bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsatellites in Historic and Ancient
DNA
Authors: Arandjelovic Mimi , Thalmann Olaf 
Published: April 2013

Abstract

Owing to their high abundance in eukaryotic genomes, bisexual mode of inheritance and hyper‐mutability, microsatellites have quickly developed into an invaluable tool in molecular and wildlife genetics. Despite their widespread application, microsatellites have only marginally been used in studies utilising ancient/historical materials. This is primarily because of the characteristics inherent to such materials, that is, a low abundance of autosomal
deoxyribonucleic acid (DNA)
and a high degree of degradation resulting in endogenous DNA of insufficient length for microsatellite amplification. The few studies that have combined microsatellites and historical materials have helped to uncover information otherwise irretrievable from contemporary materials. The last decade's advances in sequencing technologies are both foe and friend to future investigations utilising microsatellites and historical materials. Although sequencing genomes of extinct specimens has never been easier and attract a lot of attention, such projects might inadvertently identify novel microsatellite loci, a powerful prospective tool for population‐wide assessments of past genetic variation.

Key Concepts:

Owing to characteristics such as their omnipresence in eukaryotic genomes, high mutability, multiallele state and ease of typing, microsatellites have been a prominent marker in molecular ecology over the past 20 years.

The peculiarities of DNA obtained from historical and ancient specimens hamper the successful application of microsatellites to such sample materials.

Although not very numerous, studies that have combined microsatellites and historical materials have unravelled genetic variation otherwise lost in time.

Recent advances in sequencing techniques are helping to quickly discover new microsatellite loci and will potentially enable the time‐ and cost‐effective generation of multilocus genotypes of the innumerable specimens hidden in natural history museums.
Reproductive Skew Theory
Authors: Trubenová Barbora , Hager Reinmar 
Published: April 2013

AbstractAn almost universal characteristic of cooperatively breeding animal groups is the unequal sharing of reproduction within the group, referred to as reproductive skew. Reproductive skew theory has been developed to investigate the adaptive causes underlying the variation in reproduction between and within species seen in nature. From its inception in the late 1970s, skew theory has expanded over the years both conceptually and in its application. Three main types of models are distinguished:Transactional modelsassume that reproductive shares are offered as a reward for cooperative behaviour, tug‐of‐war;TOW(orcompromise)modelsassume that reproductive shares are determined by competitive abilities of individuals. Both assumptions are reconciled in the third type of models, most recently developedsynthetic models.Reproductive skew theory makes predictions about the range of skew using a set of key parameters such as relatedness and competitive abilities of group members. Skew theory has been applied to a wide variety of topics in evolutionary biology such as parent–offspring conflict, sex ratio conflict or the evolution of cooperation. Key to skew theory is the question under what conditions groups remain stable and it has thus been advanced as a framework to understand the evolution of sociality.Key Concepts:Social animals living in groups must often resolve a conflict over the allocation of reproduction.Unequal partitioning of reproduction is termed reproductive skew. Reproductive skew is a degree of reproductive bias in favour of one or a few breeders.Skew theory provides a possible explanation for conflict resolution and adaptive causes of sociality.Several indices of skew exist, suitable for different types of studies and questions.There are three main types of models: transactional, tug‐of‐war (TOW) (also referred to as compromise) and synthetic models, based on different assumptions and yielding different predictions.Transactional models are subdivided into two categories: concession and restraint models. Concession models assume full control of dominants over reproduction in the group, and reproductive share is offered as a reward for cooperation. Restraint models assume subordinates are free to claim reproduction and are only limited by the threat of eviction.TOW models are based on the assumption that both subordinates and dominants have only a limited control over the reproduction and reproductive share is determined by the mutual competitive abilities.Synthetic models combine features of transactional and TOW models. The maximal and minimal reproductive share of the subordinate for a group to remain stable is determined as in transactional models, while, within the range given by the maximal and minimal share, the exact reproductive share is determined by the competitive abilities of both subordinate and dominant in a TOW scenario.
Biochemistry and Molecular Genetics of Speech–Sound Disorder and Dyspraxia
Authors: Caylak Emrah 
Published: April 2013

Abstract

In this review, some of the most exciting recent developments in the biochemical and molecular genetic research on common learning disabilities (LD) such as speech–sound disorder (SSD) and dyspraxia have been summarised. A greater understanding of biochemical abnormalities (galactosaemia or polyunsaturated fatty acids deficiency) may provide a useful addition with other treatment procedures for these LD or improving learning abilities for them.

