bluuebunny/crossref_metadata_2025 huggingface dataset:
Sexual Selection and Life History Allocation
Authors: Houslay Thomas M , Bussière Luc F
Published: April 2013

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

Plant 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

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

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

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

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

Glial 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

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.
Genetics of Adaptation to High Altitude
Authors: Labie Dominique , Elion Jacques
Published: April 2013

From the initial observation of Monge on the Andeans in the 1920s, polycythaemia and elevated haemoglobin (Hb) were considered the universal response to life at high altitude. However, this response is maladaptive, as excessive polycythaemia leads to the potentially lethal ‘chronic mountain sickness’. Highlanders in Tibet and Ethiopia revealed different phenotypes with Hb levels similar to those of sea‐level populations. Genome‐wide search for gene selection in these highlanders pointed on candidate genes encoding proteins belonging or closely related to the hypoxia‐inducible transcription factors (HIF) pathway. However, each population exhibits distinct sets of candidate genes suggesting convergent evolution on a candidate pathway rather than candidate genes. Complexity of the candidate genes in each population suggests that altering the HIF pathway globally needs to be balanced by other changes rescuing essential hypoxia‐regulated downstream processes. These observations open new avenues of investigations to uncover the molecular bases of adaptation to hypoxia that could also improve our understanding of common hypoxia‐induced maladies in lowlanders.

Key Concepts:

Moving out of Africa, man has colonised a very diverse array of environments including high altitude.

The three most dramatic examples of long‐term high‐altitude residence are populations of the Andean Altiplano, the Tibetan plateau and the Ethiopian highlands.

Highland populations have to cope with hypobaric hypoxia and cold and still maintain exercise, energetic metabolism and reproductive success.

Based on the pioneer observation of Dr Carlos Monge on the Andean populations, polycythaemia and increased haemoglobin level have been considered the universal adaptive response to high‐altitude hypoxia for more than half a century.

Tibetan and Ethiopian highlanders exhibit haemoglobin level comparable to sea‐level residents; thus elevated haemoglobin is not the universal response to hypoxia.

Genome‐wide search for adaptive genes in the three paradigmal highland populations identified largely distinct patterns in each population, but converging towards the hypoxia‐inducible transcription factors (HIF) pathway.

Analysis of genetic adaptation to high altitude in man expands the concept of converging evolution from candidate genes to candidate pathways.

Complexity of the candidate genes in each highland population suggests that altering the central HIF‐mediated hypoxic signalling pathway globally may need to be balanced by other changes rescuing essential hypoxia‐regulated downstream processes.
Genetics of Alopecia
Authors: Inui Shigeki
Published: April 2013

A recent genome‐wide association study showed eight regions for alopecia areata (AA), including
CTLA4
,
IL‐2/IL‐22
,
HLA‐class II
,
UL16‐binding protein‐3
and
‐6
,
syntaxin 17
,
IL‐2RA
,
peroxiredoxin 5
and
Eos
. Candidate genes associated with androgenetic alopecia are divided into androgen‐related and ‐unrelated genes. The former includes
5
α‐
reductase isozymes
,
androgen receptor
and
ectodysplasin A2 receptor
, which is located close to androgen receptor (AR) gene, and possible AR coregulator such as
histone deacetylase 9
. The latter contains
PAX1
and
FOXA2
. Regarding congenital hypotrichosis, mutations in
EDA‐A1
,
EDAR
and
EDA‐RADD
,
p63
and
P‐cadherin
are pointed out for ectodermal dysplasia,
SPINK5
for Netherton syndrome, desmoglein 4,
lipase H (LIPH)
and
LPAR6 (P2RY5)
for localised autosomal recessive hypotrichosis,
lipase H (LIPH)
and
LPAR6 (P2RY5)
for autosomal recessive woolly hair,
keratin 74
for autosomal dominant woolly hair,
corneodesmosin
and
APCDD
for hypotrichosis simplex and
hairless
for Marie‐Unna hypotrichosis.

Key Concepts:

Recent studies using mainly genome‐wide association analysis revealed novel candidate genes associated with alopecia, providing informative explanation for the pathogenesis.

