bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecosystem Services
Authors: Patterson Trista M 
Published: April 2013

AbstractEcosystem services represent all the things that functioning ecosystems do for people that people generally do not have to pay for. Examples include a forested hillside filtering water and retaining topsoil/sediments, how trees remove carbon from the atmosphere, or how a mangrove buffers surrounding low‐lying lands from wave action and storm surge. When ecosystem services are lost, the human‐made substitutes (such as a water filtration plant, erosion retaining walls, etc.) are often costly, and costly to maintain. Environmental management decisions are increasingly incorporating estimates of ecosystem service values as part of the cost–benefit evaluations. The intent of many ecosystem service efforts are to internalise ecosystem contributions into decision‐making, thus stemming ecosystem service loss. However, accomplishing this requires not only stemming the loss of ecosystem services, but also addressing the increasing human demands for them.Key Concepts:Ecosystem services are those processes of ecosystems that support (directly or indirectly) human well‐being.The concept of ecosystem services is of interest to economists, ecologists and many other disciplines for its ability to create cross‐discipline dialog.Ecosystem services provide valuable social benefits, which are often not accounted in standard economic currencies. Left unaccounted, they are vulnerable to loss. Numerous tools are emerging to visualise this value, supporting protection and/or restoration of ecosystem services.Much of the current focus on ecosystem service work bases its emphasis on thesupplyof ecosystem services. For this concept to support sustainability objectives however, growingdemandsfor ecosystem services must be addressed through changes in behaviour, technology, governance and design.
Molecular Genetics of Sleep Disorders
Authors: Caylak Emrah 
Published: April 2013

Abstract

Common sleep disorders include narcolepsy, restless legs syndrome, obstructive sleep apnea syndrome, circadian sleep disorders and parasomnias. They are influenced by genes and several research groups to attempt to identify susceptibility genes of sleep disorders through the sequential analysis of genetic linkage and association. Strong evidence has now emerged for the presence of genes influencing sleep disorders at several chromosomal loci and for at least one of these, there is evidence implicating specific genes. This review highlights the genetic contribution to sleep disorders and current molecular genetic researches aimed at identifying susceptibility genes for sleep disorders.

Key Concepts:

Sleep disorders result in sleep deprivation and interfere with work, driving and social activities. Management of sleep disturbances is important to inhibit secondary to mental, medical, or substance abuse disorders.

Genetic factors are important in sleep disorders.

The association and linkage studies of sleep disorders identify genetic causes of heritable sleep disorder.

Molecular genetic researches should be aimed to identify susceptibility genes for sleep disorders.

Molecular advances in narcolepsy (NRCLP), restless legs syndrome (RLS), obstructive sleep apnea syndrome (OSAS), circadian sleep disorders (CSD) and parasomnias will help to set the research agendas for future studies to follow.

Gene‐mapping studies may help us to understand the biological basis of normal sleep variation, in addition to sleep disorders.
Molecular Genetics of Coeliac Disease
Authors: Mistry Vanisha , van Heel David 
Published: April 2013

Abstract

Coeliac disease (CD) is a common inflammatory disease of the small intestine. It has a prevalence of 1% in the population and is strongly heritable. Current germline disease risk variants explain ∼50% of known heritability, the majority contributed by a strong human leukocyte antigen (HLA)‐DQ association. The role of HLA‐DQ in the immunology of CD is well understood, for example the role of tissue transglutaminase and HLA‐DQ in modifying and binding immuno‐dominant dietary cereal (gluten) peptides. Genome‐wide association studies have found 39 loci with risk variants of more modest effect. The use of high‐throughput sequencing technologies to locate rare variants of larger effect may aid in the complete resolution of this complex trait, as well as in other autoimmune diseases, which show considerable overlap in immunological pathways.

Key Concepts:

Coeliac disease has a strong genetic component with an environmental trigger, gluten.

Coeliac disease shows strong HLA association, which is necessary but not sufficient for disease development.

Genome‐wide association studies have located common variants of modest effect size.

Rare variants with larger effect are hypothesised to contribute to common complex disease.

