bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Organisation and Chromosome Architecture from Interphase to Metaphase
Authors: Bernardi Giorgio 
Published: May 2016

Abstract

It is well established that vertebrate and other eukaryotic genomes are compositionally compartmentalised into long (≥200 Kb) sequences, the isochores, that are fairly homogeneous in their basic composition, and belong to a small number of families (five in the human genome). On the other hand, recent investigations in many laboratories have led to a new vision of interphase chromatin, which basically consists of large loops (average size ∼186 Kb in the case of the human genome) and anchors held together by ‘architectural’ proteins such as CTCF (the CCCTC‐binding factor) and cohesin. A very recent analysis has revealed correlations between isochores from different families and the architectural features of chromosomes through the cell cycle. This leads to a unifying view of the genome organisation and chromosome architecture.

Key Concepts

The long‐range compositional organisation of the genome of vertebrates and of other eukaryotes (i.e. the isochore organisation) is correlated with the chromosome architecture through the cell cycle. This leads to a unifying view of genome organisation and chromosome architecture.

In spite of very extensive investigations over many years, the organization of the eukaryotic genome and the architecture of chromosomes from interphase to metaphase are two problems that are still open because of their complexity.

A combination of a large‐scale compositional analysis of vertebrate genomes and of the recent results on the architecture of interphase chromatin led to a solution of those problems.

The large‐scale compositional analysis revealed that vertebrate genomes consist of long (≥200 kilobases) fairly homogenous DNA segments, the isochores. Cross‐linking of contact regions of chromatin and sequencing (chromosome conformation captureand its variants) provided a picture of three‐dimensional interphase chromatin structure.

The long‐range compositional organization of the genome of vertebrates and of other eukaryotes (i.e., the isochore organization) was shown to be correlated with the chromosome architecture through the cell cycle.

The correlations between the isochore organization of the genome and the chromosome architecture through the cell cycle (especially the architecture of interphase chromatin structure) led to a unifying view of genome organization and chromosome architecture.
Sociobiology, Evolutionary Psychology and Genetics
Authors: Bateson Patrick 
Published: May 2016

AbstractMuch of human behaviour, including violence and those activities thought to be characteristic of each sex, has been attributed to the heritage of human evolution. These ideas have stimulated much discussion but have been criticised for playing down the interplay between the developing individual and the environment. In modern times, their clearest expression has been those in the writings of the sociobiologists and the evolutionary psychologists.Key ConceptsThe subjects of sociobiology and evolutionary psychology drew attention to the current utilities of behaviour patterns but often confused functions with the historical processes that gave rise to them and did not consider development.The concepts of instinct and innateness have caused much confusion because so many different meanings are attached to them. It is better to state what has been demonstrated or intended than perpetuate the confusion.Plasticity and robustness are often treated as opposites, but the processes that give rise to plasticity are often highly robust and robust behavior is often the product of plasticity during development.
Plant Circadian Rhythms
Authors: McWatters Harriet G , Eriksson Maria E 
Published: May 2016

Abstract

Circadian clocks are found in most eukaryotic organisms. By allowing anticipation of daily and seasonal changes, they enable coordination of metabolism and lifecycle with the natural rhythms of the environment. Plant circadian rhythms are generated by a series of interlocking feedback loops of RNA (ribonucleic acid) and protein expression that respond to environmental cycles of light and temperature. They control essential processes in the plant's development, such as the transition to flowering or growth cessation, and thus influence yield, plant growth and biomass production. Many components of the clock are conserved across a wide variety of plant species and thus research in
Arabidopsis
translates into an understanding of the clock in agricultural crops or long‐living deciduous tree species such as hybrid aspen.

Key Concepts

Circadian clocks are found in both eukaryotes and bacteria.

Circadian clocks have a free‐running periodicity of about 24 h but are normally entrained to environmental cycles of light and temperature.

Temperature compensation is a key feature of the circadian clock and thus the free‐running period length varies relatively little across the range of ambient temperature.