Genome‐wide association studies suggested the importance of innate and acquired immunity in alopecia areata pathogenesis and possibility of androgen‐independent pathogenic pathway in androgenetic alopecia.

Novel genes associated with congenital hypotrichosis have been found, providing new clues to search not only the pathogenesis but also molecular mechanism of normal hair growth.
Molecular Genetics of Rhabdomyosarcoma
Authors: Gallego Soledad , De Toledo Jose Sanchez , Roma Josep
Published: April 2013

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and adolescents. There are two main histologic subtypes, embryonal and alveolar, with different clinical behaviour and prognosis. Embryonal RMS is commonly localised with favourable prognosis, whereas alveolar RMS is more frequently metastatic and its prognosis is poor. These clinical differences reflect different molecular genetics. Alveolar RMS has recurrent reciprocal translocations that are absent in embryonal tumours. These translocations, t(2;13)(q35;q14) and t(1;13)(p36;q14), generate the fusion genes
PAX3–FOXO1
and
PAX7–FOXO1,
respectively. The resulting fusion proteins exert effects on differentiation, proliferation and apoptosis, thereby bestowing a survival advantage on RMS cells. Recent advances in the identification of the cell of origin of RMS and a deeper knowledge of deregulated signalling pathways offer an opportunity for novel therapeutic approaches for patients with this tumour.

Key Concepts:

Embryonal and alveolar RMS have different molecular and genetic features and different clinical behaviours.

Fusion‐negative alveolar RMS have expression profiles resembling those of embryonal RMS.

The chimeric proteins resulting from the characteristic translocations of alveolar rhabdomyosarcomas exert oncogenic effects.

Numerous signalling pathways are deregulated in rhabdomyosarcoma.

Rhabdomyosarcoma derives from myogenic progenitor cells that undergo malignant transformation under the effects of a regulator programme that involves
p53
and
Rb
pathways.
Somatic Genome Variations
Authors: Iourov Ivan Y , Vorsanova Svetlana G , Yurov Yuri B
Published: April 2013

The genome of somatic cells is susceptible to change through ontogeny. These variations can take a variety of forms and occur through different mechanisms. Stochastic intercellular variations of the genome are suggested to be involved in a number of critical biological processes (pre‐natal development, cell number regulation, cell death and aging). However, somatic genome variations have been shown to be involved in pathogenesis of a broad spectrum of human diseases (from chromosomal and monogenic diseases to complex disorders). Nonetheless, the contribution of somatic genome variations to human biodiversity and disease is usually underappreciated. The latter is due to consistent questioning the possibility of techniques used for uncovering somatic genome variation. Therefore, technological aspects of studying intercellular variation of the human genome remain an additional important issue for understanding the role of somatic mosaicism in health and disease.

Key Concepts:

The cellular genome is highly variable both at molecular and at chromosomal level.

Somatic variation of the human genome is a likely mechanism for biodiversity either at intercellular or at interindividual level.

A number of critical biological processes (pre‐natal development, cell number regulation, cell death and aging) seem to be mediated by somatic genome variations.

According to current concepts, the commonest type of intercellular genome variations are those manifested as changes of chromosome numbers (aneuploidy or polyploidy).

Somatic genome variations are known to contribute to pathogenesis of hereditary and chromosomal diseases.

Intercellular genome variation is a highly probable mechanism of complex disorders (i.e. diseases of the brain and immune system), pre‐natal mortality and cancer.

Understanding of the way to uncover somatic genome variations is an important issue for determining the contribution to intercellular/interindividual diversity in health and disease as well as their functional consequences.
Syphilis: Laboratory Aspects
Authors: Wright David J , Norris Steven J , Dhillon Rishi H‐P , Edmondson Diane G
Published: April 2013

The laboratory diagnosis of syphilis remains a challenge to physicians. The organism cannot be subcultured and dark‐field microscopy requires a skilled operator. Current routine assays rely on serological‐based techniques, which cannot distinguish syphilis from other treponemal infections such as yaws and pinta. False‐positive and false‐negative results can occur, as well as difficulties between differentiating between acute and chronic infection. Concomitant infection with human immunodeficiency virus (HIV) can also skew results. Molecular analysis with polymerase chain reaction (PCR) is promising but is still in its infancy and standardisation is required. Therefore in order to diagnose syphilis correlation with the history and clinical examination findings remain of paramount importance.

