bluuebunny/crossref_metadata_2025_split huggingface dataset:
Caracterização da ictiofauna do rio Santa Catarina (Bacia do São Francisco) no município de Vazante, Minas Gerais
Authors: Amorim Nathan Pereira Lima , Giongo Patrícia , Belei Frederico , Sampaio Wagner Martins Santana 
Published: April 2014

<p>A bacia hidrográfica do rio São Francisco é a terceira maior em extensão do Brasil. O Rio Paracatu é um dos principais contribuintes do rio São Francisco. O rio Santa Catarina é afluente esquerdo do rio Paracatu, sendo o principal rio presente no município de Vazante, em Minas Gerais. A Ictiofauna da bacia do São Francisco é representada por cerca de 158 espécies de água doce, sendo as famílias Characidae, Loricariidae, Rivulidae e Anostomidae as mais diversificadas. Na região do rio Santa Catarina no município de Vazante (MG) as atividades ligadas à mineração representa a principal atividade econômica da região, porém causa vários tipos de impactos ambientais aos ecossistemas aquáticos. O presente trabalho busca caracterizar a área do Rio Santa Catarina, no município de Vazante, Minas Gerais, e desta forma propor medidas de conservação da ictiofauna da bacia do Rio Santa Catarina. Foram capturados 177 indivíduos. Estes estão distribuídos em 61 espécies, 45 gêneros, 22 famílias e 6 ordens. O rio Santa Catarina apresenta inúmeros habitats que são essenciais para manutenção da biodiversidade aquática da bacia do rio São Francisco, como veredas, dolinas naturais e rios intermitentes que apresentam peixes de vida restrita e ameaçados de extinção, além de se apresentar como importante rota migratória para o rio Paracatu um dos principais afluentes do rio São Francisco em Minas Gerais.</p><p> </p><p>10.7902/ecb.v4i1.53</p>
Spatial variability of surface irradiance measurements at the Manus ARM site
Authors: Riihimaki Laura D. , Long Charles N. 
Published: April 2014

AbstractThe location of the Atmospheric Radiation Measurement (ARM) site on Manus island was chosen because it is very close to the coast, in a flat, near–sea level area of the island, hopefully minimizing the impact of local island effects on the meteorology of the measurements. In this study, we confirm that the Manus site is indeed less impacted by the island meteorology than slightly inland by comparing over a year of broadband surface irradiance and ceilometer measurements and derived quantities at the standard Manus site and a second location 7 km away as part of the ARM Madden Julian Oscillation Investigation Experiment (AMIE)‐Manus campaign. The two sites show statistically similar distributions of irradiance and other derived quantities for all wind directions except easterly winds, when the inland site is downwind from the standard Manus site. Under easterly wind conditions, which occur 17% of the time, there is a higher occurrence of cloudiness at the downwind site likely due to land heating and orographic effects. This increased cloudiness is caused by scattered clouds often with bases around 700 m in altitude. While the central Manus site consistently measures a frequency of occurrence of low clouds (cloud base height less than 1200 m) about 25% of the time regardless of wind direction, the AMIE site has higher frequencies of low clouds (38%) when winds are from the east. This increase in low, locally produced clouds causes an additional −20W/m2shortwave surface cloud radiative effect at the AMIE site than the Manus site.
A flux‐form conservative semi‐Lagrangian multitracer transport scheme (FF‐CSLAM) for icosahedral‐hexagonal grids
Authors: Dubey Sarvesh , Mittal Rashmi , Lauritzen Peter H. 
Published: April 2014

AbstractA high‐order incremental “remap‐type” transport scheme is presented (FF‐CSLAM). The scheme utilizes bi‐quadratic polynomial subgrid‐cell reconstruction functions based on the weighted least squares method. The integration of the reconstruction functions over flux areas, which is inherent in remap schemes, makes use of CSLAM approach of line integration. Though the formal order of the scheme is second order, yet quadratic subgrid scale polynomial reconstruction does lead to improvement in the overall accuracy of the scheme. Since the rigorous search for overlap areas between flux areas and grid cells is cumbersome, two simplifications have been suggested in the literature. The main objectives of this paper are (a) to formulate flux‐form CSLAM for the icosahedral‐hexagonal grid and (b) to assess the accuracy of two flux‐integral simplifications.
G Protein‐Coupled Receptors
Authors: Bockaert Joël 
Published: April 2014

