bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Carbon Cycle
Authors: Sabine Christopher L 
Published: August 2014

Abstract

Despite the low concentrations in the atmosphere relative to nitrogen or oxygen, carbon dioxide (CO
2
) plays a significant role in the Earth's life cycle and in controlling the global climate. The positive and negative feedback mechanisms associated with the exchange of atmospheric carbon with the ocean and organic material found on the land surface (called the terrestrial biosphere) appear to have been relatively well balanced for most of humankind's existence. Since the beginning of the industrial era, however, humans have been extracting fossil carbon from the Earth's interior and combusting it for energy production. Much of this fossil carbon is converted to CO
2
gas and released into the environment where it is altering the carbon balance between the atmosphere, ocean and terrestrial biosphere. Recent changes observed in the global climate are consistent with the predicted response to increasing CO
2
and other greenhouse gases in the atmosphere.

Key Concepts:

Carbon is an essential component of life on Earth.

Atmospheric CO
2
concentrations varied considerably in the distant past depending on the balance of several geochemical processes.

Geochemical evidence suggests that atmospheric CO
2
levels dropped below 300 ppm approximately 20 million years ago and have remained below that level until the beginning of the twentieth century.

The atmosphere, terrestrial biosphere and the ocean are the only systems that have natural exchanges of carbon on time‐scales relevant to human society.

Humans are in the process of altering the global carbon cycle at a rate that is unprecedented in Earth's history through land‐use practices and the burning of fossil fuels.

As we change the balance of the carbon cycle it is clear that the global climate is changing, but it is not clear how global ecosystems might respond.
Small Nuclear Ribonucleoproteins (sn
RNP
s)
Authors: Stone Lauren B , Riley Kasandra J 
Published: August 2014

Abstract

Small nuclear ribonucleoproteins (snRNPs)
are protein–
ribonucleic acid (RNA)
complexes defined by a core noncoding RNA of approximately 100–600 nucleotides and tightly bound proteins that together accumulate in the nucleus. The snRNPs are best known for their role in RNA splicing complexes, including U1, U2, U4, U5 and U6 snRNPs found in the spliceosome. Additional snRNPs are functionally diverse, but in many cases the RNA component of snRNPs can base‐pair with a substrate for precise alignment and possible catalysis. The U7 snRNP directs 3′‐end mRNA formation for histone transcripts, and the 7SK snRNP regulates transcription. Two special groups of snRNPs,
small nucleolar RNPs (snoRNPs)
and
small Cajal‐body RNPs (scaRNPs)
, are restricted to their named subnuclear compartments in order to direct post‐transcriptional modification of ribosomal and splicing RNAs, respectively. Certain herpesviruses express high levels of novel snRNPs involved in the regulation of gene expression. Due to their important biological roles, there are many diseases associated with snRNPs.

Key Concepts:

The snRNPs are small nuclear ribonucleoprotein particles, a class of dynamic RNA–protein complexes that accumulate in the nucleus.

Major and minor splicing snRNPs form super‐complexes (spliceosomes) that direct the precise splicing of messenger RNAs.

In the special process of
trans
‐splicing, splice leader (SL) snRNPs donate RNA to the ends of transcripts.

The U7 snRNP coordinates 3′ end processing of metazoan histone messenger RNAs.

The 7SK snRNP regulates transcription by selectively sequestering and rendering inactive the P‐TEFb protein, a key modulator of RNA polymerase II.

Two groups of snRNPs are singled out for specific subnuclear localisation: small nucleolar and small Cajal‐body associated (sno/scaRNPs) direct methylation and pseudouridylation of splicing and ribosomal RNAs.

Some mammalian herpesviruses express viral snRNPs, which have enigmatic and complex functions in gene regulation.

Several diseases including lupus present autoantibody production of antibodies directed at snRNP‐affiliated proteins such as Sm, Lsm and La.