Key Concepts:

Models of the cyclical epidemics of syphilis, which have been proposed and the factors that influence their periodicity and size of recurrence.

Comparison with the Treponema species that infect man with those from primates points to the origin of the disease, whereas study of their molecular structure throws light on treponemal biology.

The role of serological tests in the diagnosis of syphilis is analysed. Rapid screening tests are contrasted with more sophisticated laboratory tests. An example of the latter is the place of confirmatory tests.

The reasons for the gradual introduction of molecular tests like PCR into the diagnostic armoury and their current shortcomings are evaluated.

The practical difficulties of manufacturing and introducing a syphilis ‘vaccine’ are addressed, despite the theoretical and experimental support for this approach.
Dayhoff, Margaret Oakley
Authors: Strasser Bruno J
Published: April 2013

The American physical chemist Margaret Oakley Dayhoff was one of the major figures in the early history of bioinformatics. In 1965, she published the initial edition of theAtlas of Protein Sequence and Structure, the first comprehensive, computerised and publicly available collection of protein sequences. It became a model for many subsequent sequence databases, including GenBank. Dayhoff developed several methods to analyse protein sequences and infer their evolutionary relationships, as well as computer models to simulate the composition of planetary atmospheres.

Key Concepts:

Margaret O. Dayhoff was one of the founders in the field of bioinformatics.

Margaret O. Dayhoff created the first public comprehensive, computerised and publicly available database of protein sequences, TheAtlas of Protein Sequence and Structure(1965).

TheAtlas of Protein Sequence and Structurewas the model for GenBank and many other molecular databases.

TheAtlas of Protein Sequence and Structurewas a key tool for the development of molecular biology, molecular evolution and bioinformatics.

TheAtlas of Protein Sequence and Structurewas tremendously successful among researchers, yet they were sometimes reluctant to contribute their data.
History of Research into Ageing/Senescence
Authors: Grignolio Andrea , Franceschi Claudio
Published: April 2013

The fact that people age and die has always stimulated extensive philosophical and medical investigations in all societies. The early theories of ageing that arose in ancient Greece and revived in the Middle Age saw old age as a consequence of the gradual consumption of the innate heat with the inevitable loss of body moisture, according to Hippocrates’ system of four‐humours (fifth century BC). The idea that senescence was itself an illness, the image of the aged body as a lamp in which life‐fuel has run out, the character alterations of elders, the attempt to prolong life through specific diet or by substituting damaged body parts were the main themes around which research into ageing and senescence revolved from the Renaissance to the eighteenth century. The fresh tools provided by evolutionary theory and molecular biology have opened new vistas, sometimes retrieving old conceptions, of the intimate mechanisms underlying the recent prolongation of life expectancy.

Key Concepts:

Early speculations on ageing were focussed on the bodily humoural imbalance and on the gradual loss of inner heat.

Rejuvenating or stopping the ageing process was a major concerns of Medieval and Renaissance medicine.

Prolonging human lifespan through specific dietetic regimens was a long running theme in the history of gerontology.

Evolutionary approaches and molecular disciplines gave a new impetus to the researches into ageing.

No more considered itself a disease, senescence is nowadays sees as a successful form of remodelling and adaptation to a lifelong series stressors.

In the past decades, ageing researches have concentrated their efforts in four major directions: cellular theories, immune‐metabolic models, evolutionary explanations and molecular biology‐based approaches.
What is life? A Historical Survey
Authors: Pancaldi Giuliano
Published: April 2013

Notions about life adopted within different cultural traditions reveal similarities. According to anthropologists, these similarities show that humans share a basic apprehension of the world, allowing them to tell the living from the nonliving. Some scholars consider this an outcome of evolutionary adaptation. The present article offers a survey of the views of life formulated over the past twenty‐four centuries that retain a bearing on the life sciences as they are practiced today. It will be argued that, at least since Charles Darwin and Louis Pasteur, notions about life and the uses of life in the social and economic sphere have been woven into a common fabric.

Key Concepts:

From Aristotle onward, answers to the question of what is life have displayed some recognisable, recurrent patterns.

At least since Darwin and Pasteur, the notions about life and the uses of life in the social and economic sphere have been woven into a common fabric.