The clock underlies many aspects of plant metabolism and physiology because it can detect and respond to both short‐term (the day:night cycle) and long‐term (the pattern of daylength variation across a year) changes in light and temperature.

The circadian clock of plants is made up of a series of interconnected transcription‐translation feedback loops (TTFLs) governing cycles of mRNA and protein expression.

Every plant cell contains its own clock. Clocks in different cells may be entrained independently of one another, although there appears to be a hierarchy of clocks within a plant dominated by the apex.

Plants with malfunctioning clocks suffer reductions in growth.

Many of the key components of the plant clock first described in the model species
Arabidopsis thaliana
are conserved across a wide range of species including trees such as hybrid aspen.
Shoot Branching and Plant Architecture
Authors: Bennett Tom , Ward Sally P , Leyser Ottoline 
Published: May 2016

Abstract

Shoot architecture is the spatial arrangement of stems, leaves and reproductive structures in plants. A major component of shoot architecture is the formation of secondary axes of growth (branches). In flowering plants, these originate from meristems located in the axils of leaves. Once initiated, axillary meristems can produce a secondary shoot immediately, or arrest as a dormant bud, resulting in a large degree of architectural plasticity. Long‐distance hormonal signals including auxin, cytokinin and strigolactone allow the outgrowth of buds to be tightly coordinated with the physiological and nutritional status of the plant as a whole. Two major models have been proposed to explain how these hormonal signals are integrated to control shoot branching. Shoot architecture is highly varied among model species, but the core regulatory mechanisms are conserved across the flowering plant group.

Key Concepts

Shoot architecture in flowering plants is highly plastic and is produced using repeating modules (phytomers), which can vary in number and type.

Production of secondary shoots (branches) is a major component of shoot architecture in flowering plants.

Branches are produced by axillary meristems, which form in the axils of leaves.

Axillary meristem formation may occur simultaneously with leaf formation, or may be delayed until a later stage.

Once initiated, axillary meristems may immediately grow out to form a branch, or can produce a dormant axillary bud.

The activity‐dormancy switch in axillary buds is the major control point for shoot branching.

Long‐distance hormonal signals control bud outgrowth in response to environmental cues.

Two major models have been proposed to explain how these hormonal signals are integrated to control shoot branching.

Different species use the same fundamental control mechanisms to produce highly varied shoot architectures.
Lipid Rafts and Neurological Diseases
Authors: Sonnino Sandro , Grassi Sara , Prioni Simona , Ciampa Maria G , Chiricozzi Elena , Prinetti Alessandro 
Published: May 2016

Abstract

The different populations of brain cells are characterised by evident membrane polarisation with the creation of distinct morphological and functional subcompartments, whose formation, stabilisation and functions require sophisticated geometric features and a high level of lateral order, which are, at least in part, driven by the collective properties of membrane lipids. Lipid‐driven membrane organisation allows the segregation of membrane‐associated components into specific ‘lipid membrane domains’ or lipid rafts, which function as dynamic platforms for signal transduction, protein processing and membrane turnover. From this point of view, sphingolipids (SLs), polar membrane lipids present as minor components in all eukaryotic cell membranes but highly enriched in neuron and myelin membranes, play crucial roles. In fact, the metabolism of SLs is precisely regulated along the differentiation and development of neurons and oligodendrocytes, leading to the expression of peculiar cell‐specific SL patterns essential for the maintenance of the functional integrity of the nervous system, while, on the other hand, alterations in SL homeostasis, which lead to abnormal lipid raft organisation and consequent deregulation of lipid raft‐dependent events, are a common trait in diverse major brain diseases.

Key Concepts

Cellular membranes are highly organised structures with multiple and multi‐dimensional levels of order where lipid components are active players.

Membrane domains are ordered structures or regions in a biological membrane that differ from the surrounding membrane in their lipid and/or protein composition.

