bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escherichia colias an Experimental Organism
Authors: Cronan John E 
Published: July 2014

AbstractEscherichia coli, a gram‐negative gamma proteobacterium, is presently the best‐understood organism. It is a paradigm organism in bacterial physiology and genetics as well as a key tool in molecular genetics in that many genetic manipulations throughout biology involveE. coli. Molecular cloning into one of manyE. colivector plasmids is a standard procedure in most molecular biology and biotechnology laboratories.E. coliis also the workhorse of recombinant protein production since conditions have been found that allow proteins from across biology to be efficiently expressed in and purified fromE. coli. Indeed, the bulk of x‐ray crystal structures are performed on proteins that were produced in this bacterium. Finally, a collection of mutantE. colistrains each deleted for a gene nonessential for growth in a rich medium provides a resource to test the functions of genes from other organisms by assaying their ability to replace the function of anE. coligene.Key Concepts:E. coliis a preferred host for gene cloning due to the high efficiency of introduction of DNA molecules into cells.E. coliis a preferred host for protein production due to its rapid growth and the ability to express proteins at very high levels.Bacterial conjugation can be used to transfer large DNA fragments from one bacterium to another.E. coliis a preferred host for the study of phage biology due to the detailed knowledge of its nucleic acid and protein biosynthetic pathways.The ability ofE. colito grow on chemically defined media coupled with its extensive genetic toolbox make it a key system in study of bacterial metabolic pathways.
Multivariate Techniques in Ecology
Authors: Reyment Richard A 
Published: July 2014

AbstractMultivariate analysis (MA) is concerned with the simultaneous examination of two or more variables (in the case of full space) or parts (in the case of simplex space) by means of procedures based on the application of standard methods of linear algebra and differential geometry. The methods are largely universally applicable. In the life sciences, MA is of wide use in animal and plant taxonomy, quantitative genetics, environmetrics, ecology and aspects of evolutionary biology.
Mutualistic Symbioses
Authors: Saffo Mary Beth 
Published: July 2014

Abstract

Mutualistic symbioses are defined as intimate inter‐species interactions beneficial to all species partners. In reality, however, mutualistic symbioses are more intricate, complex, diverse and variable than the formal definition suggests; understanding this complexity is essential to understanding mutualism dynamics. Widely distributed both geographically and taxonomically, mutualistic symbioses play a significant role in the biology of organisms. Iconic examples of mutualisms such as lichens, reef‐building corals with algal symbionts, and mycorrhizal fungi with terrestrial plants, highlight the prevalence of many symbiotic mutualisms in resource‐limited conditions. The several important examples of hereditary microbial symbiosis in insects call attention to the importance of hereditarily transmitted symbioses as well. But there are also mutualisms that do not fit the ecological paradigm of partnerships forged by nutrient scarcity, and evolutionarily persistent, horizontally‐transmitted mutualisms which challenge the notion that hereditary symbiosis is the only stable form of mutualistic symbiosis. In the face of ubiquitous immune defences among organisms, the persistence and ubiquity of mutualistic symbiosis seems a physiologically improbable phenomenon. But recent research suggests a possible resolution to this paradox, in revealing the involvement of immune mechanisms in selection, tolerance and maintenance of beneficial foreign microbes, as well as recognition and elimination of pathogens.

Key Concepts:

Given the ubiquity and effectiveness of immune defences among plants and animals, the existence of chronic, beneficial infections seems a physiologically improbable situation.

Despite its improbability, mutualistic symbiosis is widespread in the biosphere, playing key roles in the evolution and ecology of land plants, tropical and deep‐sea marine ecosystems, the biology of herbivorous animals, and more.

Mutualistic symbioses are diverse, embracing a physiologically, taxonomically, and ecologically diverse array of interactions.

Mutualistic symbioses can incorporate antagonistic as well as mutualistic elements; many can also vary in their biological effects, depending on environmental conditions.

