bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yeast Artificial Chromosomes
Authors: Arnak Remigiusz , Bruschi Carlo V , Tosato Valentina 
Published: April 2013

AbstractYeast artificial chromosomes (YACs) are shuttle‐vectors that can be amplified in bacteria and employed for the cloning and manipulation of largedeoxyribonucleic acid (DNA)inserts (up to 3 Mb pairs) in the yeastSaccharomyces cerevisiae. Artificial chromosomes can be conveniently built and modified in yeast cells usingin vivohomologous recombination, a novel process known as ‘recombineering’. The capacity of YACs to accommodate large DNA fragments is exploited to clone clusters of genes surrounded by their native DNA context, where regulatory elements are located. This is important for biotechnology, when YACs are used for engineering genetic determinants of new biochemical pathways for production of secondary metabolites and for heterologous protein expression. YACs can be retrofitted with the appropriate selectable markers and transmitted to cells of different organisms allowing the generation of transgenic animals. Finally, YACs are largely employed in the production of full‐scale genomic libraries, for mapping and functional analysis purposes.Key Concepts:Yeast artificial chromosomes (YACs) represent the top instruments for the study of eukaryotic genomes and for mobilisation of large genetic elements among bacteria and eukaryotes.YACs behave like naturally existing chromosomes, provided that they are of the proper size, showing comparable stability.YACs can be manipulated directly by classical genetic engineering as well as by modern recombineering technology.Properly retrofitted, YACs can be used in many different organisms, for cloning or genome analysis.Chromosomal translocation can be studied using disposable YACs that do not harbour genetic information essential for cell function.
Archaeal Membrane Lipids and Applications
Authors: Sprott G Dennis 
Published: April 2013

AbstractMembrane lipids ofArchaeaare unique and distinct from those found inEukaryaandBacteria. The polar lipids consist of isoprenoid chains, 20–40 carbons in length and usually saturated, which are attachedviastable ether bonds to the glycerol carbons at thesn‐2,3 positions. Polar head groups differ at the genus level of diversity and consist of mixtures of glyco groups (mainly disaccharides), and/or phospho groups primarily phosphoglycerol, phosphoserine, phosphoethanolamine or phosphoinositol. Phosphocholine headgroups are rarely found. Extremely halophilic archaea are characterised by headgroups consisting of phosphoglycerolphosphate‐O‐methyl, and sulfated‐sugars. Some of these archaea synthesise cardiolipin analogues. The inherent stability and unique features of archaeal lipids makes them a useful biomarker for Archaea within environmental samples, including ocean sediments. The polar lipids ofArchaeacan be used to make liposomes (closed vesicles referred to as archaeosomes) with characteristics that are useful for applications in biotechnology. Archaeal‐like polar lipids are being synthesised to optimise the properties of archaeosomes to serve as next‐generation adjuvants and drug delivery systems.Key Concepts:Archaeol (2,3‐diphytanyl‐sn‐glycerol), and variations thereof, define the polar lipids of the domain of life,Archaea.The structures of polar lipids biosynthesised provide a useful taxonomic feature to assign an isolate to the Genus level of classification.New polar lipid structures are being reported as the field expands to encompass novel isolates.These unique polar and neutral isoprenyl lipids can be used as biomarkers of archaea in environmental samples.Archaeal lipids can serve as a rich source for novel molecules not commonly found in nature, such as β‐l‐gulose.Archaeal polar lipid mixtures hydrate to form lipid membrane vesicles (archaeosomes) with bilayer, unilayer or a combination of uni and bilayer structure.Archaeosomes are generally nonfusogenicin vitro, but fusion can be dramatic for certain compositions by exposure to the combination of acidic pH, calcium and glycosidase.Archaeosomes function as safe vaccine adjuvants in mammals imparting long‐lasting CD8+T‐cell immunity and antibody responses.Isoprenoid lipids that retain the key archaeal‐lipid features are being synthesised to optimise their properties as vaccine adjuvants and delivery systems.
Magnetotaxis in Prokaryotes
Authors: Lefèvre Christopher T , Frankel Richard B , Bazylinski Dennis A 
Published: April 2013

