bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blastocladiomycota
Authors: Longcore Joyce E , Simmons D Rabern 
Published: April 2013

Abstract

The Blastocladiomycota, a phylum of fungi that produce motile spores and gametes, live in water or in soils, where they are active when water is present and survive with thick‐walled resting sporangia when soils are dry. Some genera are saprobic, but the phylum also contains pathogens of invertebrates and plants. Life cycles can include alternation of haploid and diploid generations and different generations may have different hosts. Sexual reproduction begins by fusion of gametes and meiosis takes place during germination of resistant sporangia. Saprobic members have been used as model organisms and genome sequencing of
Allomyces
and
Blastocladiella
continues this trend.
Coelomomyces
species parasitise mosquito larvae and are capable of causing death of up to 90% of their hosts. Obligate parasitism, narrow host ranges, need for an alternate host and unpredictable rate of control have deterred development of
Coelomomyces
species for mosquito control.

Key Concepts:

Members of the Blastocladiomycota produce spores and gametes that are motile by means of a posteriorly directed whiplash flagellum.

Motile spores, which are recognisable by their centrally located nucleus that is apically surrounded by a nuclear cap consisting of ribosomes, are recognisable at the ultrastructural level by microtubules in groups of three that extend from the apex of the kinetosome and surround the nucleus.

Some saprobic species have an alternation of morphologically similar haploid and diploid generations and some pathogens have alternation of haploid and diploid generations with different morphologies and sometimes on different hosts.

Sexual reproduction is by fusion of motile gametes and meiosis takes place during the germination of resting sporangia.

The phylum contains pathogens of crustaceans, nematodes, algae and aquatic and semi‐aquatic plants.

Saprobic species, especially
Allomyces macrogynus
and
Blastocladiella emersonii
, are used for physiological and genetic studies and the genome of
A. macrogynus
has been sequenced.
Cave Evolution
Authors: Gross Joshua B 
Published: April 2013

Abstract

Cave‐dwelling animals are fascinating because of the phenotypic extremes they frequently exhibit, such as a reduced or complete loss of vision and pigmentation. Equally interesting is the fact that irrespective of taxonomic position, organisms colonising the subterranean environment converge on highly similar phenotypic deficits and improvements. Thus, a predictable suite of morphological, physiological and behavioural changes evolve in response to low nutrient conditions of the subterranean environment. Despite several decades of enquiry, the precise genetic and molecular underpinnings of cave‐associated changes are only beginning to be elucidated through the use of high‐resolution contemporary molecular and genetic techniques. Regressive phenotypic changes, those traits that are lost in derived lineages, are particularly interesting since they evolve in the absence of obvious selective value to the organism. Continuing research utilising an increasing number of emerging cave‐dwelling models offers the exciting prospect of clarifying longstanding problems in contemporary evolutionary biology.

Key Concepts:

Widespread convergence on cave‐associated (troglomorphic) characteristics is often attributed to the paucity of nutrition and overall stability of the cave environment.

Cave‐adapted organisms are excellent models for the study of regressive phenotypic evolution, that is the loss of traits in derived organisms.

The evolutionary mechanism(s) accounting for phenotypic loss in cave‐dwelling organisms (neutralism versus selection) remains unknown.

Hybrid crosses between cave‐dwelling and intra‐specific ‘surface’ forms reveal numerous morphological changes associated with cave adaptation are recessive.

Phenotypic analyses in subsequent generations reveal many cave‐associated characteristics arise through Mendelian (single locus) and complex (polygenic) patterns of inheritance.

The cave environment likely represents an attractive habitat given that over 50 000 cave‐limited species are known worldwide, distributed across broad taxonomic groups.

Contemporary cave research has advanced significantly over the last decade thanks to integrative analyses combining developmental, genetic, genomic, behavioural, physiological and population‐level approaches.
Plastid Origin and Evolution
Authors: Chan Cheong Xin , Bhattacharya Debashish 
Published: April 2013

Abstract

Plastids (or chloroplasts in plants) are organelles within which photosynthesis takes place in eukaryotes. The origin of the widespread plastid traces back to a cyanobacterium that was engulfed and retained by a heterotrophic protist through a process termed primary endosymbiosis. Subsequent (serial) events of endosymbiosis, involving red and green algae and potentially other eukaryotes, yielded the so‐called ‘complex’ plastids found in photosynthetic taxa such as diatoms, dinoflagellates and euglenids. The field of plastid research also includes nonphotosynthetic organelles (apicoplasts) within the parasitic apicomplexans and the temporary sequestration (‘theft’) of plastids by heterotrophic organisms (kleptoplasty) such as the sea slug

Elysia chlorotica

. The gain and loss of plastids, and nonlineal gene transfer (associated with endosymbiosis) are key aspects of algal evolution that have decisive impacts on inference of their phylogenetic positions in the tree of life. Deciphering plastid origin therefore provides general insights into the evolution of eukaryote lineages.