Abstract

Among membrane‐bound receptors that recognise regulatory messages (hormones, neurotransmitters, photon, odours, etc.), the seven transmembrane receptors coupled to G proteins (G protein‐coupled receptors, GPCRs) are the most numerous. They represent 3% of the total number of genes in human genome. Following activation by those messages, GPCRs activate one or several heterotrimeric G proteins (α, β and γ subunits) by stimulating the guanosine diphosphate/guanosine triphosphate (GTP) exchange on the nucleotide binding site. The GTP form of the subunits activate effectors such as enzymes (e.g. the adenylyl cyclase) or channels. GPCRs can also trigger G protein‐independent signalling. GPCRs are targets for more than 30% of the drugs used in human therapy. Progress has been made recently on the structure and activation of GPCRs, thanks to the crystallisation of more than 60 GPCRs bound to agonists, antagonists and inverse‐agonists as well as a cocrystallisation between β2‐adrenergic receptors and its associated G protein.

Key Concepts:

Cell–cell communication involved messages (hormone, neurotransmitter growth factors, odorant, etc.) and receptors, the majority of them being GPCRs.

GPCRs are seven transmembrane receptors. They form homo‐ or heterodimers.

There are three main classes of GPCRs differing in their primary sequences.

The class 3 is the more original one having its binding site within an extracellular structure called ‘Venus fly trap’.

During evolution, mutations have tinkered the GPCR structure in order to allow recognition of ligands as diverse as photon, odorant, sugar, proteins, etc.

Virus, like human immunodeficiency virus (HIV), uses GPCRs such as those recognising chemokines (CCR5, CXCR3) to enter specialised cells such as macrophages or lymphocytes.

GPCRs are allosteric molecules and drugs can be developed enhancing or silencing the effect of the natural ligand without having any effect by themselves.

Mutations of GPCR are responsible of pathologies. These mutations can render the receptor constitutively active or inactive.

Analysis of GPCR structures using crystallisation and nuclear magnetic resonance (NMR) indicates that many ‘active’ and ‘inactive’ conformations do exist for each GPCR. They are stabilised by chemically different agonists, inverse‐agonists or antagonists.

The fully ‘active conformation’ is only obtained when the GPCR occupied by an agonist is associated with a G‐protein.
Virus Evolution
Authors: Domingo Esteban , Perales Celia 
Published: April 2014

Abstract

Viruses are transmissible
deoxyribonucleic acid (DNA)
or
ribonucleic acid (RNA)
genetic elements that require a cell for multiplication. Viruses are extremely diverse and ubiquitous in nature. They evolve in continuous interaction with their host cells and organisms, following the general Darwinian principles: genetic variation, competition among variant forms and selection of the most fit variants in a given environment. Viruses probably had an ancient origin and have survived as agents of gene transfer and promoters of cell variation. Evolution of RNA viruses and some DNA viruses can be extremely rapid, fuelled by limited template‐copying fidelity of the replicating polymerases. They form extremely complex mutant clouds termed viral quasispecies, which can acquire features not explainable from the individuals that compose the ensemble. Quasispecies dynamics not only represent a problem for disease prevention and control, but it has inspired new strategies to combat viral disease. One of them is lethal mutagenesis or viral extinction driven by an excess of mutations, often produced by mutagenic nucleotide analogues. New antiviral designs based on lethal mutagenesis are currently under investigation.

Key Concepts:

Virions are the virus particles produced on completion of the intracellular replication cycle.

Interhost transmission of virions can give rise to disease outbreaks, epidemics or pandemics.

Metagenomic studies using deep sequencing methods have unveiled great diversity of viruses in many natural habitats.

The ensemble of viruses in our biosphere is termed the ‘virosphere’.

Evidence from comparative genomics suggests a long coevolution of cells and viruses on Earth.

