bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling immersion freezing with aerosol‐dependent prognostic ice nuclei in Arctic mixed‐phase clouds
Authors: Paukert M. , Hoose C. 
Published: July 2014

AbstractWhile recent laboratory experiments have thoroughly quantified the ice nucleation efficiency of different aerosol species, the resulting ice nucleation parameterizations have not yet been extensively evaluated in models on different scales. Here the implementation of an immersion freezing parameterization based on laboratory measurements of the ice nucleation active surface site density of mineral dust and ice nucleation active bacteria, accounting for nucleation scavenging of ice nuclei, into a cloud‐resolving model with two‐moment cloud microphysics is presented. We simulated an Arctic mixed‐phase stratocumulus cloud observed during Flight 31 of the Indirect and Semi‐Direct Aerosol Campaign near Barrow, Alaska. Through different feedback cycles, the persistence of the cloud strongly depends on the ice number concentration. It is attempted to bring the observed cloud properties, assumptions on aerosol concentration, and composition and ice formation parameterized as a function of these aerosol properties into agreement. Depending on the aerosol concentration and on the ice crystal properties, the simulated clouds are classified as growing, dissipating, and quasi‐stable. In comparison to the default ice nucleation scheme, the new scheme requires higher aerosol concentrations to maintain a quasi‐stable cloud. The simulations suggest that in the temperature range of this specific case, mineral dust can only contribute to a minor part of the ice formation. The importance of ice nucleation active bacteria and possibly other ice formation modes than immersion freezing remains poorly constrained in the considered case, since knowledge on local variations in the emissions of ice nucleation active organic aerosols in the Arctic is scarce.
Large‐scale vapor transport of remotely evaporated seawater by a Rossby wave response to typhoon forcing during the Baiu/Meiyu season as revealed by the JRA‐55 reanalysis
Authors: Kudo Tadasuke , Kawamura Ryuichi , Hirata Hidetaka , Ichiyanagi Kimpei , Tanoue Masahiro , Yoshimura Kei 
Published: July 2014

AbstractThe modulation of large‐scale moisture transport from the tropics into East Asia in response to typhoon‐induced heating during the mature stage of the Baiu/Meiyu season is investigated using the Japanese 55‐year reanalysis (JRA‐55), aided by a Rayleigh‐type global isotope circulation model (ICM). We highlighted the typhoons that migrate northward along the western periphery of the North Pacific subtropical high and approach the vicinity of Japan. Anomalous anticyclonic circulations to the northeast and southeast of typhoons and cyclonic circulation to their west become evident as they migrate toward Japan, which could be interpreted as a Rossby wave response to typhoon heating. These resultant anomalous circulation patterns form moisture conveyor belt (MCB) stretching from the South Asian monsoon region to East Asia via the confluence region between the monsoon westerlies and central Pacific easterlies. The ICM results confirm that the well‐defined nature of the MCB leads to penetration of the Indian Ocean, South China Sea, Philippine Sea, and Pacific Ocean water vapors into western Japan. The typhoons have the potential to accumulate large amounts of moisture from distant tropical oceans through the interaction of their Rossby wave response with the background flow. In the case of a typical typhoon, the total precipitable water around the typhoon center as it approaches Japan is maintained by the moisture supply from distant oceans rather than from the underlying ocean, which indirectly leads to the occurrence of heavy rainfall over western Japan.
Spirochaetes
Authors: Houston Simon , Taylor John S , Cameron Caroline E 
Published: July 2014

Abstract

Species in the phylum Spirochaetes (order: Spirochaetales) are thin, spiral‐shaped or wave‐like, highly motile bacteria that are best visualised by darkfield microscopy. Spirochaetes are Gram‐negative‐like, in that they possess inner and outer membranes separated by a peptidoglycan‐containing periplasmic space. Beyond these ultrastructural similarities, few parallels exist with conventional Gram‐negative bacteria. There have been more than 90 spirochaete species identified, including the well‐known pathogenic, disease‐causing species

Treponema pallidum

(syphilis),
Leptospira
sp. (leptospirosis) and

Borrelia burgdorferi

(Lyme disease). The phylogenetic relationship among spirochaetes is evident at the level of gross phenotypic characteristics, which include a distinctive morphology derived from the presence of periplasmic flagella. In this article, the authors describe the genomic, physiologic, structural and functional features that make Spirochaetes unique among the prokaryotes.

