bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reductionism in Biology
Authors: Darden Lindley 
Published: July 2016

Abstract

Explanatory and methodological reductionism in biology emphasises the importance of building explanations and pursuing research at ever‐deeper levels of organisation. Integrationism, in contrast, emphasises the importance of building explanations at multiple levels of organisation or utilising findings from multiple scientific fields. Some of the perceived advantages of reduction are reviewed, but it is noted that reductionist tendencies are prone to biases and distortions in the description of biological systems. Attention to integrative strategies aids in avoiding the biases and distortions that reductionist strategies are prone to produce. Integration takes different forms: integrating levels, integrating temporally extended mechanisms, and integrating findings from different fields to solve a particular problem. One should look up and around, not just down. Integration is illustrated with cases from evolutionary theory and genetics.

Key Concepts

Reductionist research strategies have advantages in biology, whereas biases that they introduce can be countered by employing integrative strategies.

Reductive research strategies reveal hidden mechanisms, but neglect their context.

Multilevel integration provides a full explanatory account of a phenomenon.

Integrative strategies bridge different levels and different scientific fields to solve scientific problems.

Integrative strategies tie together sub‐mechanisms within a temporally extended mechanism.
Genetic Carrier Testing
Authors: Henneman Lidewij , Cornel Martina 
Published: July 2016

Abstract

Genetic carrier testing includes tests for the heterozygous status of a recessively inherited disorder in individuals who, although apparently healthy themselves, have a high risk of transmitting the genetic disorder to their offspring. Carrier testing will allow couples of childbearing age to make informed reproductive decisions. Genetic carrier tests are used by people who have a family history of an inherited disorder or carriership, reproductive partners of carriers and partners of individuals who have the disorder. A prerequisite for knowledge about a possible risk for relatives and the availability of testing is the dissemination of information in the family. Carrier testing can also be offered as a screening test to persons who do not have an
a priori
increased risk of being a carrier based on their family history. With new genetic testing technologies, it is possible to screen for a growing number of disorders simultaneously.

Key Concepts

Reproductive planning is the most important factor motivating genetic carrier testing.

Family disclosure of genetic information is a prerequisite to knowledge about the risk and availability of carrier testing.

Because of factors impeding the sharing of information in families and factors interfering with the decision about testing, the uptake for carrier testing in high‐risk families is often lower than expected.

To minimize (time) constraints and maximize reproductive options, carrier testing before conception is advocated.

Carrier screening is the detection of carrier status in persons who do not have an
a priori
increased risk of being a carrier based on their or their partners' personal or family history.

Rapidly evolving genetic testing technologies facilitate carrier screening for a growing number of diseases simultaneously.
Bioethics: Institutionalisation of
Authors: Engelhardt HT , Iltis Ana Smith , Jotterand Fabrice 
Published: July 2016

Abstract

Bioethics is a recognised discipline in the academy, an established practice within the clinic and a source of guidance for healthcare policy and the conduct of human research. As a complex of theoretical and practical undertakings, bioethics now commands an officially recognised cluster of norm‐setting and behaviour‐guiding roles that have become institutionalised elements of the scholarly, clinical, human research and public policy establishment. The integration of the antecedents of bioethics into these settings began in the 1960s but these activities were recognised under this name only at the end of the 1970s. By 1979, there was an established literature, numerous individuals who called themselves bioethicists and academic programmes engaged in bioethics. Efforts to professionalise bioethics by articulating a code of ethics and establishing practice standards are ongoing. Competing conceptions of expertise shape these efforts. Attention to bioethics internationally continues to grow, particularly as biotechnological developments raise new questions and concerns.

Key Concepts

The antecedents of bioethics emerged in the 1960s, and then the field took shape under this rubric in the 1970s.

Awareness of past abuses of human research subjects and the need to conduct more research to secure progress in medicine led to a focus on research ethics and the regulation and oversight of research.

Cultural shifts in the 1960s and 1970s that emphasised individuals' rights led to discussions about patients' rights and patient‐driven decisions.

The secularisation of U.S. society in the 1960s created space for discussions of medical morality among secular scholars who sought a secular source for moral guidance.

Bioethicists provide clinical and research ethics consultations, teach and conduct research in the academy and are involved in the creation of public policy.

Efforts to professionalise bioethics are ongoing.

