bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic Retrospect of Seedcotton Yield and its Components from a 6-Parent Gossypium hirsutum Diallel Cross Under Water Stress Conditions
Authors: Munaiza Baloch  , Muhammad Ibrahim Keerio  , Bashir Ahmad Ansari  , Moula Bux Kumbhar
Published: April 2014

A six-by-six complete F1 Gossypium hirsutum, L. diallel cross of three pre-screened drought tolerant and three drought susceptible varieties (CRIS-134, CRIS-342, SINDH-1, NIAB-78, SADORI and BH-160) was evaluated for genetic parameters during 2009 at Sindh Agriculture University farm, Tandojam. The characters studied were number of bolls per plant, sympodial branches per plant, seedcotton yield per plant and lintcotton yield per plant. The objective of such study was to assess the effect of irrigation stress on the genetic inheritance pattern of above quantitative traits as to how far the genetic parameters are affected due to irrigation stress in the F1 diallel generation. Irrigation treatments were four; normal seven irrigations schedule, five irrigations, four irrigations (medium stress) and three irrigations up to 150 days of crop maturity (stress conditions). CRIS-134 in seven, Sadori in five and CRIS-342 in four and three irrigations treatments were the most recessive parents contributing increasing boll number into their progenies while BH-160 in seven, CRIS-342 in five and Sindh-1 in four and three irrigations treatments proved to be the most dominant parents responsible for contributing decreased boll number per plant into their progenies. Seedcotton per plant was partial dominant in seven irrigations treatment while it inherited as an overdominant trait in five, four and three irrigations respectively. BH-160 was the most recessive of all with increased sympodia contributing attributes in seven and four irrigations whereas Niab-78 in five and CRIS-342 in stress were the most recessive parents. Sindh-1 was the most dominant parent in seven, five and three irrigation treatments while CRIS-342 in four irrigations yielded decreased sympodia contributing attributes into their progenies. Sindh-1 in seven, BH-160 in five and three and CRIS-342 in four irrigations treatments proved to be the most recessive parents with increasing seedcotton yield attributes while CRIS-342 in seven and five and Sindh-1 in four and three irrigations were the most dominant parents contributing decreased seedcotton yield into their progenies. Inheritance trend of lintcotton per plant was similar to that of seedcotton yield per plant.
Chemical Investigation of Mesua nagassarium (Burm. f.) Kosterm
Authors: Ridwan Islam  , Iftekhar Ahmed  , Al Amin Sikder  , Mohammad Rashedul Haque  , Abdullah Al-Mansur  , Mansoor Ahmed  , Munawar Rasheed  , Mohammad A. Rashid
Published: April 2014

Repeated chromatographic separation and purification of pet-ether and carbon tetrachloride soluble fractions of a methanol extract of stem bark of Mesua nagassarium (Burm. f.) Kosterm yielded five compounds. Extensive spectroscopic studies, including high field NMR analyses was conducted to identify these compounds which resulted to be friedelin (1), 3β-friedelanol (2),lupeol (3), 3-oxo-betulin(4) and spinasterol (5). Although compounds 1–3have been reported from various plant species, but 3-oxo-betulinand spinasterol have been discovered from M. nagassarium (Burm. f.) Kosterm for the first time.
La victimisation, la polyvictimisation et la délinquance chez les enfants et les jeunes adultes au Royaume-Uni1
Authors: Radford23 Lorraine , Corral Susana , Bradley Christine , Fisher Helen L.
Published: April 2014

Cette étude explore l’impact et la nature de l’accumulation de victimisations sur la déviance autodéclarée des enfants et des jeunes adultes. Dans le cadre d’une enquête représentative menée auprès de ménages au Royaume-Uni en 2009, l’exposition à une gamme élargie d’expériences de victimisation ainsi que la délinquance autodéclarée ont été évaluées grâce à 4036 interviews auprès de participants de deux groupes : des enfants âgés de 11 à 17 ans et des jeunes adultes âgés de 18 à 24 ans. L’âge, le sexe (masculin) et le fait d’avoir vécu certaines formes de victimisation augmentaient considérablement les probabilités de polyvictimisation au cours de l’enfance. L’impact de la victimisation sur la délinquance variait selon le type de victimisation, le sexe et le groupe d’âge. La victimisation sexuelle durant l’enfance était fortement associée à la délinquance chez les femmes mais avait moins d’impact chez les hommes âgés de moins de 18 ans. La polyvictimisation avait le plus d’impact sur la délinquance des enfants âgés de 11 à 17 ans mais n’influençait pas significativement celle des jeunes femmes adultes. Les professionnels qui travaillent auprès des enfants et des jeunes doivent être à l’affût des concomitances et du caractère cumulatif de la victimisation durant l’enfance. Ils doivent également être outillés afin de repérer et d’aider ceux qui sont vulnérables à la polyvictimisation.
Polyvictimisation et comportements à risque chez des élèves chinois du High School1
Authors: Chan23 Ko Ling
Published: April 2014