Key Concepts:

Spirochaetes are a genetically and morphologically distinct group of bacteria.

Spirochaetes are thin spiral‐shaped or wave‐like bacteria that are highly motile.

Endoflagella/periplasmic flagella provide spirochaetes with their characteristic corkscrew‐like motility.

Spirochaetes differ from typical Gram‐negative bacteria at the ultrastructural level.

Spirochaetes are chemo‐organotrophic, grow in diverse conditions and are comprised of both pathogenic and nonpathogenic members.

Complete genome sequencing has allowed for the characterisation and differentiation of spirochaetes at the genetic level.

Medically important spirochaetes belong to the three genera
Borrelia
,
Leptospira
and
Treponema
.
DNA
Double‐Strand Breaks and Their Consequences in Bacterial Genomes
Authors: Kobayashi Ichizo , Handa Naofumi , Kusano Kohji 
Published: July 2014

Abstract

Deoxyribonucleic acid (DNA)
double‐strand breaks, which are caused by many factors such as chemical treatments, radiations and, often, biological factors, are lethal events in organisms carrying DNA as their genome, which include bacteria. There are various mechanisms that work in the processing of these breaks, sometimes in collaboration or competition with each other. These include exonucleolytic degradation, end joining and recombination repair. These may bring about death, restoration or recombinational/mutational changes in the genome. Intragenomic collaboration and conflict between various pathways can be a force in their genome evolution. Recent analyses suggest that DNA double‐strand breaks switch on the programme of cell death in bacteria. DNA double‐strand breakage and its consequences in bacteria may provide a good model system to analyse the dynamic relationship between life, death and evolution. Understanding these processes in bacteria is important in medicine, environmental studies and industrial application.

Key Concepts:

DNA double‐strand breakage and its consequences in bacteria may provide a model system to analyse the relationship between life, death and evolution.

DNA double‐strand breakage may switch on programmes of cell death in bacteria.

Repair of DNA double‐strand breakage provides accurate products and innacurate products for host genome.

Small and large genome alterations are important in bacterial genome evolution.

The concept of intragenomic conflict may lead to meanings of the generation, processing and consequences of double‐strand breaks.
Peptidases
Authors: Rawlings Neil D , Barrett Alan J 
Published: July 2014

AbstractPeptidases are catalytically active proteins (enzymes) that cleave peptide bonds in proteins and peptides by hydrolysis. Not only do peptidases break down proteins and peptides so that the amino acids can be recycled and used during growth and remodelling, but they are also important for modifying proteins. These processing events ensure proteins are sent to the correct cellular or extracellular locations, are activated or inactivated when required, and that biologically important peptides are excised. There are six catalytic types (serine, cysteine, threonine, aspartic, glutamic and metallo). Peptidases can be classified by sequence similarities into approximately 250 families, and these in turn can be arranged into approximately 60 clans by comparing tertiary structures.Key Concepts:A peptidase is a catalytically active protein that cleaves one or more peptide bonds in a protein or peptide by hydrolysis.There are six different catalytic types of peptidases.Comparison of the amino acid sequences of peptidases allows them to be classified into about 250 families.Comparison of the structural folds of peptidases allows them to be classified into about 60 clans.A peptidase that acts only within three residues of the amino or carboxyl termini of a substrate protein is known as an exopeptidase.A peptidase that cleaves any bond in a substrate protein that is more than three residues from the amino or carboxyl termini is known as an endopeptidase.A peptidase has an active site containing amino acids that are important for catalysis and which are usually conserved in all active members of a family.The active site of a peptidase is flanked by substrate binding pockets, each of which accommodates one residue from the substrate.Some peptidases have additional substrate binding sites remote from the active site that are known as exosites.
Establishment of Left–Right Asymmetry in Chick and Mouse Embryos
Authors: Komatsu Yoshihiro , Mishina Yuji 
Published: July 2014

