bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetospheric conditions for sawtooth event development
Authors: Noah M. A. , Burke W. J.
Published: February 2014

This paper addresses two topics concerning the magnetospheric conditions that allow sawtooth events (STEs) to develop during “nonstorm” intervals yet fail to yield them during many intense/super storms. A statistical analysis by Cai et al. (2011) reported that while only 5.4% of STEs occurred outside the context of magnetic storms, their occurrence rate during intense storms was just 63.5%. They concluded that (1) STEs are not necessarily storm time phenomena and (2) particular interplanetary conditions are needed to drive the class of storms in which STEs are generated. Traces of Sym‐H indices and cross polar cap potentials during “nonstorm” STEs indicate that ring current energy remained above normal, quiet time values and open flux was continually being transferred to the magnetotail. We combined two independently generated lists of intense/super storms from the 1996 to 2007 period and found that 46 of them did not appear on the STE list of Cai et al. (2011). They divide three categories of storms in which (1) information needed to establish the presence/absence of STEs is insufficient, (2) STE signatures were present but overlooked, and (3) the magnetopause moved earthward of 6.6 RE so that energetic particles cannot gradient‐curvature drift to geosynchronous satellites in the magnetosheath near local noon. We conclude that STE identification criteria be expanded to include compressed cases in which quasiperiodic nightside injections occur. Super storms with no nightside injections are attributed to episodes of severe ring current inflation of the inner magnetosphere that inhibited the formation of sustained near‐Earth neutral lines.
The distribution of the mid‐to‐lower crustal low‐velocity zone beneath the northeastern Tibetan Plateau revealed from ambient noise tomography
Authors: Li Hongyi , Shen Yang , Huang Zhongxian , Li Xinfu , Gong Meng , Shi Danian , Sandvol Eric , Li Aibing
Published: February 2014

We collected continuous seismic data recorded between 2007 and 2010 by 208 broadband stations from the Chinese Provincial Digital Seismic Networks, A Seismic Collaborative Experiment of Northern Tibet, and the Northeastern Tibet Seismic experiment. Cross correlations of vertical component records are computed to extract the Rayleigh wave empirical Green's functions. Group and phase velocities are then constructed from the empirical Green's functions in 8 to 50 s period. At periods ≤25 s, more than 10% lower velocities are imaged beneath the Qaidam Basin, and high velocities are observed beneath the nonbasin regions. At periods ≥30 s, up to 10% lower velocities are imaged in the Qiangtang and Songpan‐Ganze Terranes. From these group and phase velocity maps, a three‐dimensional (3‐D) Vsv model of the crust is derived. The model shows that the Qiangtang and Songpan‐Ganze Terranes have a very thick crust with a prominent low‐velocity zone (LVZ) in the middle crust. The LVZ thins out in the vicinity of the eastern Kunlun Mountains, providing a new constraint on the mode of deformation across the Tibetan Plateau. The northwestern Qilian Orogen, where receiver functions reveal a Moho deeper than the surrounding areas, also features a relatively weak midcrustal LVZ, which we interpret as an intracrustal response associated with the shortening between the North China Craton and the Tibetan Plateau.
Constraining particle size‐dependent plume sedimentation from the 17 June 1996 eruption of Ruapehu Volcano, New Zealand, using geophysical inversions
Authors: Klawonn M. , Frazer L. N. , Wolfe C. J. , Houghton B. F. , Rosenberg M. D.
Published: February 2014

Weak subplinian–plinian plumes pose frequent hazards to populations and aviation, yet many key parameters of these particle‐laden plumes are, to date, poorly constrained. This study recovers the particle size‐dependent mass distribution along the trajectory of a well‐constrained weak plume by inverting the dispersion process of tephra fallout. We use the example of the 17 June 1996 Ruapehu eruption in New Zealand and base our computations on mass per unit area tephra measurements and grain size distributions at 118 sample locations. Comparisons of particle fall times and time of sampling collection, as well as observations during the eruption, reveal that particles smaller than 250 μm likely settled as aggregates. For simplicity we assume that all of these fine particles fell as aggregates of constant size and density, whereas we assume that large particles fell as individual particles at their terminal velocity. Mass fallout along the plume trajectory follows distinct trends between larger particles (d≥250 μm) and the fine population (d<250 μm) that are likely due to the two different settling behaviors (aggregate settling versus single‐particle settling). In addition, we computed the resulting particle size distribution within the weak plume along its axis and find that the particle mode shifts from an initial 1φmode to a 2.5φmode 10 km from the vent and is dominated by a 2.5 to 3φmode 10–180 km from vent, where the plume reaches the coastline and we do not have further field constraints. The computed particle distributions inside the plume provide new constraints on the mass transport processes within weak plumes and improve previous models. The distinct decay trends between single‐particle settling and aggregate settling may serve as a new tool to identify particle sizes that fell as aggregates for other eruptions.
Temporal variability and tidal modulation of hydrothermal exit‐fluid temperatures at the Lucky Strike deep‐sea vent field, Mid‐Atlantic Ridge
Authors: Barreyre Thibaut , Escartín Javier , Sohn Robert A. , Cannat Mathilde , Ballu Valérie , Crawford Wayne C.
Published: February 2014