Most snRNPs have been affiliated with diseases and are therefore promising biomarkers for diagnosis and prognosis.
Far‐field Light Microscopy
Authors: Cremer Christoph 
Published: August 2014

Abstract

Novel developments in optical technology and photophysics made it possible to radically overcome the diffraction limit (ca. 200 nm laterally, 600 nm along the optical axis) of conventional far‐field fluorescence microscopy. Presently, three principal ‘nanoscopy’ families have been established: Nanoscopy based on highly focused laser beams; nanoscopy based on structured illumination excitation; and nanoscopy based on localisation microscopy approaches. With such ‘superresolution’ or ‘nanoscopy’ techniques, it has become possible to analyse biostructures with a substantially enhanced light optical resolution down to a few tens of nanometre in 3D, and a few nanometre in the object plane, corresponding to 1/100 of the exciting wavelength. These methods allow to study individual membrane complexes, cellular protein distributions, nuclear nanostructures, bacteria or individual viruses down to the molecular level; they open new perspectives to combine molecular and structural biology to unravel the basic mechanisms of life and their emergence from fundamental laws.

Key Concepts

Light microscopy of biostructures has reemerged as an essential tool of the life sciences.

Conventional light microscopy methods suffer from the limited resolution and thus prevent the direct study of nanostructural details.

Novel developments in optics and photophysics have made it possible to overcome the conventional resolution limits.

Present ‘superresolution’/‘nanoscopy’ techniques are based either on focused laser beam excitation; or on patterned/structured illumination schemes; or on homogeneous wide‐field illumination.

In addition to advanced optical techniques, nanoscopy requires appropriate photostable/photoswitchable fluorochromes with specific spectral characteristics.

Far‐field light microscopy based ‘nanoscopy’ techniques presently allow to discriminate (resolve) in a cellular environment individual fluorescent molecules down to a minimum distance of few nanometre.

The combination of the novel nanoscopy approaches with molecular biology methods is expected to open an avenue towards a substantially improved understanding of the basic mechanisms of life and its emergence from the basic laws of nature.
Kinetochore: Structure, Function and Evolution
Authors: Liu Song‐Tao 
Published: August 2014

Abstract

Duplicated eukaryotic chromosomes are segregated into daughter cells through cell division. Faithful chromosome segregation depends on kinetochores, which are specialized macromolecular structures built upon centromeric chromatin. The dynamic kinetochore structures connect chromosomes with spindle microtubules, power chromosome movement, and signal the activation and silencing of the spindle assembly checkpoint (SAC). Molecular analyses of the components and architecture of kinetochores have advanced rapidly in recent years. A human kinetochore contains approximately 200 proteins, many of which are evolutionarily conserved in other organisms. A histone H3 variant, CENP‐A and associated constitutive centromere proteins lay the foundation for kinetochore build‐up. Multiple kinetochore‐localised microtubule‐binding proteins including the Ndc80 complex help regulate chromosome movement. The SAC signalling originates from kinetochores and contributes to the fidelity of chromosome segregation. Many fascinating properties remain to be elucidated about the kinetochore as a fundamental machinery to maintain genomic stability.

Key Concepts:

Chromosome segregation in eukaryotic cells depends upon connecting spindle microtubules with special macromolecular structures on chromosomes called kinetochores.

The centromere is the chromosomal locus where a kinetochore is built.

Laying the foundation for kinetochore assembly at centromeres are CENP‐A (a histone H3 variant) containing nucleosomes and a group of CENP‐A associated proteins (termed constitutive centromere proteins).

There are multiple microtubule motors and nonmotor microtubule‐binding proteins localised at kinetochores to coordinate chromosome movement.

A 10 protein complex called KMN network is currently thought to provide the primary end‐on microtubule‐binding activity.

The spindle assembly checkpoint (SAC) monitors the kinetochore–microtubule attachment and signals the delay of the metaphase‐to‐anaphase transition when defects are detected.