Exome sequencing a large number of individuals from multigenerational families might isolate precise causal variants.
Molecular and Cellular Basis of Learning Difficulties in Genetic Disorders
Authors: Crego Cortney , Landreth Anthony , Silva Alcino J 
Published: April 2013

Abstract

Recent advances have revealed a plethora of genes, signalling pathways, cellular and circuit processes involved in learning and memory. Convergent evidence demonstrates that molecular mechanisms that regulate long‐lasting changes in synaptic function are critical for learning and memory. This evidence has had a key role in unraveling mechanisms responsible for learning disabilities. For example, mutations in the neurofibromatosis type I (
NF1
) gene are a common genetic cause for learning disabilities. Studies in mice revealed that these learning deficits are caused by increases in Ras signalling leading to enhancements in synaptic inhibition and synaptic plasticity deficits. These deficits can be reversed by manipulations that target Ras signalling or inhibition. Current clinical trials are testing the efficacy of these treatments in
NF1
. Studies in other genetic causes for learning disabilities have shown that it is possible to develop mechanism‐based treatments for these disorders in mice that are effective even when they are started in adulthood.

Key Concepts:

The molecular mechanisms that regulate long‐lasting changes in synaptic function are critical for learning and memory.

Our growing understanding of mechanisms of memory has been effectively used to unravel the causes for memory deficits associated with animal models of several key genetic disorders, including NF1, tuberous sclerosis and fragile X.

It is possible to develop mechanism‐based treatments for developmental disorders that are effective even when treatment is started in adulthood.
Next‐generation Sequencing in Clinical Molecular Diagnostics
Authors: ten Bosch John R , Deignan Joshua L , Grody Wayne W 
Published: April 2013

Abstract

Next‐generation sequencing is based upon the concept of massively parallel chemical reactions in which millions of independent DNA sequencing events occur simultaneously, and this is achieved using a relatively similar concept across all of the currently available platforms. Current clinical molecular genetics labs offer testing mainly for single‐gene defects and a few multigene panels. However, for whole‐exome and whole‐genome sequencing, as the cost per sample continues to fall, there is little question that the clinical application of this technology will soon become abundant in diagnostic labs. Before that happens, we will need to prepare ourselves to handle certain types of unexpected and potentially unwanted information, since this technology should prove to be of tremendous value for the practice of medicine in the future.

Key Concepts:

Next‐generation sequencing is based upon the concept of massively parallel chemical reactions in which millions of independent DNA sequencing events occur simultaneously.

There are several commercial vendors of next‐generation sequencing instruments, though the market is currently dominated by Roche, Illumina and Life Technologies.

Most clinical labs prefer to sequence multiple samples or many regions of the genome in one run, and there are several methods that can be used to accomplish this.

Next‐generation sequencing can also be used to effectively detect both large and small chromosome aberrations.

Next‐generation sequencing has the potential to increase the scope of tests for sequence variants in the areas of infectious disease testing and oncology.

Clinical laboratories are currently observing caution in the adoption of this new technology.
Evolution of Genetic Resistance/Susceptibility to Malaria Infection
Authors: Ghosh Kanjaksha , Ghosh Kinjalka 
Published: April 2013

Abstract

Severe malaria infection still kills more than 2.7 million people across the globe every year. Of the few infections which has shaped human genome over the millennia through the process of natural selection, malaria infection has left its imprints on human genome. Genetic studies on malarial resistance started in the late 1940s with demonstration of protection against malaria in carriers of several haemoglobinopathy genes and further demonstration of increasing prevalence of such genes across the malarious areas of the world. As malaria parasites pass a significant period of its life inside the red cell, many red cell proteins and their genes were studied for polymorphic variants which offers protection against such infection. Total absence of

Plasmodium vivax

malaria in Western Africa and its linkage with total absence of red cell Duffy antigen is a case in point. Subsequently as a rational extension of the above idea, association of resistance or susceptibility to severe malarial infection were studied with relation to genes of innate immunity, adoptive immunity, cytokine genes, adhesion molecules, coagulation proteins, proteins involved in systemic inflammatory reactions etc. Innumerable studies have shown various kinds of association. However, at present the interest has shifted towards genome wide association studies with malarial infection. Present review stops short of genome wide association and presents a snapshot view of genome association with malaria infection.

Key Concepts:

The immune system of man has evolved to fight pathogens like malaria parasite.

Pathogens have exerted intense selective pressures on the evolution of the immune system of man.

Key elements of the adaptive immune system, such as antigen receptors and major histocompatibility complex molecules, show evidence of such selective pressures.

Mutation is the key genetic mechanism underlying the co‐evolution of the immune system and pathogens.

Evolutionary adaptation to malaria involves many more aspects than modification of adoptive and Innate Immune system.

Owing to complex life cycle of the parasite and its specific requirements of nutrition and need for protection during its growth, the parasite vulnerability increases due to changes in Nutrient (haemoglobin), Host Enzyme system (Oxidant damage), changes in specialised receptors for entry into cells (Red cells, Hepatocytes) and its ability to adhere to Key cells (Endothelium).