AbstractMagnetotaxis refers to the behaviour of some motile, aquatic, bacteria that orient and swim along magnetic field lines. These microorganisms, called magnetotactic bacteria (MTB), contain intracellular structures known as magnetosomes, which are nano‐sized, magnetic, iron‐mineral crystals, each enveloped by a biological (phospholipid bilayer) membrane. Magnetosomes are usually arranged in chains within the cell, providing it with a permanent magnetic dipole moment that facilitates location and retention in the cell's preferred habitat at or below the oxic–anoxic interface in the water column or sediment. Although all MTB are motile by means of flagella and have a cell wall structure characteristic of Gram‐negative bacteria, their diversity is reflected by the large number of different morphotypes found in environmental samples of water or sediment, and by phylogenetic analysis of both cultured and uncultured organisms.Key Concepts:Prokaryotes (bacteria), like eukaryotes, internally compartmentalise and contain organelles.The prokaryotic flagellum rotates clockwise and counter clockwise thereby propelling the cell during swimming.Magnetotaxis is bacterial motility directed by a magnetic field.Magnetotactic bacteria contain intracellular, nano‐scale, membrane‐enveloped, magnetic iron‐mineral crystals called magnetosomes.Magnetosomes impart a permanent magnetic dipole moment to cells of magnetotactic bacteria causing them to behave as miniature, motile, compass needles.Magnetotaxis works in conjunction with aerotaxis to increase energy transduction in magnetotactic bacteria.Genes for magnetosome formation are clustered in a region of the genomes of magnetotactic bacteria known as a magnetosome gene or genomic island.Magnetotactic bacteria are important in the cycling of a number of important elements including carbon, iron, nitrogen and sulfur.
Phototaxis: Microbial
Authors: Allan Claire Y , Fisher Paul R 
Published: April 2013

AbstractPhototaxis in its broadest sense is light‐regulated movement of motile organisms (microorganisms in the case of microbial phototaxis), usually resulting in their attraction to (positive phototaxis) or avoidance of (negative phototaxis) illuminated regions. Prokaryotes often use a time‐biased random walk strategy under which they choose directions randomly, but move for longer time periods in the chosen direction when that direction happens to be correct. They use type I sensory rhodopsin photoreceptors and two‐component histidine kinase‐mediated phosphotransfer systems to regulate flagellar movement. Eukaryotic microbes by contrast can sense and respond to the direction of light by regulating the direction of movement. Phototransduction pathways in eukaryotic microbes appear to involve protein phosphorylation/dephosphorylation at serine or threonine residues, and the responsible kinases and phosphatases are regulated by second messengers. This review focuses on select representative organisms from each of the three taxonomic domains whose photosensory signal transduction pathways have been studied. Although many components of the signal transduction pathways controlling phototaxis have been identified, there is still much to be elucidated.Key Concepts:Phototaxis enables microorganisms to position themselves in an environment that is optimal for survival.Organisms from all three taxonomic domains display phototaxis with differing photosensory signal transduction pathways.Photosensory signal transduction pathways in eubacteria and archaea involve the coupling of signals from photoreceptors to the same signalling pathways as are used by these organisms for chemotaxis.Phototransduction pathways in eukaryotic microbes appear to involve protein phosphorylation/dephosphorylation at serine or threonine residues, and the responsible kinases and phosphatases are regulated by second messengers.
Rhizosphere
Authors: Lynch James M , de Leij Frans 
Published: April 2013

Abstract

The rhizosphere is that part of the soil ecosystem where plant roots, soil and the soil biota interact with each other. These interactions are often of benefit to plants, improve soil fertility and enhance the degradation of toxic chemicals. Rhizodeposition from plants is the key energy supply for the rhizosphere biota. Mineral nutrients are supplied by the soil matrix, organic residues and biological nitrogen fixation. The interactive biotic community includes microorganisms, protozoa and soil fauna. Some organisms are beneficial whereas others are harmful. Some deleterious organisms can be suppressed in a variety of biological control strategies. The key physical factors governing rhizosphere activity are temperature, water availability, oxygen, pH and soil structure. The rhizosphere has strong influences on agriculture, and the bioremediation of contaminated and degraded land.

Key Concepts:

Rhizodeposition from roots generates the energy substrates for rhizosphere organisms.

Mineral nutrients are provided by the soil matrix, organic residues and biological nitrogen fixation.

