bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population Genetics: Overview
Authors: Ewens Warren J 
Published: September 2010

Abstract

Population genetics is concerned with the nature of, and the forces determining, the genetic composition of a population. Since any presently observed population is the outcome of an evolutionary process, the subject is in large part concerned with evolutionary questions. Indeed the evolutionary component of population genetics may be thought of as the rewriting of the Darwinian theory in terms of the Mendelian hereditary mechanism. This involves, for example, determining the rate of incorporation of favourable new alleles into a population, and the evolutionary effects of mutation. These activities are
prospective
, that is they discuss changes in the structure of a population forwards in time. However population genetics theory is currently largely
retrospective
, assessing the past history of a population (‘When and where did the most recent common ancestor of all currently living humans live?’) and investigating what forces led to the currently observed genetic composition of a population.

Key Concepts:

The
additive genetic variance
is that component of the variation in any character which is explained by ‘genes within genotypes’.

The
blending theory
asserts that the value of any characteristic of any child is approximately the average of the corresponding characteristics in that child's parents.

The
correlation between relatives
is the correlation in some character between close relatives (e.g. mother–daughter).

The
Fundamental Theorem of Natural Selection
relates aspects of the change in the mean fitness of a population from one generation to the next to the parental generation additive genetic variance in fitness.

The
Hardy–Weinberg law
shows that, in the absence of selection, genetic variation is maintained from one generation to the next.

The
neutral theory
claim that most of presently observed genetic variation in a population, and most of the variation from one population to another, did not arise as a result of selection but arose rather as a result of purely random changes in allelic frequencies.

Retrospective population genetics theory
focuses on the past history of a population rather than its future evolution.
Seed Banks and Gene Banks
Authors: Ambrose Michael J 
Published: September 2010

Abstract

The doomsday seed vault buried deep in the side of a frozen mountain‐side on the Island of Svalbard situated within the Arctic Circle has come to encapsulate the global imperative of conserving the biodiversity relating to the world's major food crops against the growing challenges resulting from rising human population, lost of agricultural land and climate change. Extending seed longevity in seed and gene banks is regarded as complementary to conserving plant genotypes

in situ

in their natural environment. Elucidating the basis and variation in seed physiology with respect to seed storage as well as other

in vitro

storage techniques such as cryopreservation are essential to success in this mission and in enabling ready access to these resources for future generations.

Key Concepts:

Crop wild relatives are wild plant taxa that are closely related to a crop such as a wild ancestor, from which it might be possible to find and transfer beneficial traits for crop improvement.

The classification of survival of species on the basis of the response of seeds to combinations of temperature and desiccation.

Genetic resources is the term that refers to any material that contains functional units of heredity.

Seeds with intermediate storage behaviour can tolerate moderate desiccation (8–12% moisture) but are sensitive to dry storage at temperatures at or below freezing.

Serotiny is an ecological adaptation whereby some plant species release their seeds in response to environmental cues such as wetting, burning or warmth rather than the time when the seed reaches maturity.

Seeds can be subjected to accelerated aging by storing seeds for short periods under stressed conditions of high humidity and high temperatures. This results in a fall in percentage germination that mimics the effect observed under long‐term storage.
Protein Import into the Yeast Endoplasmic Reticulum: Methods
Authors: Brodsky Jeffrey L , Morrow Michael W 
Published: September 2010

Abstract

Nascent secreted proteins and integral membrane proteins in eukaryotes must be imported, or ‘translocated’ into the endoplasmic reticulum (ER). Because approximately one‐third of all cellular proteins fall into these protein classes, the translocation machinery in the ER must operate with high efficiency and accommodate a wide variety of chemically diverse substrates. Moreover, proteins can translocate into the ER either cotranslationally or posttranslationally, and each of these modes of protein entry into the ER requires unique components. Through the years, the composition and function of the ER translocation machinery was defined by the development of

in vitro

assays in which protein translocation can be recapitulated. For example, the posttranslational translocation of a model protein into the yeast ER can be measured using ER‐derived microsomes or reconstituted proteoliposomes. The model protein for this assay is the mating pheromone precursor, prepro‐alpha factor.