While the metabolic foundation of many mutualistic host‐symbiont interactions lies in symbiotic‐enhanced nutrient exchanges in nutrient‐limited conditions, benefits of symbiotic mutualisms can also include nonnutritional factors such as bioluminescence, drought resistance and enhanced defences against predators and pathogens.

Hereditarily‐transmitted symbioses are often considered the 'ultimate' mutualisms because of the extreme interdependence and striking coevolution of hosts and endosymbionts in such interactions.

However, nonhereditary (horizontally transmitted) mutualisms also can be strongly interdependent, evolutionarily persistent associations, with major impact on the ecology and evolution of plants and animals.
Cold Spring Harbor Laboratory
Authors: Witkowski Jan A 
Published: July 2014

AbstractThe Biological Laboratory was established at Cold Spring Harbor, New York, USA, in 1890 as a summer school for teachers of biology. It began a transition to becoming a research institute in 1898, and in 1904, the Carnegie Institution of Washington created the Station for Experimental Evolution. A third institute, the Eugenics Records Office (ERO), was established in 1910. The ERO was closed in 1940 and the two remaining institutes amalgamated to create the Cold Spring Harbor Laboratory of Quantitative Biology in 1963. Genetics was and remains the central theme of the Laboratory's research, focusing on cancer, but current areas of research also include quantitative biology, neurobiology and plant genetics. The Laboratory is also the leading centre for meetings and courses in experimental biology; over 8500 scientists attend over 50 meetings and 25 courses held annually. The Laboratory's DNA Learning Center provides education in molecular genetics for high school students, whereas the Watson School of Biological Sciences, founded in 1998, grants the PhD degree.Key Concepts:Cold Spring Harbor Laboratory is located in Nassau County on Long Island, New York, USA. It is a world‐renowned institute for research on topics of biological and biomedical importance.The laboratory plays a key role in professional education through its meetings, courses and book publishing.The Watson School of Biological Science offers graduate training leading to the PhD degree.The DNA Learning Center provides teaching in molecular genetics for high school students.
Glycosidases: Functions, Families and Folds
Authors: Kötzler Miriam P , Hancock Susan M , Withers Stephen G 
Published: July 2014

AbstractGlycosidases catalyse the hydrolysis of glycosidic linkages, thereby degrading oligosaccharides and glycoconjugates, the structurally most diverse class of biopolymers. These efficient and highly specific catalysts play important roles in biological processes thus a detailed knowledge of glycosidase function is invaluable for understanding and controlling diseases and for industrial applications. The classification of this huge class of enzymes into families on the basis of amino acid sequence has provided a highly valuable tool for the analysis of structure–function relationships. Furthermore, the steady increase in three‐dimensional structural information is revealing further evolutionary relationships between glycosidase families. In addition to the majority of glycosidases that act via the classical Koshland mechanisms, a growing number of such enzymes that use unusual mechanisms are being uncovered. This confluence of bioinformatics, structural and mechanistic studies has greatly advanced glycosidase engineering and the development of specific glycosidase inhibitors.Key Concepts:Classification of glycosidases by sequence similarity in a comprehensive database CAZy has proven to be an invaluable tool to analyse their structures and functions.Glycosidases adopt a variety of folds.The vast majority of glycosidases act via Koshland mechanisms with either retention or inversion of the anomeric configuration.Some glycosidases use unusual mechanisms employing hydration, elimination and/or redox steps.Detailed mechanistic understanding of glycosidase mechanism has allowed the engineering of glycosynthases and the development of specific inhibitors.
Copy Number Variations and Neuropsychiatric Diseases
Authors: Alliey‐Rodriguez Ney , Gershon Elliot S 
Published: July 2014

Abstract

Copy number variants (CNVs) are submicroscopic deletions and duplications of
deoxyribonucleic acid (DNA)
segments, which can have a high impact on gene expression. Methods to explore CNVs include array comparative genomic hybridisation, single‐nucleotide polymorphism microarrays and whole genome sequencing. Rare CNVs are strongly associated with neuropsychiatric diseases including autism spectrum disorder, schizophrenia, bipolar disorder and disruptions to some specific loci have been related to more than one disorder. The chromosome 22q11.21 deletion is so far the locus identified with the highest risk, 82% for any psychiatric disorder.
De novo
copy number events, those present in cases but not in their parents, also have a significant risk for any of these disorders, with an overall risk of 13% to develop a neuropsychiatric disorder if present anywhere in the genome.