This review also highlights the genetic contribution to SSD and dyspraxia. These disabilities influenced by genes and several research groups to attempt to identify susceptibility and candidate genes of those through the sequential analysis of genetic linkage and association. Currently, genetic linkage studies have identified one susceptibility locus on 3p12–q13 associated with SSD, and also one susceptibility locus (speech–language disorder 1;
SPCH1
) on 7q31 and two candidate genes (
FOXP2
gene on chromosome 7, and
FOXP1
gene on chromosome 3) have been found associated with dyspraxia.

Key Concepts:

Learning disabilities may cause the learner to understand or to use language (spoken or written) with an imperfect ability to listen, think, speak, read, write, spell or do mathematical calculations.

Speech–sound disorder (SSD) is characterised by the substitution or emission of speech sounds leading to intelligible speech.

Individuals with dyspraxia seem to have problems in production of speech sounds due to poor motor skills (articulation), and applying linguistic rules to combine sounds to form words (phonological).

Biochemical and molecular genetic studies of learning disabilities may help us to understand the relationships between specific pattern deficits contributing to disordered learning. Moreover, greater understanding of biochemical abnormalities of these disabilities may provide a useful addition with other treatment procedures for them.

Genetic factors are important in SSD and dyspraxia.

Molecular genetic researches should be aimed to identify susceptibility and candidate genes for SSD and dyspraxia.

Molecular advances in SSD and dyspraxia will help to set the research agendas for future studies to follow.
Chrysophyceae and Synurophyceae
Authors: Jordan Richard W , Iwataki Mitsunori 
Published: April 2013

AbstractUntil recently, the chrysophytes were an algal group with mixed affinities and variable morphologies, united largely by their golden brown pigmentation. However, morphological and genetic studies have progressively removed many of the unaffiliated taxa, leaving two closely related classes, the Chrysophyceaesensu strictoand the Synurophyceae.Both the classes contain freshwater and marine species, although are considered more abundant and diverse in oligotrophic waters in terrestrial habitats. Cells may be solitary or colonial, having unequal flagella (heterokont), with flagellar swellings on one or both flagella acting as photoreceptors. Taxa covered by siliceous scales are present in both classes, although silicified bristles are only present in some synurophytes. Some chrysophytes may form cellulosic, chitinous, siliceous or calcareous loricae instead of possessing scales. All taxa from both classes produce resting stages known as stomatocysts, with some species forming them during both asexual and sexual phases. Since stomatocysts, and to a lesser extent scales and bristles, are preserved in the underlying sediments, their fossil record is relatively well known, with the oldest stomatocysts found in Early Cretaceous sediments.Fossil stomatocysts have proven very useful in palaeolimnological studies, particularly when reconstructing past nutrient levels, whereas their marine counterparts are a proxy for past sea‐ice distribution.Key Concepts:Genetic studies have shown that the Chrysophyceaesensu strictoand Synurophyceae are closely related, whereas the other taxa previously included in the Chrysophyceaesensu latobelong to different algal classes.Chrysophytes and synurophytes are heterokont algae, with a long ‘flimmer’ flagellum and a short ‘whiplash’ flagellum and with flagellar swellings on one or both flagella.Fucoxanthin is the main pigment responsible for their ‘golden brown’ colouration.Cells may possess silicified scales (but only synurophytes have bristles) produced by Golgi‐derived vesicles.Scale and bristle morphology appears to be species‐specific and is thus a key criterion in the identification of the taxa.Silicified resting stages bearing a plugged pore (stomatocysts) are unique to the Chrysophyceae and Synurophyceae, and may also be species‐specific.Stomatocysts are often preserved in the underlying sediments, and have been used as palaeoenvironmental indicators.The oldest stomatocysts were found in Early Cretaceous marine sediments from the Southern Ocean, whereas the oldest silicified scales and bristles were found in Middle Eocene freshwater sediments from northwest Canada.
Parmales
Authors: Konno Susumu , Jordan Richard W 
Published: April 2013