Conformational change of MAD2 and assembly of the mitotic checkpoint complex (MCC) are the key events to activate the SAC.

Comparative studies of similar and distinct kinetochore composition, structure and function in different species and during mitosis or meiosis have provided evolutionary perspectives on mechanisms regulating chromosome segregation.
Bacteriophage: Therapeutic Uses
Authors: Harper David R , Burrowes Benjamin H , Kutter Elizabeth M 
Published: August 2014

AbstractBacteriophages are viruses that grow within bacteria. Almost all bacteriophages can destroy (lyse) their bacterial host, although many are ‘temperate’ and can insert their genome into that of their bacterial host, a state referred to as lysogeny. Those that can only kill their host bacteria are termed ‘virulent’ and are preferred for therapeutic use. Lysis kills the bacterial host and releases the next generation of bacteriophages. This unique property allows localised amplification of a bacteriophage therapeutic, but only where its specific bacterial host is present. Bacteriophages are also able to target bacteria living within biofilms that can make them highly refractory to conventional antibiotics. Since their discovery in 1915, bacteriophages have been identified as having potential for the control of bacterial disease. Following the widespread appearance of resistance to conventional antibiotics, interest in this area has revived and the results of clinical trials of bacteriophage therapeutics are now being reported.Key Concepts:Bacteriophages are viruses that infect bacteria.Lytic bacteriophages kill their bacterial host rapidly, taking over host metabolism and producing a new generation of bacteriophages soon after infection.Newly produced bacteriophages can infect new host bacteria locally and can also spread to other sites of infection.This ability to kill bacteria led to their therapeutic use against bacterial infection in the pre‐antibiotic era.In most of the world, bacteriophages have been superseded since the 1940s by chemical antibiotics due to a combination of factors, including the limited understanding of basic bacteriophage biology and the far broader host ranges of chemical antibiotics.Despite many years of extensive clinical study in Eastern Europe and in earlier work in Europe and the United States, a lack of clinical trials meeting current regulatory requirements has limited the development of bacteriophage therapeutics.Interest in bacteriophages as therapeutics has been revived by the looming antibiotic resistance crisis, in an era when much more information is available about the older work and when phage biology is far better understood.Bacteriophage products for agricultural and food use are currently being marketed.
Amidohydrolase Superfamily
Authors: Liu Aimin , Huo Lu 
Published: August 2014

Abstract

The amidohydrolase superfamily is a structure‐based cluster of enzymes that contain a sturdy and versatile triosephosphate isomerase (TIM)‐like (β/α)
8
‐barrel fold embracing the catalytic active site. To date, the amidohydrolase superfamily has grown into one of the largest families of enzymes, with tens of thousand of members catalysing a wide range of hydrolytic and nonhydrolytic metabolic reactions which are important in amino acid and nucleotide metabolism as well as biodegradation of agricultural and industrial compounds. Previously, the presence of a mono‐ or dinuclear
d
‐block metal cofactor in the active site was thought to be one of the main characteristics of the members in this superfamily. However, recently new members containing a trinuclear metal cofactors or no cofactor at all were discovered. It has become apparent that activating a well‐ordered water molecule by an active site residue for nucleophilic attack on the organic substrate is a common mechanistic feature for all members of the superfamily.

Key Concepts:

Amidohydrolase superfamily is one of the largest enzyme superfamilies performing a wide array of catalytic reactions.

All members in the family employ a TIM‐barrel structural fold, although some of the amidohydrolase superfamily members present an imperfect barrel.

The vast majority, but not all, of the enzymes in this superfamily are metalloenzymes.

The hallmark of the catalytic mechanisms shared by these enzymes is to use an activated water molecule to attack the organic substrate.