We deployed autonomous temperature sensors at black smoker chimneys, cracks, and diffuse flow areas at the Lucky Strike hydrothermal field (Mid‐Atlantic Ridge, ~37°17'N) between summer 2009 and summer 2012 and contemporaneously measured tidal pressures and currents as part of the long‐term MoMAR experiment to monitor hydrothermal activity. We classify the temperature data according to the hydrogeologic setting of the measurement sites: a high‐temperature regime (>190°C) representing discharge of essentially unmixed, primary hydrothermal fluids through chimneys, an intermediate‐temperature regime (10–100°C) associated with mixing of primary fluids with cold pore fluids discharging through cracks, and a low‐temperature regime (<10°C) associated with a thermal boundary layer forming over bacterial mats associated with diffuse outflow of warm fluids. Temperature records from all the regimes exhibit variations at semi‐diurnal tidal periods, and cross‐spectral analyses reveal that high‐temperature discharge correlates to tidal pressure while low‐temperature discharge correlates to tidal currents. Intermediate‐temperature discharge exhibits a transitional behavior correlating to both tidal pressure and currents. Episodic perturbations, with transient temperature drops of up to ~150°C, which occur in the high‐temperature and intermediate‐temperature records, are not observed on multiple probes (including nearby probes at the same site), and they are not correlated with microearthquake activity, indicating that the perturbation mechanism is highly localized at the measurement sites within the hydrothermal structures. The average temperature at a given site may increase or decrease at annual time scales, but the average temperature of the hydrothermal field, as a whole, appears to be stable over our 3 year observation period.
Seismoacoustic signatures of fracture connectivity
Authors: Rubino J. Germán , Müller Tobias M. , Guarracino Luis , Milani Marco , Holliger Klaus
Published: February 2014

Wave‐induced fluid flow (WIFF) between fractures and the embedding matrix as well as within connected fractures tends to produce significant seismic attenuation and velocity dispersion. While WIFF between fractures and matrix is well understood, the corresponding effects related to fracture connectivity and the characteristics of the energy dissipation due to flow within fractures are largely unexplored. In this work, we use oscillatory relaxation simulations based on the quasi‐static poroelastic equations to study these phenomena. We first consider synthetic rock samples containing connected and unconnected fractures and compute the corresponding attenuation and phase velocity. We also determine the relative fluid displacement and pressure fields in order to gain insight into the physical processes involved in the two manifestations of WIFF in fractured media. To quantify the contributions of the two WIFF mechanisms to the total seismic attenuation, we compute the spatial distribution of the local energy dissipation. Finally, we perform an exhaustive sensitivity analysis to study the role played by different characteristics of fracture networks on the seismic signatures. We show that in the presence of connected fractures both P wave attenuation and phase velocity are sensitive to some key characteristics of the probed medium, notably to the lengths, permeabilities, and intersection angles of the fractures as well as to the overall degree of connectivity of the fracture network. This, in turn, indicates that a deeper understanding of these two manifestations of WIFF in fractured media may eventually allow for the extraction of some of these properties from seismic data.
Visualization of space competition and plume formation with complex potentials for multiple source flows: Some examples and novel application to Chao lava flow (Chile)
Authors: Weijermars R.
Published: February 2014

Fluid displacement in a continuum pressured by a variable constellation of source flows can be visualized as solutions of line integrals. The algorithms are based on complex potentials that provide exact solutions of the Navier‐Stokes equation and allow users to specify both the location and flux strength of multiple sources. If relative strength and positioning of the sources are varied, a wide range of flow patterns and particle paths can be traced. Time‐dependent variations in the strength of the sources can account for transient‐flow problems. A further expansion is superposition of a background flow, which displaces the particle paths issued from the sources into concentrated plumes. The outlined modeling technique for visualization of multiple plume displacements is potentially relevant for a wide spectrum of practical situations. Detailed applications are possible, such as time tracking of groundwater‐plume migration from a series of pollution sources, tracking of salt‐feeder‐stock flow and suture zone formation when salt issued from the stocks coalesces into a salt canopy, and designing of optimal spacing and relative pressure strength of multiple water injection wells in field‐development plans for hydrocarbon production. Further applications are highlighted in the main text, including a simulation of geometrical features exposed in the Chao coulee (Chilean Andes).
Effects of shear heating, slip‐induced dilatancy and fluid flow on diversity of 1‐D dynamic earthquake slip
Authors: Suzuki Takehito , Yamashita Teruo
Published: February 2014