AbstractThe Parmales are a group of marine microalgae, closely related to the Bolidophyceae and the diatoms. The parmalean cell includes a chloroplast (with chlorophyllsa+c1+c2+c3), Golgi body, nucleus, mitochondrion and large vacuole, but lacks flagella. The cell wall is composed of 5–8 interlocking siliceous plates, which exhibit distinct dorsal, ventral, shield and girdle plate morphologies. The group currently includes approximately 20 taxa, mostly described from high latitudes, although some tropical species also have been reported. Parmalean algae reach high absolute abundances in the spring, before sinking to the pycnocline in the summer – a strategy similar to the centric diatoms. Their rare occurrences in sediment trap and surface sediments suggest that the siliceous plates are mostly recycled in the photic zone, yet plates of parmalean algae have been discovered in older sediments, although their true stratigraphic distribution remains unknown.Key Concepts:Recent gene sequences have shown that the Parmales are closely related to the Bolidophyceae and the diatoms, with similar cell features and pigment composition.Cells are covered by 5–8 silicified plates, consisting of three or four types (shield, girdle, ventral and/or distal), arranged in a particular pattern and with distinct morphology, which defines each genus.At present no flagellate stage, ploidy level or life cycle has been identified, however, it is possible that the nonmotile silica plate‐bearing cells are diploid, and alternate with a naked bolidophyte‐like flagellate haploid stage.Most taxa inhabit high latitude areas, although tropical taxa also exist.Studies have shown their ecology is similar to that of the centric diatoms, with assemblages remaining in their silicified form throughout the year and sinking to the pycnocline in the summer.Remains of parmalean cells found in the fossil record suggest at least an early Cenozoic origin, but when molecular clock calculations are made in the future a much older origin is expected.
Plant Responses to ElevatedCO2
Authors: Barnaby Jinyoung Y , Ziska Lewis H 
Published: April 2013

AbstractCarbon dioxide (CO2) has two unique properties: physically it absorbs in the infra‐red (heat) portion of the spectrum, and plays a role in maintaining global surface temperatures; secondly, it is the source of carbon for plant photosynthesis and growth. Recent, rapid anthropogenic increases in CO2have been well‐characterised with respect to climatic change; less recognised is that increase in CO2will also impact how plants supply food, energy and carbon to all living things. At present, numerous experiments have documented the response of single leaves or whole plants to elevated CO2; however, it is difficult to scale up or integrate these observations to plant biologyin toto. To that end, a greater emphasis on multiple factor experiments for managed and unmanaged systems, in combination with simulative vegetative modelling, could increase our predictive capabilities regarding the impact of elevated CO2on plant communities (e.g. agriculture, forestry) of human interest.Key ConceptsDirect effects of rising CO2on plant biology are an underappreciated aspect of anthropogenic climate change.Differential responses to elevated CO2are observed at spatial and temporal levels.Differentiation will affect competition, diversity and plant community demographics.The basis for this differentiation is unclear, but fundamental changes in ecosystem dynamics and evolution are expected.Need to move beyond a reductionist approach and integrate ecosystem responses to elevated CO2, in conjunction with appropriate modelling techniques for better forecasting of elevated CO2impacts on plant systems (e.g. agricultural responses).
Gibberellin Biosynthesis
Authors: Hedden Peter 
Published: April 2013

Abstract

The gibberellins are a large class of tetracyclic diterpenoid carboxylic acids, which are present in flowering plants, as well as some species of lower plants, fungi and bacteria. They include endogenous growth regulators in higher plants, in which they promote organ growth and induce certain developmental switches. Production of the biologically active compounds in plants requires the activity of plastid‐localised terpene cyclases, membrane‐associated
cytochrome P450 monooxygenases
and soluble
2‐oxoglutarate‐dependent dioxygenases
. In most plant tissues the concentrations of the active compounds are tightly regulated, in a process that requires their turnover through deactivation, for which several mechanisms have been identified, including 2β‐hydroxylation. Regulation of gibberellin concentration occurs in response to environmental cues, such as light quality, temperature and stress, as well as developmental and hormonal signals. Furthermore, gibberellin biosynthesis and inactivation are subject to homoeostasis mechanisms that act through the gibberellin signalling pathway.