During the twentieth century several circumstances favoured an intertwining between the research tools of the physicists and those of the biologists, often resulting in a gene‐centered view of life.

Over the past few decades emerging specialties such as evo‐devo and systems biology have harboured growing dissatisfaction with the gene‐centered view.

The achievements associated with the Human Genome Project at the turn of the century were technological as well as scientific.

Answers to the question ‘what is life?’ are increasingly coming from technologically oriented approaches to the life sciences, sustained by the expanding bioeconomy.
Genome Evolution of
Trypanosoma cruzi
Authors: Souza Renata T , Marini Marjorie M , da Silveira José Franco
Published: April 2013

The protozoan parasite

Trypanosoma cruzi

is the etiologic agent of Chagas disease which is a major public health problem in Latin America.

T. cruzi

isolates have been classified into six main lineages (TcI–TcVI) based on genetics, phylogeographical and epidemiological studies. Its genome is complex, with a high variability among isolates, mainly as result of differences in the amount of repetitive sequences such as multigenic families encoding surface proteins and retrotransposons. Despite genome size variation and karyotype polymorphism,

T. cruzi

exhibits high conservation of chromosome structure with large syntenic groups conserved among all isolates. Comparison between

Trypanosoma brucei

and

T. cruzi

genomes suggests the occurrence of fusion and split events involving the chromosomes of these two species.

Key Concepts:

Trypanosoma cruzi
chromatin is poorly condensed during cell division, which precludes the use of conventional cytogenetic analysis.

Chromosomal bands can be separated by Pulsed‐Field Gel Electrophoresis (PFGE). A chromosomal band may contain co‐migrating chromosomes, which are not necessarily homologous.

The exact number of chromosomes remains unknown.

T. cruzi

is essentially diploid, although some larger aneuploid fragments have been described.

Six distinct

T. cruzi

lineages have been proposed on the basis of geographical, phylogenetic and epidemiological studies.

Large syntenic regions are conserved among

T. cruzi

isolates and also between trypanosomatids.

T. cruzi

lineages exhibit a striking conservation of chromosome structure.

The

T. cruzi

centromeric region consists of a GC‐rich strand‐switch domain composed mainly of degenerated retrotransposons.

T. cruzi

telomeres are composed of tandem repeats of the hexamer TTAGGG followed by a 189 bp species‐specific sequence.

The subtelomeric region is enriched with members of surface protein gene families and could be a site of generation of new variants of surface antigens.

The mapping of the syntenic regions on

T. cruzi

chromosomal bands provides evidence of the occurrence of fusion and split events involving

T. brucei

and

T. cruzi

chromosomes.
Genome Sequence of an Australian Kangaroo,Macropus eugenii
Authors: Deakin Janine E
Published: April 2013

The tammar wallaby (Macropus eugenii) is a model marsupial species that has been intensively used for research into various aspects of marsupial biology. Recently, it became one of only three marsupial species to have its genome sequenced. Comparisons of genome sequence from all three marsupials with those of other vertebrates have made it possible to begin identifying marsupial‐specific genome features. Our knowledge of the biology of the tammar wallaby has informed the interpretation of these unique features and provided insight into their evolution. Among these unique features are genes involved in the sophisticated marsupial lactation system and genes encoding for potent antimicrobial peptides. Comparisons of genome organisation have also provided insight into marsupial genome evolution.

Key Concepts:

Uncovering the genetic basis of unique marsupial features is now possible due to the availability of genome sequences for three marsupial species.

The tammar wallaby is a model species used for studies into marsupial biology, making it possible to link genomic features with the biological characteristics.

As the tammar wallaby genome was only lightly sequenced, other genomic resources such as transcriptome sequences and genome maps have enhanced the genome assembly.

A number of novel genes are associated with the complex marsupial lactation system and immunity.

Five novel genes have been identified on the marsupial Y chromosome.

The organisation of the tammar wallaby major histocompatibility complex is vastly different to that of any other species studied to date.

A decades old debate over chromosome number in the ancestral marsupial has been resolved by comparing genome organisation among the sequenced marsupials species and the outgroup species human and chicken.