We theoretically study effects of thermal pressurization, slip‐induced dilatancy and fluid flow on slip evolution assuming 1‐D fault model. We generalize the analysis made in our former papers by introducing an upper limit for the inelastic porosity evolution. The expression for nondimensional parameter Ta, which is related to the upper limit, is derived in the present paper. We find that the parameter Ta together with two nondimensional parameters Su and derived in our former papers completely determine the qualitative nature of system behavior once the initial condition is given. For example, changes in Su and Ta generate two qualitatively different slip behaviors, both of which can be models for ordinary earthquake. The slip is accelerated with time after experiencing an initial deceleration in one of them, while the slip ceases after monotonic deceleration in the other. The initial slip deceleration observed in the former case may be interpreted as a dynamic event preceding the main shock in seismological observations. We mathematically derive the expression for the ranges of the nondimensional parameters in which the above two slip behaviors appear. Slow earthquakes are also modeled in the same framework, and nonzero values of the nondimensional parameter together with relatively large values of Su and Ta are found to contribute to the generation of such slow earthquakes. The mathematical framework constructed here can be applied to understanding of some other natural phenomena such as a kind of reaction‐diffusion system.
Interaction of gravity waves with the QBO: A satellite perspective
Authors: Ern M. , Ploeger F. , Preusse P. , Gille J. C. , Gray L. J. , Kalisch S. , Mlynczak M. G. , Russell J. M. , Riese M.
Published: February 2014

One of the most important dynamical processes in the tropical stratosphere is the quasi‐biennial oscillation (QBO) of the zonal wind. Still, the QBO is not well represented in weather and climate models. To improve the representation of the QBO in the models, a better understanding of the driving of the QBO by atmospheric waves is required. In particular, the contribution of gravity waves is highly uncertain because of the small horizontal scales involved, and there is still no direct estimation based on global observations. We derive gravity wave momentum fluxes from temperature observations of the satellite instruments HIRDLS and SABER. Momentum flux spectra observed show that particularly gravity waves with intrinsic phase speeds <30m/s (vertical wavelengths <10km) interact with the QBO. Gravity wave drag is estimated from vertical gradients of observed momentum fluxes and compared to the missing drag in the tropical momentum budget of ERA‐Interim. We find reasonably good agreement between their variations with time and in their approximate magnitudes. Absolute values of observed and ERA‐Interim missing drag are about equal during QBO eastward wind shear. During westward wind shear, however, observations are about 2 times lower than ERA‐Interim missing drag. This could hint at uncertainties in the advection terms in ERA‐Interim. The strong intermittency of gravity waves we find in the tropics might play an important role for the formation of the QBO and may have important implications for the parameterization of gravity waves in global models.
A generalized beta‐advection model to improve unusual typhoon track prediction by decomposing total flow into climatic and anomalous flows
Authors: Qian Weihong , Shan Xiaolong , Liang Haoyuan , Huang Jing , Leung Cheuk‐Hin
Published: February 2014

Using a novel approach of decomposing total flow into climatic and anomalous flows, we have developed a generalized beta‐advection model to improve unusual typhoon track prediction within 2–3 days. Typhoon Megi (2010) that experienced an unusual path is first used to introduce this model. Differing from the conventional beta‐advection model (BAM) in (i) decomposing the total flow into the climatic and anomalous flows and considering their interaction and (ii) taking the layer of minimum divergence anomaly and maximum vorticity anomaly instead of any average layers done by, for example, the shallow BAM, the medium BAM, and the deep BAM, this model is a combination of the climatic‐flow BAM and the anomalous‐flow BAM. In this paper, 19 cases of sudden right‐turning typhoon and 10 cases of straight‐moving typhoon in the South China Sea are studied to examine this model's capability. Results show that 15 right‐turning and 10 straight‐moving cases were successfully predicted by this combination model.
What controls the interannual variation of the wet season onsets over the Amazon?
Authors: Yin Lei , Fu Rong , Zhang Yong‐Fei , Arias Paola A. , Fernando D. Nelun , Li Wenhong , Fernandes Katia , Bowerman Adam R.
Published: February 2014

Previous studies have established that sea surface temperature anomalies (SSTAs) in the tropical Pacific and Atlantic are the main forcing of the interannual variation of the wet season onsets in the Amazon. However, this variation appears to be complex and not uniquely determined by SSTAs. What causes such a complexity and to what extent the interannual variation of the wet season onsets is predictable remain unclear. This study suggests that such a complex relationship is the result of several competing processes, which are nonlinearly related to the SSTAs. In particular, three dry season conditions are crucial for determining interannual variation of the wet season onset. (i) A poleward shift of the Southern Hemisphere subtropical jet (SHSJ) over the South American sector, initiated from a wave train‐like structure possibly forced by south central Pacific SST patterns, can prevent cold frontal systems from moving northward into the Amazon. This delays cold air incursion and results in late wet season onset over the southern Amazon. (ii) An anomalous anticyclonic center, which enhances westerly wind at 850 hPa over the southern Amazon and also the South American low‐level jets, leads to moisture export from the southern Amazon to La Plata basin and reduces convective systems that provide elevated diabatic heating. (iii) Smaller convective available potential energy (CAPE) limits local thermodynamically driven convection. Based on the stepwise and partial least squares regressions, these three selected preseasonal conditions (Niño 4, SHSJ, and CAPE) can explain 57% of the total variance of the wet season onset.
Organic and inorganic carbon dynamics in a karst aquifer: Santa Fe River Sink‐Rise system, north Florida, USA
Authors: Jin Jin , Zimmerman Andrew R. , Moore Paul J. , Martin Jonathan B.
Published: February 2014