Key Concepts:

A large number and variety of proteins must be imported, or ‘translocated’ into the ER.

Proteins can enter the ER either cotranslationally, that is during synthesis, or posttranslationally, that is after synthesis.

The translocation reaction requires a multiprotein complex and associated factors which reside in the cytoplasm, in the ER membrane and in the ER lumenal space.

Posttranslational translocation can be recapitulated using ER‐derived microsomes prepared from the yeast
Saccharomyces cerevisiae
, or using reconstituted proteoliposomes into which the translocation machinery has been integrated.

The
in vitro
reaction has helped to define how components of the translocation machinery function.

The translocated substrate can be mutated to assess how aberrant proteins are targeted for ER‐associated degradation (also known as ERAD).
Fourier Transform Infrared (
FTIR
) Spectroscopy
Authors: Gerwert Klaus , Kötting Carsten 
Published: September 2010

Abstract

Fourier transform infrared (FTIR) spectroscopy is an experimental technique used initially for qualitative and quantitative analysis of organic compounds, providing specific information on molecular structure, chemical bonding and molecular environment. For many years, FTIR has been successfully employed for studying a wide variety of proteins, enzymes, nucleic acids, lipids and glycolipids and photobiological systems. Time‐resolved (tr)‐FTIR spectroscopy can monitor reactions of the amino acids, the ligands and specific water molecules in the active centre of a protein in the time range from nanoseconds to seconds, thereby providing a detailed understanding of the molecular reaction mechanism.

Key Concepts:

FTIR provides several advantages compared to other spectroscopic techniques.

FTIR spectroscopy is widely used for the investigation of secondary protein structure.

To obtain information on individual groups, we have to look at difference spectra.

In order to derive information on the reaction mechanism, the infrared bands have to be assigned to molecular groups of the protein.

The QM/MM (quantum mechanics/molecular mechanics) approach can be used to calculate the infrared spectra of proteins.

With the ATR (attenuated total reflection) technique it is possible to immobilise a protein on a surface and study reactions with ligands or other proteins.

Biochemical changes of tissues and body fluids can be monitored using FTIR.

By means of infrared microscopes spatial resolved information with a resolution of a few micrometer can be obtained.
Chemical Ecology
Authors: Drijfhout Falko 
Published: September 2010

AbstractChemical ecology is the study of the structure, origin and function of naturally occurring chemicals that mediate intraspecific or interspecific interactions. These chemicals are known as semiochemicals. Depending on the function of a semiochemical, this group of chemicals can be further divided into three classes: pheromones, kairomones and allomones. At the heart of the discipline are modern analytical instrumentation, careful observational biology and good bioassay design. Research during the past 50 years has identified many different semiochemicals. Several of these chemicals are currently in use as pest control agents. Although the majority of the early research focused on (lepidopteran) sex pheromones, in recent years, a shift is seen into semiochemicals from other insects as well as noninsects such as mammals, marine animals or even micro‐organisms. The field of chemical ecology has developed into a mature science with diverse practical applications, of which pest control is the most important.Key Concepts:Chemical ecology studies the structure, origin and function of naturally occurring chemicals that mediate intraspecific or interspecific interactions.Bioassays are crucial in successfully identifying active semiochemicals.Semiochemicals are divided into different categories, depending on their function in an organism.Chemical ecology has a much wider application than only its use in pest control.Chemical ecology is characterised by highly cross‐disciplinary research.
Cancer: Chromosomal Abnormalities
Authors: Mitelman Felix 
Published: September 2010

Abstract

Most cancer cells have acquired clonal chromosome abnormalities. An increasing number of characteristic aberrations, in particular balanced changes, are with remarkable specificity associated with distinctive morphological and clinical disease characteristics. The identification of these recurrent aberrations has several important implications. First, cytogenetics has become an increasingly important tool in the clinical management of cancer patients to help establish a correct diagnosis, to predict prognosis, and to select the most appropriate treatment. Second, the cytogenetic information has provided invaluable help to identify genes of importance in the carcinogenic process by focusing the attention to chromosomal sites that may harbour genes which when rearranged lead to neoplasia. Practically all balanced structural rearrangements that have been characterised at the molecular level have been found to exert their action through one of the two alternative mechanisms: deregulation, usually over‐expression, of a seemingly normal gene in one of the breakpoints, or the creation of an abnormal hybrid gene through fusion of parts of two genes, one in each breakpoint.

