bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lymphocyte Development
Authors: Zhang Yu 
Published: April 2010

Abstract

Like haematopoietic cells of other lineages, both B and T lymphocytes arise from haematopoietic stem cells. Although B‐cell development takes place in the bone marrow, T cells are generated in the thymus. With the support of specialised micro‐environmental milieus, the progenitors unfold intrinsic genetic programs and progress through multiple intermediate stages to develop into antigen‐responsive lymphocytes. A constant theme during this process is lineage diversification. The role of several critical factors has been revealed in recent years, including that of transcription factor
Pax5
(paired box 5) and
Notch1
signal in B‐ and T‐lineage specification and commitment. In addition, lymphoid development is characterised by somatic recombination of the genes encoding antigen receptors. Such a process ensures the generation of an extremely diversified repertoire of antigen receptors. This newly generated repertoire is then subjected to strict selection before being added to the peripheral pool of mature lymphocytes.

Key Concepts:

The differentiation from haematopoietic stem cells to antigen‐responsive mature lymphocytes is accompanied by sequential changes in gene expression and orderly rearrangements of the genes encoding antigen receptors.

Division of the lymphoid developmental pathways into multiple stages provides a useful framework to dissect the cellular and molecular mechanisms of cell differentiation. But it should be recognised that the transition from one stage to the next is not necessarily as sharp as implied in the diagram.

Lineage specification and commitment is a protracted process, during which cells destined for one lineage does not lose potentials for alternative lineages until relatively late. It is always important to distinguish potential from predominant cell fate.

Cells at different developmental stages are associated with specialised micro‐environmental niches, and migration in and out of these niches is essential for the orderly progression of differentiation.

The micro‐environmental milieus either determine the fate to be adopted by a progenitor or provide signals to allow cell‐intrinsic developmental programs to progress.

Lymphocyte development is an expensive process for the host as the majority of the developing cells die by apoptosis as the result of selection against cells with nonproductively rearranged antigen receptor genes, cells incapable of recognising self‐MHC, or cells reactive to self‐antigens.

The quantitative differences in signal strength have a remarkable impact on fate choice by developing lymphocytes, such as positive‐versus‐negative selection, αβ‐versus‐γδ‐lineage diversification, CD4‐versus‐CD8‐lineage decision and Treg cell development.
Proteins: Fundamental Chemical Properties
Authors: Cozzone Alain J 
Published: April 2010

Abstract

Proteins are the most abundant class of biological macromolecules as they represent over 50% of the dry weight of cells. They are involved in virtually all chemical reactions and processes occurring in life forms as well as in the mechanical support and filamentous architecture within and between cells. Irrespective of their functional or structural role, they all are formed from the same 20 building blocks, called amino acids, which are joined end‐to‐end through covalent linkages termed peptide bonds.
The size, ionisation properties and hydrophobicity/hydrophilicity of the constituent amino acids influence the solubility, stability and structural organisation of proteins that exist essentially in either aqueous or membrane environments.
The amino acid sequences (primary structures) determine the higher structural levels (secondary and tertiary) of proteins and specify their biological properties.

Key Concepts:

Proteins occupy a prominent position in all biological systems, both quantitatively and qualitatively.

Irrespective of their structural or functional role, all proteins are built from the same fundamental blocks, the amino acids.

The physico‐chemical properties of the constituent amino acids determine the structure and biological function of proteins.
Plant Organ Primordia
Authors: Kidner Catherine A 
Published: April 2010

Abstract

Plants are made up of the shoot axis, the root axis and the organs produced by each including leaves, petals, some tendrils, some thorns and lateral roots. These organs are produced throughout the lifespan of the plant, their production involves changes in cell fate, delineating boundaries, patterning the new organ and controlling its outgrowth. Shoot organs are formed in a regular pattern on the flanks of the shoot apical meristem. They lose the indeterminacy of meristem cells. Signals from the meristem pattern the organ, establishing an upper (adaxial) and a lower (abaxial) side. Organs of the root are produced from nonmeristematic cells the peri‐cycle cells which surround the vasculature. If these cells receive the correct signal they start to divide and produce a new indeterminate meristem. This meristem activates as it breaks through the primary root tissues.