Key Concepts:

The plastid organelle in eukaryotes originated from primary endosymbiosis involving a cyanobacterium.

The secondary (and tertiary) plastids show a history of multiple (serial) endosymbiosis involving red and/or green algae.

Plastid research is complicated by the presence of nonphotosynthetic plastids in parasitic apicomplexans and by the theft of temporary plastids referred to as kleptoplasty.

Understanding plastid origin enhances our understanding of eukaryote evolution.
Evolution of Multicellularity
Authors: Nedelcu Aurora M 
Published: April 2013

AbstractMulticellularity has evolved multiple times, independently, in lineages from all three domains of life. The transition from a unicellular to a multicellular life‐style entails the integration of previously independent individuals into a new kind of individual. The emergence of individuality at the higher level requires the evolution of cooperative and altruistic behaviours, division of labour (including the separation of reproductive and somatic activities among cells), the reorganisation of basic life properties (such as immortality and totipotency), and the reorganisation of fitness (with cells specialising in one or the other fitness components – survival or reproduction). At a more mechanistic level, a new genotype–phenotype map has to be created to reflect the emergence of a new kind of individual. Notably, many traits associated with multicellularity appear to have involved the co‐option of genes and pathways already present in unicellular lineages. The evolution of multicellularity has been driven by a combination of selective pressures, developmental constraints and life history trade‐offs specific to each lineage.Key Concepts:The transition from a unicellular to a multicellular life‐style constitutes a transition in individuality, a process whereby a group of previously independent individuals become stably integrated into a new functional, physiological and reproductively autonomous and indivisible evolutionary unit – that is, a new individual.The successful integration of previously independent individuals into a new kind of individual requires the evolution of cooperative and altruistic behaviours, division of labour, the reorganisation of basic life properties, and the reorganisation of fitness.Multicellularity has evolved independently in at least 25 lineages from all three domains of life.The evolution of multicellularity has been driven by a combination of selective pressures, developmental constraints and life history trade‐offs specific to each lineage.Many traits associated with multicellularity involved the co‐option of genes and pathways already present in unicellular lineages.
Sexual Selection and Life History Allocation
Authors: Houslay Thomas M , Bussière Luc F 
Published: April 2013

Abstract

A comprehensive explanation for sexual trait diversity depends on integrating life history theory and sexual selection to compare costs and benefits of sexual traits. A universal cost for all sexual traits involves the resources required to create and maintain them, which are consequently unavailable to other life history characters. This resource trade‐off typically causes covariance between an organism's resource budget and its level of sexual trait expression, which is known as condition‐dependence. Condition‐dependence has several implications. It may be particularly important for ornaments signalling genetic quality, by helping to maintain the genetic variation that favours mate choice. It may also reduce extinction risk in sexually selected populations. Further life history studies of sexually selected traits are required, mindful of the inherent difficulties in quantifying resource acquisition and allocation, not least of which is that these processes are not independent of one another.

Key Concepts:

Trait evolution is restricted by trade‐offs, where the benefit of increased investment in a trait is opposed by the cost of investment.

The acquisition and allocation of resources is central to life history theory, but these processes are extremely difficult to quantify.

Phenotypic correlations are not necessarily good metrics for the strength or importance of a trade‐off between traits.

Condition‐dependence in mating systems featuring choice for indirect genetic benefits can help to maintain genetic variation for ornamental traits.

Sex‐role reversed systems have life history features that may clarify some of the outstanding questions in sexual selection.
Quantitative Trait Loci and Breeding
Authors: Fleury Delphine , Delannay Xavier , Langridge Peter 
Published: April 2013

AbstractPlant breeding methodologies have changed greatly over the past century as new techniques and tools become available to breeders. The introduction of computer technologies, new statistical methods and molecular markers have greatly enhanced the rates of genetic gain that can be achieved in breeding programs. Many important traits for crop improvement, such as yield, quality and quantitative or durable disease resistances, are regarded as quantitative traits and are controlled by multiple quantitative trait loci (QTL). Recent advances in molecular marker systems have created new opportunities and strategies to select for quantitative traits. Strategies for deploying QTL in breeding programs vary from monitoring specific loci through to the deployment of molecular markers flanking the target QTL to the use of whole‐genome marker scans to identify individual plants that will offer the greatest opportunity for genetic gain.Key Concepts:Yield, many aspects of quality and durable disease resistance are all examples of quantitative traits.Interactions between the genotype of the plants and the growing environment can be critical in determining the expression of quantitative traits.Breeding programs usually select for quantitative traits at multiple stages in the breeding process and using replicated trials across multiple locations.The regions of the genome controlling quantitative traits, QTL, can be mapped by measuring the association between molecular markers and the phenotype across multiple environments in populations segregating for the trait.The stability of QTL across environments and the proportion of the variation accounted for by the QTL are key criteria in determining the value of the QTL to a breeding program.Genomic selection, based on whole‐genome scan with markers, offers an opportunity to select for large numbers of minor QTL without prior knowledge of the location of the QTL.Effective delivery of molecular breeding technologies to breeding programs, particularly in poor countries, is dependent on providing access to marker screening platforms resources, and training.
Calcium Signalling in Plants
Authors: Bickerton Peter D , Pittman Jon K 
Published: April 2013

