bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diatoms
Authors: Theriot Edward C 
Published: April 2013

Abstract

Diatoms are single‐celled autotrophic organisms with highly ornate siliceous walls. They account for more than 20% of the world's primary production, are responsible for much of the petroleum humans use, and deposits of their shells are mined for numerous uses. The most taxonomically diverse groups of photosynthetic protists, diatoms are of ecological importance in nearly every freshwater and marine habitat. Their closest relatives are a poorly known group of microflagellates, some silicified and some not. Efforts to reconstruct diatom phylogeny are hampered by the fact that their true diversity and that of their closest relatives remains unknown. Genomic studies are creating tremendous new opportunities for study of this important group. Perhaps as much as a third of the diatom nuclear genome is now thought to be recently laterally transferred from bacteria. Diatom adaptation to such a wide range of environments may be a result of the resulting novel gene combinations.

Key Concepts:

Diatoms are a highly diverse group of protists, with perhaps more than 200 000 species, most of which remain undescribed.

There are four major structural groups, radial centrics, polar centrics, araphid pennates and raphid pennates.

Among the four major structural groups of diatoms, only the raphid pennates are robustly supported as monophyletic.

Diatoms dominate the world's oceans, lakes and streams, conducting more than 20% of the world's photosynthesis.

Diatoms are critical indicators of aquatic ecosystem conditions, past and present.

Fossil diatoms have significant economic importance as stratigraphic indicators for mineral exploration, particularly petroleum and as a source of diatomite, which is used in numerous industrial applications.

Diatoms make a diverse number of nanoscale siliceous structures, an order of magnitude smaller than that presently attainable by human technology.

Understanding how diatoms make their shells may lead to breakthroughs in nanotechnology.

Nearly a third of the diatom nuclear genome appears to be the result of relatively recent horizontal gene transfer from bacteria.

Horizontal gene transfer may play a role in the apparent rapid adaptation and diversification of diatoms.
Mumps Virus
Authors: Duprex W Paul , Rima Bertus K 
Published: April 2013

Abstract

Mumps virus
causes a childhood disease that is characterised by swelling of the salivary glands (parotitis) and the testes (orchitis). Though it causes what is usually a mild disease infection, in adolescents and adults, it can be seriously discomforting and lead to meningitis and other sequelae. It was the main cause of viral meningitis before vaccines controlled the numbers of cases. Some of the clinical signs develop only after the onset of immune responses and may result from immunopathological reactions. Its pathogenesis is not well understood and relatively under researched for a human pathogen.
Mumps virus
is a nonsegmented negative‐stranded ribonucleic acid virus belonging to the family
Paramyxoviridae.
The molecular description of the virus, the understanding of the genome expression and the role of most viral proteins, though far from completely understood, has advanced in recent years and we are now able to introduce mutations into the virus at will and make recombinant viruses that express autofluorescent proteins or other foreign proteins from additional transcription units within the genome and hence the opportunity exists now to study pathogenesis in a number of animal and human tissue models using novel bioimaging modalities.

Key Concepts:

Mumps virus
is a relatively simple enveloped, negative‐sensed RNA virus which contains only seven genes.

Mumps virus
is a highly infectious agent which causes a relatively mild systemic disease in susceptible individuals.

A highly efficacious vaccine has been developed, although the molecular basis of the attenuation remains an enigma.

Inadequate virus attenuation caused aseptic meningitis in vaccinees and resulted in the withdrawal of mumps vaccines, public resistance to vaccination in the 1990s. In some countries, such as Japan this led to the complete cessation of national vaccination programmes.

Recombinant
mumps viruses
have helped to define the molecular determinants of neurotropism.
Filamentous Bacteriophages: Biology and Applications
Authors: Rakonjac Jasna 
Published: April 2013

Abstract

Filamentous bacteriophages contain a circular
single‐stranded deoxyribonucleic acid (ssDNA)
genome packaged into long filaments. These phages do not reproduce by lysing bacteria; instead, they are secreted into the environment without killing the host. Well‐studied

Escherichia coli

K12‐infecting Ff phages (f1, fd or M13) always replicate episomally; however a growing number of ‘lysogenic’ or chromosomally integrated filamentous phages of Gram‐negative bacteria are being discovered. The ‘lysogens’ can be induced; however phage reproduction does not require genome excision from bacterial chromosome and does not lyse the host cells. Some filamentous phages enhance the virulence of their host organisms, the most striking example being the CTXφ of

Vibrio cholerae

, which encodes cholera toxin.