Key Concepts:

Plant organs form throughout the lifespan of the plant.

Shoot organs include leaves, floral organs and some tendrils or thorns.

Shoot organs form on the flanks of the shoot apical meristem.

Root organs include lateral roots and nodules.

Root organs form by the dedifferentiation of pericycle cells and activation of new meristems.

Auxin plays a key role in the origin of new organs.

Patterning of organs occurs early in their development.
Lateral/Secondary Roots
Authors: Guyomarc'h Soazig , Lucas Mikaël , Laplaze Laurent 
Published: April 2010

Abstract

The plant root system is made of an elongating primary root of embryonic origin as well as multiple lateral or secondary roots initiated post‐embryonically. Initiation, organisation and emergence/elongation of lateral roots are tightly regulated by local and global, as well as endogenous and environmental factors, resulting in the adaptation of the whole root system to its functions. The plant hormone
auxin
is a key player in lateral root initiation, development and elongation. Yet, complex interactions with other hormones such as cytokinins, ethylene, brassinosteroids or abscisic acid (ABA) are also involved. Transcription factors and other proteins of unknown function have been identified in the signalling cascades regulating lateral root formation in response to endogenous or environmental cues. Progresses in understanding the multiple regulations of lateral root formation open new possibilities to use these strategies for plant adaptation to abiotic stresses such as drought or nutrient deprivation.

Key Concepts:

The regulation of lateral root formation influences the overall architecture of the root system and its adaptation to various constraints.

The commitment of pericycle cells to become lateral root founder cells is the first step of formation of secondary roots and determines their positioning.
Positional Information in Plant Development
Authors: Pallakies Helge , Simon Rüdiger 
Published: April 2010

Abstract

Tissue patterning during organogenesis in plants is based on precise cell fate determination of undifferentiated cells, which are derived from stem cells that reside in meristems. Cell fate determination has been shown to be largely dependent on the position of the differentiating cell in the plant body, and not on the lineage. A number of mechanisms were identified that provide positional information to cells or cell populations. Plant hormones like
auxin
establish gradients or local concentration maxima; cell–cell signalling enables communication between adjacent cell layers via secreted ligands and membrane‐associated receptors; transcription factors can act noncellautonomously and integrate cell behaviour, and long range signals can be transported between cells through plasmodesmata. In addition, the cell wall itself may trigger position‐dependent differentiation. In most developmental processes, a variety of information from different sources acts on the same cell to control cell fate decisions.

Key Concepts:

Cell fate determination depends on the position of a cell within the plant, not on its clonal origin.

A cell gains positional information from a combination of sources in a constant process until differentiation.
Plant Cuticle
Authors: Kerstiens Gerhard 
Published: April 2010

Abstract

Plant cuticles are protective lipophilic membranes that cover leaves and many stems and fruits. They consist of a polymer matrix that is covered with epicuticular waxes and incorporates intracuticular waxes. Together, these constituents provide a good but imperfect barrier against the loss of water and solutes and ingression by pests and pathogens. The thickness, structure and chemical composition of cuticular matrices and epicuticular and intracuticular waxes vary very widely, and the potential functional consequences of such differences are poorly understood. Transport across the cuticle can occur by random diffusion within the lipophilic network (relevant for lipophilic and moderately polar substances) or along clusters of water molecules that form a continuous hydrophilic phase reaching across the membrane (relevant for polar and ionic substances).

Key concepts:

All leaves and nonwoody stems are covered by a protective and resilient membrane called the cuticle.

Its permeability is low but it can accumulate lipophilic xenobiotics. Thicker or waxier cuticles are generally not less permeable than thinner or less wax‐rich ones.

