bluuebunny/crossref_metadata_2025 huggingface dataset:
Quorum sensing control of Type VI secretion factors restricts the proliferation of quorum-sensing mutants
Authors: Majerczyk Charlotte , Schneider Emily , Greenberg E Peter
Published: May 2016

Burkholderia thailandensis uses acyl-homoserine lactone-mediated quorum sensing systems to regulate hundreds of genes. Here we show that cell-cell contact-dependent type VI secretion (T6S) toxin-immunity systems are among those activated by quorum sensing in B. thailandensis. We also demonstrate that T6S is required to constrain proliferation of quorum sensing mutants in colony cocultures of a BtaR1 quorum-sensing signal receptor mutant and its parent. However, the BtaR1 mutant is not constrained by and outcompetes its parent in broth coculture, presumably because no cell contact occurs and there is a metabolic cost associated with quorum sensing gene activation. The increased fitness of the wild type over the BtaR1 mutant during agar surface growth is dependent on an intact T6SS-1 apparatus. Thus, quorum sensing activates B. thailandensis T6SS-1 growth inhibition and this control serves to police and constrain quorum-sensing mutants. This work defines a novel role for T6SSs in intraspecies mutant control.
Origin of the unidentified positive mobile ions causing the bias temperature instability in SiC MOSFETs and their diffusion process
Authors: Shirakawa Hiroki , Kamiya Katsumasa , Araidai Masaaki , Watanabe Heiji , Shiraishi Kenji
Published: May 2016

For SiC metal–oxide–semiconductor field-effect transistors (MOSFETs), it has been shown that unidentified positive mobile ions are generated in SiO2 after conventional hydrogen annealing, which leads to significant reliability degradation known as bias temperature instability (BTI). Discovering the origin of these mobile ions is important for fabricating highly reliable SiC MOSFETs. On the basis of first-principles calculations, we verified that the BTI of SiC MOSFETs is caused by hydrogen ions combining with CO3-like defects in SiO2. These hydrogen ions dissociate from the CO3-like defects and diffuse “as protons” in SiO2. These results indicate that the observed positive mobile ions are protons.
Silicon on-chip wavelength-selective switch composed of Mach–Zehnder-interferometer-based switches and microring resonators
Authors: Miura Kengo , Shoji Yuya , Mizumoto Tetsuya
Published: May 2016

We fabricated a wavelength-selective switch composed of microring resonators as wavelength filters and Mach–Zehnder-interferometer-based thermo-optic switches as routing switches. Nonblocking wavelength-selective switching operations for several channels were successfully demonstrated. A wavelength-selective transmittance change of 9.7 dB was obtained at a wavelength channel of 1548 nm, which is one of four wavelength channels in a wavelength range between 1535 and 1570 nm. An electric power of 17.9 mW was applied for switching the thermo-optic switch from a cross state to a bar state. The change in transmittance in other wavelength channels is <1.7 dB.
First-principles study of electronic structures of graphene on Y2O3
Authors: Kaneko Tomoaki , Ohno Takahisa
Published: May 2016

We investigate the structures, stability and electronic properties of graphene adsorbed on Y2O3(111) using first-principles calculations based on density functional theories. When the interface of Y2O3(111) is terminated by an Y-layer, graphene is chemisorbed on Y2O3, resulting in the strong modification of electronic band structures. When the Y2O3(111) surface is terminated with O atoms and extra O atoms, on the other hand, graphene is physisorbed on Y2O3(111). Therefore, an O-rich environment is preferable for the graphene and Y2O3 interface.
Top-gated graphene field-effect transistors by low-temperature synthesized SiNx insulator on SiC substrates
Authors: Ohno Yasuhide , Kanai Yasushi , Mori Yuki , Nagase Masao , Matsumoto Kazuhiko
Published: May 2016

Top-gated devices made from an epitaxial graphene film on a 4H-SiC substrate were fabricated. Atomic force microscopy and Raman spectroscopy results showed that a large-scale highly uniform monolayer graphene film was synthesized on the SiC substrate. A SiN
x
passivation film was deposited on a SiC graphene device as a top gate insulator by catalytic chemical-vapor deposition (Cat-CVD) below 65 °C. After the top gate electrode was formed on the SiN
x
film, no leakage current flowed between the gate and source electrodes. The transport characteristics showed clear ambipolar characteristics from 8 to 280 K, and the temperature dependences of the conductance and field-effect mobility of the devices implied that monolayer graphene devices can be successfully fabricated. Moreover, the position of the charge neutrality point after SiN
x
deposition was around 0 V, indicating p-doping characteristics. These results indicate that SiN
x
films synthesized by Cat-CVD can be used as gate insulators and that the carrier type may be controlled by adjusting the deposition conditions.
Fabrication of single TiO2 nanotube devices with Pt interconnections using electron- and ion-beam-assisted deposition
Authors: Lee Mingun , Cha Dongkyu , Huang Jie , Ha Min-Woo , Kim Jiyoung
Published: May 2016

