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Proceedings of the Japan Academy. Series B, Physical and Biological Sciences

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https://www.readbyqxmd.com/read/28496055/organization-and-dynamics-of-yeast-mitochondrial-nucleoids
#1
Isamu Miyakawa
Mitochondrial DNA (mtDNA) is packaged by association with specific proteins in compact DNA-protein complexes named mitochondrial nucleoids (mt-nucleoids). The budding yeast Saccharomyces cerevisiae is able to grow either aerobically or anaerobically. Due to this characteristic, S. cerevisiae has been extensively used as a model organism to study genetics, morphology and biochemistry of mitochondria for a long time. Mitochondria of S. cerevisiae frequently fuse and divide, and perform dynamic morphological changes depending on the culture conditions and the stage of life cycle of the yeast cells...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28496054/days-weaving-the-lagging-strand-synthesis-of-dna-a-personal-recollection-of-the-discovery-of-okazaki-fragments-and-studies-on-discontinuous-replication-mechanism
#2
Tsuneko Okazaki
At DNA replication forks, the overall growth of the antiparallel two daughter DNA chains appears to occur 5'-to-3' direction in the leading-strand and 3'-to-5' direction in the lagging-strand using enzyme system only able to elongate 5'-to-3' direction, and I describe in this review how we have analyzed and proved the lagging strand multistep synthesis reactions, called Discontinuous Replication Mechanism, which involve short RNA primer synthesis, primer-dependent short DNA chains (Okazaki fragments) synthesis, primer removal from the Okazaki fragments and gap filling between Okazaki fragments by RNase H and DNA polymerase I, and long lagging strand formation by joining between Okazaki fragments with DNA ligase...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28496053/chemical-and-structural-biology-of-protein-lysine-deacetylases
#3
Minoru Yoshida, Norio Kudo, Saori Kosono, Akihiro Ito
Histone acetylation is a reversible posttranslational modification that plays a fundamental role in regulating eukaryotic gene expression and chromatin structure/function. Key enzymes for removing acetyl groups from histones are metal (zinc)-dependent and NAD(+)-dependent histone deacetylases (HDACs). The molecular function of HDACs have been extensively characterized by various approaches including chemical, molecular, and structural biology, which demonstrated that HDACs regulate cell proliferation, differentiation, and metabolic homeostasis, and that their alterations are deeply involved in various human disorders including cancer...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28496052/data-management-issues-in-mobile-ad-hoc-networks
#4
Takahiro Hara
Research on mobile ad hoc networks (MANETs) has become a hot research topic since the middle 1990's. Over the first decade, most research focused on networking techniques, ignoring data management issues. We, however, realized early the importance of data management in MANETs, and have been conducting studies in this area for 15 years. In this review, we summarize some key technical issues related to data management in MANETs, and the studies we have done in addressing these issues, which include placement of data replicas, update management, and query processing with security management...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28496051/molecular-investigations-of-development-and-diseases-of-the-brain-of-higher-mammals-using-the-ferret
#5
Hiroshi Kawasaki
The brains of higher mammals such as primates and carnivores contain well-developed unique brain structures. Uncovering the physiological functions, developmental mechanisms and evolution of these brain structures would greatly facilitate our understanding of the human brain and its diseases. Although the anatomical and electrophysiological features of these brain structures have been intensively investigated, our knowledge about their molecular bases is still limited. To overcome this limitation, genetic techniques for the brains of carnivores and primates have been established, and molecules whose expression patterns correspond to these brain structures were identified recently...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28496050/multiple-system-atrophy-clinicopathological-characteristics-in-japanese-patients
#6
Tetsutaro Ozawa, Osamu Onodera
Multiple system atrophy (MSA) is an adult-onset neurodegenerative disorder that has both clinical and pathological variants. Clinical examples include MSA with predominant cerebellar ataxia (MSA-C) and MSA with predominant parkinsonism (MSA-P), whereas olivopontocerebellar atrophy and striatonigral degeneration represent pathological variants. We performed systematic reviews of studies that addressed the relative frequencies of clinical or pathological variants of MSA in various populations to determine the clinicopathological characteristics in Japanese MSA...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28413199/rapid-and-coordinated-processing-of-global-motion-images-by-local-clusters-of-retinal-ganglion-cells