L’étude vise à évaluer la prévalence et les facteurs associés à la polyvictimisation chez l’enfant, ainsi qu’à fournir une estimation fiable du problème dans le contexte chinois. En utilisant une procédure d’échantillonnage stratifiée à deux niveaux, 18 341 élèves chinois ont été recrutés dans six villes de Chine. Ils ont été invités à remplir un questionnaire autoadministré contenant des questions sur leurs victimisations dans l’enfance, leurs comportements de dépendance et leurs comportements sexuels à l’adolescence. La version chinoise validée du questionnaire sur la victimisation juvénile (JVQ pour l’acronyme anglophone) a été utilisée. Les taux de prévalence obtenus, portant sur l’année précédente, sont de 23,2 % pour tout type de victimisation des enfants et 9,2 % pour la polyvictimisation. Vivre en Chine continentale, être parmi les plus jeunes et avoir des frères et soeurs, sont les facteurs associés à l’augmentation du rapport de cote (« odds ratio ») de polyvictimisation. Certains comportements de dépendance et sexuels des adolescents, incluant les jeux de hasard, le tabagisme, l’alcoolisme, les relations sexuelles précoces, les multiples partenaires sexuels, et la grossesse chez les adolescentes, sont également significativement associés à une probabilité accrue de polyvictimisation. Les résultats de cette étude révèlent de fortes associations entre la victimisation des enfants et les comportements à risque, ce qui souligne la nécessité d’une intervention prioritaire en cas de polyvictimisation.
Effects of RF/MW Exposure from Mobile-phone Base-Stations on the Growth of Green Mint Plant using Chl a Fluorescence Emission
Authors: Kafi S. T. , Ahmed A. M. , Sabah-Alkhair M. K. , Mohamed D. A. , Ahmed R. S. , Hassaan Z. O.
Published: April 2014

We report on the effects of RF/MW on plants.Green Mint plant exposed to different levels ofradiation (from 0.5 to 10.5 μW/cm2) for thispurpose. A USB2000 spectrophotometer wasused to record fluorescence signals from intactleaves.Spectroscopic data (P.I.R and A.R)together with vegetative data (leafdimensions and weight), revealed stressingeffects on plant due to RF/MW in all groupsexcept the control which was free of exposure.
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

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.

 

10.7902/ecb.v4i1.53
Perturbed physics ensemble simulations of cirrus on the cloud system‐resolving scale
Authors: Muhlbauer Andreas , Berry Elizabeth , Comstock Jennifer M. , Mace Gerald G.
Published: April 2014

In this study, the effect of uncertainties in the parameterization of ice microphysical processes and initial conditions on the variability of cirrus microphysical and radiative properties are investigated in a series of cloud system‐resolving perturbed physics ensemble (PPE) and initial condition ensemble (ICE) simulations. Three cirrus cases representative of midlatitude, subtropical, and tropical anvil cirrus are examined. The variability in cirrus properties induced by perturbing uncertain parameters in ice microphysics parameterizations outweighs the variability induced by perturbing the initial conditions in midlatitude and subtropical cirrus. However, in tropical anvil cirrus the variability spanned by the PPE and ICE simulations is on the same order of magnitude. Uncertainties in the parameterization of ice microphysical processes affect the vertical distribution of cloud fraction, ice water content, and cloud thickness, whereas cirrus cloud cover is only marginally affected. The top three uncertainties controlling the microphysical variability and radiative impact of cirrus clouds are the mode of ice nucleation, the number concentrations of ice nuclei available for heterogeneous freezing, and the threshold size of the parameterized ice autoconversion process. Uncertainties in ice fall speeds are of minor importance. Changes in the ice deposition coefficient induce only transient effects on the microphysical properties and radiative impacts of cirrus except in cases of very low ice deposition coefficients of about 0.05. Changes in the sulfate aerosol number concentration available for homogeneous freezing have virtually no effect on the microphysical properties and radiative impact of midlatitude and subtropical cirrus but a minor effect on tropical anvil cirrus.
Spatial variability of surface irradiance measurements at the Manus ARM site
Authors: Riihimaki Laura D. , Long Charles N.
Published: April 2014