The
trans
‐cuticular diffusion paths for ions and lipophilic compounds are different.
Centrosomes: Methods for Preparation
Authors: Habermann Karin , Lange Bodo MH 
Published: April 2010

Abstract

The centrosome of higher eukaryotic cells is the main microtubule‐organising centre. To understand the molecular mechanisms underlying this organelle's biogenesis and important functions in several cellular processes, such as microtubule nucleation, cell division and stress response, it was critical to develop methods for isolating biochemically meaningful quantities of centrosomes. Centrosomes have been isolated from a variety of organisms and based on these preparations, numerous aspects of this intriguing organelle's morphological, functional and biochemical properties have been uncovered. Better isolation procedures along with the development of new technologies, like RNAi (
ribonucleic acid
interference) and the increasing accuracy of mass spectrometry and electron microscopy techniques, have profoundly improved our knowledge of the centrosome, leading to a better understanding of its implications in various cellular processes and in diseases.

Key concepts

Cultured animal cells, animal tissue, Drosophila embryos, green algae, budding yeast, fungi and surf clams are suitable starting materials for centrosome isolation.

Centrosome isolation from animal cells requires cell lysis in low ionic strength buffers.

Enrichment of centrosomes is achieved by density centrifugation in sucrose step gradients.

Immunoaffinity purification has been employed to further enrich centrosomes from Drosophila embryos.

Isolated centrosomes are competent to nucleate microtubules.

The analysis of isolated centrosomes has provided a wealth of information on their biochemical composition and novel structural and functional features.

Many centrosome components have been identified by applying mass spectrometry and antibody approaches.

RNAi has been used to study centrosome functions in cellular signalling pathways and the cell cycle and to identify novel components.

Electron tomography will be an informative tool to study the supramolecular structures of isolated centrosomes.
Proline Residues in Proteins
Authors: Deber Charles M , Brodsky Barbara , Rath Arianna 
Published: April 2010

AbstractAs the only commonly occurring imino acid in proteins, proline has been found to play unique structural and dynamic roles in guiding protein folding, fibre formation and protein–protein interactions. The cyclic pyrrolidine side‐chain fixes the backbone dihedral ϕ angle and renders proline unable to act as a hydrogen bond donor. These properties are reflected in its preference for protein secondary structure elements such as turns and polyproline II helices, and its generally destabilizing effect on α helix and β‐strand conformation. The ability of proline to undergocis‐transisomerization is important in protein folding and forms the basis of molecular switches that help to control cellular growth and regulation. Proline and its posttranslationally modified analogue, hydroxyproline, are additionally the major components of collagens, proteins that are the major fibrous proteins in animals and account for approximately 30% of total human body protein.Key Concepts:The structural and dynamic properties imparted to proteins by the amino acid proline arise from the unique cyclic structure of its side‐chain.Interconversion of proline fromcistotransconformation, which can be facilitated by peptidylprolyl isomerases, is a rate‐limiting step in protein folding and can act as a molecular switch in the regulation of cellular growth and signalling.Proline residues facilitate the formation of protein secondary structure elements such as turns and the polyproline II helix, but typically disfavour α helix and β‐strand conformations.Proline and its posttranslationally modified analogue hydroxyproline are key components of the structural protein collagen.Regions of water‐soluble proteins rich in proline residues are often sites of protein–protein interaction.
Polymerase Chain Reaction (PCR): Specialised Reactions
Authors: Tsirka Stella E , Frohman Michael A 
Published: April 2010