Device fabrication using nanostructured materials, such as nanotubes, requires appropriate metal interconnections between nanotubes and electrical probing pads. Here, electron-beam-assisted deposition (EBAD) and ion-beam-assisted deposition (IBAD) techniques for fabrication of Pt interconnections for single TiO2 nanotube devices are investigated. IBAD conditions were optimized to reduce the leakage current as a result of Pt spreading. The resistivity of the IBAD-Pt was about three orders of magnitude less than that of the EBAD-Pt, due to low carbon concentration and Ga doping, as indicated by X-ray photoelectron spectroscopy analysis. The total resistances of single TiO2 nanotube devices with EBAD- or IBAD-Pt interconnections were 3.82 × 1010 and 4.76 × 108 Ω, respectively. When the resistivity of a single nanotube is low, the high series resistance of EBAD-Pt cannot be ignored. IBAD is a suitable method for nanotechnology applications, such as photocatalysis and biosensors.
Influence of 700 °C vacuum annealing on fracture behavior of micro/nanoscale focused ion beam fabricated silicon structures
Authors: Goshima Yoshiharu , Fujii Tatsuya , Inoue Shozo , Namazu Takahiro
Published: May 2016

In this paper, we describe the influence of 700 °C vacuum annealing on strength and fracture behavior of micro- and nano-scale Si structures fabricated by focused ion beam (FIB). Si nanowires (NWs) made from silicon-on-nothing (SON) membrane are fabricated using FIB. Microscale Si specimens are fabricated by conventional micromachining technologies and FIB. These specimens are tensioned to failure using specially developed microelectromechanical systems (MEMS) device and thin-film tensile tester, respectively. The mean fracture strengths of the nano- and microscale specimens are 5.6 and 1.6 GPa, respectively, which decrease to 2.9 and 0.9 GPa after vacuum annealing at 700 °C for only 10 s. These strength values do not vary with increasing annealing time. Fracture origin and its behavior are discussed in the light of fracture surface and FIB damage layer observations.
Shape control of self-organized porous silica submicron particles and their strength evaluation
Authors: Kiyohara Keita , Inoue Keita , Inoue Shozo , Namazu Takahiro
Published: May 2016

In this paper, precise control of the shape, size, and porosity of porous silica submicron particles and their strength evaluation are described. Self-organization phenomenon of silica nanopowders and submicron polystyrene latex (PSL) balls in an atomized mist is used for the fabrication of the particles. When temperatures of lower- and upper-zone heaters are 100 and 600 °C, and N2 gas flow rate is 0.4 l/min, spherical particles are produced. When PSL concentration increases, the number of pores increases. Particles with uniformly-arranged pores are produced at the PSL concentration of around 3 wt %. By using the PSL balls of different diameters, porous silica particles including different size pores are made. Also, compressive fracture test is conducted to check the effect of vacuum annealing on the strength of particles. The annealed particle shows higher fracture force than the unannealed particle, which indicates that the annealing would be effective for improving the mechanical reliability.
Visible and Infrared Remote Sensing
Authors: Emery William J.
Published: May 2016

Visible and infrared satellite remote sensing originated with the need to provide satellite imagery of the Earth's weather from Earth‐orbiting satellites. Visible images would provide the distribution of clouds over the Earth during daytime, while the infrared would provide a similar picture at night. These satellite systems were developed by the National Aeronautics and Space Administration (NASA) and then turned over to the National Oceanic and Atmospheric Administration (NOAA) for their operations as part of the weather forecast system. Later an emphasis was put on using narrow visible bands to study the Earth's surface in detail. This satellite series became a joint project between NASA and the U.S. Geological Survey (USGS). The meteorological satellites began as a polar‐orbiting series but later gave rise to a geostationary satellite program. This geostationary program has gone through many changes but is now the backbone of weather forecasting operations. There continues to be a polar‐orbiting weather satellite system for weather forecasting as well but data from this series have been used for a great many other applications to both ocean and land surfaces. The Landsat cooperation between NASA and USGS continues and has recently seen some dramatic improvements in sensing capability.
Finite‐Difference Time‐Domain Solution of Maxwell's Equations
Authors: Taflove Allen , Hagness Susan C.
Published: May 2016

For over 100 years after the publication of Maxwell's equations in 1865, essentially all solution techniques for electromagnetic fields and waves were based on Fourier‐domain concepts, assuminga prioria time‐harmonic (sinusoidal steady‐state) field variation and possibly the existence of a particular Green's function or a set of spatial modes. In 1966, Kane Yee's seminal paper introduced a complete paradigm shift in how to solve Maxwell's equations, reporting a field evolution‐in‐time technique that subsequently evolved into the finite‐difference time‐domain (FDTD) method. In the decades since the publication of Yee's paper, there has been an explosion of interest in FDTD and related grid‐based time‐marched solutions of Maxwell's equations among scientists and engineers. During this period, FDTD modeling has evolved to an advanced stage enabling large‐scale simulations of full‐wave time‐domain electromagnetic wave interactions with volumetrically complex structures over large frequency ranges, spatial scales, and timescales. Currently, FDTD modeling spans the electromagnetic spectrum from ultralow frequencies to visible light. FDTD modeling is routinely conducted as an invaluable virtual laboratory bench in scientific inquiry and exploration in electrodynamics; as an integral part of the electromagnetic engineering design and optimization process; and as a powerful forward solver in imaging and sensing inverse problems. This article reviews the technical basis of the key features of FDTD solution techniques for Maxwell's equations and provides 18 modeling examples spanning the electromagnetic spectrum to illustrate the power, flexibility, and robust nature of FDTD computational electrodynamics simulations.
Multi‐channel MAC Protocols and Power Control for Wireless Ad hoc Networks
Authors: Minh Dang Duc Ngoc , Hong Choong Seon
Published: May 2016