Abstract

All vertebrates have consistent left–right structural asymmetry, and deviations from the typical asymmetry in humans are clinically important. Studies elucidating the mechanisms that establish left–right asymmetry have lead to some of the most elegant advances in the field of embryology. In the past several decades, while we have gained an extensive understanding of the development of left–right asymmetry during embryogenesis, many questions remain to be addressed to fully appreciate the molecular mechanisms underlying its establishment. In this review article, the authors summarise the gene regulatory network that controls left–right patterning. They also focus on our current understanding of how left–right symmetry is broken.

Key Concepts:

Primary cilia rotating in a clockwise direction generate a unidirectional leftward fluid flow at a structure called the node, resulting in left–right symmetry breakage in mouse embryos. Similar leftward flow is observed in many vertebrate embryos.

Planar cell polarity (PCP) signalling, initially identified in the fruitfly, controls the uniform orientation of hairs and bristles on the body.

A primary cilium is a microtubule‐based antenna‐like structure lacking the central pairs of microtubules. This ‘9+0’ microtubular structure and lack of dynein arms render them immotile, whereas motile cilia have a ‘9+2’ microtubular structure with dynein arms.

BMP signalling negatively regulates cell cycle at the ventral surface of the node.

The posterior tilt of nodal cilia regulated by planar cell polarity is critical to generate a unilateral leftward flow from the rotation of the nodal cilia.

The ventral surface of the node is quiescent that allows formation of cilia.
Immunological Tolerance: Mechanisms
Authors: Zouali Moncef 
Published: July 2014

AbstractImmunological tolerance refers to a reduction or complete inhibition of the ability of an individual to mount a specific immune response upon immunisation. Several mechanisms are involved in induction and maintenance of tolerance, including clonal deletion, clonal anergy, receptor editing, receptor down‐modulation and lymphocyte sequestration. The number of antigen presenting cells, the number and activity of regulatory T cells and regulatory B cells, the nature and amount of antigenic peptides generated and the presence of co‐stimulatory signals in a particular tissue are also important. Depending on the site and the level of antigen expression, different states of peripheral B‐cell and T‐cell tolerance can be reached. In certain situations, they could act in an additive manner. In humans, induction of immunological tolerance is an important issue in both transplantation biology and autoimmune diseases, and present research aims at designing novel strategies to induce specific tolerance.Key Concepts:Tolerance induction is easier in animals with an immature immune system or with a mature immune system that has been compromised by irradiation, drugs or thoracic drug drainage.In general, when a given antigen is used over a wide range of concentrations, intermediate doses induce immunity, and low and high doses induce tolerance.The introduction route is a key variable in tolerance induction, particularly in adult animals, presumably by determining the accessibility of the antigen to professional antigen presenting cells.The tolerant state is not absolute and tolerance is rarely complete. With time, it gradually wanes and eventually disappears, but it can be deliberately terminated by several means.Persistence of the tolerogen in the periphery and its accessibility to the immune system are generally required to maintain tolerance, which continuously inactivates newly emerging T and B cells that develop in lymphoid organs.T lymphocytes specific for self‐peptides bound to major histocompatibility complex peptides are eliminated by clonal deletion, a process known as negative selection. Similarly, self‐reactive B cells are purged from the functional repertoire during the transition from the pre‐B to mature B‐cell stage in the bone marrow.Anergy is a functionally silent state induced in B cells and T cells, allowing them to persist functionally inactivated in tolerant animals.Receptor editing is a form of receptor processing that markedly alters the variable region genes expressed by B cells and, consequently, changes the specificity of the surface immunoglobulin and maintains B‐cell tolerance to self.Two functional lymphocyte subsets, called regulatory T cells and regulatory B cells, have recently been found to contribute to the maintenance of the fine equilibrium required for immune tolerance.In humans, induction of immunological tolerance in the adult is an important issue in both transplantation biology and autoimmune diseases, and present research aims at designing novel strategies to induce specific tolerance.
Meiosis
Authors: Cha Rita S , Hartsuiker Edgar 
Published: July 2014