Key Concepts:

Chromosome aberrations are a characteristic feature of neoplasia.

Chromosome abnormalities have been reported in almost 60 000 human neoplasms.

Recurrent balanced chromosome rearrangements, in particular translocations, are associated with distinctive tumour characteristics.

Cancer‐associated chromosome changes are of clinical importance for diagnosis, prognosis and treatment.

The breakpoints of balanced structural chromosome aberrations point at the locations of cancer‐relevant genes.

Cancer‐associated structural chromosome abnormalities lead to the formation of hybrid genes through fusions of parts of two genes located in the breakpoints.

More than 600 gene fusions created by an acquired chromosome change are known, and about 30% of human cancer cases contain a fusion gene.
Meiosis
Authors: Hultén Maj A 
Published: September 2010

Abstract

Meiosis is a specialised type of cell division, the principal function of which is to produce spores/gametes (sperm and eggs in mammals) that have the haploid number of chromosomes. In humans, this represents a reduction from 46 (23 pairs) to 23 chromosomes (one complete set) in sperm and eggs. The normal somatic number of 46 chromosomes is restored at fertilisation. The most complex part of meiosis (prophase I) involves intimate pairing and synapsis of the homologous chromosomes followed by reciprocal recombination/crossing‐over/chiasma formation. In most organisms, chiasma formation is obligatory to allow the regular segregation of the (rearranged) homologues at the first (reductional) division (anaphase I). In mammals, there are substantial differences between the two sexes as regards the meiotic process. Mammalian female prophase I takes place during foetal development, and the second meiotic cell division is not completed until after fertilisation. In sharp contrast, mammalian male meiosis does not start until puberty and is continuous throughout life.

Key Concepts:

Meiosis is the term used for the cell divisions leading to gametes, sperm and eggs in mammals.

At meiosis, the chromosome number is halved compared to that in somatic cell nuclei.

Meiosis takes place in the germ line, testes and ovaries in mammals.

The meiotic process is very different in the two mammalian sexes.

Female mammalian meiosis is subdivided into three stages: the first taking place during foetal development, the second just before ovulation and the third after fertilisation.

Male mammalian meiosis starts at puberty and is ongoing throughout life.

Reciprocal recombination/crossing‐over/chiasma formation (taking place during foetal development in mammalian females) is necessary for normal first meiotic cell division (taking place just before ovulation in mammalian females).

Many of the proteins involved in the meiotic recombination process, as well as some structural components of meiotic chromosomes, are conserved from yeast to man.

Human females produce only 300–400 mature eggs in a lifetime, in stark contrast to human males who normally produce around 300–400 million sperm daily.

An abnormal chromosome number (aneuploidy) is common in humans and is thought to arise due to abnormalities in meiotic cell divisions.
Glucose‐6‐phosphate Dehydrogenase (G6PD) Deficiency: Genetics
Authors: Mason Philip J , Vulliamy Thomas J 
Published: September 2010