Lipid‐driven collective interactions are a major factor in determining the local structure of a membrane.

Among amphipatic membrane lipids, gangliosides are known to be major players in the creation of lateral order within biological membranes.

Sphingolipid metabolism is deeply altered in several neurological diseases.
Molecular Genetics of Pancreatic Endocrine Tumours
Authors: Katabathina Venkata S , Wilcoxson Robert (Dan) , Prasad Srinivasa R 
Published: May 2016

Abstract

Pancreatic tumours with neuroendocrine phenotype comprise 1–2% of all pancreatic tumours and commonly occur in a sporadic setting. Up to 10% of pancreatic neuroendocrine tumours (PNETs) may occur as part of inherited tumour‐predisposing syndromes, including multiple endocrine neoplasia type 1, von Hippel–Lindau disease, neurofibromatosis type 1, tuberous sclerosis complex and glucagon cell adenomatosis. Recent advances in genetics and pathology have allowed better understanding of the role of genetic abnormalities that underlie hereditary and sporadic PNETs. Ongoing research in this fast‐changing field has led to the discovery of mutations in key genes that determine how tumours begin, evolve and behave. Major specific tumour pathways of PNETs involve abnormalities of
MEN1
,
DAXX
/
ATRX
, and mammalian target of rapamycin (
mTOR
) pathway genes (
PTEN
,
TSC2,
and
PIK3CA
). New knowledge in the field of genetics of PNETs potentially permits development of effective diagnostic methods and targeted therapies aimed at improving prognosis and disease‐free survival rates.

Key Concepts

Hereditary and sporadic pancreatic neuroendocrine tumours (PNETs) demonstrate characteristic histo‐morphology and genetics that determine biology, treatment response and prognosis.

Tumour‐predisposing syndromes with increased risk of developing PNETs include multiple endocrine neoplasia type 1 (MEN1), von Hippel–Lindau disease (VHL), neurofibromatosis type 1 (NF1) and tuberous sclerosis complex (TSC).

Recent advances in the pathology and genetics of PNETs have unraveled the role of genetic abnormalities in tumour pathways that may lead to better diagnostic and therapeutic paradigms.

Major specific tumour pathways of PNETs involve abnormalities of
MEN1
,
DAXX
/
ATRX
, and mammalian target of rapamycin (
mTOR
) pathway genes (
PTEN
,
TSC2,
and
PIK3CA
).
VincentBrianWigglesworth (1899–1994)
Authors: Gawne Richard , Clarke Jameson 
Published: May 2016

AbstractVincent Brian Wigglesworth (1899–1994) had played a fundamental role in the creation of the modern science of insect physiology. He is best known for making some of the first significant contributions to research in insect endocrinology. Through a series of simple experiments, Wigglesworth was able to demonstrate the existence of the ‘status quo’ juvenile hormones and the molting hormone ecdysone. Later, he made advances in our understanding of the sources and functions of these hormones. HisPrinciples of Insect Physiologywas especially influential, serving as the canonical guide to research in the field for nearly 40 years.
Clovis Technology
Authors: Eren Metin I , Buchanan Briggs 
Published: May 2016

AbstractColonising hunter‐gatherer populations in North and Central America at the end of the Pleistocene utilised Clovis technology. Clovis technology is known for ‘fluted’ flaked stone points that were used to hunt prey and served as knives, but it also included the production, use and discard of a diversity of other implements made from stone, bone and other materials. Clovis technology lasted for several centuries, perhaps as long as a millennium and a half. Clovis technology shares some similarities with Siberian Paleolithic technology, which is consistent with current genetic evidence, indicating that ancestors of the people using Clovis technology originated in Asia. Clovis technology, as archaeologists generally recognise it, likely emerged piecemeal as people dispersed into the New World – some aspects of it can be tied to ancestry in Siberia, while other aspects are likely indigenous to North and Central America. Several studies have shown that Clovis technology was subjected to both micro‐ and macroevolutionary forces.Key Concepts‘Clovis technology’ is just an archaeologist's shorthand to refer to what is in actuality an inferred, fuzzy set of human–tool interactions found across North and Central America during the terminal Pleistocene.There is a diversity of Clovis tools made from stone, bone and other materials.Evidence for Clovis technology can be found across the lower 48 states of the United States, throughout southern Canada, and Central America.The ancestors of people who used Clovis technology came from Asia.What archaeologists generally recognise, and refer to, as Clovis technology likely emerged piecemeal as people from Asia dispersed into the New World.Clovis technology evolved at both the micro‐ and macroevolutionary scales.
X
‐Chromosome Dosage Compensation
Authors: He Xionglei , Zhang Jianzhi 
Published: May 2016