AbstractThe polymerase chain reaction (PCR) is a technique that rapidly amplifies selected subsets of DNA (deoxyribonucleic acid) or complementary DNA (cDNA) from initially complex biological mixtures. The efficiency of amplification or sequence of the amplified material can then be examined for any of many purposes, including genotyping or the characterisation of new genes, gene expression patterns, mutations or polymorphisms. Quantitative‐PCR (QT‐PCR) has become practical and popular over the past decade with the generation of libraries of individual primer sets and arrayed sets of primers by commercial entities. QT‐PCR machines can assay up to 384 samples at once, permitting the complete analysis of expression of families of genes, such as signalling kinases or cytokines, in a single experiment. RACE (rapid amplification of cDNA ends)‐PCR has also become popular to identify microRNAs (ribonucleic acid). PCR is highly useful in structural biology to rapidly modify the boundaries of protein domains intended for crystallisation.Key Concepts:PCR can be conducted on vanishingly small amounts of material.PCR can be used for rapid genotyping or sequencing.PCR is useful for quantitative analysis of gene expression of entire gene families or signalling networks in arrayed assays.PCR is frequently the method of choice for genetic engineering involving mutations, truncations or extensions of existing genes.
Physcomitrella patens
: A Model Bryophyte
Authors: Knight Celia D , Perroud Pierre‐François 
Published: April 2010

Abstract

Physcomitrella patens

is a species of moss that has been studied experimentally for over half a century. The techniques that have been developed for the study of this model organism allow us to answer biological questions relating to plant growth and development, adaptation to environments and plant evolution. The recent completion of the

P. patens

genome sequence as the first non‐angiosperm land plant allows comparative genomic analyses and identification of conserved genes as well as genes with novel functions.

P. patens

has a special feature among plants, that of an efficient gene‐targeting mechanism, enabling gene functions to be identified by targeted mutations. Such comparative and experimental approaches allowed the determination of similarities and differences between mosses and angiosperms in their response to light and hormones. Finally, we may be able to learn how plants deal with environmental stresses by studying these processes in

P. patens

.

Key concepts:

P. patens
is a model organism because it can be studied simply within a controlled environment to address biological questions.

P. patens
is easy to culture
in vitro
because the cells are totipotent.

P. patens
undergoes highly efficient gene targeting that allows
in vivo
analysis of a gene's function by mutating the endogenous gene after introduction of a cloned homologue.

It is easy to identify mutant phenotypes in
P. patens
because the gametophytic cells are haploid.

P. patens
is the first nonangiosperm land plant to have its genome sequence published.

Genomic comparisons and other studies suggest that there are many similarities in the ways in which mosses and angiosperms use environmental cues to develop, indicating conserved evolution; however, mosses also possess some unique sequences which might present novel gene functions.
Insurance and Genetic Information
Authors: Bombard Yvonne , Lemmens Trudo 
Published: April 2010

Abstract

With the accelerating pace of genetic technology comes increased opportunity for individuals to obtain additional risk estimates about their susceptibilities to disease. Insurers argue that they need to have access to any information that predicts disease risk because the amount that policyholders pay for insurance coverage is determined by assessing their level of risk. Without access to genetic information, insurers are concerned that individuals may purchase more insurance at unadjusted premiums, which may lead to the collapse of the market. However, people are reluctant to share genetic test results with insurers due to the potential risk of insurance discrimination. As genetic testing becomes more prevalent, there are concerns that sections of the population will be denied insurance because of their genetic profiles. The question of what governments should do about this is one that has been debated in many countries.

Key concept:

Despite the public's fear of insurance discrimination, insurers argue that genetic health information should be shared with them to enable underwriters to make an accurate assessment of the risk.
Glycosyltransferases of Small Molecules: Their Roles in Plant Biology
Authors: Bowles Dianna , Lim Eng‐Kiat 
Published: April 2010

Abstract

Glycosyltransferases
are enzymes that transfer sugars from nucleotide sugars to a wide range of small molecule acceptors, from hormones and secondary metabolites to biotic and abiotic chemicals. This alters the hydrophilicity of the acceptors, their stability and chemical properties, their subcellular localization and often their bioactivity.
Glycosyltransferases
form a large multigene family in the plant kingdom and can be identified by a signature motif in their primary sequence. Considerable progress has been made in understanding the biochemistry of
glycosyltransferases
and the role of these enzymes in the plant. This article outlines our current knowledge of these enzymes, drawing on information gained from recent

in vitro

and

in planta

studies.

