bluuebunny/crossref_metadata_2025_split huggingface dataset:
History of Scientific Agriculture: Crop Plants
Authors: Hancock JF 
Published: April 2013

AbstractThe first farming communities appeared in the Fertile Crescent above the Tigris River in what is now Iran approximately 13 000 years ago. Agriculture was also invented independently at several other locations in the world including Africa, Asia, China, India, Japan, Mesoamerica, South America and the Eastern US. Most of the early crops were annual types that were self‐pollinating and polyploid. The crops emerging in each region spread gradually across the world. Once humans began to plant and harvest, several profound changes occurred in the crop species due to conscious and unconscious selection. Some of the major changes were nonshattering of seed pods, more determinate growth, more uniform ripening, larger seed size and increased seed production. Levels of genetic diversity were also greatly reduced during the process of crop domestication when humans selected only those types that were most beneficial to them.Key Concepts:Homo sapiensdid not begin agriculture until approximately 13 000 years ago, even though the modern form of humans appeared approximately 50 000 years ago.The domestication of crops by humans began in what is called the ‘Fertile Crescent’ on the western edge of modern Iran, but at least 13 other locations across the world spawned agriculture.The act of planting and harvesting plants dramatically altered the genetic and physiological makeup of crop species, effecting traits such as seed retention, growth patterns, uniformity of ripening and levels of seed production.The earliest crops represented a broad array of plant families, but most were herbaceous annuals and self‐pollinated.During the domestication process, levels of genetic variation were dramatically reduced as humans selected a narrow range of plant types.
Nucleic Acids: Hybridisation
Authors: Kim Ji Hun , Kalitsis Paul , Pertile Mark D , Magliano Dianna , Wong Lee , Choo Andy , Hudson Damien F 
Published: April 2013

Abstract

Nucleic acid hybridisation is the pairing of complementary
deoxyribonucleic acid
(DNA) strands to produce DNA–DNA hybrids or the pairing of complementary DNA–RNA strands to produce DNA–RNA hybrids. Nucleic acid hybridisation is the basis of many research and diagnostic applications with all relying on simple base pairing specificity of nucleic acids to generate a signal through a labelled probe. This fundamental principle has led to DNA/RNA detection and quantification on solid phase blots, DNA/RNA cytogenetic localisation on cells, detection and purification of specific DNA and comparative gene expression analysis. Most recently, principles of nucleic acid hybridisation have been combined with next generation sequencing technology to create powerful new platforms for analysis which will increase in utility as we enter this new age of genomics and personalised medicine. The concepts and applications of nucleic acid hybridisation will be discussed in this review.

Key Concepts:

Nucleic acid hybridisation using base paring complementary allows detection of genes, mutations and RNA permitting accurate diagnosis of disease in the clinic and providing researchers with many powerful tools to analyse and interpret their work.

Traditional hybridisation technologies have enabled detection of target DNA or RNA sequences on a solid‐base membrane or on chromosomes.

Development of radioactive and nonradioactive probe labelling systems allowed for significantly improved sensitivity and specificity of detection of the target nucleic acids.

Nucleic acid hybridisation in quantitative analysis permits detection of mutations such as deletion, insertion and copy number variation for disease diagnosis.

Incorporation of next‐generation sequencing with nucleic acid hybridisation has opened a new genomic era and has enabled high‐throughput sophisticated analysis for personalised medicine by discovering novel genes and single nucleotide polymorphisms (SNP).
Parasitism: The Variety of Parasites
Authors: Phillips R Stephen 
Published: April 2013