Spatiotemporal variations in dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), major ions concentrations and other geochemical parameters including stable carbon isotopes of DIC (δ13CDIC), were measured in surface water and deep and shallow well water samples of the Santa Fe River Sink‐Rise eogenetic karst system, north Florida, USA. Three end‐member water sources were identified: one DOC‐rich/DIC‐poor/δ13CDIC‐depleted, one DOC‐poor/DIC‐rich/δ13CDIC‐enriched, and one enriched in major ions. Given their spatiotemporal distributions, they were presumed to represent soil water, upper aquifer groundwater, and deep aquifer water sources, respectively. Using assumed ratios of Na+, Cl, and SO42− for each end‐member, a mixing model calculated the contribution of each water source to each sample. Then, chemical effects of biogeochemical reactions were calculated as the difference between those predicted by the mixing model and measured species concentrations. In general, carbonate mineral dissolution occurred throughout the Sink‐Rise system, surface waters were net autotrophic and the subsurface was in metabolic balance, i.e., no net DOC or DIC production or consumption. However, there was evidence for chemolithoautotrophy, perhaps by hydrogen oxidizing microbes, at some deep aquifer sites. Mineralization of this autochthonous natural dissolved organic matter (NDOM) led to localized carbonate dissolution as did surface water‐derived NDOM supplied to shallow well sites during the highest flow periods. This study demonstrates linkages between hydrology, abiotic and microbial processes and carbon dynamics and has important implications for groundwater quality, karst morphologic evolution, and hydrogeologic projects such as aquifer storage and recovery in karst systems.
The sensitivity of global wildfires to simulated past, present, and future lightning frequency
Authors: Krause Andreas , Kloster Silvia , Wilkenskjeld Stiig , Paeth Heiko
Published: February 2014

In this study, components of the Max Planck Institute Earth System Model were used to explore how changes in lightning induced by climate change alter wildfire activity. To investigate how climate change alters global flash frequency, simulations with the atmospheric general circulation model ECHAM6 were performed for the time periods preindustrial, present‐day, and three future scenarios. The effect of changes in lightning activity on fire occurrence was derived from simulations with the land surface vegetation model JSBACH. Global cloud‐to‐ground lightning activity decreased by 3.3% under preindustrial climate and increased by up to 21.3% for the RCP85 projection at the end of the century when compared to present‐day, respectively. Relative changes were most pronounced in North America and northeastern Asia. Global burned area was little affected by these changes and only increased by up to 3.3% for RCP85. However, on the regional scale, significant changes occurred. For instance, burned area increases of over 100% were found in high‐latitude regions, while also several regions were identified where burned area declined, such as parts of South America and Africa.
A 170 year spring phenology index of plants in eastern China
Authors: Ge Quansheng , Wang Huanjiong , Zheng Jingyun , This Rutishauser , Dai Junhu
Published: February 2014

Extending phenological records into the past is essential for the understanding of past ecological change and evaluating the effects of climate change on ecosystems. A growing body of historical phenological information is now available for Europe, North America, and Asia. In East Asia, long‐term phenological series are still relatively scarce. This study extracted plant phenological observations from old diaries in the period 1834–1962. A spring phenology index (SPI) for the modern period (1963–2009) was defined as the mean flowering time of three shrubs (first flowering of Amygdalus davidiana and Cercis chinensis, 50% of full flowering of Paeonia suffruticosa) according to the data availability. Applying calibrated transfer functions from the modern period to the historical data, we reconstructed a continuous SPI time series across eastern China from 1834 to 2009. In the recent 30 years, the SPI is 2.1–6.3 days earlier than during any other consecutive 30 year period before 1970. A moving linear trend analysis shows that the advancing trend of SPI over the past three decades reaches upward of 4.1 d/decade, which exceeds all previously observed trends in the past 30 year period. In addition, the SPI series correlates significantly with spring (February to April) temperatures in the study area, with an increase in spring temperature of 1°C inducing an earlier SPI by 3.1 days. These shifts of SPI provide important information regarding regional vegetation‐climate relationships, and they are helpful to assess long term of climate change impacts on biophysical systems and biodiversity.
CMIP5 multi‐model hindcasts for the mid‐1970s shift and early 2000s hiatus and predictions for 2016–2035
Authors: Meehl Gerald A. , Teng Haiyan
Published: February 2014