E. coli

Ff phages are the workhorse of phage display technology, whose most notable ‘products’ are therapeutic recombinant antibodies. Ff are also being used in nanotechnology as templates for assembly of nanostructures, which has already led to their incorporation into a working nanobattery.

Key Concepts:

Filamentous bacteriophages are long filaments (6–7 nm×>500 nm) that contain a single‐stranded circular DNA genome.

Filamentous bacteriophages replicate via a rolling circle mechanism, one strand at a time.

Filamentous bacteriophages do not lyse the cells; they are released by secretion, using a dedicated filamentous phage assembly secretion system.

Filamentous phage secretion‐assembly requires the proton‐motive force and ATP.

Some filamentous phages replicate exclusively as episomes, while others also integrate their genomes into the host chromosome, forming a lysogen. Induction of the lysogen does not result in cell lysis.

Ff filamentous phages of

E. coli

(f1, M13 and fd) have been used interchangeably as vectors and helper phages in DNA sequencing, as a protein display platform in phage display technology and as a template for assembly of nanostructures in nanotechnology.
Hibernation: Endotherms
Authors: Geiser Fritz 
Published: April 2013

Abstract

The main function of hibernation and daily torpor in heterothermic mammals and birds (i.e. species capable of expressing torpor) is to conserve energy and water and thus to survive during adverse environmental conditions or periods of food shortage no matter if they live in the arctic or the tropics. However, the reduced energy requirements also permit survival of bad weather during reproduction to prolong gestation into more favourable periods, conservation of nutrients for growth during development, and overall result in reduced foraging needs and thus exposure to predators, which appear major contributing reasons why heterotherms are often long lived and have lower extinction rates than strictly homeothermic species that cannot use torpor. Known heterothermic mammals and birds are diverse with about 2/3 of mammalian orders and 1/3 of avian orders containing heterothermic species, and their number continues to grow.

Key Concepts:

Hibernation and daily torpor are the most effective means of energy conservation available to mammals and birds and are crucial for survival of adverse conditions of many species.

Use of torpor often is enhanced by low ambient temperatures and limited food.

Because torpor reduces energy requirements, its opportunistic use allows extension of gestation, nutrient sparing during development, and permits survival in modified and degraded habitats and also reduces the need for foraging and thus exposure to predators.

As the rate of extinction in heterothermic mammals is much lower than in homeotherms, thermal energetics are of concern to conservation biologists because mammals and birds that can use and cannot use torpor differ enormously in their energy requirements and thus foraging needs.
Human Behavioural Ecology
Authors: Borgerhoff Mulder Monique , Schacht Ryan 
Published: April 2013

Abstract

Human behavioural ecology emerged in the mid‐1970s as a result of applying the theory of evolution by natural selection to the study of human behaviour. Using explicit models to derive hypotheses that are tested with quantitative data primarily drawn from traditional human communities, it offers a natural science of sociocultural diversity. Recent activity in this field lies in the study of the family, in life history theory and in individual and collective interests, and increasingly the field of enquiry moves from traditional communities to modern industrial societies. Current challenges include incorporating the mechanisms underlying adaptive behaviour, and the developmental and historical causes of human behavioural variability.

Key Concepts:

Human behavioural ecology (HBE) relies on the phenotypic gambit, the claim that how a trait is inherited does not seriously constrain adaptive responses to ecological variation.

HBE derives testable hypotheses from either graphical or mathematically explicit models anchored in basic principles of evolution by natural selection.

An HBE perspective integrates topics that are typically somewhat distinct in conventional anthropology – subsistence, marriage, reciprocity, kinship, demography, politics, ritual and health – into a unified theoretical enquiry.