Key Concepts:

Gibberellins are a group of tetracyclic diterpenoid carboxylic acids, which includes endogenous plant growth factors.

The biosynthesis of gibberellins requires the action of plastid‐localised terpene cyclases, membrane‐bound cytochrome P450 monoxygenases and soluble 2‐oxoglutarate‐dependent dioxygenases.

Several mechanisms for deactivating gibberellins have been identified, the most prevalent being 2β‐hydroxylation by two families of 2‐oxoglutarate‐dependent dioxygenases.

The concentration of the biologically active gibberellins is tightly regulated in most plant tissues at the level of biosynthesis and deactivation.

Gibberellin biosynthesis is regulated through feedback and feed‐forward mechanisms as well as by auxin and a range of environmental stimuli.
Improving Nutrient Use Efficiency in Crops
Authors: Hawkesford Malcolm John 
Published: April 2013

Abstract

Optimum use of mineral nutrients (fertilisers) by crops is essential for sustainable agricultural production. With increasing world demands for food and energy, this is set to become an ever‐increasing priority. Fertilisers are costly to produce and apply, both financially and environmentally. There is an absolute requirement to maximise efficiency using both agronomic and plant breeding approaches. Nutrient use efficiency may be defined as yield per unit fertiliser input or in terms of recovery of fertiliser applied. Improving yield alone may be at the expense of mineral nutrient content and hence quality, therefore yield improvements must be matched by appropriate increases in nutrient uptake. Multiple complex processes contribute to the overall nutrient use efficiency trait, and all are multigenic and developmentally and environmentally modulated. Key breeding traits for improvement includes root characteristics to enhance acquisition, canopy functioning for yield generation, and sink tissue attributes for final yield and quality aspects. Multidisciplinary approaches involving traditional breeding and biotechnology will contribute to future improvements.

Key Concepts:

Optimum use of mineral fertilisers by crops is essential for sustainable agriculture.

Some fertilisers are nonrenewal resources.

Nutrient use efficiency may be defined as yield per unit fertiliser input or in terms of recovery of fertiliser applied.

Nutrient use efficiency comprises two main traits, uptake efficiency and utilisation efficiency.

Agronomic practice is an important part of nutrient use efficiency.

Crop improvement may be targeted at roots, canopy or harvested material.

Root systems and transporters are required for capture of nutrients to produce an effective canopy.

An effective canopy will result in high yield.

Efficient captures and partitioning of nutrients contributes to quality components of crops.

Huge unexploited natural germplasm diversity for nutrient use efficiency exists for most crops.
Boron
Authors: Sakamoto Takuya 
Published: April 2013

Abstract

Boron (B), a metalloid element, is atomic number 5 of periodic table. Element B and some B compounds have industrial values. B essentiality is proven in some living organisms including plants, but probably in human. At present, the only role of B in plants is demonstrated as the structural maintenance of cell wall. Soil B, as boric acid, is acquired through roots and then distributed around the plant via the passive and active transport pathway. To adapt variations in the environmental B status, the active B transport system is tightly regulated at the molecular level in plants. In agriculture, both deficient and excess levels of soil B impair plant growth, resulting in the reduction of quantity and quality of crops. The major causes of B toxicity in plants contain oxidative stress, metabolism alteration and
deoxyribonucleic acid
damage. Several plant traits/genes that ensure tolerance to B stress have been isolated.

Key Concepts:

Boron has numerous biological functions in almost all living organisms including plants although its biochemical importance is poorly understood.