The 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

A 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

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

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

Systematics 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

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

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

Respiring 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

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

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

Paul 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

Creatures 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.
Genetically Modified Plants
Authors: Halford Nigel G
Published: April 2014

The genetic modification of plants is now an established tool for plant breeders in many parts of the world, with the area of land used for genetically modified (GM) crop cultivation rising to 170 million hectares by 2012. This article puts genetic modification of plants into the context of scientific plant breeding, and describes the techniques that are used to transform plants and that define the term genetically modified. The design of transgenes is described, as is the use of selectable and visible marker genes. The use of GM crops in commercial agriculture is covered in detail, including GM crops that may be developed for commercial use in the near future. The barriers to the continued development of crop biotechnology are considered, notably the cost, the associated issue of regulatory compliance and the problem of consumer acceptance. The consequences of science losing the GM crop debate are discussed.

Key Concepts:

Genetic modification (GM) is a term used to describe the artificial introduction of a gene or genes into an organism's genome.

Genetic modification is now an established tool in plant breeding in many parts of the world.

Genetically modified crops were grown on 170 million hectares of land in 2012.

‘Input’ traits such as herbicide tolerance and insect resistance are by far the most successful GM traits.

Other GM traits in commercial crops include virus resistance, modified oil content, increased nutritional value, drought tolerance and the synthesis of high‐value, nonfood products (biopharming).

Increased vitamin A content, improved food safety and bioremediation are targets for GM crop programmes that may be commercialised in the next few years.

GM is the most heavily regulated area of plant breeding, and over‐regulation is a significant barrier to the development of the technology.

Consumer acceptance of GM crops remains a difficult issue in some regions, notably Europe.
Leucine Zippers
Authors: Hakoshima Toshio
Published: April 2014

The leucine zipper (ZIP) motif consists of a periodic repetition of a leucine residue at every seventh position (heptad repeat) and forms an α‐helical conformation, which facilitates dimerisation and in some cases higher oligomerisation of proteins by forming a parallel helix–helix association stabilised by formation of an interhelical hydrophobic core involving leucine side chains. These nonpolar interactions are important for stabilisation of the ZIP structures, whereas specificity of these dimerisation and oligomerisation is mediated by electrostatic interactions, such as formation of salt bridges. In many eukaryotic gene regulatory proteins, the ZIP motif is flanked at its
N
‐terminus by a basic region containing characteristic residues that facilitate
deoxyribonucleic acid (DNA)
binding and is referred to as bZIP. ZIP‐related heptad repeats are frequently found in a variety of proteins and catalyse dimerisation/oligomerisation by forming both parallel and antiparallel coiled coils.

Key Concepts:

A heptad repeat of leucine residues, leucine zipper (ZIP), is an important sequence motif facilitating protein–protein interactions.

ZIP forms an amphiphilic α helical structure, in which two residues that are separated by seven residues in sequence are located at nearly the same molecular surface in an α helix.

The amphiphilic nature of the ZIP helix facilitates protein dimerisation by forming a parallel helix–helix association.

Leucine side chains extending from one α helix interdigitate with those displayed from an α helix of a second polypeptide like a zipper to stabilise formation of an interhelical hydrophobic core.

The specificity of the ZIP dimerisation is mediated by electrostatic interactions, such as formation of salt bridges.

ZIP is frequently fused with other sequence motifs to produce biologically important functional structural modules.

The ‘basic region ZIP’ (bZIP motif) is a fusion between a segment that is rich in basic residues facilitating DNA binding and ZIP, forming a class of eukaryotic transcription factors.

The DNA binding specificity of bZIP is determined by the basic region that directly binds a class of palindromic DNA sequences.

ZIP‐related sequence motifs containing an incomplete heptad repeat are frequently found in a variety of proteins and catalyse dimerisation/oligomerisation by forming both parallel and antiparallel coiled coils.
Chromosome Preparation
Authors: Blennow Elisabeth , Iwarsson Erik
Published: April 2014

Standard chromosome preparations can be obtained from various tissues containing dividing cells. The easiest way to obtain metaphases for constitutional karyotyping is to take a blood sample and culture the lymphocytes. Amniotic fluid obtained by amniocentesis, or preparation of chromosomes from chorionic villi, may be used for prenatal diagnosis. Bone marrow is the tissue of choice for studies of acquired chromosome abnormalities in haematological malignancies. Chromosome preparations can also be made from cultures of solid tissues, like tumours, fetal skin, muscle, placenta, lung, kidney and liver. To have an unlimited source of cells, immortalised cell lines may be established, like tumour‐derived cell lines or cell transduction of normal cells with genes from adeoxyribonucleic acid (DNA)tumour virus. To achieve a higher resolution using fluorescentin situhybridisation, methods for preparation of released, less‐condensed and linearised DNA fibres have been developed.