The wallaby genome assembly in combination with other genomic resources are proving valuable for the discovery of marsupial‐specific features.
Evolution of the Major Histocompatibility Complex: Insights from Characterisation of Marsupial Genes
Authors: Cheng Yuanyuan , Belov Katherine
Published: April 2013

The major histocompatibility complex (MHC) is a multigene family that plays an essential role in the innate and adaptive immune system. The MHC has been intensely studied in a variety of vertebrate species and comparative analyses of the MHC in distantly related species have revealed changes in gene complexity and organisation during the evolution of this gene cluster. Marsupials occupy a unique phylogenetic position that bridges the gap between eutherians and nonmammal species. Characterisation of MHC genes and genomic regions in marsupials has greatly improved our knowledge on MHC evolution, including our understanding of changes in genomic organisation, the effect of translocation or loss of genes on gene function and the influence of natural selection on genetic variations at MHC loci.

Key Concepts:

The genomic organisation of MHC class I genes differs between nonmammalian and eutherian species.

The organisation of the marsupial MHC resembles that of nonmammals.

Separation of class I genes from class II and antigen‐processing genes occurred after the divergence of marsupial and eutherian mammals.

Classical class I genes are not linked to the MHC in the tammar wallaby.

The nonclassical class I geneUKis conserved in marsupials and likely plays a significant functional role.

Loss of a class II gene family in the Tasmanian devil may have an adverse impact on immunity in this species.

Balancing selection acts to maintain high MHC diversity in the Kangaroo island tammar wallaby population.

Selective sweeps may have contributed to the low MHC diversity in the Tasmanian devil.
Evolution of the Human Genome: Adaptive Changes
Authors: Crisci Jessica L , Jensen Jeffrey D
Published: April 2013

The study of human evolution is of interest to many both for the potential it has to improve our understanding of heritable disease, as well as for the possibility of illuminating evidence for adaptations that may help to tell the story of our origin. But uncovering evidence of positive selection at the genetic level has been a challenge. It remains unclear how much of the human genome has been affected by positive selection, what the main mechanism of selection is, and what types of patterns we should be looking for to identify adaptations. With whole‐genome sequencing and high performance computation, we are quickly shifting to a field in which data is no longer a limiting factor. Here we will discuss the progress that has been made towards these ends, explore the best examples of human‐specific adaptations to date, and discuss the implications of these findings within the context of classical population genetic theory.

Key Concepts:

An abundance of genomic data allows for a genotype‐first approach to discover selection in humans.

Ancient hominin genomic sequences provide a nearer outgroup to humans than chimpanzee, and therefore can help elucidate selective targets in humans.

Hard sweeps may have been rare in human evolution, whereas soft sweeps are a much more likely mechanism of selection.

The genomic signatures of sweeps, background selection, and demography all look similar and can be difficult to distinguish.

Genomic scans for selection make use of various signatures of selection and they rarely identify overlapping targets.

More accurate modelling of selection in humans is needed to find true signals of selection.
Impulsivity and Anxiety
Authors: Fernando Anushka
Published: April 2013

Impulsivity and anxiety are traits often found in many psychiatric disorders ranging from ADHD and bipolar disorder to post‐traumatic stress disorder (PTSD), social phobia and generalised anxiety disorder. Recent advances in both clinical and preclinical research propose further division of these two traits into distinct subconstructs. Specific cognitive tasks used across species suggest differing neurobiology underlying these processes, advocating their sub‐division. The further categorisation of these two traits is hoped to lead to specific treatments which can then be given in combination to the patient, rather than trying to treat a single disorder in its entirety. This is beginning to be explored with the use of complementary cognitive tasks in both animals and humans.

Key Concepts:

Psychiatry is advancing to treat defined symptoms rather than single disorders.

Impulsivity and anxiety are two traits thought to be distinct entities both in neural and psychological terms.

Division of these traits into subforms has been shown to correlate better with symptom diagnosis and therapeutic potential.

Establishment of these subforms is achieved with cross‐species tasks that model cognitive processes.

