http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Synthetic molecular motors and mechanical machines.

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

Over the 100 years since its discovery, liquid crystals have been the intriguing subject for both academia and industries. The textbook of de Gennes The Physics of Liquid Crystals published in 1974 is still the bible for many LC researchers, but new subjects unmentioned in the book have also risen for these years. This chapter describes the story of the recent developments and the future perspectives in physics of liquid crystals, especially focusing on the contributions by Japanese research groups for the last decade.

Physics of Liquid Crystals

Dynamic atomic force microscopy methods

A novel dichiral azobenzene compound which shows two kinds of highly ordered liquid-crystalline phases was prepared. One of the mesophases was found, by miscibility studies, to be a chirality-induced three-dimensional (3D) liquid crystal phase. We, for the first time demonstrate the photoinduced phase transition of the liquid-crystalline 3D structure.

Novel Photoinduced Phase Transition Observed in Three-dimensional Liquid-crystalline Phase of Azobenzene Compound

An experimental approach to investigate anomalous electrical conduction in a 100 nm width silicon wire by scanning Maxwell-stress microscopy (SMM) has been reported. The silicon wire exhibited negative resistance and hysteresis characteristics by sweeping the applied voltage up to 50 V. Potential profile along the wire obtained from the SMM images exhibited that lateral electric field significantly increased at the ground-side end of the wire after the hysteresis characteristics emerged. The field increase is interpreted as the conductivity decrease. The origin of the conductance decrease is considered to be generation and trapping of hot holes at the ground-side end.

Characterization of electrical conduction in silicon nanowire by scanning Maxwell-stress microscopy

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Myxobolus koi (Myxozoa: Myxosporea) forms large- and small-type "cysts" in the gills of common carp.

We investigate how the interaction of particles mediated by an elastic deformation of a nematic liquid crystal is influenced by the initial deformation of the director field. To this end, we calculate the interaction energy between particles in a nematic cell with hybrid boundary conditions, homeotropic on the surface of one confining plate and planar on the other. We find an analytic form of the interaction energy in the case of weak anchoring on the surface of the particle. This interaction energy sensitively depends on the position of the two particles as well as the interparticle distance and can be nonmonotonic with a minimum in its landscape. This nontrivial energy landscape might lead to a chainlike superstructure of particles.

Interaction of particles in a deformed nematic liquid crystal

Anglerfish from the genus Lophius are a globally important commercial fishery. The microsporidian Spraguea infects the nervous system of these fish resulting in the formation of large, visible parasitic xenomas. Lophius litulon from Japan were investigated to evaluate the intensity and distribution of Spraguea xenomas throughout the nervous system and to assess pathogenicity to the host and possible transmission routes of the parasite. Spraguea infections in L. litulon had a high prevalence; all fish over 403 mm in standard length being infected, with larger fish usually more heavily infected than smaller fish. Seventy percent of all fish examined had some gross visible sign of infection. The initial site of development is the supramedullary cells on the dorsal surface of the medulla oblongata, where all infected fish have parasitic xenomas. As the disease progresses, a number of secondary sites typically become infected such as the spinal, trigeminal and vagus nerves. Fish with infection in the vagus nerve bundles often have simultaneous sites of infection, in particular the spinal nerves and along the ventral nerve towards the urinary bladder. Advanced vagus nerve infections sometimes form xenomas adjacent to kidney tissue. Spraguea DNA was amplified from the contents of the urinary bladders of two fish, suggesting that microsporidian spores may be excreted in the urine. We conclude that supramedullary cells on the hindbrain are the primary site of infection, which is probably initiated at the cutaneous mucous glands where supramedullary cells are known to extend their peripheral axons. The prevalence of Spraguea infections in L. litulon was very high, and infections often extremely heavy; however, no associated pathogenicity was observed, and heavily infected fish were otherwise normal.

Spraguea (Microsporida: Spraguidae) infections in the nervous system of the Japanese anglerfish, Lophius litulon (Jordan), with comments on transmission routes and host pathology.

Hiroshi Yokoyama

Papers

Novel Photoinduced Phase Transition Observed in Three-dimensional Liquid-crystalline Phase of Azobenzene Compound

Characterization of electrical conduction in silicon nanowire by scanning Maxwell-stress microscopy

Myxobolus koi (Myxozoa: Myxosporea) forms large- and small-type "cysts" in the gills of common carp.

Interaction of particles in a deformed nematic liquid crystal

Spraguea (Microsporida: Spraguidae) infections in the nervous system of the Japanese anglerfish, Lophius litulon (Jordan), with comments on transmission routes and host pathology.