IEEE 802.11 provides multiple channels for wireless communications at the physical layer, however the Medium Access Control (MAC) protocol is designed only for single channel. Moreover, the Carrier Sense Multiple Access (CSMA)‐based MAC protocol in IEEE 802.11 suffers from the starvation problem. By exploiting the multiple channels and employing the power control algorithm to increase the spatial reuse, we can improve the network performance. Motivated by this, herein we present multichannel MAC protocols and power control algorithms proposed for wireless ad hoc networks.
RWG
Functions: Evolution and Progress
Authors: Rao Sadasiva M. , Wilton Donald R. , Glisson Allen W.
Published: May 2016

The Rao–Wilton–Glisson (RWG) functions, defined over a pair of planar triangles, originally were developed for solving electromagnetic scattering and radiation problems from metallic bodies. Later, these functions found applications in other numerical electromagnetic research problems as well involving non‐metallic and combinations of metallic and nonmetallic bodies. Further, RWG functions were applied successfully in various other research areas. In this work, we present the underlying concepts while developing the functions, extensions to solve other closely related problems, and a detailed list of applications in other research areas.
Cellulose Fibers, Regenerated
Authors: Woodings Calvin
Published: May 2016

Fibers manufactured from cellulose are either derivative or regenerated; historically, they are designated man‐made fibers and distinguished from fibers based on synthetic organic polymers. A derivative fiber is one formed when a chemical derivative of a natural polymer, for example, cellulose, is dissolved and extruded as a continuous filament, and the chemical nature of the derivative is retained after the fiber formation process. A regenerated fiber is one formed when a natural polymer, or its chemical derivative, is dissolved and extruded as a continuous filament, and the chemical nature of the natural polymer is either retained or regenerated after the fiber formation process. The difficulties of making solutions of natural cellulose from which fibers can be spun has led to most fabricated cellulosic fibers being regenerated from more readily soluble derivatives of cellulose. It is the technology of making these fibers that is the subject of this article.

Textile fibers and filaments composed of regenerated cellulose are called rayons. In Europe, the fibers are now generally known as viscose or lyocell; the term viscose rayon is used whenever confusion between the fiber and the cellulose xanthate solution (also called viscose) is possible. In addition to the viscose process, the cuprammonium rayon and direct dissolution–or lyocell processes are also covered. Fiber properties and environmental and commercial issues are discussed.
A statistical study of proton pitch angle distributions measured by the Radiation Belt Storm Probes Ion Composition Experiment
Authors: Shi Run , Summers Danny , Ni Binbin , Manweiler Jerry W. , Mitchell Donald G. , Lanzerotti Louis J.
Published: May 2016

A statistical study of ring current‐energy proton pitch angle distributions (PADs) in Earth's inner magnetosphere is reported here. The data are from the Radiation Belt Storm Probes Ion Composition Experiment (RBSPICE) on board the Van Allen Probe B spacecraft from 1 January 2013 to 15 April 2015. By fitting the data to the functional form sinnα, where α is the proton pitch angle, we examine proton PADs at the energies 50, 100, 180, 328, and 488 keV in the L shell range from L = 2.5 to L = 6. Three PAD types are classified: trapped (90° peaked), butterfly, and isotropic. The proton PAD dependence on the particle energy, magnetic local time (MLT), L shell, and geomagnetic activity are analyzed in detail. The results show a strong dependence of the proton PADs on MLT. On the nightside, the n values outside the plasmapause are clearly lower than those inside the plasmapause. At higher energies and during intense magnetic activity, nightside butterfly PADs can be observed at L shells down to the vicinity of the plasmapause. The averaged n values on the dayside are larger than on the nightside. A maximum of the averaged n values occurs around L = 4.5 in the postnoon sector (12–16 MLT). The averaged n values show a dawn‐dusk asymmetry with lower values on the dawnside at high L shells, which is consistent with previous studies of butterfly PADs. The MLT dependence of the proton PADs becomes more distinct with increasing particle energy. These features suggest that drift shell splitting coupled with a radial flux gradient play an important role in the formation of PADs, particularly at L > ~ 4.5.
Rainouts over the Arabian Sea and Western Ghats during moisture advection and recycling explain the isotopic composition of Bangalore summer rains
Authors: Rahul P. , Ghosh Prosenjit , Bhattacharya S. K.
Published: May 2016