The catalytic centre is diverse, with one, two, three or zero metal ion(s).
Plant Virus Silencing Suppressors and
RNA
Silencing in Plants
Authors: Zhang Xiuchun , Qu Feng 
Published: August 2014

Abstract

Plants use
ribonucleic acid (RNA)
of virus origins to produce
small interfering RNAs (siRNAs)
that guide sequence‐specific destruction of viral RNAs through a process termed RNA silencing. In addition to siRNAs, antiviral RNA silencing requires the participation of at least four families of plant proteins, namely the dicer‐like (DCL) nucleases that process virus‐specific double‐stranded (ds) RNA to siRNAs, Argonaute proteins (AGO) that use siRNAs as the sequence‐specific guide to cleave (slice) complementary single‐stranded viral RNA, as well as dsRNA‐binding proteins (DRBs) that assist DCL processing and/or DCL‐AGO communication, and RNA‐dependent RNA polymerases (RDRs) that produce a subset of dsRNA substrates of DCLs by converting viral ssRNAs into dsRNAs. To survive the RNA silencing‐based plant defence, plant viruses have evolved to encode strong suppressors of RNA silencing (VSR). Known targets of VSRs include all major steps/components of the RNA silencing pathway(s).

Key Concepts:

RNA silencing is an RNA‐mediated, sequence‐specific surveillance system in plants and other eukaryotes.

The sequence specificity of RNA silencing is conferred by siRNAs generated through the processing of dsRNAs originated from viruses and other molecular parasites.

RNA silencing is analogous to RNA interference (RNAi) in animals. It is a highly conserved mechanism of genome defence in almost all eukaryotic organisms.

Evolutionary successful viruses encode VSRs to engage diverse components of the RNA silencing pathway and subvert this robust defence mechanism.
Sleep and Memory
Authors: Aton Sara J , Seibt Julie , Frank Marcos G 
Published: August 2014

Abstract

Current behavioural evidence indicates that sleep plays a central role in memory consolidation. Neural events during post‐learning sleep share key features with both early and late stages of memory consolidation. For example, recent studies have shown neuronal changes during post‐learning sleep which reflect early synaptic changes associated with consolidation, including activation of shared intracellular pathways and modifications of synaptic strength. Sleep may also play a role in later stages of consolidation involving propagation of memory traces throughout the brain. However, to date the precise molecular and physiological aspects of sleep required for this process remain unknown. The behavioural effects of sleep may be mediated by the large‐scale, global changes in neuronal activity, synchrony and intracellular communication that accompany sleep, or by synapse‐specific ‘replay’ of activity patterns associated with prior learning.

Key Concepts:

Memory consolidation involves plastic changes at the synaptic and brain‐systems levels; these changes occur over timescales of minutes (synaptic consolidation) to days or months (systems consolidation).

Cellular changes occurring during early post‐learning sleep suggest that synaptic consolidation may occur preferentially during sleep.

Brain‐imaging and gene expression studies have provided limited evidence that sleep may facilitate the gradual redistribution of memory traces throughout the brain.

Sleep may facilitate consolidation through large‐scale changes in neural activity, neurotransmission or gene expression associated with REM and NREM sleep.

It remains unclear whether sleep‐dependent consolidation is mediated by permissive (global) or instructive (synapse‐specific) mechanisms.
Memory (Mechanisms Other than
LTP
)
Authors: Debanne Dominique , Campanac Emilie 
Published: August 2014

Abstract

Synaptic plasticity is not the exclusive mode of memory storage, and persistent regulation of voltage‐gated ionic channels also participates in information storage. Long‐term changes in neuronal excitability have been reported in several brain areas following learning. Synaptic activation of glutamate receptors initiates long‐lasting modification in neuronal excitability at the pre‐ or postsynaptic side, that is, in the axon, soma and dendrites of central neurons. Intrinsic plasticity is expressed in virtually all neuronal types including principal cells and interneurons. It is mediated by changes in the expression level or biophysical properties of voltage‐gated ion channels in the membrane and can affect many different neuronal operations such as dendritic integration and action potential generation and propagation. Similarly to synaptic plasticity, long‐lasting intrinsic plasticity is bidirectional and expresses a certain level of input or cell specificity. Synaptic and intrinsic plasticities not only share common learning rules and induction pathways but also contribute in synergy with these synaptic changes to the formation of a coherent mnesic engram.