Key Concepts:

Metaphase spreads may be obtained from various tissues on condition that the cells are spontaneously dividing or may be cultured and in some cases chemically stimulated to divide by the addition of a mitogen.

The easiest way to obtain metaphase chromosomes for constitutional karyotyping is to take a blood sample and culture the lymphocytes.

Amniotic fluid or chorionic villi cells may be used for preparation of chromosomes for prenatal diagnosis.

Chromosome preparations from bone marrow may be used for studies of acquired chromosome abnormalities in haematological malignancies.

The cultures may be synchronised in order to achieve a better quality of chromosome preparation.

Chromosome preparations can be made from cultures of solid tissues after disaggregation.

To have an unlimited source of cells, immortalised cell lines may be established.

To achieve a higher resolution using fluorescentin situhybridisation (FISH), methods for preparation of released, less‐condensed and linearised DNA fibres may be used.
Sex Chromosomes
Authors: Lucchesi John C
Published: April 2014

Sexual reproduction increases the number of different genetic constitutions that are present at each generation and that can be acted on by natural selection. In many organisms, the genetic information required for the differentiation of fertilised eggs into individuals of different sexes is contained on a special pair of chromosomes: the sex chromosomes. All sex chromosomes were derived from pairs of ordinary chromosomes (autosomes). In some instances, the autosomes acquired a gene represented by two alleles, one of which was male determining. In other instances, the presence of one of the two alleles of the sex‐determining gene on both chromosomes led to the differentiation of one sex, whereas its presence on only one of the two autosomes led to the differentiation of the other sex. In this case, the allele on the other chromosome was neutral with respect to any effect on sex determination. The autosome with the male‐determining allele or with the neutral allele accumulated mutations that inactivated most of the other genes present throughout their length. This led to a difference in the dosage of these genes between the sexes and to the evolution of mechanisms that compensate for this dosage difference.

Key Concepts:

In many organisms, sex is determined by the presence of specific chromosomes – the sex chromosomes.

These chromosomes have evolved from particular pairs of autosomes.

In all cases, the determination of sex is achieved by the expression of one or a few genes that are present on the sex chromosomes.

The expression of these genes causes the differentiation of one of the two sexes; the other sex develops by default.

The presence of different sex chromosomes in the two sexes can cause differences in the dosage of genes that are present on these chromosomes but that have critical functions in both sexes.

When such a difference in these genes would be harmful to one of the two sexes, regulatory mechanisms that compensate for the difference in the dosage of these genes have evolved.
Gene Targeting by Homologous Recombination
Authors: Reh Wade A , Vasquez Karen M
Published: April 2014

Gene targeting by homologous recombination involves the exchange of genetic information between genomic and exogenous
deoxyribonucleic acid (DNA)
molecules via crossover events. These exchanges are guided by homologous sequences acted on by enzymatic machinery of the cell. Homologous recombination provides a mechanism for targeting defined modifications into genes of interest, making gene‐targeting technologies valuable tools to explore gene function and to develop human, genetic disease models. Gene targeting, however, is inefficient, making the process challenging. Advances in technology now allow us to direct repair enzymes to the targeted site by inducing site‐specific DNA damage using zinc‐finger nucleases, transcription activator‐like effector nucleases, clustered regularly interspaced short palindromic repeats and triplex‐forming oligonucleotides. Further, antirecombinogenic pathways can now be transiently suppressed using
ribonucleic acid (RNA)
interference (RNAi) and other small molecule approaches. These and other techniques can greatly enhance gene‐targeting efficiency. The coincident development of human stem cell technology brings forth the potential of gene‐targeting strategies for therapeutic application.

Key Concepts:

Homology‐directed gene targeting utilises homologous recombination to introduce defined modifications into sequences of interest in mammalian genomes.

Gene‐targeted knockout and knock‐in models are instrumental in elucidating gene function and studying human genetic diseases.

Combining stem cell and gene‐targeting technologies opens potential avenues for gene therapy.

Recent technological advances have greatly enhanced gene‐targeting efficiencies.