Compared to uninitialized climate change projections, a multi‐model ensemble from the CMIP5 10 year decadal prediction experiments produces more warming during the mid‐1970s climate shift and less warming in the early 2000s hiatus in both the tropical Indo‐Pacific region and globally averaged surface air temperature (TAS) in closer agreement with observations. Assuming bias in TAS has stabilized in the 10 year predictions, after bias adjustment, TAS anomalies for the 2016–2035 period in the 30 year predictions initialized in 2006 are about 16% less than the uninitialized projections. One contributing factor for the improved climate simulation is the bias adjustment, which corrects the models' systematic errors and higher‐than‐observed decadal warming trend. Another important factor is the initialization with observations which constrains the ocean such that the starting points of the initialized simulations are close to the observed initial states.
Crustal structure beneath SE Tibet from joint analysis of receiver functions and Rayleigh wave dispersion
Authors: Sun Xiaoxiao , Bao Xuewei , Xu Mingjie , Eaton David W. , Song Xiaodong , Wang Liangshu , Ding Zhifeng , Mi Ning , Yu Dayong , Li Hua
Published: February 2014

New constraints on the pattern of crustal flow in SE Tibet are obtained from joint analysis of receiver functions and Rayleigh wave dispersion with a newly deployed seismic array. The crust in the Sichuan‐Yunnan Diamond Block has an average thickness of ~45 km and gradually thins toward the Indo‐China Block to the west and the Yangtze Block to the east. High VP/VS ratios are detected to the west of the Xiaojiang fault, but not in the Yangtze Block to the east. The S wave velocity profile reveals that intra‐crustal low‐velocity zones (IC‐LVZs) are strongly heterogeneous, with two LVZs in the middle and mid‐lower crust, respectively, in marked contrast to previous observations of a single LVZ. Combined with other observations, the two IC‐LVZs are interpreted as isolated channels of crustal flow at different depths beneath SE Tibet, resulting in the observed complex pattern of radial anisotropy and further elucidating patterns of flow and deformation.
Applying bicoherence analysis to spacecraft observations of Langmuir waves
Authors: Graham D. B. , Malaspina D. M. , Cairns Iver H.
Published: February 2014

In type II and type III solar radio bursts and planetary foreshocks, the processes which convert Langmuir waves (LWs) to transverse waves are not well understood. One of the proposed mechanisms for generating transverse waves involves electrostatic (ES) decay followed by coalescence of two LWs. One of the tests used to identify this process is bicoherence analysis. Bicoherence has been applied to spacecraft observations of LWs to yield results consistent with ES decay and coalescence. However, recent work has shown that the harmonic fields produced by LWs are more consistent with sheath rectification and nonlinear currents. It is shown here that sheath rectification and nonlinear currents yield bicoherences similar to those expected for ES decay and coalescence, explaining the bicoherences associated with spacecraft observations of LWs. These results show that bicoherence alone cannot be used to identify ES decay and coalescence and emphasize the importance of sheath rectification.
Bacterial Endospores
Authors: Mury Sean P , Popham David L
Published: February 2014

The spores of bacteria formed mainly by members of the genera
Bacillus
and
Clostridium
are termed endospores because they develop singly within the mother or sporangial cells. Spore formation is a complex differentiation process involving two cells and a programme of gene expression requiring intracellular communication. Endospores exhibit complete metabolic dormancy and extreme resistance to multiple environmental insults, and can survive for centuries. The production of resistant spores by certain pathogenic bacterial species contributes to their transmission and difficulties in preventing their reoccurrence. Dormancy and resistance properties derive from alterations in the spore cell cytoplasmic contents, including dehydration, and from multiple integument layers. When presented with a nutrient‐rich environment, spores can rapidly germinate and re‐enter vegetative growth cycle.

Key Concepts:

Bacterial endospores can survive for decades and are highly resistant to numerous environmental insults.

The resistance properties of bacterial endospores contribute to their roles in food spoilage and in human and animal pathogenesis.

Bacterial endospores are cells with specialised modifications to their structure and contents.

Bacterial endospores are produced via a simple developmental process involving cooperative and regulated gene expression of two cells.

Heat resistance of bacterial endospores is determined by several factors, the most important being the relative dehydration of the spore core.

Bacterial endospores possess a unique mode of resistance to UV irradiation involving specialised DNA‐binding proteins.
Archaeal Cell Walls
Authors: Meyer Benjamin H , Albers Sonja‐Verena
Published: February 2014

Next to the bacterial and eukaryal domains, Archaea form the third domain of life. One major difference to bacteria is the composition of the cell wall. The cell wall of most Archaea is formed by a proteinaceous surface (S‐) layer. S‐layer proteins have the intrinsic ability to form two‐dimensional crystals, which can have an oblique (p2), square (p4) or hexagonal (p3 or p6) symmetry. All currently studied archaeal S‐layer proteins were found to be modified by the attachment ofN‐linked and, in some cases, additionally byO‐linked glycans. Next to the S‐layer (glyco‐)proteins, sugar polymers like pseudomurein, methanochondroitin or heteropolysaccharides are also found in archaeal cell walls. These polymeric cell wall structures can either form the sole cell wall structure or be supported by an additional S‐layer cover. A few archaeal species even completely lack a cell wall.

Key Concepts:

Archaeal cell envelopes lack murein or a lipopolysaccharide (LPS)‐containing outer membrane.

Most Archaea posses a glycosylated proteinaceous surface layer (S‐layer) as their sole cell wall structure.

