describes key features of the coupling analysis system developed, and we perform tests to validate its performance for several AFSI problems. The system runs efficiently in a parallel environment, and it is capable of analyzing three-dimensional-complex-shaped structures with more than 20 million degrees-of-freedom (DOFs). Its numerical results also show good agreement with experimental results.     

N‐Heterocyclic Carbene‐Catalyzed Benzoin Strategy for Divergent Synthesis of Cyclitol Derivatives from Alditols

A divergent synthesis of cyclitol derivatives has been developed utilizing an N‐heterocyclic carbene‐catalyzed benzoin‐type cyclization of C₂‐symmetrical dialdoses. The resulting inososes are versatile intermediates, which are readily converted into not only inositols but also amino‐, deoxy‐, O‐methyl‐ and C‐methyl‐inositols.

     

Theoretical performance analysis on transmission reserve table buffer with triage ranking for resource‐limited control networks

Performance of the ‘transmission reserve table’ (TRT) buffer, which the authors recently proposed, is theoretically investigated. The buffer's triage ranking queuing was designed for resource‐limited control networks that are possibly exposed to a rush of control commands. Our previous study analyzed the performance of the TRT buffer by means of computer simulation. In this paper, we derive a stochastic analytical model for the TRT buffer and verify the model in comparison with computer simulations. Theoretical calculation demonstrates that the triage ranking of the TRT plays a crucial role in keeping the real‐timeness of the control network even in a rush of commands by our triage ranking mechanism. © 2015 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.     

Comparison of the Reactivity of Carbohydrate Photoaffinity Probes with Different Photoreactive Groups

A judicious choice of photoreactive group is critical in successful photoaffinity labeling studies of small molecule–protein interactions. A set of carbohydrate‐based photoaffinity probes was prepared to compare the effects of three major photoreactive groups on the efficiency and selectivity of crosslinking a binding protein with low affinity. We showed that, despite the low crosslinking yield, the diazirine probe displayed the high ligand‐dependent reactivity consistent with the ideal mechanism of photoaffinity labeling. Moreover, we demonstrated that, among the three photoreactive groups, only the diazirine probe achieved highly selective crosslinking of a low‐affinity binding protein in cell lysate.     

Improvement of Mechanical Properties of Softwood Lignin-Based Carbon Fibers

PEG-lignin fibers obtained by a solvolysis pulping of Japanese cedar with polyethylene glycol (PEG) 400 were successfully converted into defective-free, infusible fibers as a precursor for carbon fibers (CFs) by chemical curing followed by oxidative thermostabilization. The curing was performed by immersing PEG-lignin fibers in an aqueous mixed solution of hexamethylenetetramine (60 g/L) and hydrochloric acid (3 M) at 85°C for 1 h, resulting in the formation of crosslinkages between lignin molecules through methylene groups. These cured fibers were completely thermostabilized upon heating up to 250°C at a heating rate of 2°C/min under an air atmosphere. Finally, the thermostabilized fibers were carbonized to yield CFs, which showed about 1.5 times the tensile strength of our CFs previously prepared.