#7
Akihiro Matsumoto, Masao Tachibana
Even when the body is stationary, the whole retinal image is always in motion by fixational eye movements and saccades that move the eye between fixation points. Accumulating evidence indicates that the brain is equipped with specific mechanisms for compensating for the global motion induced by these eye movements. However, it is not yet fully understood how the retina processes global motion images during eye movements. Here we show that global motion images evoke novel coordinated firing in retinal ganglion cells (GCs)...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28413198/engineering-the-lodging-resistance-mechanism-of-post-green-revolution-rice-to-meet-future-demands
#8
REVIEW
Ko Hirano, Reynante Lacsamana Ordonio, Makoto Matsuoka
Traditional breeding for high-yielding rice has been dependent on the widespread cultivation of gibberellin (GA)-deficient semi-dwarf varieties. Dwarfism lowers the "center of gravity" of the plant body, which increases resistance against lodging and enables plants to support high grain yield. Although this approach was successful in latter half of the 20th century in rice and wheat breeding, this may no longer be enough to sustain rice with even higher yields. This is because relying solely on the semi-dwarf trait is subject to certain limitations, making it necessary to use other important traits to reinforce it...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28413197/structure-and-function-of-helicobacter-pylori-caga-the-first-identified-bacterial-protein-involved-in-human-cancer
#9
REVIEW
Masanori Hatakeyama
Chronic infection with Helicobacter pylori cagA-positive strains is the strongest risk factor of gastric cancer. The cagA gene-encoded CagA protein is delivered into gastric epithelial cells via bacterial type IV secretion, where it undergoes tyrosine phosphorylation at the Glu-Pro-Ile-Tyr-Ala (EPIYA) motifs. Delivered CagA then acts as a non-physiological scaffold/hub protein by interacting with multiple host signaling molecules, most notably the pro-oncogenic phosphatase SHP2 and the polarity-regulating kinase PAR1/MARK, in both tyrosine phosphorylation-dependent and -independent manners...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28413196/the-molecular-cues-regulating-immune-cell-trafficking
#10
REVIEW
Akira Takeda, Naoko Sasaki, Masayuki Miyasaka
Lymphocyte recirculation between the blood and the lymphoid/non-lymphoid tissues is an essential homeostatic mechanism that regulates humoral and cellular immune responses in vivo. This system promotes the encounter of naïve T and B cells with their specific cognate antigen presented by dendritic cells, and with the regulatory cells with which they need to interact to initiate, maintain, and terminate immune responses. The constitutive lymphocyte trafficking is mediated by particular types of blood vessels, including the high endothelial venules (HEVs) in lymph nodes and Peyer's patches, and the flat-walled venules in non-lymphoid tissues including the skin...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28413195/purinergic-signaling-in-microglia-in-the-pathogenesis-of-neuropathic-pain
#11
REVIEW
Kazuhide Inoue
Nerve injury often causes debilitating chronic pain, referred to as neuropathic pain, which is refractory to currently available analgesics including morphine. Many reports indicate that activated spinal microglia evoke neuropathic pain. The P2X4 receptor (P2X4R), a subtype of ionotropic ATP receptors, is upregulated in spinal microglia after nerve injury by several factors, including CC chemokine receptor CCR2, the extracellular matrix protein fibronectin in the spinal cord, interferon regulatory factor 8 (IRF8) and IRF5...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28413194/dual-role-of-cellular-prion-protein-in-normal-host-and-alzheimer-s-disease
#12
REVIEW
Takashi Onodera
Using PrP(C)-knockout cell lines, it has been shown that the inhibition of apoptosis through STI1 is mediated by PrP(C)-dependent SOD activation. Antioxidant PrP(C) may contribute to suppression of inflammasome activation. PrP(C) is functionally involved in copper metabolism, signal transduction, neuroprotection, and cell maturation. Recently several reports have shown that PrP(C) participates in trans-membrane signaling processes associated with hematopoietic stem cell replication and neuronal differentiation...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28302962/finite-block-length-analysis-in-classical-and-quantum-information-theory
#13
REVIEW
Masahito Hayashi