AbstractDeficiency ofglucose‐6‐phosphate dehydrogenase(G6PD) is the most common enzyme deficiency in humans and is due to many different local variants with point mutations in the X‐linked G6PD gene. In populations that have a history of malaria infection G6PD alleles causing deficiency can reach frequencies of 10% or more. Though often asymptomatic, the enzyme deficiency can lead to acute haemolytic anaemia caused by failure to maintain sufficiently high levels of nicotinamide–adenine dinucleotide phosphate reduced form (NADPH) to prevent oxidative damage in red cells. Rare sporadic variants that can occur in all human populations can cause more severe chronic haemolytic anaemia. G6PD deficiency is also one of the major causes of neonatal jaundice. The prevalence of G6PD‐deficient alleles is likely due to the fact that they confer a selective advantage against malaria infection.Key Concepts:G6PD deficiency is widespread because deficient individuals have a selective advantage against malaria infection.G6PD in red cells maintains the levels of NADPH, essential for reducing oxidising agents.Deficient variants cannot maintain high NADPH levels and reactive oxygen species cause haemolysis.Deficient variants can reach polymorphic levels and different populations have different variants.This pattern of variation arose recently, coincident with the spread of malaria in human populations.Most deficient variants are unstablein vivoand therefore cause very low levels in red cells, where the enzyme is not turned over.Knowledge of the G6PD variants in a population can be useful in limiting illness caused by G6PD deficiency.
Macrophage Foam Cells
Authors: Valledor Annabel F , Lloberas Jorge , Celada Antonio 
Published: September 2010

Abstract

Foam cells are lipid‐loaded macrophages that are generated from the massive uptake of modified low‐density lipoproteins and the intracytoplasmatic accumulation of cholesteryl esters. Foam cells are present in all stages of atherosclerosis and participate in inflammatory responses and tissue remodelling within the arterial intima. Foam cells can also be generated as a consequence of infection by persistent pathogens, such as

Mycobacterium

,

Chlamydia

and

Toxoplasma

. These pathogens meet nutritional advantages by residing within cells that accumulate lipids. When the immune system is unable to eliminate substances perceived as foreign, it produces a granuloma, composed mostly of macrophages, attempting to wall off the nonself‐material. This article reviews the processes that lead to the regulation of foam cell formation in atherosclerosis and infection.

Key Concepts:

Foam cells are lipid‐loaded macrophages.

Foam cells are generated from the massive uptake of modified low‐density lipoproteins and the intracytoplasmatic accumulation of cholesteryl esters.

Foam cells are present in several diseases as atherosclerosis and as result of different infections.

Foam cells participate in inflammatory responses and tissue remodelling.

Endothelial transmigration of monocytes is the first step in the development of atherosclerosis.

Once monocytes have taken residence in the arterial wall intima, they undergo phenotypic transformation into macrophages, and can internalise large amounts of modified LDLs and become foam cells.

Liver X receptors (LXR) and the retinoid X receptors (RXR) heterodimers directly upregulate the expression of a number of genes involved in lipid and lipoprotein homeostasis.

When the immune system is unable to eliminate substances that it perceives as foreign it attempts to wall off the nonself‐material by producing granulomas; a ball‐like structures composed of immune cells, mostly activated macrophages, that are surrounded by lymphocytes predomintantly of the T
H
1 type.
Heliobacteria
Authors: Asao Marie , Madigan Michael T 
Published: September 2010

AbstractHeliobacteria are the most recently discovered of the anoxygenic phototrophic bacteria. Heliobacteria contain bacteriochlorophyllg, a pigment unique to species of this group, and synthesise the simplest photosynthetic complexes of all known phototrophs. Also, unlike all other phototrophs, heliobacteria produce endospores but cannot grow autotrophically. Four genera of heliobacteria are known. Species ofHeliobacterium,HeliobacillusandHeliophilumgrow best at neutral pH, whereas species ofHeliorestisare alkaliphilic.Heliobacterium,HeliobacillusandHeliophilumspecies form one phylogenetic clade whereasHeliorestisspecies form a second within the phylum Firmicutes of the domain Bacteria. Heliobacteria have a unique ecology, being primarily terrestrial rather than aquatic, and some species may have evolved a mutualistic relationship with rice plants. The genome sequence of the thermophileHeliobacterium modesticaldumsupports the hypothesis that heliobacteria are minimalist phototrophs, and because of this, heliobacteria may have played a pivotal role in the evolution of phototrophic bacteria.Key Concepts:Heliobacteria are unlike all known anoxygenic phototrophic bacteria because of their unique bacteriochlorophyll, Gram‐positive phylogeny, and primarily soil habitat.Heliobacteria employ the simplest of all photosynthetic energy‐generating systems and thus their study may yield important clues to when and how photosynthesis evolved.In addition to being phototrophic, heliobacteria are strong nitrogen‐fixing bacteria and possibly associate with plants such as rice in a type of symbiotic association.
Apoptosis in Developmental Processes
Authors: Entezari Maria , Zakeri Zahra , Lockshin Richard A 
Published: September 2010