B is widely distributed in the earth, and its main form in soils is boric acid that is available for plants.

B availability in soils depends on factors such as soil type and climates, and it is a key determinant for the crop yields in agriculture.

Plants uptake and distribute B via two distinct pathways: passive diffusion and active transport mediated by B transport molecules.

The molecules working in the active B transport system are tightly regulated dependently to the environmental B conditions to promote B acquisition under limited B supply or to avoid accumulating toxic levels of B in plants.

The active B efflux from cells to soils or outside of cells and the protection of cellular mechanism from B attack are key molecular processes for B‐toxicity tolerance in plants.
Cellulose Biosynthesis in Higher Plants and the Role of the Cytoskeleton
Authors: Li Shundai , Gu Ying 
Published: April 2013

Abstract

Cellulose is a polysaccharide consisting of a linear chain of β (1→4) linked
D
‐glucose and it is the most abundant polymer on earth. As a major structural component of the cell wall, cellulose accounts for about one‐third of plant mass. The regulation of cellulose biosynthesis is essential to plant development. Cellulose is synthesised by the cellulose synthase (CESA) complex in the plasma membrane. This article reviews the composition and regulation of the cellulose synthase complex with a focus on the role of cytoskeleton in higher plants. In this article, the evolving views in the field of cellulose biosynthesis are discussed and the unresolved questions, such as

in vitro

cellulose synthesis, structure of CESA and mechanism underlying microtubule–microfibril alignment hypothesis, are highlighted.

Key Concepts:

Cellulose is a polysaccharide consisting of a linear chain of β (1→4) linked
D
‐glucose.

Cellulose is synthesised by large membrane‐bound protein complexes known as cellulose synthase complexes (CSCs).

Microtubule–microfibril alignment hypothesis states that there is a causal link between the orientation of cortical microtubules and nascent microfibrils.

Primary cell wall surrounds all plant cells and is formed during cell division and expansion.

Secondary cell wall is formed between the primary cell wall and the plasma membrane in cells that are subject to mechanical stress.
Molecular Genetics of Dravet Syndrome
Authors: Weckhuysen Sarah , Suls Arvid , de Jonghe Peter 
Published: April 2013

Abstract

Dravet syndrome is a severe epilepsy disorder characterised by infantile onset of fever‐sensitive seizures. Seizures are therapy resistant, and although children develop normal in the first year of life, progressive cognitive decline occurs soon after seizure onset. Dravet syndrome has a genetic etiology and mutations in the sodium channel α1 subunit gene (
SCN1A
) are found in approximately 70% of patients. Most mutation occur

de novo

, although some familial
SCN1A
mutations have been reported. A small percentage of female patients with a phenotype resembling Dravet syndrome have a mutation in the protocadherin 19 gene (
PCDH19
) on the X‐chromosome. Rare mutations have been found in a few other ion channel genes, but still the genetic cause of approximately 20% of patients with Dravet syndrome remains unknown.

Key Concepts:

Dravet syndrome is the most frequent indication for DNA analysis within the group of epileptic encephalopathies.

In approximately 70% of patients with Dravet syndrome, a heterozygous dominant

de novo

mutation in
SCN1A
can be identified.

In patients with a clinical diagnosis of Dravet syndrome who test negative for
SCN1A
sequence‐based mutations, additional tests that are capable of detecting copy number variations such as MAQ, MLPA or aCGH are required as
SCN1A
whole gene or exonic deletions/duplications can be missed on Sanger sequencing.

SCN1A
mutations in Dravet syndrome lead to haploinsufficiency of the gene.

Dravet syndrome is at the most severe end of the GEFS+ spectrum.

SCN1A
germline and somatic mosaicisms are important causes of recurrence of Dravet syndrome within siblings and intrafamilial clinical heterogeneity.

In 25% of female patients with Dravet syndrome who test negative for
SCN1A
mutations a
PCDH19
mutation can be found.

In 20% of patients with Dravet syndrome the etiology remains unknown after diagnostic testing of all relevant genes.