Variations in the isotope ratios (18O/16O and D/H) of meteoric water at continental stations serve as valuable tracers for the hydrological cycle. In the present study, we investigated the role of sea surface temperature, wind speed, relative humidity, and rainout processes on the stable isotopic composition of the 2010 monsoon rainwater of Bangalore. The wind over the ocean influences the sea surface temperature and humidity which in turn influence the vapor isotopic composition. The rainout over the Arabian Sea and the land mass (Western Ghats) during advection of the air parcel to Bangalore and its recycling further modify the vapor composition. The isotopic ratios (δ18O, δD, and d‐excess) of the precipitation at Bangalore was estimated following a Rayleigh fractionation model involving rainout and recycling processes yield values consistent with our observation. In some samples, however, the observed isotopic ratios are higher (by 2 to 5‰), and a few of them are associated with high d‐excess values. These discrepancies could be due to limitation of the model assumptions.
Simulating 2 Ga of geodynamo history
Authors: Driscoll Peter E.
Published: May 2016

The paleomagnetic record indicates the geodynamo has been active over much of Earth history with surprisingly little trend in paleointensity. Variability, however, is expected from models that predict a sharp increase in intensity following inner core nucleation (ICN) and implied by Neoproterozoic anomalies that hint at a highly variable field over several hundred million years. Here we demonstrate with a suite of numerical dynamos driven by a new thermal evolution model that the geodynamo could have transitioned from a multipolar to dipolar regime around 1.7 Ga, then to a weak‐field dynamo around 1.0 Ga, and finally to a strong‐field dipole following ICN around 650 Ma that is maintained to the present day. The occurrence of a weak‐field geodynamo in the Neoproterozoic may be consistent with the observed anomalous apparent polar wander paths and reversal behavior. Recovery to a dipolar geodynamo in the Phanerozoic could be a signature of inner core nucleation. Index terms: 1507, 1560, and 1521.
Modeling the response of a top hat electrostatic analyzer in an external magnetic field: Experimental validation with the Juno JADE‐E sensor
Authors: Clark G. , Allegrini F. , McComas D. J. , Louarn P.
Published: May 2016

We investigate the response function of an electrostatic analyzer when electron gyroradii in a magnetic field become comparable to the scale size of the sensor. This occurs when electrons have sufficiently small energies and are in a strong magnetic field. Through simulations and laboratory experiments with the Jovian Auroral Distribution Experiment‐Electron (JADE‐E) sensor, we observe the energy response, detection angle distribution, and geometric factor to change significantly. Using electro‐optics simulation results, we develop semiempirical and empirical relationships that can be used for top hat electrostatic analyzers. We present a model based on these relationships that covers an energy range between 0.1 keV and 5 keV with a uniform external magnetic field magnitude between 0–3 G and verified that these relationships apply to JADE‐E in a specially designed testing environment by comparing with the model. We find that the model agrees well with the JADE‐E sensor validating it for top hat electrostatic analyzers more generally.
Functional and Molecular Diversity of Native Neuronal

K
+

Channels
Authors: Nerbonne Jeanne M
Published: May 2016

Multiple types of potassium (K
+
) currents have been distinguished in central and peripheral neurons based on differences in gating, time‐ and voltage‐dependent properties and pharmacological sensitivities. The various K
+
currents function to control neuronal resting membrane potentials, action potential waveforms and repetitive firing properties. In addition, the cellular and sub‐cellular expression patterns of the underlying K
+
channels are distinct, suggesting unique roles in regulating axonal and dendritic excitability and mediating the responses to synaptic inputs, as well as influencing short‐ and long‐term changes in neuronal functioning, plasticity and homeostasis. Molecular cloning has revealed considerable diversity of K
+
channel pore‐forming (α) and of cytosolic and transmembrane accessory (β) subunits, and accumulating evidence suggests that native neuronal K
+
channels, like other types of ion channels, function in macromolecular protein complexes. The individual (or combinations of) channel accessory subunits in these complexes, post‐translational modifications of channel subunits, as well as interactions with intracellular mediators and other types of voltage‐gated ion channels, influence the properties and the functioning of neuronal K
+
channels. The theme of this article is the electrophysiological and molecular diversity of neuronal K
+
channels and the molecular mechanisms that control the expression, distribution and functioning of native neuronal K
+
channels with a focus on rapidly activating and inactivating voltage‐gated A‐type K
+
channels for illustrative purposes.

Key Concepts

Multiple types of voltage‐dependent and voltage‐independent K
+
currents have been distinguished in mammalian peripheral and central neurons based on differences in biophysical and pharmacological properties.

The electrophysiological diversity of neuronal K
+
currents has a functional significance in that the different K
+
currents contribute to determining resting membrane potentials, action potential waveforms, repetitive firing properties and responses to neurotransmitters and modulators.

In most mammalian neurons, multiple functionally distinct types of K
+
currents/channels are co‐expressed and several are differentially distributed in neuronal cell bodies, dendrites and axons.