Initial explorations of HBE were in the field of foraging (hunter‐gatherer) subsistence behaviour, drawing explicitly from optimal foraging theory.

An early and enduring focus in HBE is why human communities exhibit such variable culturally sanctioned mating patterns, formalised as marriage rules and marital payments.

Organisms face two major allocation decisions, the first between growth and reproduction, and the second between the number of offspring produced and the amount to be invested in each.

Distinctive features of human life histories, compared to those of other primates and mammals, include: a very large brain, an exceptionally long lifespan, an extended period of juvenile dependence, support of reproduction by older post‐reproductive individuals and other kin, and men's support of reproduction through the provisioning of women and their offspring.

The individual selectionist perspective of behavioural ecology highlights the conflict of interests among individuals at each level as well as the potential for cooperation within and between groups, as do some schools within economics, political science and sociology.

The focus of behavioural ecology (both human and other) is principally on adaptive function, whereas evolutionary psychology focuses on mechanism, and cultural evolutionary theory on the transmission of cultural traits.

Behavioural ecologists predict matching between behavioural strategy and context irrespective of whether humans reach this adaptive strategy as a consequence of genes, psychological mechanism or the learning of culture.
Triticum AestivumL (Wheat)
Authors: Snape John W , Pánková Katerina 
Published: April 2013

AbstractWheat seeds, known as grain, are a primary source of calories for the human race, and for animal feed, with more than 650 million tonnes being produced annually, worldwide. There are two agricultural species, bread wheat (Triticum aestivum) and durum (pasta) wheat (Triticum durum), both of which belong to the botanical tribe Triticeae in the grass family Poaceae, which also contains the related crop species, rye and barley. The centre of origin of the species is the ‘fertile crescent’ in the Middle East from where they have travelled to all continents of the world, although typically they are major annual crops of the temperate regions. The dried grains are crushed to produce flour, which is mixed by adding water and other ingredients to make dough, which is then cooked to produce a variety of breads and cakes.Key Concepts:Wheat belongs to the botanical tribe Triticeae in the grass family Poaceae, which also contains the related crop species, rye and barley.Because of the relatively close genetic relationships between cultivated wheat and related species, it is possible to artificially hybridise cultivated wheat with many of their wild relatives to create hybrids for gene transfer, and even new cereal species, such as Triticale, the artificial hybrid between wheat and rye.Triticum turgidumsubspeciesdurum(durum wheat) is atetraploid wheat with 14 pairs of chromosomes (2n=2x=28; AABB genomes) and was domesticated by ancient farmers from a wild species still growing in the Middle East, calledTriticum dicoccoides.Bread wheat is a hexaploid species (2n=6x=42; AABBDD genomes) with 21 pairs of chromosomes.Bread wheat is the most widely grown species of the cultivated wheat species and accounts for approximately 30% of all the cereal grain consumed in the world today, 650 million tonnes were produced in 2010, and it ranks alongside rice and maize as the world's most important crops.Most archaeological evidence suggests that the earliest domestication of wheat occurred around 7500–6500 BCin the ‘Fertile Crescent’ consisting of mountain chains flanking the plains of Mesopotamia and the Syrian Desert.Evidence suggests that wheat first reached Europe via the south‐east Balkans and spread by two main routes across Europe, one inland and the other coastal.The major production areas are now in Europe, Russia, North and South America, Australia and China.As a foodstuff for humans, wheat is distinguished from other cereals by its property of making viscoelastic dough when the ground seeds (flour) are mixed with water.
Gene Evolution and Human Adaptation
Authors: Harris Eugene E 
Published: April 2013

Abstract

Regions of the human genome that have been subject to past positive selection contain patterns of genetic variation that are markedly different in specific ways from regions that have not experienced positive selection. By uncovering these so‐called signatures of positive selection in the genome we can discover the unique ways in which humans have evolved. Genome‐wide scans have revealed signatures of positive selection on the human lineage since we diverged from chimpanzees, as well as signatures of positive selection specific to regional human populations. New research has found that much of human population adaptation may have occurred by positive selection causing modest increases in frequency of beneficial variants at multiple loci that all result in the shift of the expression of a feature (like height) in a particular direction.