Key concepts:

There is a class of glycosyltransferases (GTs) that transfers sugars to small molecule acceptors.

In plants, these acceptors can be natural products such as hormones and secondary metabolites, as well as nonnatural products, such as herbicides and pesticides.

Glycosylation changes the properties of the acceptors, increasing water solubility and leading to transport of glycosides from the cytosol.

Glycosylation can also affect activity of the acceptors, both in the plant, such as inactivation of hormones and in industrial applications, such as bioactivity and bioavailability.
Genome Analysis of the Platypus
Authors: Wong Emily SW , Lillie Mette , Belov Katherine 
Published: April 2010

Abstract

The sequencing of the platypus genome represents a significant milestone in the study of mammalian evolution. The platypus is an egg‐laying mammal, a member of the order Monotremata, the most divergent mammalian clade. It is the first monotreme to have its genome sequenced. Its unique evolutionary position, as an offshoot between the early divergence of birds and the later emergence of therian (eutherian and marsupials) mammals, provides an unrivalled opportunity to understand the evolution of all mammals. Much like the physical characteristics of the platypus, the platypus genome shows traces of an amalgamation of mammalian and reptilian traits. Key findings to emerge from the genome project include the complex evolution of mammalian sex chromosomes, the transition from egg‐laying to live birth in mammals, and the evolution of immune genes and venom molecules in this unique species.

Key concepts:

The platypus genome is the first monotreme genome to be sequenced. The platypus's unique evolutionary position, as an offshoot between the early divergence of birds and the later emergence of therian (eutherian and marsupials) mammals, provides an opportunity to increase our understanding of the evolution of all mammals.

The platypus genome shows features of mammalian and reptilian traits.

The platypus has 10 sex chromosomes, some of which have homology to chicken Z. The mechanism used by platypuses to determine sex is not known.

The density of interspersed repeat elements in the platypus genome is greater than that seen in any other vertebrate genome.

The platypus genome contains a high G+C content (45.4%).

The platypus possesses a unique class of over 40 000 noncoding RNA known as snoRTE.

The platypus contains the largest repertoire of V1R vomeronasal receptors seen in any vertebrate.

The platypus genome contains the major egg yolk protein, vitellogenin.

Key mammalian milk genes, caseins, are present in the platypus.

The platypus genome contains an expansion of antimicrobial peptide genes.

Platypus venom molecules evolved independently to snake venom molecules.
Aneurysms:
CNS
Authors: Rubin Mark N , Lanzino Giuseppe , Rabinstein Alejandro 
Published: April 2010

Abstract

Intracranial aneurysms are a source of clinical concern because their rupture can cause subarachnoid haemorrhage, which is associated with high risk of death and disability. The prevalence of intracranial aneurysms has been difficult to assess but is estimated to be roughly 2% of the general population in North America. The size of an intracranial aneurysm is the greatest predictor of rupture. Other predictors of rupture include a prior history of subarachnoid haemorrhage and the location of the aneurysm. The majority of intracranial aneurysms discovered incidentally in the general population are smaller than 10 mm in diameter and pose little risk of rupture. Aneurysms requiring treatment can be treated with surgical clipping or endovascular coil embolisation. A large randomised study has shown that the functional outcome at 1 year is better after endovascular coiling than with surgical clipping in patients suitable for either therapy.

Key concepts:

Intracranial aneurysms occur in an estimated 2% of the North American general population.

Rupture of an intracranial aneurysm leads to a devastating type of stroke called subarachnoid haemorrhage.

Size of an intracranial aneurysm is the greatest predictor of rupture.

More than 90% of unruptured aneurysms are less than 10 mm in diameter and have a low yearly risk of rupture.

Intracranial aneurysms at risk for rupture can be treated with surgical clipping or endovascular embolisation.

Ruptured aneurysms require prompt treatment to prevent a catastrophic recurrent haemorrhage.