Microorganisms interact with protozoa and soil fauna in the rhizosphere.

Deleterious organisms can be suppressed by beneficial organisms in biological control.

Temperature, water availability, oxygen, pH and soil structure govern biotic activity.

The rhizosphere activity can optimise crop production and remediate contaminated and degraded land.
Herpesviruses (Human)
Authors: Whitley Richard J 
Published: April 2013

Abstract

Human herpesviruses are a family of eight
deoxyribonucleic acid
(DNA) viruses. There are three subfamilies, reflecting size and sites of latency. The alphaherpesviruses consist of
Herpes simplex virus type 1
(HSV‐1),
Herpes simplex virus type 2
(HSV‐2) and
Varicella‐zoster virus
(VZV), all of which have a predisposition to infect neuronal tissues and establish latency in sensory ganglia. The betaherpesviruses are
Cytomegalovirus
(CMV),
Human herpesvirus 6
(HHV‐6) and
Human herpesvirus 7
(HHV‐7) which infect endothelial cells and secretory glands. Finally, the gamma herpesviruses are
Epstein
–
Barr virus
(EBV) and
Kaposi sarcoma‐associated herpesvirus
(KSHV or HHV‐8). These viruses commonly infect humans but generally cause only trivial disease. However, in high‐risk patient populations (e.g. the newborn or immunocompromised host) disease can be associated with significant morbidity and mortality. Therapy exists for many but not all of the resultant diseases.

Key Concepts:

Human herpesviruses are a family of eight
deoxyribonucleic acid
(DNA) viruses:
Herpes simplex virus type 1
(HSV‐1),
Herpes simplex virus type 2
(HSV‐2),
Varicella‐zoster virus
(VZV),
Cytomegalovirus
(CMV),
Epstein‐Barr virus
(EBV),
Human herpesvirus 6
(HHV‐6),
Human herpesvirus 7
(HHV‐7) and
Kaposi sarcoma‐associated herpesvirus
(KSHV or HHV‐8).

Membership in the
Herpesviridae
family is based on the structure of the virion, and herpesvirus is categorised into three subfamilies and six groups (classified A–F) based on genomic sequence arrangement.

Replication of herpesviruses occurs in a multistep process, though this process is considered inefficient, with a high ratio of noninfectious to infectious viral particles.

Latency is established in specific host cells, and the latent viral genome may be either extrachromosomal or integrated into host cell DNA.

Reactivation of latent virus can be triggered by such stimuli as stress, menstruation and exposure to ultraviolet light, though reactivation in not clearly understood from a biochemical of genetic standpoint.

The definitive diagnosis of a herpesvirus infection usually requires either isolation of virus or the amplification of viral DNA by molecular techniques, namely polymerase chain reaction (PCR).

A critical factor for the transmission of HSV‐1 and HSV‐2 is the requirement for intimate contact between a person who is shedding virus and a susceptible host.

Varicella‐zoster virus
is one of the most common encountered by humans, and is generally transmitted via airborne routes. Varicella (chicken pox) is the manifestation of primary infection, and Herpes zoster (shingles) is the recurrent form, resulting from latent virus. Vaccines are available for the prevention of both these types of infection.

Infections due to HSV, VZV and CMV are the most amenable to therapy with antiviral drugs.
Rhinoviruses
Authors: Arden Katherine E , Mackay Ian M 
Published: April 2013

AbstractHuman rhinovirus (HRV) infections cause 70% of virus‐related wheezing exacerbations and cold and flu‐like disease. They are associated with otitis media, sinusitis and pneumonia. Annually, the health and socioeconomic impact of HRV infections costs billions of dollars. Since 1987, 100 officially recognised HRV serotypes have resided in two genetically distinct species, HRV‐A and HRV‐B. Their genome sequences were deduced in 2009. Recently a new species, HRV‐C was recognised, containing 60 genotypes, of which only two have been isolated in primary tissue. Little is known about HRV‐Cs. The HRVs reside within the genusEnterovirus, familyPicornaviridae. What drives the development and maintenance of so many distinct viruses is unknown. What role recombination plays in generating this diversity and whether there are species‐specific circulation patterns and clinical outcomes remains unclear. In short, much remains uncertain about the HRVs but the current key features and clinical outcomes from HRV infection are presented.Key Concepts:The nonenveloped HRVs have a small RNA genome of approximately 7000 base pairs.A third, new species of HRV, HRV‐C was described in 2007; all species reside within the genusEnterovirus, familyPicornaviridae.HRV prevalence peaks twice per year.HRVs cause cold and flu‐like symptoms and trigger asthma and chronic obstructive pulmonary disease exacerbations.HRVs are associated with diseases such as otitis media, sinusitis and pneumonia.HRV infections are associated with considerable direct and indirect healthcare expenditure annually.
Viral Classification and Nomenclature
Authors: Fauquet Claude M , Martelli Giovanni P 
Published: April 2013