Product of metabolism of malaria parasite (Hemozoin) exerts strong immunomodulatory effect.

As malaria parasite from different regions of the world exerted selection pressure on different population groups with different genetic endowment (polymorphisms), this resulted in evolution of different key resistant molecules against malaria in different parts of the world.
Molecular Genetics of Tourette Syndrome
Authors: Valenti Antoinette , Grados Marco 
Published: April 2013

Abstract
Tourette Syndrome (TS) is a neurodevelopmental disorder characterised by chronic motor and vocal tics, which fluctuate over time. The molecular genetics of TS is supported by genetic epidemiology studies, which strongly suggest the presence of susceptibility genes for TS. Epidemiologic family, segregation and linkage studies, as well as candidate gene studies, have yielded limited specific results to date, however, pathophysiology models that support a molecular genetics approach in TS are emerging. Whole‐genome approaches, including genome‐wide association studies (GWAS) and whole‐genome sequencing, may yield more definitive genomic findings. Uncovering the biological substrate of TS will spur the development of novel, more precisely targeted, treatments for this disabling disorder.
Optical Control of Neuronal Activity
Authors: de Lecea Luis , Carter Matthew E 
Published: April 2013

Abstract

Optogenetics has become an invaluable method to establish causal relationships between the activity of genetically defined neuronal circuits and behaviour.
Channelrhodopsin 2
is a light‐activated channel that, when introduced in neurons allows temporally precise control of the activity of genetically identified neuronal networks. Conversely, halorhodopsins are light sensitive ion pumps that allow us to reversibly inhibit neuronal transmission with single action potential resolution. These optical tools offer new approaches to deconstruct neuronal circuits in freely moving animals. New variants of light‐activated channels and pumps offer a menu of optogenetic tools that allow us to determine functional connectivities and dynamic properties of brain networks. The development of optogenetics has profound implications in our understanding of brain organisation and mechanisms of neuropsychiatric disease.

Key Concepts:

Introduction of Channelrhodopsin 2 in neurons allows millisecond optical control of genetically identified neurons.

Different mutants of ChR2 show different kinetic properties, spectral sensitivity.

Different gene delivery methods allow dissection of neuronal circuits even in the absence of genetic markers and in multiple model organisms.

Combination of optogenetics with gene deficiencies and imaging systems will allow significant improvements in our understanding of circuit dynamics and mechanisms of disease.
Advanced Techniques for Cell Lineage Labelling in Drosophila
Authors: Hafezi Yassi , Nystul Todd G 
Published: April 2013

Abstract

The ability to mark and genetically manipulate clonally related cells in live organisms is invaluable for investigating the mechanisms of tissue development, homeostasis and repair. A wide variety of techniques have been developed in

Drosophila melanogaster

for this purpose. These cell lineage labelling techniques range from simple methods for randomly marking cells to complex schemes for differentially labelling and genetically altering specific cells or more than one clone at a time. For example, coupled MARCM makes it possible to simultaneously label both halves of a cell lineage with positive markers; FINGR uses a combinatorial approach, using Gal4 and Gal80, to provide finer spatial control over clone induction; Flybow and Drosophila Brainbow increase the resolution and efficiency of clonal analysis through multicolour labelling; and G‐trace differentially marks cells that currently express a driver from cells that expressed the driver in the past. These labelling techniques each have their own advantages and disadvantages. But together they create a powerful arsenal of tools for the study of many diverse topics in tissue biology.

Key Concepts:

Cell lineage labelling is a technique, which allows populations of clonally related cells to be traced
in vivo
.

Modern cell lineage labelling techniques in Drosophila allow cells to be labelled and genetically modified without invasive procedures.

Cell lineage labelling has become the gold standard for the identification of stem cells in Drosophila.

Recently developed cell lineage labelling techniques offer more flexibility, precision and control.
Cilia and Human Disease
Authors: Albee Alison J , Dutcher Susan K 
Published: April 2013

Abstract

Cilia and centrioles are highly conserved organelles that have hundreds of proteins associated with them. Studies in mice have shown that these organelles are essential for mammalian development and mice that cannot assemble them die

in utero

. However, mutations in many cilia and centriole genes cause human diseases that show a great range in defects. Defects in centrioles are associated with microcephaly and mental retardation. The reduction in brain size is related to the loss of neuronal progenitor cells. Defects in centrioles may also be associated with Sjögren syndrome, an autoimmune disease, because of defects in formation of the immunological synapse. Defects that cause immotile cilia result in chronic respiratory infections, infertility, and congenital heart defects. Defects in primary cilia share various symptoms that include loss of vision, obesity, diabetes, cystic kidney disease, mental retardation, polydactyly, and short bones. Many of these diseases are associated with the transport and sorting of receptors onto the ciliary membrane for sensing the environment.