AbstractMeiosis is a differentiation programme used by sexually reproducing organisms for generating reproductive cells. Its purpose is to reduce the genetic complement by half to ensure restoration of the correct number of chromosomes upon union of two sex cells. The halving of the genome is achieved by a single round of genome duplication followed by two successive rounds of genome division. During the period between completion of genome duplication and the first division, homologous maternal and paternal chromosomes pair with one another and exchange genetic material, culminating in formation of crossovers, which physically link the homologous chromosomes until they are separated at anaphase I. During the second genome division, the duplicated sister chromatids, which remain connected during meiosis I, are separated. Following the second division, four separated haploid genomes undergo a series of developmental steps, which give rise to reproductive cells capable of forming a diploid organism upon fertilisation.Key Concepts:Meiosis is a specialized cell division programme for generating reproductive cells.The aim of meiosis is to generate haploid reproductive cells from a diploid precursor.Reduction of the genome content by half is achieved by a single round of genome duplication followed by two successive rounds of genome divisions.During the first meiotic genome division (meiosis I), homologous maternal and paternal chromosomes separate; during the second genome division (meiosis II), the newly duplicated sister chromatids separate.Physical connection between homologous maternal and paternal chromatids or a crossover is essential for homologue separation during meiosis I.Crossover formation depends on meiosis‐specific pairing of the homologues and genetic recombination between the homologues.Meiotic recombination is initiated by developmentally programmed formation of DNA double‐strand breaks.Meiotic recombination leads to exchange of genetic information between homologous maternal and paternal DNA and contributes to genome variation and evolution.Meiotic homologue pairing and recombination are evolutionarily conserved from yeast to humans.Defects in meiotic homologue pairing and recombination contribute to infertility, birth defects and aneuploidy (e.g. Downs syndrome) in humans.
Thrombin
Authors: Thiagarajan P , Narayanan AS 
Published: July 2014

Abstract

Thrombin (factor IIa) is a serine protease that converts fibrinogen into fibrin in blood coagulation. The precursor of thrombin, prothrombin (inactive zymogen), is one of the several coagulation proteins containing γ‐carboxyglutamic acid. Prothrombin is synthesised in the liver and secreted into blood circulation, and is activated by vascular injury by limited proteolysis following upstream activation of the coagulation cascade. Thrombin activity is regulated by serum inhibitors and by its own action. With its procoagulant and anticoagulant functions, it plays a central role in thrombosis and haemostasis. It is an agonist for a number of cellular responses during inflammation and wound repair. Many diseases including stroke and myocardial infarction involve thrombosis; therefore, thrombin is a preferred target of antithrombotic drugs. Drugs available to block thrombin action include heparins, hirudins (lepirudin and bivalirudin), vitamin K antagonists and a new generation of direct thrombin inhibitors such as dabigatran and argatroban.

Key Concepts:

Thrombin is a serine protease that converts fibrinogen into fibrin and plays a crucial role in haemostasis and thrombosis.

During coagulation, factor Xa/Va complex formed on phospholipid or platelet membrane converts prothrombin to thrombin in the presence of Ca
2+
.

Thrombin also activates platelets and factors V, VIII and XI to enhance haemostasis.

In addition to haemostasis, thrombin plays a major role in inflammation and wound healing, and it is a potent mitogenic factor.

Thrombin has anticoagulant effects by activating the protein C pathway and by releasing plasminogen activators from endothelial cells, which promote fibrinolytic cascade.

Consequences of thrombosis include vascular diseases such as stroke, myocardial infarction and deep‐vein thrombosis and pulmonary embolism.