Key Concepts:

Hundreds of genes have been found that bear signatures of positive selection on the human lineage with genes mainly falling into categories of chemoreception, immune defence, reproduction and fertilisation as well as apoptosis.

Most studies of positive selection have focused their work on the protein‐coding portion of the genome, yet many sites of positive selection may fall in noncoding regions where new research is detecting many functional elements.

There is much active research trying to identify the extent to which DNA substitutions in regulatory elements underlay our adaptations.

Much needed in future research is experimental work that aims to pinpoint causal variants within genomes and the phenotypic effects of genomic regions showing signatures of positive selection.

The traditional signature of selection, a ‘classic selective sweep’, appears to be rare in large resequencing datasets of diverse world populations leading researchers to begin searching for signatures of ‘soft selective sweeps’ where weak positive selection acts to subtly increase the frequency of DNA variants at multiple loci with all variants contributing to a shift in a phenotype's expression in the same direction.
Toward systems metabolic engineering of Aspergillus and Pichia species for the production of chemicals and biofuels
Authors: Caspeta Luis , Nielsen Jens 
Published: April 2013

AbstractRecently genome sequence data have become available for Aspergillus and Pichia species of industrial interest. This has stimulated the use of systems biology approaches for large‐scale analysis of the molecular and metabolic responses of Aspergillus and Pichia under defined conditions, which has resulted in much new biological information. Case‐specific contextualization of this information has been performed using comparative and functional genomic tools. Genomics data are also the basis for constructing genome‐scale metabolic models, and these models have helped in the contextualization of knowledge on the fundamental biology of Aspergillus and Pichia species. Furthermore, with the availability of these models, the engineering of Aspergillus and Pichia is moving from traditional approaches, such as random mutagenesis, to a systems metabolic engineering approach. Here we review the recent trends in systems biology of Aspergillus and Pichia species, highlighting the relevance of these developments for systems metabolic engineering of these organisms for the production of hydrolytic enzymes, biofuels and chemicals from biomass.
Monitoring of post‐translational modification dynamics with genetically encoded fluorescent reporters
Authors: Hertel Fabian , Zhang Jin 
Published: April 2013

ABSTRACTPost‐translational modifications (PTMs) of proteins are essential mechanisms for virtually all dynamic processes within cellular signaling networks. Genetically encoded reporters based on fluorescent proteins (FPs) are powerful tools for spatiotemporal visualization of cellular parameters. Consequently, commonly used modular biosensor designs have been adapted to generate several protein‐based indicators for monitoring various PTMs or the activity of corresponding enzymes in living cells, providing new biological insights into dynamics and regulatory functions of individual PTMs. In this review, we describe the application of general design strategies focusing on PTMs and discuss important considerations for engineering feasible indicators depending on the purpose. Moreover, we present developments and enhancements of PTM biosensors from selected studies and give an outlook on future perspectives of this versatile approach. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 180–187, 2014.
Chemical and biological methods to detect post‐translational modifications of arginine
Authors: Slade Daniel J. , Subramanian Venkataraman , Fuhrmann Jakob , Thompson Paul R. 
Published: April 2013