A rather large number of K
+
‐channel pore‐forming (α) subunits have been identified, many of which are expressed in peripheral and in central neurons, and considerable progress has been made in defining the relationships between the expressed K
+
‐channel α subunits and functional neuronal K
+
channels.

A number of cytosolic and transmembrane K
+
‐channel auxiliary subunits have also been identified, and increasing evidence suggests that neuronal K
+
channels function in macromolecular protein complexes.

Multiple transcriptional, post‐transcriptional, and post‐translational mechanisms contribute to native neuronal K
+
‐channel diversity, distribution and functioning.
Regeneration in Invertebrates: Model Systems
Authors: Allen John M , Ross Kelly G , Zayas Ricardo M
Published: May 2016

The ability of animals to replace lost tissues or body parts has captured the imagination of humans for centuries. Animals with simple body parts, such as hydra and planarians, are able to re‐form complete organisms from small tissue fragments. Echinoderms such as sea urchins, starfish and sea cucumbers display a broad and diverse range of regenerative capacities that allows for the regeneration of lost organs, limbs or in some cases entire organisms. In contrast, arthropods (insects and crustaceans), which have been the most amenable invertebrates to genetic manipulation, are more limited in regenerative potential but can still faithfully regenerate complex structures of the limb. The diverse modes and capacities for regeneration in invertebrates and the advent of molecular tools to inhibit gene function and study genome‐wide changes in gene expression associated with tissue repair provide outstanding opportunities for scientists to decode the cellular and molecular underpinnings of regeneration. Here we provide an overview of prominent invertebrate organisms that are interesting models to investigate stem cell biology, cellular reprogramming and regeneration.

Key Concepts

Regeneration is the regrowth of lost tissues and body structures.

The ability to (and extent of) regeneration is diverse and distributed across many phyla and cannot necessarily be predicted by phylogenic relationships.

Regeneration broadly consists of four phases: wound healing, generation of proliferating cells, cell differentiation and tissue remodelling.

The two dominant modes of regeneration are epimorphosis, where proliferation occurs prior to differentiation, and morphallaxis, where existing tissue is re‐proportioned via transformation to restore lost body parts. Importantly, these processes are not exclusive and may occur concurrently.

Wound healing consists of muscle contractions and epidermal cell spreading that work together to limit further damage. In contrast to non‐regenerative organisms, this process does not involve the creation of scar tissue.

Crucial to epimorphic regeneration is the formation of a blastema. A blastema is a growing mass of undifferentiated cells that will eventually re‐form lost tissues.

Blastemal cells rely on positional cues to differentiate into proper tissues with the appropriate higher order organisation. These cues are often similar to those guiding embryonic development and consist largely of chemical morphological gradients and cell–cell signalling factors.

New techniques to manipulate gene expression including RNAi‐mediated gene knockdowns, targeted transgenesis using CRIPSR/Cas nucleases and transcriptomic profiling (even at single‐cell resolution) are helping to provide insights into the molecular mechanisms underlying regeneration.
Plant Genetic Mapping Techniques
Authors: Hyten David L , Lee Donald J
Published: May 2016

Plant genetic maps are graphic representations of the organisation of chromosomes. These genetic maps are used in several applications to link a phenotype to a gene or a region on a chromosome. While genetic maps were classically dependent on morphological markers, recent advances in technology have allowed modern maps to be composed of hundreds to thousands of molecular markers. Since many plants have the ability to self‐fertilize, several different types of population structures can be created to facilitate genetic linkage map construction. Polyploidy and aneuploidy are also common in plants and require modified techniques that increase genetic mapping complexity or help facilitate marker placement onto chromosomes.

Key Concepts

Plant genetic maps are the foundation of many techniques used to map genes that contribute to plant traits.

Classical genetic maps provided the basis for determining the linkage order and distance between genes but were limited by the number of observable markers available.

Advances in modern molecular techniques have led to the ability to create genetic maps that contain thousands of markers.

The ability of plants to self‐fertilize allows for multiple population structures to be used for creating genetic maps.

Since polyploidy and aneuploidy are present in plants, modified techniques are required to create genetic maps.
Cork
Authors: Zajączkowska Urszula
Published: May 2016

Cork occurs in stems, roots, petioles as well as in some fruits or bud scales. It is usually formed from phellogen. Cork cells are usually tightly packed, dead and filled with air. Suberin is deposited along with waxes on the primary wall of cork cells. In addition to natural cork in intact plants, wound cork can develop after wounding. There are also specific structures of cork in some groups of plants, such as aerenchymatous phellem, polyderm, interxylary cork and the storied cork which is formed without the involvement of phellogen in some monocotyledons. Cork creates a physico‐chemical barrier that protects against water loss and pathogen invasion, but in some cases, it facilitates an exchange of gases between a plant's roots and its stem. Cork is characterised by low density; high elasticity; high resistance to compression; a low Poisson's ratio; low thermal, water and gas conductivity and the slow propagation of sound waves.

Key Concepts

Typical cork with tightly packed cells forms a physico‐chemical barrier, protecting a plant against water loss and pathogen invasion.