Coding technology is used in several information processing tasks. In particular, when noise during transmission disturbs communications, coding technology is employed to protect the information. However, there are two types of coding technology: coding in classical information theory and coding in quantum information theory. Although the physical media used to transmit information ultimately obey quantum mechanics, we need to choose the type of coding depending on the kind of information device, classical or quantum, that is being used...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28302961/getting-to-the-heart-of-the-matter-in-cancer-novel-approaches-to-targeting-cancer-stem-cells
#14
REVIEW
Hugh Colvin, Masaki Mori
Cancer is one of the leading causes of deaths worldwide. While cancers may initially show good response to chemotherapy or radiotherapy, it is not uncommon for them to recur at a later date. This phenomenon may be explained by the existence of a small population of cancer stem cells, which are inherently resistant to anti-cancer treatment as well as being capable of self-renewal. Therefore, while most of the tumour bulk consisting of cells that are not cancer stem cells respond to treatment, the cancer stem cells remain, leading to disease recurrence...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28302960/development-of-chemical-and-chemo-enzymatic-glycosylations
#15
REVIEW
Shin-Ichiro Shoda
Glycosidic compounds are indispensable molecules in living systems. Biological phenomena such as cell wall formation, energy storage, and cell recognition strongly depend on the multi-functional characters of these substances. Development of highly regio- and stereoselective glycosylation reactions is necessary to provide sufficient amounts of specific compounds in basic research as well as for applications in industry. This review presents an overview of chemical and chemo-enzymatic glycosylations that have been developed during my forty-year academic career in the field of glyco-science...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28190871/heating-mechanisms-of-the-solar-corona
#16
REVIEW
Takashi Sakurai
The solar corona is a tenuous outer atmosphere of the Sun. Its million-degree temperature was discovered spectroscopically in the 1940s, but its origin has been debated since then without complete convergence. Currently there are two classes of models; the wave theory and the microflare/nanoflare theory. Both models have merits and disadvantages, but the essential issues are nearly pinned down. Recent revival of the wave theory is one of the many contributions from Japanese solar observing satellite Hinode launched in 2006...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28190870/the-complexity-of-glycoprotein-derived-glycans
#17
REVIEW
Johannes F G Vliegenthart
A brief review is presented of our studies on the structure of glycoprotein-derived glycans. The emphasis is on the introduction of high-resolution (1)H-NMR spectroscopy for the unambiguous determination of primary structures. For this purpose, we developed the structural reporter group concept. Structural reporters are defined as unique markers of structural elements in the NMR spectra. Application of this concept led to the discovery of numerous new structures. Furthermore, a number of structures presented in the literature could be corrected...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28190869/single-molecule-detection-thermal-fluctuation-and-life
#18
REVIEW
Toshio Yanagida, Yoshiharu Ishii
Single molecule detection has contributed to our understanding of the unique mechanisms of life. Unlike artificial man-made machines, biological molecular machines integrate thermal noises rather than avoid them. For example, single molecule detection has demonstrated that myosin motors undergo biased Brownian motion for stepwise movement and that single protein molecules spontaneously change their conformation, for switching to interactions with other proteins, in response to thermal fluctuation. Thus, molecular machines have flexibility and efficiency not seen in artificial machines...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28077808/rupture-waves-and-earthquakes
#19
REVIEW
Koji Uenishi
Normally, an earthquake is considered as a phenomenon of wave energy radiation by rupture (fracture) of solid Earth. However, the physics of dynamic process around seismic sources, which may play a crucial role in the occurrence of earthquakes and generation of strong waves, has not been fully understood yet. Instead, much of former investigation in seismology evaluated earthquake characteristics in terms of kinematics that does not directly treat such dynamic aspects and usually excludes the influence of high-frequency wave components over 1 Hz...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28077807/folding-of-apomyoglobin-analysis-of-transient-intermediate-structure-during-refolding-using-quick-hydrogen-deuterium-exchange-and-nmr
#20
REVIEW
Chiaki Nishimura
The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
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