ABSTRACTPost‐translational modifications (PTMs) of protein embedded arginines are increasingly being recognized as playing an important role in both prokaryotic and eukaryotic biology, and it is now clear that these PTMs modulate a number of cellular processes including DNA binding, gene transcription, protein–protein interactions, immune system activation, and proteolysis. There are currently four known enzymatic PTMs of arginine (i.e., citrullination, methylation, phosphorylation, and ADP‐ribosylation), and two non‐enzymatic PTMs [i.e., carbonylation, advanced glycation end‐products (AGEs)]. Enzymatic modification of arginine is tightly controlled during normal cellular function, and can be drastically altered in response to various second messengers and in different disease states. Non‐enzymatic arginine modifications are associated with a loss of metabolite regulation during normal human aging. This abnormally large number of modifications to a single amino acid creates a diverse set of structural perturbations that can lead to altered biological responses. While the biological role of methylation has been the most extensively characterized of the arginine PTMs, recent advances have shown that the once obscure modification known as citrullination is involved in the onset and progression of inflammatory diseases and cancer. This review will highlight the reported arginine PTMs and their methods of detection, with a focus on new chemical methods to detect protein citrullination. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 133–143, 2014.
Development of a high‐volume, multiple‐operator program for percutaneous chronic total coronary occlusion revascularization: procedural, clinical, and cost‐utilization outcomes
Authors: Karmpaliotis Dimitri , Lembo Nicholas , Kalynych Anna , Carlson Harold , Lombardi William L. , Anderson Chad N. , Rinehart Sarah , Kirkland Ben , Shemwell Kathie C. , Kandzari David E. 
Published: April 2013

BackgroundDevelopment of a specialized chronic total coronary occlusion (CTO) revascularization program attentive to procedural guidelines, quality oversight, and cost/resource utilization has not been described.MethodsA single‐center CTO interventional program was initiated with requirements including: extensive didactic training, on‐site proctorship, routine determination of case appropriateness, adherence to procedural safety guidelines, and a 2‐operator/case approach. Clinical and angiographic characteristics, procedural outcomes, in‐hospital clinical events, and cost/resource utilization were examined.ResultsAmong 145 patients, 160 consecutive CTO revascularization procedures were attempted between October 2009 and December 2010. Selected procedural and technical characteristics included: bilateral femoral access, 90.0%; planned retrograde guidewire placement, 37.5%; re‐entry catheter, 10.0%; reattempt, 10.6%; fluoroscopic time, 67.4 ± 45.5 min; contrast volume, 403 ± 215 mL. Average stent number and total stent length per CTO vessel were 2.6 ± 1.1 and 64.7 ± 30.7 mm, respectively. Overall CTO success rate was 85.6% (137/160). In‐hospital adverse outcomes included: death 0.6%; emergency bypass surgery, 0.6%; tamponade, 0.6%; myocardial infarction, 1.9%; transient nephropathy, 1.2%. Compared with patients undergoing non‐CTO PCI, procedural and total cost per patient were significantly higher among the CTO cohort despite overall similar contribution margins ($5,173 ± 12,052 versus $5,730 ± 8,958, P = 0.58).ConclusionsFollowing initiation of a dedicated program with implementation of quality and performance guidelines, complex CTO revascularization may be safely performed with outcomes comparable with reports from established centers. Despite higher resource utilization, CTO revascularization is associated with a positive contribution margin. Requirement of educational and performance standards, mentorship from experts, consensus review for appropriateness and provision of catheterization laboratory policies may represent a model for program development. © 2013 Wiley Periodicals, Inc.
Continuous Micro Liquid‐Liquid Extraction
Authors: Assmann N. , Ładosz A. , Rudolf von Rohr P. 
Published: April 2013

AbstractAmong the different separation processes, liquid‐liquid extraction especially benefits from microfluidics as the short molecular diffusion distance and large specific interfacial area in microchannels are advantageous for effective liquid/liquid contacting. An overview is given on different examples of continuous micro liquid‐liquid extraction. As contacting of the two phases as well as phase separation strongly depend on the flow pattern, one chapter is devoted to each parallel flow, segmented flow, and emulsions. Advantages and disadvantages of the three flow patterns are compared to each other. Additionally, possibilities for scaling up microfluidic concepts for higher‐throughput systems are presented.
ChemInform Abstract: Perovskite‐Like Mn2O3: A Path to New Manganites.
Authors: Ovsyannikov Sergey V. , et al. et al. 
Published: April 2013

AbstractTwo new metastable phases of Mn2O3, ε‐Mn2O3 (I) and ζ‐Mn2O3 (II) are obtained by heating bixbyite‐structured Mn2O3 to 800—2200 K at 10—20 GPa for 2—3 h.