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

Existing experimental techniques for measuring the orientational anchoring strength at a substrate-nematic interface are critically analyzed with a particular emphasis on their macroscopic basis and on the range of applicability and precision. Conceptual basis of the anchoring strength is first clarified by making a distinction between the macroscopic and the microscopic approaches toward the substrate-nematic interface, and the significance of the Gibbs’ dividing surface is emphasized together with some thermodynamic properties of the anchoring strength and pretilt angle. The principles of some typical experimental techniques are next reviewed from a fundamental viewpoint, and possible complications and sources of error in these methods, when applied to an interface with strong anchoring, are discussed. Drawing upon the result of the “high-electric-field technique” which yields an anchoring energy apparently larger than 10−3 J/m2, the greatest value ever observed, for a planar-aligned nematic on...

Surface Anchoring of Nematic Liquid Crystals

IL-1 is a pro-inflammatory cytokine consisted of two molecular species, IL-1alpha and IL-1beta, and the IL-1 receptor antagonist (IL-1Ra) is a natural inhibitor of both molecules. Although it is suggested that IL-1 potentiates immune responses mediated by T(h)2 cells, the role of IL-1 in asthma still remains unclear. In this study, we demonstrate that the ovalbumin (OVA)-induced airway hypersensitivity response (AHR) in IL-1alpha/beta-deficient (IL-1alpha/beta(-/-)) mice was significantly reduced from the levels seen in wild-type mice, whereas the responses seen in IL-1Ra(-/-) mice were profoundly exacerbated, suggesting that IL-1 is required for T(h)2 cell activation during AHR. OVA-specific T cell proliferation, IL-4 and IL-5 production by T cells, and IgG1 and IgE production by B cells in IL-1alpha/beta(-/-) mice were markedly reduced compared with these responses in wild-type mice; such responses were enhanced in IL-1Ra(-/-) mice. Using IL-1alpha(-/-) and IL-1beta(-/-) mice, we determined that both IL-1alpha and IL-1beta are involved in this reaction. Both IgG1 and IgE levels were reduced in IL-1beta(-/-) mice, while only IgE levels were affected in IL-1alpha(-/-) mice, indicating a functional difference between IL-1alpha and IL-1beta. These observations indicate that IL-1 plays important roles in the development of AHR.

/pdf/il-1-is-required-for-allergen-specific-th2-cell-activation-koyhz9y9br.pdf

IL‐1 is required for allergen‐specific Th2 cell activation and the development of airway hypersensitivity response

More than 30 species of marine fish are cultured in Japan and a wide variety of parasites are recognized as serious pathogens of these fish. In most cases, marine fish are cultured in floating net cages, which can provide a suitable substrate for monogenean eggs to become entangled with. This characteristic is most typically exemplified by the monogenean Heterobothrium okamotoi of tiger puffer; the parasite deposits a very long string of eggs, almost all of which become entangled with the net meshing, resulting in an accumulation of eggs within the culture system. Life cycles of important parasites of cultured marine fish, such as myxosporeans (e.g. Kudoa amamiensis and Myxobolus buri of yellowtail), microsporidians (Microsporidium seriolae of yellowtail and an unidentified species from tiger puffer) or blood flukes (Paradeontacylix spp. of amberjack) have not been elucidated. This is a large obstacle to the establishment of control measures against these parasitic diseases. Generally, parasitic diseases of cultured marine fish are much more difficult to control than their counterparts in fresh water. No single method has proved sufficient for the effective control of parasitic diseases of marine fish. Future efforts to control marine infections should be directed not only to chemical treatments, but also to biological measures, and to prophylaxis and quarantine through parasite detection and early diagnosis.

https://www.jstage.jst.go.jp/article/jsfp1966/33/4/33_4_303/_pdf

Parasitic diseases of cultured marine fish in Japan

The out‐of‐plane anchoring strength at the interface between 4‐n‐pentyl‐4’‐cyanobiphenyl (5CB) and an obliquely evaporated SiO was measured as a function of temperature by applying the ‘‘high‐electric‐field technique’’ recently developed by Yokoyama and van Sprang [J. Appl. Phys. 57, 4520 (1985)]. The orientational ‘‘extrapolation length’’de for the interface was found to remain virtually constant at about 30 nm up to nearly 1 K below the clearing temperature Tc=308.4 K. At temperatures closer to Tc, however, it was observed to show an apparently critical increase, which approximately follows de∝[(Tc−T)/Tc]−0.45. At 0.043 K below Tc, de=183±3 nm, yielding the anchoring energy of (1.13±0.03)×10−5 J/m2. The implications of the observed temperature dependence are first investigated by extending Gibbs’ surface thermodynamics to a nematic‐wall interface, deriving a general relationship between the temperature variation of de and the surface excess entropy. In particular, it is concluded on thermodynamic grounds that the exponent of −0.45 can never be associated with a real critical behavior, but is indicative of the occurrence of crossover to a more singular or noncritical behavior. To draw specific connections between the temperature dependence of de and the orientational order near the interface,we develop a simple statistical mechanical theory of the anchoring strength, based on a van der Waals picture of the nematic‐wall interface. We show that the extrapolation length consists of two essentially distinct contributions: one is from the anisotropic interactions at the interface and the other is unconventionally from the interfacial inhomogeneity of the order parameter itself. For the most relevant cases, the van der Waals theory states that a reduction of the anchoring strength should always be accompanied by a depression of the surface order parameter. By comparing the theory with the experiment, the surface order parameters just below and above Tc are found to be 0.04 and 0.01, respectively, in agreement with the estimates from the contact angle and the pretransitional birefringence experiments. It is also argued, based on the present model, that the order parameter inhomogeneity is predominantly responsible for the quasicritical behavior of the anchoring strength.

Hiroshi Yokoyama

Papers

Surface Anchoring of Nematic Liquid Crystals

IL‐1 is required for allergen‐specific Th2 cell activation and the development of airway hypersensitivity response

Parasitic diseases of cultured marine fish in Japan

Temperature dependence of the anchoring strength at a nematic liquid crystal‐evaporated SiO interface

Nitrogen removal from animal waste treatment water by anammox enrichment.