Loosely arranged cork cells may facilitate gas exchange in flooded plants.

Cork is usually formed in plants during secondary growth through activity of the phellogen, a secondary meristem.

In monocotyledons with abnormal secondary growth, the storied cork is formed which develops from parenchyma cells.

The cell walls of cork are subject to various modifications, the most important of which is adcrustation with suberin.

The degree of cork cell wall suberisation may be modified depending on the environment.

Cork can be considered as a natural form of the so‐called cellular solid structures known in technology.
Genome Organisation and Chromosome Architecture from Interphase to Metaphase
Authors: Bernardi Giorgio
Published: May 2016

It is well established that vertebrate and other eukaryotic genomes are compositionally compartmentalised into long (≥200 Kb) sequences, the isochores, that are fairly homogeneous in their basic composition, and belong to a small number of families (five in the human genome). On the other hand, recent investigations in many laboratories have led to a new vision of interphase chromatin, which basically consists of large loops (average size ∼186 Kb in the case of the human genome) and anchors held together by ‘architectural’ proteins such as CTCF (the CCCTC‐binding factor) and cohesin. A very recent analysis has revealed correlations between isochores from different families and the architectural features of chromosomes through the cell cycle. This leads to a unifying view of the genome organisation and chromosome architecture.

Key Concepts

The long‐range compositional organisation of the genome of vertebrates and of other eukaryotes (i.e. the isochore organisation) is correlated with the chromosome architecture through the cell cycle. This leads to a unifying view of genome organisation and chromosome architecture.

In spite of very extensive investigations over many years, the organization of the eukaryotic genome and the architecture of chromosomes from interphase to metaphase are two problems that are still open because of their complexity.

A combination of a large‐scale compositional analysis of vertebrate genomes and of the recent results on the architecture of interphase chromatin led to a solution of those problems.

The large‐scale compositional analysis revealed that vertebrate genomes consist of long (≥200 kilobases) fairly homogenous DNA segments, the isochores. Cross‐linking of contact regions of chromatin and sequencing (chromosome conformation captureand its variants) provided a picture of three‐dimensional interphase chromatin structure.

The long‐range compositional organization of the genome of vertebrates and of other eukaryotes (i.e., the isochore organization) was shown to be correlated with the chromosome architecture through the cell cycle.

The correlations between the isochore organization of the genome and the chromosome architecture through the cell cycle (especially the architecture of interphase chromatin structure) led to a unifying view of genome organization and chromosome architecture.
Sociobiology, Evolutionary Psychology and Genetics
Authors: Bateson Patrick
Published: May 2016

Much of human behaviour, including violence and those activities thought to be characteristic of each sex, has been attributed to the heritage of human evolution. These ideas have stimulated much discussion but have been criticised for playing down the interplay between the developing individual and the environment. In modern times, their clearest expression has been those in the writings of the sociobiologists and the evolutionary psychologists.

Key Concepts

The subjects of sociobiology and evolutionary psychology drew attention to the current utilities of behaviour patterns but often confused functions with the historical processes that gave rise to them and did not consider development.

The concepts of instinct and innateness have caused much confusion because so many different meanings are attached to them. It is better to state what has been demonstrated or intended than perpetuate the confusion.

Plasticity and robustness are often treated as opposites, but the processes that give rise to plasticity are often highly robust and robust behavior is often the product of plasticity during development.
Plant Circadian Rhythms
Authors: McWatters Harriet G , Eriksson Maria E
Published: May 2016

Circadian clocks are found in most eukaryotic organisms. By allowing anticipation of daily and seasonal changes, they enable coordination of metabolism and lifecycle with the natural rhythms of the environment. Plant circadian rhythms are generated by a series of interlocking feedback loops of RNA (ribonucleic acid) and protein expression that respond to environmental cycles of light and temperature. They control essential processes in the plant's development, such as the transition to flowering or growth cessation, and thus influence yield, plant growth and biomass production. Many components of the clock are conserved across a wide variety of plant species and thus research in
Arabidopsis
translates into an understanding of the clock in agricultural crops or long‐living deciduous tree species such as hybrid aspen.

Key Concepts

Circadian clocks are found in both eukaryotes and bacteria.

Circadian clocks have a free‐running periodicity of about 24 h but are normally entrained to environmental cycles of light and temperature.

Temperature compensation is a key feature of the circadian clock and thus the free‐running period length varies relatively little across the range of ambient temperature.

The clock underlies many aspects of plant metabolism and physiology because it can detect and respond to both short‐term (the day:night cycle) and long‐term (the pattern of daylength variation across a year) changes in light and temperature.

The circadian clock of plants is made up of a series of interconnected transcription‐translation feedback loops (TTFLs) governing cycles of mRNA and protein expression.

Every plant cell contains its own clock. Clocks in different cells may be entrained independently of one another, although there appears to be a hierarchy of clocks within a plant dominated by the apex.

Plants with malfunctioning clocks suffer reductions in growth.