Both direct and indirect inhibitors are used clinically to treat thrombotic disorders.
Bioluminescence
Authors: De Abhijit 
Published: July 2014

Abstract

Bioluminescence is the active luminescence light producing event encountered among diverse group of living organisms in nature, more commonly in deep sea organisms. The event is a result of high‐quantum yield enzyme–substrate catalysis reaction resulting in the production of light devoid of any heat. The chemical reactions behind bioluminescence light emission can be broadly categorised as
adenosine triphosphate (ATP)
‐dependent and ATP‐independent mechanisms. Bioluminescence identified from firefly beetle is an example of ATP‐dependent photo‐production, whereas in jellyfish and
Renilla
sp. bioluminescence is an ATP‐independent process. In recent years several new biotechnology applications have used bioluminescence demonstrating their utility as highly sensitive assays for measuring cellular functions
in vivo
. Often genetic modifications in the luciferase structure or chemical modifications of their substrate have added new functionalities making these assays even more robust. Finally, noninvasive bioluminescence imaging has also evolved as an attractive tool for interrogating human cellular biology in rodent models.

Key Concepts:

Bioluminescence is light producing event caused by luciferase enzyme mediated substrate catalysis.

Bioluminescence can be co‐factor (e.g. ATP and Ca
2+
) dependent or independent process.

Evolutionary relationship among the structure of various luciferase proteins or their organic chemical substrates are hard to establish, with little or no commonality.

Luciferase proteins obtained from diverse organisms are used as bioluminescent reporters because they enable monitoring of intracellular events with high sensitivity, and without destroying the cells or tissues.

In biotechnology, mutations can be performed on luciferase gene sequence obtained from nature to make it suitable for use in higher order organisms and/or attribute better characters such as brightness, change spectral properties or protein stability.

Bioluminescence is extensively used in basic laboratory experiments for biotechnology and biomedical research, particularly in the format of various assays such as BRET and other diagnostic methods.

Noninvasive small animal imaging using luciferase reporter is gaining ground to provide simultaneous qualitative and quantitative measurements of disease interrogation
in vivo
.
Mimicry
Authors: Speed Mike 
Published: July 2014

Abstract

In its most general form mimicry refers to phenotypes of an organism that are adaptively modified to resemble living or nonliving components of its environments. Phenotype mimicry can be used in a number of different ways, most notably, to protect individuals against predators and other enemies. Such protective mimicry includes masquerade (copying an inanimate object in the environment), Batesian mimicry (an edible prey copies a defended prey) and Müllerian mimicry (shared warning signals between defended prey species). Phenotype mimicry may also be used aggressively, where for example, a predaceous mimic uses mimicry to hide from or to lure victims. In sexual mimicry (e.g. females look like males or vice versa), phenotype mimicry may be used to remove costs of sexual selection. In song mimicry, mimicry may be used to attract mates, to deter predation or facilitate grouping. Although mimicry is used in very diverse ways in nature, there may be similarities in the evolutionary ecology of mimetic phenotypes. A key point is that if the fitness of individual mimics increases with the number of mimics in a habitat then we may expect monomorphisms in the phenotypes; but if fitness declines as abundance increases we may anticipate the opposite.

Key Concepts:

Mimicry refers to phenotypes of an organism that are adaptively modified to resemble living or nonliving components of their environments.

The most extensively studied forms of mimicry are those used to protect prey from predators (especially mimetic resemblance of the colour patterns of a warningly coloured animal: Batesian and Müllerian mimicries).

In masquerade edible prey mimics inanimate objects in their environment (twigs and stones) to prevent predators noticing and attacking them.

Nature has found many different uses for phenotype mimicry in addition to avoidance of predation (e.g. aggressive use by predators to enable predation; by nectarless flowers to attract pollinators and by sexual mimicry and vocal mimicry).

Though mimicry is used in various ways there may be some common evolutionary issues; for example, how phenotype mimicry can evolve when the intermediate forms are less fit than both the original ancestral and the perfectly mimetic trait.

The benefits to a mimic are likely to change with the local abundance of the mimetic phenotype in a locality. Sometimes mimics benefit when there are many present (and we expect monomorphism in mimicry).

Often mimics lose benefits as the mimetic phenotype increases in abundance (in which case diversification of mimetic phenotypes may be expected).

When mimicry harms another organism we may expect counteractive measures in the form of adaptive change within an organism's lifetime (by learning) or by adaptive change across generations (coevolution).