Abstract

The X and Y chromosomes of placental and marsupial mammals originated from a pair of autosomes. Ohno hypothesised nearly 50 years ago that the expression levels of X‐linked genes should be doubled to compensate for the degeneration of their Y‐linked homologues during sex chromosome evolution. The advent of microarray and RNA (ribonucleic acid) sequencing technologies in the past decade prompted a series of empirical tests of Ohno's hypothesis. Surprisingly, X‐chromosome dosage compensation is found to be largely absent in mammals. Studies of multiple independently evolved sex chromosome systems from a variety of species revealed a large variation in sex‐chromosome dosage compensation, ranging from absence of compensation to complete compensation, although further scrutiny is required because of the high heterogeneities in expression data acquisition and analysis methods among studies. The lack of sex chromosome dosage compensation in at least some lineages has important implications for understanding gene expression evolution and sex chromosome evolution.

Key Concepts

Ohno proposed that the expression levels of mammalian X‐linked genes should be doubled to compensate for the degeneration of their Y‐linked homologues during sex chromosome evolution.

Initial microarray studies of genome‐wide gene expression levels found an X : AA ratio of ∼1, consistent with Ohno's hypothesis.

Subsequent analysis of transcriptomic data generated by the more sensitive RNA sequencing method found an X : AA ratio of ∼0.5, inconsistent with Ohno's hypothesis.

Some argued that Ohno's hypothesis is supported because X : AA is about 1 for actively expressed genes, but this assertion is caused by a common misunderstanding of Ohno's hypothesis.

A direct comparison between human X‐linked genes and their one‐to‐one orthologues located in chicken autosomes that are homologous to the mammalian proto‐X found no upregulation in mammalian X‐linked gene expression, refuting Ohno's hypothesis.

A human proteomic analysis found no evidence for a twofold upregulation of protein concentrations of X‐linked genes.

Transcriptome analyses of multiple species with independently evolved sex chromosomes revealed a large variation in the presence/absence and degree of sex chromosome dosage compensation, but further scrutiny is required due to the high heterogeneities in the data and methods used in the published studies.

The lack of sex chromosome dosage compensation in at least some lineages suggests that halving the expression level of a gene usually has no appreciable fitness consequences.
Role of Plakins in Human Genetic Disease
Authors: Favre Bertrand , Borradori Luca 
Published: May 2016

Abstract

The mammalian plakins comprise a small family of seven large proteins: bullous pemphigoid antigen 1, desmoplakin, envoplakin, epiplakin, microtubule‐actin crosslinking factor 1, periplakin and plectin. Their main functions consist of organising the different components of the cytoskeleton, crosslinking them to each other and anchoring them to various cell–matrix and cell–cell adhesion complexes. Thereby, these cytolinkers regulate cell stiffness, adhesion, migration and polarisation in a dynamic way. They can also interact with signal transducers, serve as scaffolds for signalling complexes and modulate vesicle trafficking. Congenital or engineered mutations in human and mouse plakin genes, respectively, reveal their essential functions in tissues either subjected to mechanical stress, such as the skin, skeletal and cardiac muscle, or highly sensitive to cytoskeletal and vesicle transport disorganisation, the nervous system. The pleiotropic diseases caused by plakin mutations reflect their multiple functions that have not yet been fully elucidated.