Key Concepts:

Copy number variants are so far the most potent sources of genetic risk for neuropsychiatric disease.

Rare and
de novo
events are associated with neuropsychiatric disorders.
Plant Mineral Nutrition
Authors: Miller Anthony J 
Published: July 2014

Abstract

Several inorganic minerals are essential for plant growth and these are usually obtained by roots from the soil. Availability of minerals in the soil is determined by the physical and chemical characteristics of the soil. Plants can directly influence nutrient availability around the root surface; this zone is called the rhizosphere. Plants adjust root architecture and exudation according to their nutrient requirements and under deficiency these changes can be a marker for nutrient status. Nutrients are taken up from the soil using plasma‐membrane located transporter proteins and excess is stored in the cell vacuole or converted into polymerised storage forms. For crops it is essential to match nutrient supply to demand throughout the growth season to obtain the maximum yield. These nutrient storage forms can be used as agricultural indicators of crop nutrient status and the potential for fertilizer leaching losses. Membrane transporters provide a gateway for nutrient entry into plants, but the selectivity of these filters can breakdown when chemically similar minerals are present at very high concentrations. The minerals may not be essential for growth, but they can enter plant cells and cause toxicity.

Key Concepts:

Several mineral elements are essential for plant growth.

These nutrients are usually obtained from the soil and their availability depends on the physical and chemical properties of the soil.

Plants adjust their root growth according to their nutrient requirements and these changes can be a marker for nutrient status.

It is necessary to matching nutrient supply to demand throughout the growth season to obtain maximum crop yield.

Excess nutrients can be stored in the plant and these storage pools can be used as indicators of nutrient status.

Root plasma membrane located transporters are the gateway for entry of nutrients into the plant and their selectivity is important for determining the toxicity of some elements.
Determinism and Total Explanation in the Biological and Behavioral Sciences
Authors: Winther Rasmus Grønfeldt 
Published: July 2014

AbstractShould we think of our universe as law‐governed and ‘clockwork’‐like or as disorderly and ‘soup’‐like? Alternatively, should we consciously and intentionally synthesise these two extreme pictures? More concretely, how deterministic are the postulated causes and how rigid are the modelled properties of the best statistical methodologies used in the biological and behavioural sciences? The charge of this entry is to explore thinking about causation in the temporal evolution of biological and behavioural systems. Regression analysis and path analysis are simply explicated with reference to a thought experiment of painting three universes (clockwork, soup and conscious) useful for imagining our actual universe. Attention to historical, structural and mechanistic explanatory perspectives broadens the palette of methodologies available for analysing determinism in, and explanation of, biological and behavioural systems. Each justified methodology provides a partial perspective on complex reality. Is a total explanation of any system ever possible and what would it require?Key Concepts:A thought experiment delineating three universes – clockwork, soup, and conscious – assists in understanding statistical methodologies.Neither extreme rigid determinism nor radical chancy indeterminism permit accurate depictions of a ‘Laplacian chance’, conscious universe.Standard statistical methodologies related to the General Linear Model (GLM), such as regression analysis and path analysis, synthesise determinism and indeterminism in important ways (e.g. via error terms).History of science illustrates the plurality of scientific methods.Inferring causes using statistical analysis is not impossible.Indeed, randomised experiments and rigorous statistical methodologies can licence causal claims.An analogy from the physical sciences, displacement of springs, provides a running example for the variety of questions asked of system behaviour from statistical, historical, structural, and mechanistic perspectives.Historical explanation and mechanistic explanation remain autonomous explanatory perspectives interested, respectively, in the origin and part‐whole structure of a biological or behavioural system.The general methodological analyses here presented should be complemented with more concrete case studies of, for example, sexuality, intelligence, autism, and ‘criminality’.Are explanations from distinct explanatory perspectives ‘miscible’ or do we reach an ‘impasse when we attempt to integrate and mix them?
Genetic Profiling in Disaster Victim Identification
Authors: Montelius Kerstin , Stenersen Marguerethe , Sajantila Antti 
Published: July 2014