Key Concepts:

Cilia perform functions in many different tissues and during development.

Many ciliary mutations affect multiple tissues and organs.

Key signalling pathways require cilia.

Orientation of the spindle during mitosis requires functional centrioles.
Selection of Phylogenetic Models of Molecular Evolution
Authors: Posada David 
Published: April 2013

Abstract

The use of different models of molecular evolution can change the conclusions derived from the evolutionary analysis of
deoxyribonucleic acid (DNA)
and protein sequence alignments. Several methods have been developed for the selection of the probabilistic model of nucleotide substitution or amino acid replacement that best fits the particular data at hand. Simulation studies indicate that these techniques work very well, and in recent years these methods have been implemented in a number of programs such as ModelTest, ProtTest and recently jModelTest. These programs also provide various tools for quantifying uncertainty in model selection, model averaging or multimodel inference.

Key Concepts:

Models of molecular evolution allow us to calculate probabilities of change between nucleotide and amino acid sequences.

The use of different models of evolution can change the outcome of the phylogenetic analysis.

Different datasets can be best‐fitted by distinct models.

Model selection techniques are quite accurate at identifying the generating model in simulations.

Programs like jModelTest and ProtTest facilitate the routinary selection of models of evolution in phylogenetics.
Evolution of Transcription Factors inCaenorhabditis
Authors: Jovelin Richard 
Published: April 2013

AbstractTranscription factors (TFs) are regulatory proteins controlling gene expression by binding specific motifs associated with their target genes and playing essential roles during development and physiological response to stimuli. The evolution of transcriptional regulation is an important source of phenotypic diversity. The genome of the nematodeCaenorhabditis elegansencodes a similar proportion of TFs as the human genome, although TF families show different patterns of expansion in human and in worm. The TF repertoire ofC. elegansis well diversified with over 50 TF families. Alternative splicing and gene duplication contribute to the functional diversity of TFs and the rapid evolution of TF protein sequence suggests that TF evolution plays important roles in developmental evolution. Many of the principles that guided the diversification of the worm TFs are likely to be applicable to the evolution of TFs in other organisms.Key Concepts:The genome ofC. elegansencodes 988 TFs belonging to 50 distinct families based on the type of DNA‐binding domain.The worm and human genomes encode a similar proportion of TFs, and in both species a third of the TFs show tissue‐specific gene expression.Alternative splicing increases the number of TF transcripts by 22%.Gene duplication contributes significantly to the functional diversification of TFs, and several examples illustrate the different evolutionary trajectories taken by TF duplicates.Tissue‐specific expression, alternative splicing, gene duplication and the combinatorial regulatory activity of TFs reduce the pleiotropic constraints operating on TF sequence evolution.TF factor sequence evolution plays an unappreciated role in developmental evolution.TFs can harbour high level of amino acid variation both between species and within populations.
Advances in High‐Throughput Crystallisation
Authors: Meijers Rob , Mueller‐Dieckmann Jochen 
Published: April 2013

Abstract

Molecular biologists attempt to understand the inner workings of the cell, the smallest unit of all life forms on earth. The constituents that perform cellular functions are the proteins, enzymes and nucleotides. A full appreciation of the chemical and biological functions of the cellular constituents, and therefore life itself, requires knowledge of their three‐dimensional structures. X‐ray crystallography is among the most powerful methods to derive structural information from biological macromolecules. Before the three‐dimensional structure of biological macromolecules can be determined by X‐ray crystallography, they have to be assembled into the regular and periodic arrangements, which define a crystal. Biological macromolecules are irregularly shaped and inherently flexible, which makes their crystallisation very difficult. It frequently implies the testing of many different sample variations under many hundred conditions. This is the reason for the establishment of automated high‐throughput crystallisation facilities.

Key Concepts:

Progress in the life sciences requires knowledge of the cellular processes at a molecular level.

The principal components of the cell are proteins and nucleic acids.

The three‐dimensional structures of the cellular components define their functions.

X‐ray crystallography is the method of choice to determine the structure of biological macromolecules.

Crystallisation of biological macromolecules for X‐ray crystallography requires the testing of hundreds to thousands of conditions.

Automation supports many processes in molecular biology, by performing routine operations with the help of robotics.

High‐throughput crystallisation has significantly improved success rates in crystallography through the rapid and comprehensive screening of many sample constructs under many different conditions.