Key Concepts

The plakins are a family of cytolinker proteins that connect the three components of the cytoskeleton, intermediate filaments (IFs), microfilaments and microtubules (MTs), to each other and to junctional complexes at the cell membrane.

The plakin family can be subdivided into three classes: (1) the canonical IF‐anchoring plakins: BPAG1e, desmoplakin, envoplakin, periplakin and plectin, (2) the atypical IF‐interacting plakin: epiplakin and (3) the MT‐binding spectraplakins: BPAG1a/b and MACF1a/b.

The plakins often have a dynamic function on the cytoskeleton organisation, can modulate cell signalling and serve as scaffolds for signal transducers.

The plakins also play a role in the positioning and function of organelles and regulate vesicular trafficking.

Mutations in plakin genes can cause pleiotropic diseases, such as skin blistering, muscular dystrophy, cardiomyopathy and autonomic neuropathy.

Despite the delimitation of plakin subdomains and the present knowledge of plakin functions, there is no obvious genotype–phenotype relationship.
Use of Citizens' Juries to Address Complex Bioethical Challenges
Authors: Iredale Rachel 
Published: May 2016

Abstract

The ethical and social principles that guide decision making in relation to the human genome are well known. However, new bioethical challenges are emerging, such as gene editing, which require wider public discussion. One way of involving the public is by a Citizens' Jury. Originating almost 50 years ago, Citizens' Juries involve ordinary members of the public in policy discussions, not in their capacity as service users or consumers, but as citizens. The first Citizens' Jury in the United Kingdom on the topic of genetics took place in Wales in 1997. Whilst the method may vary, the fundamental premise remains the same; that given enough time and support, any person is capable of arriving at an informed decision about a complex policy matter. The defining characteristics of Citizens' Juries are that they are deliberative and inclusive and have an important role to play in addressing the new bioethical challenges that society faces.

Key Concepts

Complex bioethical challenges require public participation in policy making.

A Citizens' Jury involves the public in their capacity as citizens and not as users of services, or consumers, or members of specific interest groups.

The fundamental premise upon which every Citizens' Jury is based is that ordinary members of the public, given enough time, support and resources, are capable of arriving at decisions about complex policy matters.

The defining characteristics of Citizens' Juries are that they are deliberative and inclusive and have the aim of delivering high‐quality citizen input into any decision‐making process.

The complex bioethical challenges that society will face this century, such as human gene editing, are too important not to involve the public.
Disruption of the gene C12orf35 leads to increased productivities in recombinant CHO cell lines
Authors: Ritter Anett , Rauschert Tatjana , Oertli Mevion , Piehlmaier Daniel , Mantas Panagiotis , Kuntzelmann Genevieve , Lageyre Nadine , Brannetti Barbara , Voedisch Bernd , Geisse Sabine , Jostock Thomas , Laux Holger 
Published: May 2016

ABSTRACTRecently, we reported that the loss of a telomeric region of chromosome 8 in Chinese Hamster Ovary (CHO) cells correlates with higher recombinant productivities. New cell lines lacking this region, called CHO‐C8DEL, showed several advantages during cell line generation and for the production of recombinant proteins (Ritter et al., 2016, Biotechnol Bioeng). Here, we performed knock‐down and knock‐out experiments of genes located within this telomeric region of chromosome 8 to identify the genes causing the observed phenotypes of CHO‐C8DEL cell lines. We present evidence that loss or reduced expression of the gene C12orf35 is responsible for higher productivities and shorter recovery times during selection pressure. These effects are mediated by increased levels of mRNA of the exogenes heavy chain (HC) and light chain (LC) as well as dihydrofolate reductase (DHFR) and neomycin phosphotransferase (Neo) during the stable expression of antibodies. Biotechnol. Bioeng. 2016;113: 2433–2442. © 2016 Wiley Periodicals, Inc.