Bioethics continues to seek substantive moral insight from secular sources.
Nutrigenetics
Authors: Savini Isabella , Gasperi Valeria , Catani Valeria M 
Published: July 2016

Abstract

In the past decades, extensive usage of omic technologies applied to nutrition has led to the concept of personalised dietary recommendations. It is now widely accepted that gene–diet interaction is a complex, bidirectional mechanism: food components can modulate the flow of genetic information by regulating genes at transcriptional, translational and post‐translational levels, whereas the individual's genotype determines specific responses to nutrient intake. Genetic variants (that represent the focus of nutrigenetic studies) influence the metabolism of almost all macro‐ and micronutrients, thus differentially impacting on human health. Although still a young field of research, nutrigenetics appears to be a promising tool for monitoring susceptibility to chronic pathologies, as well as for designing personalised nutrition in order to prevent (or eventually treat) the most common Western diet‐associated diseases.

Key Concepts

Several lines of evidence indicate that diet is a key determinant of health status and that many chronic degenerative diseases (including obesity, diabetes, cardiovascular disease, cancer, neurodegenerative diseases) could be prevented by adopting a correct lifestyle.

Nutrigenetic studies indicate that there is a different susceptibility to development of these diseases in relation to food intake, due to specific genetic variants.

Nutrigenomic studies indicate that macronutrients, micronutrients and bioactive compounds can modulate gene expression, thus affecting physical and mental health.

Gene–diet interaction is a complex network; and data interpretation is not easy, as foods contain many components usually acting in combination and dietary patterns are quite variable.

It is not easy to translate scientific evidence into nutritional advice, because the organism is complex and different environmental and genetic factors have to be taken into account, especially considering the wide interindividual variability in metabolic responses.

Although holding strong promise, personalised nutrition is far from being applicable, as much accurate research is needed before application to dietetic practice.
Plant Actin Biology
Authors: Deeks Michael J , Hussey Patrick J 
Published: July 2016

Abstract

Actin is a major component of the plant cytoskeleton. Filamentous actin (F‐actin) contributes to the maintenance of the internal architecture of the cell, drives cytoplasmic streaming (the movement of components around the cytosol) and contributes to the process of cell division. The biochemistry of plant actin has many similarities to that of yeast and animals, but has developed its own strategies and molecular machinery to organise actin filaments. F‐actin provides tracks for myosin molecular motors to transport organelles at high velocities, and actin is required for specific stages of vesicle trafficking that underpin cell growth and development. The means by which plant cells control the nucleation of new actin filaments from G‐actin have diverged considerably from yeast and metazoans. The unique aspects of the plant actin cytoskeleton are likely to have arisen from a combination of the environmental challenges to a sessile multicellular existence and an ancient diversification from the ancestors of the Opisthokonta and Amoebozoa model organisms from which the majority of eukaryote cytoskeletal paradigms have been established.

Key Concepts

The basic principles of actin biochemistry applicable to animals, fungi and protists are conserved in plants but there are a number of specific modifications as plants do not possess the full complement of animal actin‐binding proteins.

Actin filaments in plants have to fulfil unique functions. Actin focuses on the expansion of tip growing cells, maintains cytoarchitecture and responds to the environment (e.g. polarising in response to pathogen stimulation). During cell division actin filaments participate in all major plant‐specific arrays.

A stationary cell is NOT a physically inactive cell. Actin cables are exploited for organelle transport. Actin‐based transport tends to dominate over microtubule‐based movement. Plants utilise the fastest known type V myosin (known in plants as type XI) within the eukaryote kingdom. Polymerisation dynamics are thought to add to trafficking capabilities as low levels of antiactin drugs disrupt vesicle delivery and fusion during cell growth yet preserve myosin‐mediated transport.

Plant‐specific proteins and novel domain combinations have become established in plants to regulate the actin cytoskeleton in accordance with the demands of sessile multicellular photosynthetic autotrophy. These cytoskeletal adaptations to sedentary life within a cell wall are distinct from fungi, possibly reflecting the ancient diversification between the opisthokonts and plants.
Molecular Genetics of Macular Degeneration
Authors: Cooke Bailey Jessica N , Haines Jonathan L 
Published: July 2016

Abstract

Age‐related macular degeneration (AMD) is a complex disease; the presentation and progression of this disease are varied among patients as are risk factors. Genetics substantially influences risk for this disease, and the pursuit of localising genetic risk factors for AMD has been quite successful over the past decade through the application of increasingly sophisticated genomic techniques. To date, researchers have rigorously applied statistical genetic methods to reveal more than 30 genetic loci associated with AMD. Connecting these loci to functional impact on disease aetiology has proved challenging, and a great deal of knowledge remains to be elucidated about this disease in order to understand the molecular mechanisms by which loci influence AMD. We herein review the history of AMD genetics and the currently known AMD genetics loci.

Key Concepts

Age‐related macular degeneration is a major cause of blindness worldwide.