AbstractAssociations between animals of different species can take a variety of forms, ranging from commensalism where the partners live independent lives but benefit each other, to parasitism where one partner of the relationship benefits at the expense of the other, the host. In between, we have mutualism where the partners have an intimate relationship which is obligatory for both partners but is also beneficial to both. The majority of parasites in the animal kingdom are invertebrates. Amongst the protozoa, parasites of medical or veterinary importance are found amongst the amoebae (e.g.Entamoeba histolytica), the flagellates (e.g. trypanosomes) and the sporozoa (such as the malarial parasites), all of which are parasitic. The parasitic worms (helminths) are very important parasites of man and his domestic animals including the flukes (e.g. schistosomes causing bilharzia), round worms or nematodes such asAscaris lumbricoides, the large round worm of humans, and the tapeworms or cestodes (it is the larval stages of tapeworms which are the cause of morbidity). Finally, the arthropods include important parasites such as ticks and mites (arachnids), and insects such as lice and fleas. Many insects such as mosquitoes, of course, act as vectors of parasites. Parasites are also identified as either endoparasites or ectoparasites depending on whether they are located internally or externally with respect to the host. Parasites often have incredibly complicated life cycles and employment of control measures against parasites requires detailed knowledge of these life cycles.Key Concepts:Associations between different species of animals can take various forms ranging from commensalism, through mutualism to parasitism.In commensalism both partners live independently, in mutualism there is an obligatory intimate relationship between the partners which is beneficial to both and, in parasitic relationship one partner benefits at the expense of the other.Most parasitic species are invertebrates but there are some vertebrate parasites such as the cuckoo.Parasitic species are found in both single‐celled organisms, the protozoa, and the multi‐celled metazoan organisms.There are important medical and veterinary parasites in all the major groups of protozoan and metazoan animals.Parasites can be found inside their host and are known as endoparasites whereas some found outside their hosts and are known as ectoparasites.Devising strategies to control parasites and avoid infection depends on an understanding of the life cycle of the parasites.
Trophic Cascades
Authors: Gruner Daniel S 
Published: April 2013

Abstract

Trophic cascades in ecological communities are defined as the propagation of indirect effects between nonadjacent trophic levels in a food chain or food web. Typically, cascades are driven by predation from the top‐down, with altered herbivore densities mediating the ultimate effects on the biomass of primary producers. Predator traits and nonconsumptive changes in the behaviour of prey also can propagate cascading indirect effects, and variation in nutrients or energy at the base of food webs may mediate cascades from the bottom‐up. Significant debate has revolved around the relative dynamical strength of top‐down versus bottom‐up forces and over the importance of trophic cascades in different aquatic and terrestrial ecosystems. Polarisation has eased with the increased availability of experimental and comparative case studies, meta‐analytic syntheses of these data and development of theory. The basic conceptual construct of trophic cascades has been applied to classical biological control of agricultural pests, biomanipulation of lakes and streams and the conservation and restoration of apex predators for fisheries and wildlife management.

Key Concepts:

Limited nutrient availability and high C:N and C:P stoichiometry can constrain biomass turnover and the strength of trophic cascades.

Many lake and stream ecosystems support four trophic levels, with piscivorous fish ultimately suppressing phytoplankton in a consumptive interaction chain.

Trophic cascades can occur via direct consumption and density reductions of prey and through behavioural changes in prey foraging from predation risk.

Fisheries intensification has selectively reduced top predators and large‐bodied species and reduced the length of oceanic food chains.

Reintroduction of top predators, such as wolves, to the American west has facilitated recruitment of woody shrubs and trees and reduced stream erosion.

Long‐term studies are critical to testing for and identifying trophic cascades on landscape and regional spatial scales.
Phosphorus Availability in the Environment
Authors: Tiessen Holm 
Published: April 2013

Abstract

Phosphorus is a key element in biological reactions so that small changes in phosphorus availability can have major impacts on ecosystem function and structure. In soils and ecosystems, P is derived from the parent rocks. Although phosphate is relatively insoluble it is eventually weathered and leached out so that many old soils are P deficient and their associated ecosystems are P limited. High productivity agriculture relies on P fertilisation. Phosphorus is highly concentrated in plant seeds (grains), animals and animal (and human) excrements. Consequently environments with intensive animal production or high population density receive a surplus of P that commonly causes environmental pollution. The imbalance between regions of low and of surplus P must be addressed through more efficient P management, both in fertilisation practices and efforts to recycle P from wastes. This is particularly important as the principal source of P, rock phosphates are becoming more expensive, reserves more difficult to find and mine, and are globally strategically unevenly distributed.