Key Concepts:

Synaptic plasticity is a major mode of memory storage.

Persistent regulation of voltage‐gated ionic channels also participates in information storage following learning.

Synaptic activation of glutamate receptors initiates long‐lasting modification in neuronal excitability at the pre‐ or postsynaptic side.

Intrinsic plasticity is mediated by changes in the expression level or biophysical properties of voltage‐gated ion channels in the membrane.

Intrinsic plasticity can affect many different neuronal operations such as dendritic integration, action potential generation, action potential shape, action potential propagation and backpropagation.

Synaptic and intrinsic plasticities share common learning rules and induction pathways.

Synaptic and intrinsic plasticities contribute in synergy to the formation of a coherent mnesic engram.
Genetic Differences Between Chimpanzee Populations
Authors: Mitchell Matthew W , Gonder Mary Katherine 
Published: August 2014

Abstract

The evolutionary history of chimpanzees has been widely studied by researchers for a number of years. The number, and evolutionary relationship, of chimpanzee subspecies has been disputed for a number of years. In recent years researchers have used genomic data to investigate these questions. A consensus has emerged that chimpanzees are divided into four subspecies ranging across tropical Africa. However, little is known about underlying evolutionary processes that generated these patterns. Two major mechanisms have been proposed to drive the evolutionary diversification of chimpanzees: (1) isolation and subsequent diversification of taxa in Pleistocene Refugia and (2) isolation on opposite banks of riverine barriers. Additionally, the role of intraspecific differentiation and speciation through divergent selection across habitat gradients has been the focus of several recent studies, but this mechanism is relatively understudied in primates.

Key Concepts:

There have been recent breakthroughs into understanding the genetic differences between chimpanzee populations.

Genomic science has provided a window into the evolutionary history of chimpanzees.

Understanding evolutionary processes is vital to understanding chimpanzee evolution.

Understanding chimpanzee evolutionary history is of great interest to scientists.

Common chimpanzees can be divided into four genetically distinct subspecies.
MALDI
‐Mass Spectrometric Imaging of Endogenous Metabolites in Biological Systems
Authors: Gemperline Erin , Li Lingjun 
Published: August 2014

Abstract

Matrix‐assisted laser desorption/ionisation (MALDI)‐mass spectrometric imaging (MSI) is a powerful, relatively new technology that allows for the detection of molecules directly from biological systems and also provides the spatial distribution for these analytes within the tissue sample. MSI has gained considerable popularity for the study of endogenous metabolites as metabolites are the end product of various biochemical processes, and represent a biological snapshot of an organism's biochemistry at a given time. Although the underlying concept is simple, factors such as choice of ionisation method, sample preparation, instrumentation and data analysis must be taken into account and tailored for successful applications of MSI, especially for the study of small molecules. MALDI‐MSI has been successfully applied to the study of endogenous metabolites in animal, plant, bacteria and fungal tissues and has provided new insights into biological functions and pathways, interspecies interactions and novel natural products.

Key Concepts:

A metabolic profile provides a snapshot of an organism's metabolism and underlying biochemistry at a given time.

MALDI‐MSI provides spatial distribution of endogenous or exogenous molecules in a sample.

Advantages of MALDI‐MSI include the ability to detect a broad mass range of compounds, the ability to detect multiple analytes in a single experiment without the need for labels or prior knowledge of the analytes and the preservation of biologically relevant spatial information.

The study of small molecules with MALDI‐MSI presents unique challenges due to matrix interference and potential analyte delocalisation.

MALDI‐MSI has been extensively used to study metabolites and other compounds in animal tissue and has recently been applied to the study of small molecules in plant, bacteria and fungi.