Age‐related macular degeneration is a complex phenotype.

Risk for age‐related macular degeneration is substantially influenced by genetic factors.

The
CFH
and
ARMS2
/
HTRA1
loci are the most predictive genetic indicators of age‐related macular degeneration risk.

Statistical genetic analyses have revealed more than 30 genetic loci that influence risk for age‐related macular degeneration.
Counselling Issues around Preimplantation Genetic Diagnosis
Authors: Ross Sarah 
Published: July 2016

Abstract

Preimplantation genetic diagnosis (PGD) is a highly specialised process that uses assisted reproductive techniques to help couples increase their chances of having a child that is unaffected by a serious known genetic disorder. It requires a multidisciplinary team of professionals including specialists in both assisted reproduction and genetics.
Before a decision by a couple to undergo PGD treatment, the counsellor needs to assess their situation, discuss their genetic risk and the process of PGD including the advantages and disadvantages, while taking into account the emotional, practical and financial issues. This should enable the couple to make an informed decision about whether PGD is the most appropriate treatment for them. Counselling opportunities arise during and after a treatment cycle ensuring that couples are supported and fully aware of the implications of decisions that need to be made at each stage of the process.

Key Concepts

Preimplantation genetic diagnosis uses assisted reproductive techniques to obtain embryos that are then tested for a known serious genetic condition, before transfer to the uterus.

Assisted reproductive techniques used in PGD involve artificially stimulating the ovaries to release large numbers of eggs, which are collected and then fertilised using
in vitro
fertilisation (IVF) or in most cases, intracytoplasmic sperm insertion (ICSI).

Genetic counselling is a communication process that focuses on the occurrence or risk of a genetic disorder in the family.

FISH analysis – fluorescent in situ hybridisation is a cytogenetic technique used to detect and localise the presence or absence of specific DNA sequences on chromosomes. It uses fluorescent probes that bind to parts of the chromosome that show a high degree of sequence similarity.

Preimplantation genetic haplotyping (PGH) involves taking a single cell and extracting DNA, which is then amplified before being used for DNA fingerprinting. PGH can be used where the exact mutation is not known or cannot be identified, as long as the correct gene is identified, because the technique scans for the presence of the genetic haplotype that is associated with the familial disease gene region.

Array CGH (comparative genomic hybridisation) is a laboratory technique used to look for alterations in chromosomes that are too small to see down a microscope.
Plant Virus
RNA
Replication
Authors: Carbonell Alberto , García Juan Antonio , Simón‐Mateo Carmen , Hernández Carmen 
Published: July 2016

Abstract

Plant RNA (ribonucleic acid) viruses are obligate intracellular parasites with single‐stranded (ss) or double‐stranded RNA genome(s) generally encapsidated but rarely enveloped. For viruses with ssRNA genomes, the polarity of the infectious RNA (positive or negative) and the presence of one or more genomic RNA segments are the features that mostly determine the molecular mechanisms governing the replication process. RNA viruses cannot penetrate plant cell walls unaided and must enter the cellular cytoplasm through mechanically induced wounds or assisted by a biological vector. After desencapsidation, their genome remains in the cytoplasm where it is translated, replicated and encapsidated in a coupled manner. Replication occurs in large viral replication complexes (VRCs), tethered to modified membranes of cellular organelles and composed by the viral RNA templates and by viral and host proteins. Cis‐acting elements located in viral RNA templates regulate the recognition by the virus‐encoded RNA‐dependent RNA polymerase and possibly contribute to VRC assembly and/or activation.

Key Concepts

The vast majority of plant RNA viruses have positive (mRNA sense) single‐stranded RNA genome.

Some plant RNA viruses have negative single‐stranded, or double‐stranded RNA genome.

Replication is at the core of the infection cycle of plant RNA viruses and occurs solely through RNA intermediates of positive and negative polarities.

Replication of most plant RNA viruses takes place in viral replication complexes tethered to modified membranes of cytoplasmic organelles.

Viral replication complexes are dynamic and contain the viral RNA, viral replication proteins and proteins from the host.

A viral‐RNA‐dependent RNA polymerase is responsible for the synthesis of new genomic RNA using parental genome as template.

Viral proteins and co‐opted host factors orchestrate the targeting of the genomic RNA to the membranes where replication takes place; they also contribute to the remodelling of the membranes that are used as scaffolds for tethering the viral replication complexes.

In addition to the role of co‐opted host factors in controlling the biogenesis of replication organelles and the composition, assembly and/or activity of the viral replication complex, they can post‐translationally modify viral proteins to regulate replication.