Abstract

About 30 years ago, Professor Sir Alec Jeffreys described the first
deoxyribonucleic acid (DNA)
‐profiling technique, and genetic profiling was soon implemented for immigration cases, paternity investigations and crime casework. Today, the methods have evolved from the original ‘DNA fingerprints’, to ‘DNA profiling’, which have been adopted as a standard procedure for human identification. New technological innovations, such as next‐generation sequencing, continue to improve the methods to be more efficient, such as throughput. In the disaster victim identification (DVI) context, DNA profiling is one of the primary tools in the aftermath of massive catastrophes and an important part in the process in repatriation of victims to their relatives. The first time DNA profiling was effectively used in a DVI process, was in 1990 in the identification of the victims of the fire on the Norwegian ferry ‘Scandinavian Star’. Since then, DNA profiling has been a mainstay in DVI work, and in some situations the method has proven to be the only doable method for victim identification.

Key Concepts:

Genetic profiling is a primary tool for identification of disaster victims.

A common ante‐mortem (AM) sample is often samples collected from a close relative(s) of the missing person.

Postmortem (PM) samples are appropriate tissue samples collected from the dead body or body part.

Potential contamination should be minimised during all processes.

AM samples and PM samples are analysed with the same genetic markers.

STR markers are at present the most widely used markers for genetic profiling for DVI.

A Bayesian approach regarding statistics (use of prior odds combined with genetic data) when evaluating associations between AM and PM genetic data, allows for an assessment of the strength of the alleged relationship in the identification process.
Genetics of Age at Menarche
Authors: He Chunyan 
Published: July 2014

AbstractAge at menarche, defined as the age at first menstruation, is a complex trait influenced by both environmental and genetic factors. A younger age at menarche has been linked to increased risks later in life for a number of diseases including reproductive cancers, cardiovascular and metabolic disorders and osteoporosis. A better understanding of the genetic factors influencing menarche may not only help us to gain more mechanistic insight into normal reproduction functions and those associated diseases, but may also have important clinical implications for the identification of high‐risk subgroups that may benefit from early intervention. Our current knowledge of the genetic basis of age at menarche mainly comes from the results from linkage analysis, and candidate gene and genome‐wide association studies. New technologies and approaches, such as next‐generation sequencing and integrative molecular epidemiology, may provide useful tools for the further discovery of the genetic factors impacting age at menarche.Key Concepts:Age at menarche varies substantially between individuals. A younger age at menarche has been linked to increased risks for cancer, cardiovascular, and metabolic disorders.Age at menarche is a complex trait that is influenced by both environmental and genetic factors. It is estimated that approximately 50% of the observed variation in age at menarche is contributed by genetic factors.Different genetic approaches have identified genetic loci that are responsible for age at menarche. However, the confirmed genetic loci can only explain a small proportion of the observed variation.Future studies of the genetics of age at menarche will focus on rare genetic variations, gene–environment interactions and functional characterisation of the identified genetic variations.Identification of the genetic factors impacting age at menarche may help us to understand normal reproduction functions and diseases associated with menarche timing. This information may then be translated into clinical applications that might allow us to predict early menarche and to identify high‐risk subgroups that might benefit from early interventions.
Genetics of