In some Archaea, the cell wall is composed of glycan polymers, like glutaminylglycan, heterosaccharide, methanochondroitin or pseudomurein.
Heterochromatin and Euchromatin
Authors: Eissenberg Joel C , Elgin Sarah CR
Published: February 2014

Eukaryotes are characterised by the extensive packaging of their genomes, initially in a nucleosomal array, and further into higher order domains. Differential packaging is used as a mechanism of gene regulation, with stable silencing of large domains achieved by packaging the
deoxyribonucleic acid (DNA)
into a heterochromatic structure. Chromosome rearrangements and transgene insertions that misplace euchromatic genes near or within the heterochromatin result in silencing of the euchromatic genes, testifying to a distinct heterochromatin assembly that can antagonise transcription. Most heterochromatic regions are rich in repetitious sequences, frequently derived from transposable elements, and such packaging helps to silence such elements. Domains of heterochromatin and euchromatin are defined by specific covalent modifications of histones and, in some cases, DNA, as well as by associations with a specific subset of nonhistone chromosomal proteins. Chromosomal domains may be targeted for heterochromatin formation by specific noncoding
ribonucleic acids (RNAs)
.

Key Concepts:

The chromatin of eukaryotes is differentially packaged into domains of euchromatin and heterochromatin.

Displacing a euchromatic gene to near or within the heterochromatin often results in silencing of the euchromatic gene in some of the cells in which it should be active, resulting in a variegating phenotype.

Euchromatin and heterochromatin are distinguishable biochemically by different covalent modifications of histones (and in some cases DNA) and by distinct nonhistone proteins.

Members of the HP1a chromo domain protein family bind methylated histone H3 and interact with the H3K9 histone methyltransferase to organise transcriptionally repressive heterochromatin.

The piRNA pathway is implicated in targeting transposon silencing through local heterochromatin formation.
Binary Fission in Bacteria
Authors: Margolin William
Published: February 2014

Given a suitable environment, most free‐living prokaryotic cells (including bacteria) will grow continually until, on reaching a critical size, they divide into two equal‐sized parts in a process called binary fission. To be successful, this process requires the accurate duplication and partition of the chromosomes, and subsequent splitting of the cytoplasm precisely at the cell midpoint. The latter process, known as cytokinesis, often uses a large transmembrane protein machine that includes homologues of actin and tubulin as well as enzymes that synthesise and degrade specific portions of the cell wall. The placement of this machine is often regulated by negatively acting morphogen gradients. Once assembled, numerous accessory proteins respond to various inputs to regulate how and when the machine constricts and cells physically separate.

Key Concepts:

The timing of chromosome duplication in bacteria responds to cell growth rate and initiates at a specific location only once per cell cycle.

Bacterial chromosomes are organised and condensed by DNA‐binding proteins, some of which are conserved from bacteria to humans.

Bacterial cells use homologues of eukaryotic cytoskeletal proteins actin and tubulin to organise their growth and division.

Morphogen gradients of negative spatial regulators help to position the cytokinetic ring in many bacteria.

Recent advances in synthetic biology of bacterial cytokinesis are increasing our understanding of key components.
Antibiotic Resistance Plasmids in Bacteria
Authors: Clewell Don B
Published: February 2014

Antibiotic resistance plasmids are bacterial extrachromosomal elements that carry genes conferring resistance to one or more antibiotics. They are notorious for their ability to transfer by conjugation between bacterial species and are significantly involved in the emergence and dissemination of multiple drug resistance associated with bacterial infections in humans. The information provided here includes some of the history and nature of antibiotic resistance as well as how plasmids have become significantly involved as intercellular carriers via the phenomenon of bacterial conjugation. The manner by which resistance determinants are able to move onto plasmids via their initial association with transposons and integrons is discussed. The existence of elements with both transpositional and conjugative properties, such as the conjugative transposons and integrative conjugative elements, is also noted.

Key Concepts:

Multiple antibiotic resistance represents a serious and growing clinical problem with regard to bacterial infections in humans.

Resistance genes are commonly found on plasmids, which are small extrachromosomal elements commonly found in bacteria.

Plasmids can vary widely with regard to their size and copy number in the cell.

Plasmids are commonly able to move from one bacterial cell to another by a mechanism known as conjugation, which involves cell‐to‐cell contact followed by transfer of a copy of plasmid DNA from a donor to a recipient.

Genes conferring antibiotic resistance are commonly found on elements known as integrons and transposons, which facilitate movement between different replicons such as between the bacterial chromosome and a plasmid.

Some transposable elements, known as conjugative transposons, also carry resistance traits; and, although unable to replicate autonomously, they can move from one bacterial cell to another by a plasmid‐like mechanism.

Excessive use of antibiotics in the treatment of human infections has, over time, contributed to the emergence and selection of resistant bacteria in the gut, a phenomenon that includes passage of resistance traits between nonpathogens and pathogens.
Bacterial Antibiotic Resistance
Authors: Martins Ana , Spengler Gabriella , Molnár József , Amaral Leonard
Published: February 2014

The mechanisms by which antibiotic resistance of bacteria takes place are discussed in detail. Among the mechanisms that have been recently elucidated are overexpressed efflux pumps that render the bacterium multidrug resistant; downregulation of porins; target modification; quorum sensing; biofilm production and secretion and plasmids that carry antibiotic resistance genes. The mechanisms discussed also include modulation by agents or genetic regulation that may provide improved antibiotic therapies.