Primary sequence and structure elements of viral RNAs regulate template selection, initiation of the synthesis of complementary RNA strands and the assembly and activation of viral replication complexes.
SWI
/
SNF
Chromatin Remodelling and Human Cancer
Authors: Reisman David , Thompson Kenneth , Marquez‐Vilendrer Stefanie , Lu Li 
Published: July 2016

Abstract

Brahma (BRM) and Brahma‐related gene 1 (BRG1) are two mutually exclusively catalytic subunits of the switch in mating type/sucrose nonfermenting complex. These two key anticancer proteins are frequently targeted and silenced during cancer development. The anticancer function of BRM can be abrogated when it becomes acetylated or when it is epigenetically silenced. Central to BRM silencing is the presence of two inherited insertional polymorphisms within the BRM promoter that are statistically linked to cancer risk. Both BRM acetylation and silencing can be reversed by a number of compound families and might be important to how flavonoids and NSAIDS inhibit cancer. While BRG1 is very frequently mutated in most human cancers, it is more commonly inactivated by aberrant splicing and by an AKT‐pathway‐mediated‐translation block. While BRG1 and BRM are tied to deoxyribonucleic acid repair, growth control, differentiation, development, as well as epithelial–mesenchymal transition and are estimated to regulate 4–8% of the human genome, the inactivation of either protein is only modestly tumourigenic. This occurs in part because BRG1 and BRM are functionally redundant, which blunts the tumourigenic effect when only one gene is aberrantly silenced. Further insights into the mechanisms that regulate these genes may lead to novel therapeutic strategies that may reverse the silencing of these two important anticancer genes.

Key Concepts

Reversal of the epigenetic silencing of a gene may serve as a basis for drug therapy.

Anticancer genes are epigenetically regulated by insertional polymorphisms.

The functional redundancy of BRG1 and BRM thwarts cancer development.

Post‐translational modification of BRM and BRG1 alters the cellular roles of these proteins from growth inhibitors to growth promoters.

The loss of cofactors (i.e. BRG1 and/or BRM) for RB‐mediated‐growth inhibition could preclude the function of CDK inhibitors used clinically.

Specific SWI/SNF subunits are commonly mutated and inactivated in specific cancer types.

Diminished SWI/SNF activity, but not the complete abrogation of function, is tumourigenic.
Evolutionary History of Polar and Brown Bears
Authors: Hailer Frank , Welch Andreanna J 
Published: July 2016

Abstract

Taxonomists have long recognised polar and brown bears as separate species with distinct ecological niches and largely nonoverlapping ranges. Surprisingly, phylogenetic studies of maternally inherited mitochondrial DNA (mtDNA) found polar bears nested within brown bears, with an estimated divergence time of <170 000 years. This indicated an unusually rapid speciation and adaptation of polar bears. However, several recent studies of autosomal and Y‐chromosomal DNA have revisited these findings, giving independent perspectives of bear evolutionary history. Results show that polar bears cluster separately from brown bears, and divergence time estimates are older than those based on mtDNA, ranging from >300 000 to 4–5 million years. These studies confirm uniqueness of the polar bear lineage, provide more time for speciation and adaptation, and have uncovered numerous candidate genes for evolutionary adaptations. Several instances of introgressive hybridisation between polar and brown bears have been inferred, revealing trans‐species transmission of mtDNA and some nuclear loci.

Key Concepts

DNA sequences in conjunction with a calibration of the mutation rate (e.g. inclusion of a previously estimated mutation rate, geological information or inclusion of a radiocarbon‐dated ancient sample) can be used to estimate the timing of speciation between species.

Differentially inherited loci can reveal different aspects of evolutionary history.

The genome of polar bears contains a wealth of alleles that are not found in brown bears, and vice versa.

Polar bears have passed through bottlenecks during their evolutionary history, leaving them much less genetically variable than brown bears.

When analysing DNA sequences that have passed through the species boundary due to introgressive hybridisation, studies will obtain information about the hybridisation event rather than the (earlier) speciation event.

Brown bears have acted as vectors for polar bear alleles, transporting introgressed genetic material far beyond the species' contact zones.

Incomplete lineage sorting (see ‘Glossary’) complicates phylogenetic inferences among rapidly and/or recently diverged taxa. Lineage sorting takes on average four N
e
generations, which for many taxa can span at least several hundred thousand years (N
e
being the effective population size). The time needed for lineages to be reciprocally monophyletic can therefore take very long, even under complete reproductive isolation.

Molecular studies have found signals of positive selection in polar bear genes that are involved in fat metabolism, energy production and cardiovascular function. These genes are exciting candidates that may help us better understand the genetic basis of polar bear adaptations to Arctic conditions.