Recombination and horizontal gene transfers between viral and cellular genes have been abundant during evolution of life.

Some proteins that play physiological functions in cells can be recruited as part of the innate immunity against viruses.

Population bottlenecks may alter viral fitness and influence evolutionary outcomes.

The adaptive potential of viral quasispecies has encouraged research in new strategies for viral disease prevention and control.
Prokaryotic Systematics: Theoretical Overview in the Light of Molecular Advances
Authors: Kurtböke Ipek 
Published: April 2014

AbstractSystematics describes the ordering of information on organisms and plays an important role in communicating information within biological sciences. Systematics seeks to reveal the phenotypic and genotypic diversity of organisms while relating this information to natural interactions and evolutionary history. Systematics may utilise a wide range of data and is not limited to the experimental methods that it may draw on in order to make sensible comparisons between organisms. Systematics requires an underlying order, and both systematics and taxonomy are strongly dependent on theory and philosophy, which are used to create this order. Systematics is a complex area, which has seen much change and progress in the last century. Developments in molecular biology have been adapted in line with the theory and philosophy and have become established in systematics. In the molecular era, accumulated data including those genomics‐derived will be the driving force behind the revalidation of currently used theories and hypotheses formulated in systematics and lead towards the establishment of a ‘genomic taxonomy’.Key Concepts:Systematics seeks to discover phenotypic and genotypic diversity of organisms.Taxonomy, the theory and practice of identifying, describing, naming and classifying organisms.Current systematists make extensive use of molecular biology and bioinformatics to study microorganisms.The basis of molecular phylogeny refers to evolutive relationship of microorganisms that can be inferred from the relationships of their genes and their genomes.Genomics explores the biology of organisms through their genetic blueprints.Metagenomics provide access to genome for prediction of the ecological role of members of microbial communities.Current comparative genomics approaches will lead towards establishment of a ‘genomic taxonomy’.
Hepatitis C virus
Authors: Harris Mark 
Published: April 2014

Abstract

Hepatitis C virus
is a positive‐sense RNA virus that is parenterally transmitted and is associated with chronic liver disease – fibrosis, cirrhosis, liver failure and hepatocellular carcinoma. The virus infects an estimated 123 million individuals worldwide with 5 million new infections occurring per annum. The prevalence of the virus, and the persistent nature of the infection, has led to the prediction that it will become an ever‐increasing burden on global healthcare resources. There is no vaccine to prevent infection; however, treatment options, until recently limited to a combination of interferon and ribavirin, have been improved by the advent of direct‐acting antivirals. These therapeutic advances have been underpinned by recent developments in our understanding of the molecular biology of virus infection, which are described in this article. In particular, the establishment of a system for the study of the complete virus lifecycle in tissue culture has led to many major advances and provides opportunities for further therapeutic developments.

Key Concepts:

Hepatitis C virus
(HCV) is a major human pathogen infecting approximately 3% of the world population.

HCV causes chronic liver disease – fibrosis, cirrhosis and hepatocellular carcinoma.

HCV is a positive‐strand RNA virus that infects hepatocytes in the liver.

Recent developments in HCV biology have allowed a deeper understanding of mechanisms of replication and pathogenesis.

New direct‐acting antiviral compounds promise to improve therapeutic options.
Lassa Fever Virus
Authors: Garry Robert F 
Published: April 2014

Abstract

Lassa virus, a member of the
Arenaviridae
family, is an enveloped virus with a bisegmented, linear, single‐stranded
ribonucleic acid
genome. Infection with Lassa virus can result in a range of outcomes from a mild or asymptomatic infection to Lassa fever, a severe and often fatal viral haemorrhagic fever. Human infection with Lassa virus occurs through contact with the reservoir

Mastomys natalensis

or infected humans. There are an estimated 300 000–500 000 cases of Lassa fever in West Africa each year, with most recorded cases occurring in Sierra Leone and Nigeria. Presently, there is no licensed vaccine or immunotherapy available for preventing or treating this disease. Although the antiviral drug ribavirin can be beneficial, it must be administered at an early stage of infection to successfully alter the disease outcome, thereby limiting its utility.