Key Concepts:

Efflux pumps, porins and plasmid acquisition play an essential role in the development of multidrug resistance by bacteria.

Quorum sensing is essential in biofilm formation.

Efflux pumps must be essential for bacterial communication (quorum sensing).

Quorum sensing must play an important role in the development of resistance and bacterial survival.

Inhibition of EP and QS appear to be crucial to inhibit biofilm formation.
Peroxisomes: Methods for Preparation
Authors: Islinger Markus , Fahimi H Dariush , Völkl Alfred
Published: February 2014

Peroxisomes are ubiquitous cell organelles particularly enriched in the mammalian liver and kidney. They contain oxidases producing hydrogen peroxide and catalase, which degrades it. The majority of 60 enzymes, so far, localised to mammalian peroxisomes is involved in lipid metabolism. However, they catalyse via β‐oxidation the degradation of saturated and unsaturated long and very long‐chain fatty acids and fatty acid derivatives including complex lipids, such as bile acids, leucotrienes and prostaglandins. On the other, they are engaged in the biosynthesis of lipids, such as polyunsaturated fatty acids, ether glycerolipids and polyisoprenoids. The essential metabolic role of peroxisomes in humans is shown quite plainly by inherited disorders, the so‐called peroxisomopathies, which are partly associated with severe peroxisomal dysfunctions. Commonly, peroxisomes are isolated by classical density gradient centrifugation. Meanwhile, however, advanced alternatives have been established, for example, immunochemical techniques as well as zonal free‐flow electrophoresis.

Key Concepts:

Peroxisomes are multipurpose organelles playing a pivotal metabolic role in humans as is revealed by a variety of inherited peroxisomal disorders.

They display a remarkable plasticity in both morphology and biochemistry not only between species and tissues but also regarding different regions of the same organ.

In mammalian and wild‐type yeast cells, peroxisomes are considered commonly to multiply by growth and division and usually do not form
de novo
. There is, however, growing evidence that peroxisomes can also arise
de novo
from the ER, and even new perspectives are provided on the potential contribution of the mitochondria to peroxisomal biogenesis.

The overall heterogeneity of peroxisomes and the consistency in the buoyant density of the subpopulations with other cell organelles hamper their purification by classic cell fractionation methods, inevitably calling for adequate techniques based upon alternative physicochemical traits.
Nicotinic Receptors
Authors: Marger Laurine , Itier Valérie , Bertrand Daniel
Published: February 2014

Fast neurotransmission in the central and peripheral nervous systems is mediated by the activity of ligand‐gated ion channels. Nicotinic acetylcholine receptors (nAChRs) belong to the family of cation‐permeable channels and result from the assembly of five subunits that form both the ligand‐binding site and the ionic pore. Sixteen genes encoding for these receptors have been identified in mammals and show differential expression throughout the body. Endogenously activated by ACh, nAChRs are the primary target of nicotine contained in tobacco leaves and mediate its addiction. The use of a partial agonist of nicotinic receptors significantly reduces craving and show good outcomes in smoking cessation. Spontaneous variations occurring in the genes encoding for nAChRs are associated with neurological diseases such as myasthenia gravis, to genetically transmissible epilepsies and to nicotine dependence. Dysfunction of the nAChR transmission is associated with diseases including schizophrenia, autism and neurodegenerative diseases such as Alzheimer's. Small molecules have recently shown beneficial outcomes in Alzheimer disease opening new avenues to treat neurological affections.

Key Concepts:

Neurotransmission is mediated by integral membrane proteins and can be subdivided into ligand‐gated ion channels and G‐coupled proteins.

Nicotinic acetylcholine receptors belong to the family of cationic ligand‐gated ion channels that comprises four transmembrane domains and result from the assembly of five subunit around an axis of pseudosymmetry.

Nicotinic acetylcholine receptors are key players in nicotine addiction and the primary target for this natural alkaloid that is contained in tobacco leaves.

Nicotinic acetylcholine receptors at the neuromuscular junction play a determinant role in mediating transmission from the motor nerve to the muscle cell. Impairment of these receptor function leads to myasthenia gravis, which can be decomposed in its most common form to an autoimmune disease and in rarer forms in mutations of one or more genes.

Dysfunction of the cholinergic system is associated with cognitive impairment and with neurological diseases such as schizophrenia, autism, genetically transmissible epilepsies and neurodegenerative diseases such as Alzheimer's.