Abstract

As any classification is essentially an arbitrary human invention, it is imperative to have a unique source of classification also for viruses. The International Committee on Taxonomy of Viruses (ICTV), a committee of the Virology Division of the International Union of Microbiological Societies, has been in charge of this task since 1966 and has already published nine Reports updating the status of viral taxonomy. Contrary to other biological entities (vertebrates, invertebrates, plants, fungi and bacteria), viruses are not classified according to a Linnean latinised binomial system but, like these, they are arranged into species, genera, subfamilies, families and orders, whose names are written in italics with an initial capital letter. The last ICTV report (2011) lists 6 orders, 94 families, 22 subfamilies, 395 genera and 2480 recognised species. Species are the building blocks of the taxonomic construction. Although species identification is based on discriminating traits, their allocation into higher taxa takes into account common characters of increasingly hierarchical significance.

Key Concepts:

Taxonomy is an arbitrary organisation of biological entities to facilitate scientific studies and to identify common traits within similar taxonomic levels.

Classification and nomenclature are the two facets of taxonomy.

Classification is the arrangement of biological entities into taxonomic categories (taxa) on the basis of similarities and/or relationships (phylogeny).

Nomenclature is the assignment of names to taxa, according to international rules.

Virus classification is a rapidly evolving science particularly with the input of viral genome sequencing.

Viruses are not named according to a Linnean latinised binomial system and instead are named with international English‐based names and
de novo
international taxonomic names.

The ICTV is entrusted with the task of classifying and naming virus taxa.
Chlamydiae
Authors: Everett Karin DE 
Published: April 2013

Abstract

Chlamydiae
are bacterial species with a developmental cycle requiring replication in eukaryotic cells. They infect the cells of mammals, birds, marsupials, fish, reptiles, amphibians, insects and protozoa. The most famous species,

Chlamydia trachomatis

, causes sexually transmitted disease in humans. Analysis of available genome sequences for these bacterial species has shown that their common ancestor lived over a billion years ago. Because of their diversity,
Chlamydiae
are often recognised and grouped by using rDNA PCR methods. All
Chlamydiae
have 16S or 23S ribosomal
ribonucleic acid
(rRNA) sequences that are at least 80% identical to the rRNA of the
Chlamydiaceae
family.
Chlamydiae
are also characterised by four unique phenotypic traits: they have an electron dense infectious form (0.2
μ
m), they have a morphologically and physiologically distinct replicative form (approximately 1.0
μ
m), the outer membrane has lipopolysaccharide and is structurally dependent on disulfide‐crosslinked cysteine‐rich proteins, and in host cells Chlamydiae generally are located within membrane‐bound inclusions.

Key Concepts:

Chlamydia
was long believed to be a simple and mysterious disease.

Today we know it is a tiny intracellular bacterium so unique that it is classified at the highest level: phylum
Chlamydiae
.

Chlamydiae
probably includes thousands of species.

So far (since 1980) 25 chlamydial species have been described in some detail.

These species are found in animals, amoebae, insects and a worm living on the bottom of the ocean.

The complete genomes of 12 chlamydial species have been DNA sequenced.

Genome sequencing reveals that
Chlamydiae
existed a billion years ago.

The common ancestor of all
Chlamydiae
was directly related to the ancestors of plants and animals and other bacteria.

All genome‐sequenced
Chlamydiae
have 493 genes in common – approximately one quarter to one half of each genome.