Key Concepts:

Lassa virus, a member of the
Arenaviridae
family, is the aetiologic agent of Lassa fever.

Infection with Lassa virus can result in a range of outcomes from a mild or asymptomatic infection to severe and often fatal viral haemorrhagic fever.

Signs and symptoms of Lassa fever are highly variable, which challenges early diagnosis.

Lassa virus has an enveloped virion with a bisegmented, linear, single‐stranded ribonucleic acid genome.

The Lassa virus virion contains nucleoprotein NP, zinc protein Z, glycoproteins GP1 and GP2 and an unusually long and stable signal peptide SSP.

Human infection with Lassa virus occurs through contact with its reservoir
Mastomys natalensis
or infected humans.

An estimated 300 000–500 000 cases of Lassa fever occur in West Africa each year, with most recorded cases occurring in Sierra Leone and Nigeria.

No licensed vaccine or immunotherapy is presently available for preventing or treating Lassa fever.

The antiviral drug ribavirin can be beneficial, but must be administered early, limiting its utility.
Oxidative Stress
Authors: Fridovich Irwin 
Published: April 2014

AbstractRespiring organisms derive multiple benefits from molecular oxygen. However, some fraction of the oxygen used is unavoidably converted into dangerously reactive substances such as the superoxide radical (O2−), hydrogen peroxide (H2O2) and the hydroxyl radical (HO). These intermediates of oxygen reduction to water threaten the integrity of diverse biological molecules and hence the life of cells and organisms. The seeming comfort of aerobes in the presence of oxygen is due to their content of multilayered defences against these reactive metabolites of oxygen. There are superoxide dismutases that eliminate O2−by efficiently dismuting it to oxygen and H2O2. There are catalases that eliminate H2O2by dismuting it into water plus oxygen and there are also peroxidases that eliminate H2O2and organic peroxides by reducing them to H2O and to alcohols, respectively. Removing O2−and H2O2prevents the formation of HO. However, no defence is perfect, so backing up these frontline defences that in large measure prevent oxidative damage, are others that repair the damage caused by the reactive derivatives of oxygen and, when that is not possible, eliminate the damaged molecules and replace them with newly synthesised ones.Key Concepts:The spin restriction facing oxygen reduction that favours the univalent pathway of oxygen reduction.Superoxide, hydrogen peroxide and hydroxyl radical are intermediates on the univalent pathway.These intermediates are reactive and can cause damage.Defences are essential and have been evolved.Superoxide dismutases protect against superoxide by converting it into hydrogen peroxide plus oxygen.There are superoxide dismutases that contain copper plus zinc, manganese, iron or nickel at their active sites.Catalases protect against hydrogen peroxide by converting it into oxygen plus water.There are catalases with haem iron at the active site and others with manganese.Peroxidases protect against hydrogen peroxide and against organic peroxides by reducing them to water and to alcohols, respectively.Removing both superoxide and hydrogen peroxide prevents the formation of hydroxyl radical.Oxidative stress contributes to multiple pathologies and to normal aging.
Drift: Introduction
Authors: Whitlock Michael C , Phillips Patrick C 
Published: April 2014

Abstract

Genetic drift is the random change in allele frequencies by the chance success of some alleles relative to others. Genetic drift is more important in small populations, where chance plays stronger role. If the population size is small enough relative to the strength of selection, genetic drift can sometimes cause slightly deleterious alleles to rise in frequency or beneficial alleles to be lost from a population. Drift can lead to the fixation or loss of alleles, and therefore drift can contribute to the loss of genetic variation. As a consequence, genetic drift in small populations is a source of concern for the future evolutionary potential for some endangered species.

Key Concepts:

Alleles may increase or decrease in frequency by chance.

The effects of chance on allele frequency change are most pronounced in small populations.

Genetic drift tends to lead to fixation or loss of alleles over time, and therefore contributes to the loss of genetic variation.

If the population size is small enough relative to the strength of selection, genetic drift can cause the fixation of deleterious alleles or loss of beneficial alleles.

Genetic drift can cause genetic divergence between species or populations. Most genetic differences between species are probably due to genetic drift.