Future research using this approach aims to elucidate neurocognitive endophenotypes that may be symptomatic of more than one psychological disorder but readily treatable due to their defined characteristics.
Ethics of Human Enhancement and its Relevance to Disability Rights
Authors: David Wasserman
Published: April 2013

The prospect of biotechnological enhancement has provoked opposing and sometimes ambivalent responses from scholars concerned with the interests and rights of people with disabilities. The divergence is particularly sharp with respect to radical enhancement, which would raise human functions above current species norms. Disability scholars and activists fall on both sides of this debate. Critics regard radical enhancement as a threat to people with disabilities, increasing their comparative disadvantage and exacerbating their stigmatisation. Proponents regard radical enhancement as potentially liberating for people with disabilities, enabling them to dramatically improve their practical functioning and freeing them from the oppressive sway of species norms. Both sides of the debate have legitimate concerns; both may oversimplify the complex and varied effects of biotechnological enhancement on disability interests and rights.

Key Concepts:

There is a sharp disagreement about the impact of enhancement, especially radical enhancement, on the rights and interests of people with disabilities.

Proponents of radical enhancement argue that it would dramatically increase the opportunities and reduce the stigmatisation of most people with disabilities.

Critics of radical enhancement argue that it would worsen the comparative disadvantage of people with disabilities and increase the proportion of people stigmatised as disabled.

The claims of proponents may be more plausible with respect to physical disabilities; the claims of critics with respect to intellectual disabilities.

Disability scholars and advocates are on both sides of this complex debate.
Alien Hand Syndrome: Ethical Issues
Authors: Cheshire William P
Published: April 2013

At the nexus of theories of mind and the science of the brain is alien hand syndrome, a rare neurologic disorder in which one hand displays complex nonvolitional behaviours. The causative lesion disconnects brain regions that initiate hand movement from those needed for conscious recognition of volition. The aberrant behaviours may be unwilled and automatic, or in other cases they may be unconsciously willed yet unrecognised as the patient's own. Although sometimes touted as proof that free will does not exist, scientific descriptions of alien hand phenomenon are neutral in regard to competing philosophical theories attributing human decision to free agency or to determined physical processes. How one thinks about the nature of free will is important for ethics, which respects the validity of personal autonomy in moral decision making. Demonstration that some purposeful actions may be unwilled does not mean that all thoughts are predetermined. Therefore, neuroscientific explanations of alien hand syndrome can help to inform but do not dismantle traditional approaches to biomedical ethics.

Key Concepts:

Alien hand syndrome is a neurologic condition in which the affected hand exhibits complex nonvolitional behaviours.

It results from disconnection of brain regions that control the hand from those that signal conscious recognition of volition.

Other clinical examples of complex involuntary behaviours are recognised.

Purposeful yet nonvolitional behaviour calls into question common understandings of free will.

If no human decisions were freely made, then the ethical principle of respect for autonomy would be meaningless.

Personal culpability for unwilled harmful actions is ethically and legally diminished.

Just because some actions may be unwilled does not mean that all are.

Scientific accounts of alien hand syndrome are philosophically neutral with respect to theories of agency versus determinism.

Some instances of alien hand syndrome may be a form of agnosia of agency.
Catalysis of Disulfide Bond Formation by the Quiescin Sulfhydryl Oxidases
Authors: Alon Assaf , Fass Deborah
Published: April 2013

Quiescin sulfhydryl oxidase (QSOX), an enzyme that catalyses disulfide bond formation in the late secretory pathway and extracellular environment, is emerging as an important player in extracellular matrix assembly, with apparent physiological and pathological functions in development and cancer, respectively. High‐resolution views into the QSOX catalytic machinery are providing information not only on the QSOX enzymes themselves but also on the larger protein disulfide isomerase family of oxidoreductases and on thioredoxin‐fold superfamily proteins more generally. The two redox‐active sites of QSOX are present within domains flexibly tethered to one another, but the sites cooperate tightly and productively to generate disulfide bondsde novoand transfer them to substrate proteins. Backbone and side‐chain dynamics in the vicinity of the redox‐active disulfides of QSOX enzymes appear to modulate the local electrostatics during catalysis, facilitating electron transfer in dithiol/disulfide exchange reactions.

Key Concepts:

QSOX enzymes accomplish both the generation of disulfidesde novoand the delivery of disulfides to substrate proteins using a redox relay.

The amino (N)‐terminal portion of QSOX is structurally and functionally similar to domains of protein disulfide isomerase family proteins.