Chlamydial phenotypes today display the observable effects of these genes.
Chlorinated Hydrocarbon Metabolism
Authors: Reineke Walter , Mandt Christian , Kaschabek Stefan R , Pieper Dietmar H 
Published: April 2013

Abstract

The widespread global distribution of chlorinated hydrocarbons, their high lipophilicity and their recalcitrance have contributed to their importance as environmental toxicants. Their metabolism under oxic and anoxic conditions mediated by prokaryotic and eukaryotic cells is discussed. Various aerobic bacteria are able to use chlorinated hydrocarbons as the sole source of carbon and energy and some anaerobic bacteria can use some of these as an artificial electron acceptor in reductive dechlorination. Liver enzymes are responsible for the formation of hydrophilic metabolites ready for excretion which often lead to highly reactive and potentially toxic intermediates. Whereas fungi, especially ligninolytic ones, usually only exhibit ‘side activities’ for chlorinated hydrocarbons. The capabilities of bacteria had led to the development of various bioremediation processes. Both, successes and failures within these processes are known. Therefore, current research aims at a better understanding of global community interactions.

Key Concepts:

Chlorinated hydrocarbons have been produced by the chemical industry since nearly a decade in large amounts, but they can also be observed as natural compounds, sometimes exceeding the industrially produced amounts.

Even though toxicological properties have pushed the chlorochemistry into the focus of considerable debate and governmental regulatory action, chlorinated hydrocarbons remain essential for certain applications.

The aerobic metabolism of chlorinated hydrocarbons by bacteria has been studied in detail and an immense amount of information is available on pathways, enzymes and genes involved in the mineralisation of chloroaromatics.

The anaerobic degradation of chlorinated hydrocarbons is due to the capablity of anaerobic bacteria to use them in anaerobic respiration, which results in dechlorination.

Dehalococcoides
organisms are the most versatile reductive dehalogenators as being capable to dehalogenate chlorinated dioxins, biphenyls, benzenes and vinyl chloride, among others.

Microbial activities have been widespread used for bioremediation purposes through natural attenuation, biostimulation and bioaugmentation.

The poor understanding of the functioning of the complex microbial activities
in situ
made bioremediation efforts quite unreliable.

The rapid development of molecular techniques in recent years allows immense insights into the processes
in situ
, but also on the overall physiology of biocatalysts.
Fetal–Maternal Immunological Relationships
Authors: Chaouat Gérard 
Published: April 2013

AbstractDespite inheriting half of its genetic material from its father, the fetoplacental unit is not rejected by the maternal immune system because of a unique immunological relationship with the mother. Despite maternal immune recognition of the conceptus as evidenced by alloantibodies, unlike for conventional allografts, the immune response is spared, cytotoxic effectors being downregulated or suppressed, whereas several cytokinic responses, including inflammatory ones, are used or even provoked for their preimplantation or later on ‘immunotrophic’ effects. This unique relationship is partly due to the peculiar antigen expression in the placenta, culminating in humans with the sole expression of human leucocyte antigen C (HLA‐C) and monomorphic HLA‐G on invading cytotrophoblasts and also many immunoregulatory pathways, with special emphasis presently put on regulatory T cells. Moreover, uterine natural killer (uNK) cells are a distinct, specialised NK subset, endowed with immunoregulatory and angiogenic properties, necessary for local (spiral) arteries development. Consequences for abortion eclampsia are discussed, as well as antibody‐induced fetal haemolytic disease.Key Concepts:The fetus is usually seen as an allograft in mother's womb, which should be rejected by the maternal immune system.Pregnancy induces systemic modifications in the maternal immune system but these do not really account for fetal survival.Recognition of the ‘foreign’ nature of the fetus is good and even sometimes required for successful pregnancy.Placenta acts as a barrier between the fetus and maternal cells.Uterine natural killer cells are not endowed with the same properties as the ones found in peripheral blood.One of the keys to fetal survival is the peculiar expression of MHC antigens in the placenta, including in human the expression of a nonpolymorphic antigen, HLA‐G, in membrane bound and soluble forms both endowed with immunoregulatory properties.Uterine natural killer cells control local uterine angiogenesis.The placenta bathes in/secretes immunotregulatory materials.Regulatory T cells mitigate the effects of allorecognition by maternal immune system in placental mammals.Allopregnancy is a Th2 phenomenon.In variance with MHC antigens, red blood cells antigens can induce maternal antibodies which can cross the placenta, and destroyin uterofetal red blood cells.