Due to technological advances, most genes in a variety of mammalian species can now be manipulated by homology‐directed gene targeting.
Strigolactones: A New Class of Plant Hormones with Multifaceted Roles
Authors: Prandi Cristina , Cardinale Francesca
Published: April 2014

Strigolactones (SLs) are terpenoid lactones produced mainly in plant roots and initially identified as seed germination stimulants for parasitic weeds. In 2005, they were described also as boosters of hyphal branching in arbuscular mycorrhizal fungi, and thereby as promoters of arbuscular mycorrhizal symbiosis. In 2008, they emerged as a new class of plant hormones controlling plant architecture through repression of shoot branching. Since then, several new roles were discovered for SLs: in the adaptive responses to a number of environmental stimuli (including light, osmotic stress, interaction with pathogens and nodulating bacteria), and in several aspects of plant development (including seed germination for nonparasitic plants, hypocotyl elongation, reproduction, leaf senescence and nodulation). The biosynthetic and perception/transduction systems of SLs are being elucidated, and the first mechanistic models presented.

Key Concepts:

Strigolactones are the key nutrient allocators regulating plant development at the interface between plants, beneficial and detrimental (micro)organisms, and abiotic factors.

Strigolactones induce hyphal branching in AM fungi and facilitate the establishment of symbiosis.

Strigolactones inhibit shoot branching.

Strigolactones affect root architecture and root development depending on nutrients availability.

Synthetic SLs (analogues and mimics) are used in pharmacological applications to plants and fungi to decipher the structure–activity relationship.

Structure–activity relationship (SAR): Different structures are tested for bioactivity in order to pinpoint which part of the molecule is essential for bioactivity and which can be considered only ‘decoration’.
Two‐Component Signalling in Plants
Authors: Burr Christian A , Sacks Carly M , Kieber Joseph J
Published: April 2014

Two‐component signalling pathways are used by bacteria to perceive and respond to a wide variety of environmental signals. In their simplest form, these are comprised of a histidine kinase receptor, whose activity is regulated by a signal, and a response regulator, whose activity is controlled by Asp phosphorylation mediated by the histidine kinase. Plants use two‐component elements to respond to endogenous and environmental signals. The plant pathways are either an extended version of the two‐component pathway called a phosphorelay or include degenerated elements that no longer function as histidine kinases. These elements are conserved throughout the plant kingdom, although they are best understood in the model

Arabidopsis thaliana

. The most complete and best understood of these is the signalling pathway for the phytohormone cytokinin, which is perceived by endoplasmic reticulum‐localised histidine kinase receptors and ultimately regulates the phosphorylation of a set of response regulators that mediate the transcriptional response to cytokinin.

Key Concepts:

The canonical two‐component system consists of a histidine kinase and response regulator protein.

Multiple permutations of the canonical two‐component system exist, including a multistep phosphorelay system.

Plants respond to a variety of signals using two‐component signalling systems, including cytokinin, ethylene and light.

Two‐component signalling elements are conserved in both dicot and monocot plant species.

Cytokinin, a plant hormone, uses a multistep phosphorelay system to transduce its signal from membrane‐bound receptors to the nucleus to mediate transcription of cytokinin response genes.
Water Use Efficiency of Cultivated Crops
Authors: Katerji Nader , Mastrorilli Marcello
Published: April 2014

The concept of crop water use efficiency (WUE), determined by the ratio between the marketable yield and the seasonal values of actual evapotranspiration, has become a suitable tool for analysing the strategies that allow attaining the best use of water in agriculture. Crop WUE is easy to quantify from field measurements, but it is a complex indicator because wide differences can be observed for the WUE values of the same species cultivated under the same site.

In this article, the major causes of the large range of WUE values are identified and analysed. The authors demonstrate that the WUE variability can be ascribed mainly to three factors: agro‐techniques (water regime, mineral supply and water quality), crop (species, varieties and sensitivity of the growth stage to the stress) and environment (climate, atmospheric pollution, soil texture and climate change).

Understanding and taking into consideration the WUE variability are primary conditions for advanced studies on WUE. The paths for further research and management programmes, allowing to valorise the water in agriculture, can be drawn from the analysis reported here.

Key Concepts:

To ameliorate the efficiency of water used by cultivated crops is one of the three possible strategies for increasing water sustainability in agriculture.

To attain this objective, ecophysiological and agronomical approaches can be used.

The ecophysiological approach refers to values of carbon assimilation and transpiration rates per leaf unit area. It helps in understanding global results obtained from the agronomical approach.

In the agronomic approach, the concept of crop use water efficiency (WUE) refers to final yield and to total water consumed by crops, under field conditions. They are key data to manage the crop production.

Crop WUE is easy to quantify from field measurements, but it is a complex indicator because of its intrinsic variability.

The major causes of WUE variability are identified and analysed in this review: crop, environment and agro‐techniques.

If the causes of such variability are known and taken in the right consideration, the concept of WUE can represent an interesting tool for studying how to valorise the water in agriculture.