Many of the key components of the plant clock first described in the model species
Arabidopsis thaliana
are conserved across a wide range of species including trees such as hybrid aspen.
Shoot Branching and Plant Architecture
Authors: Bennett Tom , Ward Sally P , Leyser Ottoline
Published: May 2016

Shoot architecture is the spatial arrangement of stems, leaves and reproductive structures in plants. A major component of shoot architecture is the formation of secondary axes of growth (branches). In flowering plants, these originate from meristems located in the axils of leaves. Once initiated, axillary meristems can produce a secondary shoot immediately, or arrest as a dormant bud, resulting in a large degree of architectural plasticity. Long‐distance hormonal signals including auxin, cytokinin and strigolactone allow the outgrowth of buds to be tightly coordinated with the physiological and nutritional status of the plant as a whole. Two major models have been proposed to explain how these hormonal signals are integrated to control shoot branching. Shoot architecture is highly varied among model species, but the core regulatory mechanisms are conserved across the flowering plant group.

Key Concepts

Shoot architecture in flowering plants is highly plastic and is produced using repeating modules (phytomers), which can vary in number and type.

Production of secondary shoots (branches) is a major component of shoot architecture in flowering plants.

Branches are produced by axillary meristems, which form in the axils of leaves.

Axillary meristem formation may occur simultaneously with leaf formation, or may be delayed until a later stage.

Once initiated, axillary meristems may immediately grow out to form a branch, or can produce a dormant axillary bud.

The activity‐dormancy switch in axillary buds is the major control point for shoot branching.

Long‐distance hormonal signals control bud outgrowth in response to environmental cues.

Two major models have been proposed to explain how these hormonal signals are integrated to control shoot branching.

Different species use the same fundamental control mechanisms to produce highly varied shoot architectures.
Lipid Rafts and Neurological Diseases
Authors: Sonnino Sandro , Grassi Sara , Prioni Simona , Ciampa Maria G , Chiricozzi Elena , Prinetti Alessandro
Published: May 2016

The different populations of brain cells are characterised by evident membrane polarisation with the creation of distinct morphological and functional subcompartments, whose formation, stabilisation and functions require sophisticated geometric features and a high level of lateral order, which are, at least in part, driven by the collective properties of membrane lipids. Lipid‐driven membrane organisation allows the segregation of membrane‐associated components into specific ‘lipid membrane domains’ or lipid rafts, which function as dynamic platforms for signal transduction, protein processing and membrane turnover. From this point of view, sphingolipids (SLs), polar membrane lipids present as minor components in all eukaryotic cell membranes but highly enriched in neuron and myelin membranes, play crucial roles. In fact, the metabolism of SLs is precisely regulated along the differentiation and development of neurons and oligodendrocytes, leading to the expression of peculiar cell‐specific SL patterns essential for the maintenance of the functional integrity of the nervous system, while, on the other hand, alterations in SL homeostasis, which lead to abnormal lipid raft organisation and consequent deregulation of lipid raft‐dependent events, are a common trait in diverse major brain diseases.

Key Concepts

Cellular membranes are highly organised structures with multiple and multi‐dimensional levels of order where lipid components are active players.

Membrane domains are ordered structures or regions in a biological membrane that differ from the surrounding membrane in their lipid and/or protein composition.

Lipid‐driven collective interactions are a major factor in determining the local structure of a membrane.

Among amphipatic membrane lipids, gangliosides are known to be major players in the creation of lateral order within biological membranes.

Sphingolipid metabolism is deeply altered in several neurological diseases.
Molecular Genetics of Pancreatic Endocrine Tumours
Authors: Katabathina Venkata S , Wilcoxson Robert (Dan) , Prasad Srinivasa R
Published: May 2016

Pancreatic tumours with neuroendocrine phenotype comprise 1–2% of all pancreatic tumours and commonly occur in a sporadic setting. Up to 10% of pancreatic neuroendocrine tumours (PNETs) may occur as part of inherited tumour‐predisposing syndromes, including multiple endocrine neoplasia type 1, von Hippel–Lindau disease, neurofibromatosis type 1, tuberous sclerosis complex and glucagon cell adenomatosis. Recent advances in genetics and pathology have allowed better understanding of the role of genetic abnormalities that underlie hereditary and sporadic PNETs. Ongoing research in this fast‐changing field has led to the discovery of mutations in key genes that determine how tumours begin, evolve and behave. Major specific tumour pathways of PNETs involve abnormalities of
MEN1
,
DAXX
/
ATRX
, and mammalian target of rapamycin (
mTOR
) pathway genes (
PTEN
,
TSC2,
and
PIK3CA
). New knowledge in the field of genetics of PNETs potentially permits development of effective diagnostic methods and targeted therapies aimed at improving prognosis and disease‐free survival rates.

Key Concepts

Hereditary and sporadic pancreatic neuroendocrine tumours (PNETs) demonstrate characteristic histo‐morphology and genetics that determine biology, treatment response and prognosis.