Abstract

Ca
2+
is an important signal transduction molecule that has been shown to regulate responses to a large number of environmental stimuli in plants and control many developmental processes. These stimuli induce the formation of Ca
2+
signals within a cell, which are generated through the action of Ca
2+
release and uptake from and into internal cellular stores or the apoplast by the activity of Ca
2+
channels, pumps and exchangers. These signals take the form of elevations of Ca
2+
with specific spatio‐temporal characteristics which are thought to denote the initial stimulus and mediate an appropriate cellular response. Information is therefore hypothesised to be encoded in these signals, which are decoded and relayed to downstream gene expression regulators and protein kinases via an array of Ca
2+
‐binding sensor proteins.

Key Concepts:

Calcium signals allow plants to specifically sense and respond to environmental stimuli.

Calcium signals are generated through the coordinated action of calcium influx channels and calcium efflux transporters.

A large network of calcium‐binding proteins act as calcium sensors and relay calcium signals to downstream effector proteins.
Virus–Plant Co‐evolution
Authors: Fraile Aurora , García‐Arenal Fernando 
Published: April 2013

Abstract

Virus infection and plant defences may, respectively, reduce the fitness of plants and viruses, which could result in virus–plant co‐evolution. It is commonly assumed that viruses and plants co‐evolve, but evidence supporting this hypothesis is scant, refers mostly to the virus partner, and almost totally derives from the study of highly virulent viruses in agricultural systems, in which host genetic structure is manipulated leading to genetic changes in the virus population. Research has focussed on processes driven by qualitative resistance, either dominant or recessive, which conform, respectively, to the gene‐for‐gene and matching‐alleles models of host–pathogen co‐evolution. A serious limitation is the limited information available for systems in which the host might also evolve in response to virus infection, that is, wild hosts in natural ecosystems, an area of research that should be encouraged.

Key Concepts:

Requirements for co‐evolution have not been yet shown to be fully met for any virus–plant system.

Infection of plants by viruses does not necessarily decrease plant fitness.

Virus–plant interactions determined by single, dominant resistance genes conform to the gene‐for‐gene model of host–pathogen interaction.

Most dominant resistance genes of plants to viruses encode NB‐LRR proteins (R proteins).

There is no current evidence for diversifying selection of R proteins targeting viruses.

The product of any virus gene can be an avirulence determinant eliciting the defence determined by resistance genes.

Virus–plant interactions determined by single, recessive resistance genes conform to the matching‐alleles model of host–pathogen interaction.

Pathogenicity on dominant resistance genes may have important fitness costs.

Pathogenicity on recessive resistance genes may have fitness costs depending on the virus and host genotypes.

Constraints to virus evolution may determine the durability of resistance factors bred into crops.
Recognition and Response in Plant
PAMP
‐Triggered Immunity
Authors: Godfrey Dale , Rathjen John P 
Published: April 2013

Abstract

Pathogen‐associated molecular pattern (PAMP)‐triggered immunity (PTI) describes the first events after pathogen invasion, whereby the plant identifies the presence of an invader and mounts a response. A race ensues in which the pathogen deploys its array of virulence molecules that act in opposition to host defence mechanisms and promote establishment of a pathogenic niche. Since the seminal work identifying the first pathogen receptor, FLAGELLIN‐SENSING 2 (FLS2), the field has worked to define receptor complexes and downstream signalling pathways. This article describes recent progress in this area. In addition, many pathogen effectors target the PTI machinery. Thus, identifying PTI components as effector targets helps to validate those molecules as components of the defence machinery. As such, early molecular interactions are key to the outcome of infection. Indeed it is thought that nonhost resistance, in which most plants species are resistant to most pathogens, is likely to be a result of the PTI system.

Key Concepts:

Plants have multilayered recognition systems which detect invading pathogens.

The first line of recognition involves detection of PAMPs via host pattern‐recognition receptors (PRRs).