PTEN

Hamartoma Tumour Syndrome
Authors: Pilarski Robert T 
Published: July 2014

Abstract

The
PTEN
hamartoma tumour syndrome (PHTS) represents a group of clinically related syndromes caused by germline mutations in the
PTEN
gene. These include Cowden syndrome (CS), Bannayan–Riley–Ruvalcaba syndrome, adult Lhermitte–Duclos disease and autism spectrum disorders with macrocephaly.
PTEN
mutations lead to increased cancer risks (including breast, thyroid, uterine, renal cell and colon cancers) and benign overgrowth of multiple tissues, presenting in part as dermatologic lesions, gastrointestinal polyps, thyroid structural lesions, lipomas and vascular lesions. Historically, data on the clinical features of PHTS have been based primarily on collected case reports from the literature. More recently, findings from several large United States and European cohorts have added greatly to our understanding of PHTS. The bulk of these data are on patients with CS, the most common of the PHTS component syndromes. Testing and management criteria and recently revised clinical diagnostic criteria have been established for PHTS.

Key Concepts:

PHTS is an important group of clinical disorders, including Cowden syndrome and Bannayan–Riley–Ruvalcaba syndrome, which are defined by presence of a mutation in the
PTEN
gene.

These conditions are of relevance to many clinical specialties because of significantly increased risks for benign and malignant tissue overgrowth.

The data that are available on risks for malignancy and other features of the syndrome have been almost entirely obtained on cohorts of patients who presented to medical attention and were tested because they demonstrated a significant number of PHTS features. This inherently should lead to overestimates of the prevalence of these features.

Projected lifetime cancer risks in recent studies have been approximately 77–85% for breast cancer (women only), 20–38% for thyroid cancer, 20–30% for uterine cancer, 15–34% for renal cell carcinoma and 9–16% for colon cancer.

Common nonmalignant features include gastrointestinal polyps, macrocephaly, specific skin lesions and structural thyroid lesions. Less common features include Lhermitte–Duclos disease, autism spectrum disorder, mental retardation/developmental delay, testicular lipomatosis and vascular anomalies.

Criteria for making a clinical diagnosis of this syndrome have been recently updated to reflect current literature.

The US National Comprehensive Cancer Network has developed testing criteria and medical management criteria which are updated annually.
Acoustical and Anatomical Determination of Sound Production and Transmission in West Indian (Trichechus manatus) and Amazonian (T. inunguis) Manatees
Authors: Landrau‐giovannetti Nelmarie , Mignucci‐giannoni Antonio A. , Reidenberg Joy S. 
Published: July 2014

ABSTRACTWest Indian (Trichechus manatus) and Amazonian (T. inunguis) manatees are vocal mammals, with most sounds produced for communication between mothers and calves. While their hearing and vocalizations have been well studied, the actual mechanism of sound production is unknown. Acoustical recordings and anatomical examination were used to determine the source of sound generation. Recordings were performed on live captive manatees from Puerto Rico, Cuba and Colombia (T. manatus) and from Peru (T. inunguis) to determine focal points of sound production. The manatees were recorded using two directional hydrophones placed on the throat and nasal region and an Edirol‐R44 digital recorder. The average sound intensity level was analyzed to evaluate the sound source with a T test: paired two sample for means. Anatomical examinations were conducted on six T. manatus carcasses from Florida and Puerto Rico. During necropsies, the larynx, trachea, and nasal areas were dissected, with particular focus on identifying musculature and soft tissues capable of vibrating or constricting the airway. From the recordings we found that the acoustical intensity was significant (P < 0.0001) for both the individuals and the pooled manatees in the ventral throat region compared to the nasal region. From the dissection we found two raised areas of tissue in the lateral walls of the manatee's laryngeal lumen that are consistent with mammalian vocal folds. They oppose each other and may be able to regulate airflow between them when they are adducted or abducted by muscular control of arytenoid cartilages. Acoustic and anatomical evidence taken together suggest vocal folds as the mechanism for sound production in manatees. Anat Rec, 297:1896–1907, 2014. © 2014 Wiley Periodicals, Inc.