The development of small chemical molecules such as the partial agonist varenicline is shown to help in smoking cessation programmes and, more recently, for α7 EVP‐6124 in the treatment of Alzheimer disease.
Evolution of Human Gene Expression Control
Authors: Boyd J Lomax , Wray Gregory A
Published: February 2014

The evolutionary history of our species is associated with the emergence of numerous phenotypic traits thought to be unique to humans. Comparative analysis of gene expression between human and nonhuman primates has revealed thousands of genes differentially expressed across multiple tissues. Comparative and functional genomic studies have implicated variation in
cis
‐regulatory regions, or enhancer elements, as a major component of species‐specific expression differences. Additionally, adaptive evolution between modern human populations has also been attributed to variation in
cis
‐regulatory regions of the genome. Despite these advances, the genetic basis of most derived human traits, population‐specific differences and heritable variation in gene expression remains unidentified. Gene regulation is known to proceed through the combinatorial interaction of multiple loci, acting cooperatively or redundantly, to regulate contextual gene expression in different tissues or at different times during development. The role of epistasis, the genetic interaction between loci, may, therefore, have a significant influence on the evolution of regulatory elements underlying trait difference between primate species and human populations.

Key Concepts:

Numerous highly conserved noncoding elements are rapidly evolving in humans and many function as tissue‐specific developmental enhancers.

Variation in phenotypic traits, including disease susceptibility, has been mapped to noncoding,
cis
‐regulatory loci.

Comparison of multiple primate genomes has enabled the identification of loci under both adaptive evolution (positive selection) and evolutionary constraint (negative selection).

Natural selection within protein‐coding and noncoding regions of genome is not uniform but more preferentially targets certain biological categories of genes.

The role of epistasis in the evolution of human gene expression control is unknown for most traits but may be significant.
Pseudogene Evolution in the Human Genome
Authors: Zhang Zhaolei , Zheng Deyou
Published: February 2014

Pseudogenes are those regions in a genome that have sequence similarity to functional genes but have decayed and have no obvious functions. It is estimated that the human genome contains more than 10 000 easily recognisable pseudogenes and many more fragmented sequences, that arose mainly through one of the following three mechanisms: duplication, retrotranposition and spontaneous loss of function. The majority of the human retrotransposed (i.e. processed) pseudogenes are primate specific, arising from a burst of retrotransposition activities approximately 45 Ma. Although most of the human pseudogenes are most likely too degenerated to perform a biological function, ∼20% of them exhibit evidence of transcriptional activity based on data from multiple genomic studies. Furthermore, a handful of pseudogene transcripts have been demonstrated experimentally to gain novel functions as noncoding
ribonucleic acids (RNAs)
, indicating that pseudogenes could be a reservoir for evolution innovation.

Key Concepts:

Pseudogenes are prevalent in the human genome and other mammalian genomes.

Most human pseudogenes are from past retrotranspositions occurring before the split of primate from other lineages.

Pseudogenes are a good source of DNA sequences for studying genome evolution.

Most human pseudogenes are most likely ‘dead’ but many of them can be transcribed.

Some human pseudogenes have adopted functions as noncoding RNAs.
Plant Pathogen Dispersal
Authors: West Jonathan S
Published: February 2014

Plant disease epidemics require plant pathogens to be dispersed to infect new hosts. Understanding dispersal is important for devising methods to improve detection and control of plant pathogens. This is not straightforward, as plant pathogens can be dispersed by air, rain, water or soil, and by vectors such as animals, pollen, various microbes, people and machinery and on infected plant material including seeds. Epidemics vary in time and space as a result of complex processes affecting inoculum availability and production, dispersal and survival processes, and also the coincidence of susceptible crop plants, which each interact with the weather. To reduce disease, exposure of crops to inoculum is often limited by separating crops in time and space, using crop rotation, including different varieties. A wide range of diagnostic methods are increasingly used to help with this by detecting plant pathogens before infection occurs to prevent introduction of exotic inoculum, or to improve applications of crop protection products.

Key Concepts:

Plant pathogens include fungi, protists (such as oomycetes and plasmodiophorids), bacteria, phytoplasmas, viruses and viroids. For plant disease epidemics to occur, these plant pathogens must be dispersed to infect new hosts.

Plant pathogens can be dispersed by air, rain, water, soil, by animals, people and machinery and through infected plant material including pollen and seeds.

A key method for crop protection is to limit dispersal by separating susceptible crops in time and space by crop rotation, use of different varieties, hygiene or management of inoculum and use of crop protection products (biologicals and pesticides) at key growth stages or when infection conditions are suitable.

Some pathogens that are dispersed by air are adapted to survive freezing temperatures, high UV light levels and desiccation, whereas others only remain viable for short periods or in certain less extreme conditions. Some may even induce ice nucleation to promote rainfall to return them to the ground.

Some plant pathogens are dispersed in rain‐splash, usually short distances but occasionally longer when combined with strong winds. Pathogens can be dispersed in water films and groundwater or rivers.

Insects and other invertebrates, pollen and protists may vector some pathogens, mainly viruses, viroids and phytoplasmas.

One of the main reasons for new introductions of plant pathogens to a territory is introduction by people, as infected plant material, infected seeds or as contamination on clothing, machinery, food or other imported materials. Various statutory quarantine regulations and inspections by plant health professionals aim to reduce introductions.

Climate change may help pathogens to establish in new territories where they were previously absent.