AbstractEmbryonic development and differentiation to adult form depends on orchestration of cell division and death. In embryos, programmed death sculpts form, opens lumens, separates or splits tissue layers, allows tissue layers to fuse and removes vestigial organs. Both the central nervous and immune system overproduce cells and destroy those that do not form successful synapses or produce unusable antibodies. Cell death is first seen in mammalian embryos when the blastocyst expands, but elsewhere, the first deaths are not seen before the maternal‐zygotic transition. Abnormal timing, amount or localisation of cell death leads to abnormalities or death of embryos.Several signalling pathways trigger cell death. Usually the signals activate caspases (first discovered in embryonic cell death in nematodes) and lead to apoptosis, although apoptosis is not the only form of cell death. The signalling mechanisms that control cell death in embryos are not well understood, but should be if we hope to understand normal and teratological development.Key Concepts:Cell death can be seen in both embryonic development and normal growth of adult tissue.The embryonic cell deaths are highly programmed in that they are predictable in location, time and amount. In the simplest instances, such as in nematodes, control of cell death is under direct control of a small number of genes.Most but not all of the embryonic deaths are apoptotic.Embryonic cell to sculpt the embryo and define the boundaries of tissues and organs. In the central nervous system and the immune system, overgrowth (production of excessive cells) and subsequent pruning by cell death generate the high specificity that characterises these systems.Deregulation of apoptosis can produce many embryonic abnormalities and teratologies and, later in life, produces cancers, autoimmune disease or neurodegenerative disease.There are many means to study cell death, but only a few are directly applicable to the study of cell death in embryos. Nevertheless, further study is needed to understand the signalling mechanisms that decide the death of cells in specific locations and times.Learning more about cell death in embryos will help us to understand how it is controlled in adults.
Neuroscience of Autism
Authors: Blatt Gene J 
Published: September 2010

Abstract

Autism is a pervasive developmental disorder characterised by abnormal social–emotional behaviours, repetitive or stereotyped behaviours and delayed or impaired development of language skills. Neuropathological studies have revealed that multiple brain areas are affected in the disorder including the limbic system (hippocampus, amygdala and cingulate cortex), cerebellum, brain stem (inferior olivary nucleus) and parts of the cerebral cortex. There is a decrease in the number of cerebellar Purkinje cells in many individuals with autism. The cerebellum normally functions as an error correction system for fine motor behaviours and has also been implicated in cognitive behaviours. Over the past decade, research has focused on two transmitter systems, serotonin and γ‐aminobutyric acid (GABA). It has been reported that specific types of enzymes and receptors are deficient in individuals with autism. Despite these research findings, effective pharmacotherapies have not yet been developed and treatment outcomes vary.

Key Concepts:

Autism is characterised by deficits in social–emotional behaviour, stereotyped or repetitive behaviours and delayed/impaired development of language.

Many individuals with autism have decreased numbers of cerebellar Purkinje cells.

Neuropathology findings indicate that changes in the brain begin in prenatal development and extend into the postnatal period.

Brain overgrowth occurs during the early postnatal period especially in the frontal lobe region in individuals with autism suggesting abnormal connectivity.

Consistent results from postmortem studies indicate that in the central nervous system, the inhibitory GABA neurotransmitter system is involved in the disorder.

Specific types of GABA, serotonin, acetylcholine and glutamate neurotransmitter receptors appear to be affected in the disorder.

Imaging studies have demonstrated that in some brain areas in autistic individuals, differential activation patterns within a particular structure and in laterality.

Research efforts are continuing to report interesting findings but no cure or consistent effective treatments have been found.