PRRs are transmembrane receptor‐like kinases or receptor‐like proteins that perceive PAMPs at the cell surface.

PRRs act as a major point of control for PTI.

Biogenesis and localisation of PRRs to the plasma membrane requires the proteins are processed by the secretory pathway and individual PRRs have varying requirements for endoplasmic reticulum‐quality control pathways.

Following PAMP perception, a series of downstream defence responses results in PTI.

Attenuation of PRR signalling is necessary to restrict immune responses.
Genomics and the Rhizosphere
Authors: Tett Adrian J , Turner Thomas R , Poole Philip S 
Published: April 2013

Abstract

The rhizosphere is a nutrient‐rich area surrounding roots with increased microbial number and activity compared with bulk soil. Plant–microbe interactions in the rhizosphere are an essential determinant of plant health and productivity, as well as biogeochemical cycling. Traditionally, genomics has focussed on the small proportion of cultivable microbes, but recent advances in culture‐independent molecular tools, high‐throughput
deoxyribonucleic acid
(DNA) sequencing, and bioinformatics are revolutionising our understanding of plant–microbe interactions. Identification of total DNA (metagenomics),
ribonucleic acid
(RNA) (metatranscriptomics) and expressed proteins (metaproteomics) and metabolites (metabolomics) are now applicable to complex microbial communities such as those in the rhizosphere. Combining these genomic technologies will enable us to analyse the rhizosphere at the systems level.

Key Concepts:

Soil microbial diversity is vast and plant interfaces are a focus of microbial activity.

Plant–microbial interactions are an essential determinant of plant health and productivity.

Microbes in the rhizosphere play a key role in biogeochemical cycling.

Genomic technologies enable the investigation of the genetic and functional diversity of noncultivable microbes.

Next generation sequencing technologies are revolutionising the study of microbial community analysis.
Glial Cells in Neural Development
Authors: Trébuchet Guillaume , Giangrande Angela 
Published: April 2013

AbstractGlial cells and neurons depend on each other from birth to death. Glial cells accomplish many tasks for the proper development of the nervous system and for the maintenance of neurological functions. This review focuses on recent findings in the simpleDrosophilamodel and underlines the similarities and differences between fly and vertebrate glia. The molecular and cellular mechanisms underlying gliogenesis will be reviewed as well as the role of the master regulatory gene of the glial fate:glial cells deficient/glial cells missing (glide/gcm).All along the review, the features shared between glia and macrophages are highlighted, asglide/gcmis also required in macrophage development and fly glia behave as nervous system‐specific scavenger cells. Finally, the recent data about the developmental pathways and the role of fly glia prompt us to reconsider the origin of glial cells during evolution.Key Concepts:Glial cells are very diversified in terms of morphology, function and gene expression profile.Glial cells are absolutely required for nervous system development and to support neuronal functions.Vertebrate and invertebrate nervous systems share many similarities.Glial cells are the immune cells of theDrosophilanervous system.Glial cells are very dynamic and migrate collectively over long distances.Most glia and neurons arise from common precursors.glide/gcmtranscription factor represents the master gene of the glial fate inDrosophilaacting as a genetic switch between neuron and glia.glide/gcmis expressed and required inDrosophilaglia and macrophages.Glia and macrophages share molecular and cellular pathways.Thegcmortholog genes are not necessary in vertebrate glial development.
Transcriptional Regulation in Plants
Authors: Macrae Rhiannon K , Long Jeffrey A 
Published: April 2013

Abstract

Transcriptional regulation encompasses all of the events leading up to a change in gene expression status, either activation or repression. Although many of the mechanisms of transcriptional regulation are shared between plants and animals, plants are distinctly different in that they rely more heavily on subtle environmental cues than animals do because they are sessile, and they continue to develop new organs post‐embryonically. These unusual features require constant refinement at the transcriptional level to implement large‐scale gene expression changes. Many signalling pathways converge at the level of transcription in plants, including hormone‐response pathways and light‐response pathways, forming complex gene regulatory networks and intricate feed‐back loops to control the growth and development of plants. Additionally, alterations to the chromatin such as
deoxyribonucleic acid (DNA)
methylation and histone modifications can also affect transcriptional regulation and even lead to the formation of epialleles and genomic imprinting.

Key Concepts:

Transcriptional regulation in plants relies on many of the same mechanisms as transcriptional regulation in animals but with subtle variations.

Plant hormones, such as auxin, play a major instructive role in gene expression.

Because plants are sessile organisms, environmental cues (e.g. quality and quantity of light) are critical for regulating transcription and affect the timing of developmental decisions.

DNA and histone methylation can alter gene expression and contributes to the formation of heritable epialleles and imprinting.