Genetic drift is nonadaptive and nondirectional.
Cell‐to‐Cell Signalling in Development: Wnt Signalling
Authors: Hoppler Stefan , Nakamura Yukio 
Published: April 2014

Abstract

Wnt signalling is an important cell‐to‐cell signalling mechanism, which is generally conserved among multicellular animals. Wnt signalling operates in the embryo and in adult stem cells, but also in human cancers. Frizzled receptors in the cell membrane are critical functional intermediaries between the extracellular Wnt signal and diverse signal transduction mechanisms that can be activated inside different responding cells. Coreceptors are involved in selecting more specific intracellular signal transduction mechanisms. Frizzled receptors and other Wnt signalling molecules are localised in cells to coordinate planar cell polarity in epithelial tissues and also to regulate morphogenetic movements in embryos. A well‐studied intracellular Wnt signal transduction mechanism promotes stabilisation and nuclear localisation of the protein β‐catenin to regulate transcription of specific target genes by interacting with
deoxyribonucleic acid (DNA)
‐binding transcription factor proteins, such as the TCF/LEF proteins.

Key Concepts:

Wnt signalling functions in the embryo, to regulate stem cells and in disease such as cancer.

Wnt signalling mechanisms regulate important cellular processes, such as cell fate specification, cell proliferation, cell differentiation, axon guidance and morphogenesis.

Wnt proteins are lipid‐modified secreted signals.

Frizzled proteins function as cell membrane receptors for Wnt signals.

Wnt/Frizzled signalling activates a network of diverse intracellular signal transduction pathways.

One conserved branch of Wnt signal transduction causes stabilisation and nuclear localisation of the protein β‐catenin.

Nuclear β‐catenin regulates transcription of specific target genes by interacting with DNA‐binding proteins, such as TCF/LEF proteins.

Other, β‐catenin‐independent Wnt signal transduction mechanisms also regulate the cytoskeleton and planar cell polarity.

Feedback regulation and cross‐regulation between different Wnt signal transduction branches is characteristic of Wnt signalling.
Kammerer, Paul
Authors: Gratzer Walter 
Published: April 2014

AbstractPaul Kammerer (1880–1926) was an Austrian biologist who carried out ingenious experiments aimed at demonstrating the inheritance of acquired characteristics, most famously onAlytes, the midwife toad. The only surviving specimen after interruption of Kammerer's work by the First World War was examined by other zoologists who found the evidence for Kammerer's conclusions to be fraudulent. Soon thereafter Kammerer committed suicide. Whether or not the entire corpus of Kammerer's work was based on fraud and/or self‐delusion is a live issue in some quarters still.
Luciferases and Light‐emitting Accessory Proteins: Structural Biology
Authors: Sharpe Miriam L , Hastings J Woodland , Krause Kurt L 
Published: April 2014

AbstractCreatures that glow have mesmerised people for aeons. During the last few hundred years, scientists have been trying to reveal exactly how organisms produce this light, or bioluminescence. It has been estimated that approximately 30 or more chemically distinct bioluminescence systems have evolved independently. The luciferase enzymes that catalyse bioluminescent reactions use a variety of different structures to produce light. This article looks at the X‐ray crystal structures known for five different types of luciferases: bacterial, dinoflagellate, firefly, and two classes of coelenterates (anthozoan and hydrozoan). The structures of these enzymes reveal details of how they catalyse bioluminescence reactions, and their remarkable diversity of structure, mechanism and substrate specificity. Two accessory fluorescent proteins are also described.Key Concepts:Luciferases are enzymes that catalyse reactions that produce bioluminescence.Approximately 30 distinct bioluminescent systems have evolved.Bioluminescent reactions all involve oxygenation of a substrate to generate a peroxide intermediate, which then breaks down to give an electronically excited product that emits light.X‐ray crystallographic structures are known for the luciferases in five different bioluminescent systems: bacteria, dinoflagellates, fireflies, hydrozoa and anthozoa.Each of these luciferases has an entirely different molecular structure and catalyzes bioluminescence in a unique way.