Tumour‐predisposing syndromes with increased risk of developing PNETs include multiple endocrine neoplasia type 1 (MEN1), von Hippel–Lindau disease (VHL), neurofibromatosis type 1 (NF1) and tuberous sclerosis complex (TSC).

Recent advances in the pathology and genetics of PNETs have unraveled the role of genetic abnormalities in tumour pathways that may lead to better diagnostic and therapeutic paradigms.

Major specific tumour pathways of PNETs involve abnormalities of
MEN1
,
DAXX
/
ATRX
, and mammalian target of rapamycin (
mTOR
) pathway genes (
PTEN
,
TSC2,
and
PIK3CA
).
VincentBrianWigglesworth (1899–1994)
Authors: Gawne Richard , Clarke Jameson
Published: May 2016

Vincent Brian Wigglesworth (1899–1994) had played a fundamental role in the creation of the modern science of insect physiology. He is best known for making some of the first significant contributions to research in insect endocrinology. Through a series of simple experiments, Wigglesworth was able to demonstrate the existence of the ‘status quo’ juvenile hormones and the molting hormone ecdysone. Later, he made advances in our understanding of the sources and functions of these hormones. HisPrinciples of Insect Physiologywas especially influential, serving as the canonical guide to research in the field for nearly 40 years.
Clovis Technology
Authors: Eren Metin I , Buchanan Briggs
Published: May 2016

Colonising hunter‐gatherer populations in North and Central America at the end of the Pleistocene utilised Clovis technology. Clovis technology is known for ‘fluted’ flaked stone points that were used to hunt prey and served as knives, but it also included the production, use and discard of a diversity of other implements made from stone, bone and other materials. Clovis technology lasted for several centuries, perhaps as long as a millennium and a half. Clovis technology shares some similarities with Siberian Paleolithic technology, which is consistent with current genetic evidence, indicating that ancestors of the people using Clovis technology originated in Asia. Clovis technology, as archaeologists generally recognise it, likely emerged piecemeal as people dispersed into the New World – some aspects of it can be tied to ancestry in Siberia, while other aspects are likely indigenous to North and Central America. Several studies have shown that Clovis technology was subjected to both micro‐ and macroevolutionary forces.

Key Concepts

‘Clovis technology’ is just an archaeologist's shorthand to refer to what is in actuality an inferred, fuzzy set of human–tool interactions found across North and Central America during the terminal Pleistocene.

There is a diversity of Clovis tools made from stone, bone and other materials.

Evidence for Clovis technology can be found across the lower 48 states of the United States, throughout southern Canada, and Central America.

The ancestors of people who used Clovis technology came from Asia.

What archaeologists generally recognise, and refer to, as Clovis technology likely emerged piecemeal as people from Asia dispersed into the New World.

Clovis technology evolved at both the micro‐ and macroevolutionary scales.
X
‐Chromosome Dosage Compensation
Authors: He Xionglei , Zhang Jianzhi
Published: May 2016

The X and Y chromosomes of placental and marsupial mammals originated from a pair of autosomes. Ohno hypothesised nearly 50 years ago that the expression levels of X‐linked genes should be doubled to compensate for the degeneration of their Y‐linked homologues during sex chromosome evolution. The advent of microarray and RNA (ribonucleic acid) sequencing technologies in the past decade prompted a series of empirical tests of Ohno's hypothesis. Surprisingly, X‐chromosome dosage compensation is found to be largely absent in mammals. Studies of multiple independently evolved sex chromosome systems from a variety of species revealed a large variation in sex‐chromosome dosage compensation, ranging from absence of compensation to complete compensation, although further scrutiny is required because of the high heterogeneities in expression data acquisition and analysis methods among studies. The lack of sex chromosome dosage compensation in at least some lineages has important implications for understanding gene expression evolution and sex chromosome evolution.

Key Concepts

Ohno proposed that the expression levels of mammalian X‐linked genes should be doubled to compensate for the degeneration of their Y‐linked homologues during sex chromosome evolution.

Initial microarray studies of genome‐wide gene expression levels found an X : AA ratio of ∼1, consistent with Ohno's hypothesis.

Subsequent analysis of transcriptomic data generated by the more sensitive RNA sequencing method found an X : AA ratio of ∼0.5, inconsistent with Ohno's hypothesis.

Some argued that Ohno's hypothesis is supported because X : AA is about 1 for actively expressed genes, but this assertion is caused by a common misunderstanding of Ohno's hypothesis.

A direct comparison between human X‐linked genes and their one‐to‐one orthologues located in chicken autosomes that are homologous to the mammalian proto‐X found no upregulation in mammalian X‐linked gene expression, refuting Ohno's hypothesis.

A human proteomic analysis found no evidence for a twofold upregulation of protein concentrations of X‐linked genes.

Transcriptome analyses of multiple species with independently evolved sex chromosomes revealed a large variation in the presence/absence and degree of sex chromosome dosage compensation, but further scrutiny is required due to the high heterogeneities in the data and methods used in the published studies.

The lack of sex chromosome dosage compensation in at least some lineages suggests that halving the expression level of a gene usually has no appreciable fitness consequences.