The carboxy (C)‐terminal portion of QSOX appears to have arisen by domain duplication and fusion from an Erv‐family sulfhydryl oxidase precursor.

QSOX enzymes have structural features and appropriately positioned functional groups to enhance electron transfer between the two modules.
Accounting for Genetic Testing: Familial and Professional Perspectives
Authors: Arribas‐Ayllon Michael , Sarangi Srikant , Clarke Angus
Published: April 2013

Genetic testing is more than a laboratory procedure; it is a complex social activity involving clients, their families and genetic‐counselling professionals. This complexity is occasioned by the fact that genetic testing is distinct from other kinds of medical testing because the hereditary nature of risk and disease accentuates issues of responsibility and blame. The rise of genetic counselling with its ethos of nondirectiveness seeks to help clients make difficult decisions in the face of risk/uncertainty and unintended consequences following the test results. Genetic counselling thus requires challenging and encouraging clients to engage in socio‐moral reflection. The notion of ‘accounts’ is central to understanding how professionals and families routinely explain, defend and negotiate the consequences of genetic risk. A comprehensive review of the literature to date examines the extent to which decisions to (not) test and (not) disclose test results are experienced as tensions across autonomy, responsibility and blame.

Key Concepts:

Genetic testing is an inherently complex socio‐moral activity in which clients, families and professionals navigate dilemmas that often centre on themes of autonomy, responsibility and blame.

Genetic counselling maintains an ethos of nondirectiveness to promote an ethic of self‐governance and client‐centred practice.

In contemporary liberal society, the high premium placed on rational autonomy shifts the burden of responsibility and blame to the bearer of choices and to their ability to make decisions wisely.

Genetic counselling often requires eliciting ‘accounts’ to challenge or encourage clients to engage in socio‐moral reflection.

Accounts are linguistic/rhetorical devices that involve subtle negotiation of individual actionsvis‐à‐viscultural values, moral norms and social expectations.
Mitochondrial Carriers
Authors: del Arco Araceli , Satrústegui Jorgina
Published: April 2013

In eukaryotic cells, the exchange of metabolites across the inner mitochondrial membrane is performed by members of the mitochondrial carrier family (MCF), the largest family of solute transporters. Mutations in MCF genes are associated with rare genetic diseases underscoring the relevance of individual MCF members. Mitochondrial carriers have a common tripartite structure made up by tandem repeats of 100 amino acids each containing two transmembrane α‐helices and one conserved MCF signature. MCF members are present in two states, c and m, with binding sites for substrates facing either the intermembrane (c) or matrix (m) space. X‐ray crystallography of the mitochondrial ADP/ATP carrier in the c‐state has shown that the six α‐helices form a compact bundle shaping a cavity sealed on the matrix side by a salt‐bridge network. Substrate binding perturbs the salt‐bridge network triggering conformational changes that cause the opening of the carrier towards the matrix coupled to substrate transport.

Key Concepts:

Mitochondrial carriers perform the exchange of metabolites, nucleotides and cofactors through the inner mitochondrial membrane.

Mitochondrial carriers form an evolutionary conserved family present in all eukaryotic cells.

Mitochondrial carriers share a tripartite structure made up by repeats of 100 amino acids containing two α‐helices connected by a hydrophilic loop.

Phylogenetic analyses have shown the existence of a limited number of mitochondrial carrier subfamilies involved in the transport of structurally related substrates.

Mutations in nine mitochondrial carriers cause autosomal recessive disorders in humans.

Mitochondrial carriers are present in either one of two different states, c and m, in which binding sites for substrates face the intermembrane (c) or matrix (m) spaces.

During the transport cycle, substrate binding in each of these states induces a transition to the other state which is coupled to substrate transport.

The three‐dimensional structure solved for the ADP/ATP carrier in the c state is consistent with a bundle of six transmembrane α‐helices forming an aqueous cavity closed towards the matrix by electrostatic interactions. Specific interactions of substrates with the substrate‐binding site within the aqueous cavity will disturb the electrostatic interactions that maintain the carrier closed to the matrix side.

Substrate translocation by mitochondrial carriers occurs coupled to conformational movements of the α‐helices that open the carrier.