Key Concepts:

The only source of P in soils are the parent rocks or added fertilisers.

Weathering slowly removes P from soils, so that many old and tropical environments are P deficient.

P is essential to all life and is concentrated by organisms to levels thousands of times higher than environmental concentrations.

High environmental P concentrations usually result from the excretions or residues of organisms.

Being limiting to life, P stimulates biological growth and when in excess will cause ecosystem disruptions through eutrophication.

The principal source of fertiliser P are rock phosphates which are sedimentary deposits of marine organisms.

Approximately 1000 million t of P have been mined and added to the environment.

Finite P resources have caused concern about ‘peak production’ occurring near the middle of the twenty‐first century, followed by declines and higher prices that may limit food production.
Nitrogen Budgets
Authors: Kätterer Thomas 
Published: April 2013

Abstract

The compilation of inputs and outputs of nitrogen across the boundaries of a system defined in time and space comprises a nitrogen budget. This budget contains information about internal nitrogen fluxes within the system and can be used as an efficiency indicator or policy instrument. Nitrogen cycling at global and ecosystem scale is described as well as transformations of nitrogen between different chemical forms occurring in nature. Chemical and biological processes governing the distribution and transformation of nitrogen within ecosystems are presented including ammonification, nitrification, denitrification and plant uptake. Examples for agricultural systems are shown for illustrating how different nitrogen fluxes can be selected for calculating nitrogen budgets depending on definitions of system boundaries. Environmental consequences due to human interactions with the nitrogen cycle are also presented and discussed.

Key Concepts:

The compilation of inputs and outputs of nitrogen across the boundaries of a system defined in time and space comprises a nitrogen budget.

Nitrogen is an essential element of all living matter and, in addition to carbon, the main building block of many macromolecules, such as proteins and nucleic acids.

Although nitrogen makes up about 78% of the air we breathe it must be transformed into reactive chemical forms for being available for vascular plants.

The amount of nitrogen cycled within ecosystems is about one order of magnitude larger than the amounts crossing ecosystem boundaries.

Generally, more than 90% of the nitrogen needed for primary production is recycled through within ecosystems.

Production of mineral fertilisers is essential for feeding a growing human population.

Human impacts on nitrogen cycling are significant.

Environmental concerns due to human interactions with the nitrogen cycle are mainly related to the presence of nitrate in water and emissions of nitrogen oxides contributing to stratospheric ozone depletion and to the greenhouse effect.

Farmgate nitrogen balances, defined as the difference between nutrient input and output at farm level, are increasingly used as environmental performance indicators or as policy support tools for emission control.
Ecophysiological Responses of Plants to Air Pollution
Authors: Caporn Simon JM 
Published: April 2013

Abstract

In industrialised and heavily populated regions of the world, air pollution has an important influence on vegetation, affecting the production, abundance and distribution of plants. The principal primary pollutants are reactive compounds of sulphur, nitrogen and hydrocarbons emitted during the combustion of fossil fuels in industry, transport and from intensive farming. Increasing in importance is the secondary pollutant ozone. The direct effect of pollutants on plants is strongly influenced by the extent of their uptake into the plant tissues. Pollution also affects soils through increasing soil acidity and altering the balance of soil nutrients affecting roots and plant nutrition. Air pollution affects plants interactions with pests and pathogens and the sensitivity of vegetation to cold and drought stress. Understanding the ecophysiological responses and mechanisms by which air pollutants affect plants helps policymakers to set guidelines for air pollution to protect vegetation, crops and ecosystems.

Key Concepts:

Fossil fuel combustion and intensive agriculture are the main sources of air pollutants, which may be transported over long distances to affect plant life on a global scale.

In developed nations, sulphur dioxide, smoke and acid rain were the main acute air pollution concerns in the past, but now ozone and reactive nitrogen may pose the greatest threats.

Pollutants are deposited to plants as dry deposition of gases and particles and wet deposition in rain and cloudwater.

Stomata and cuticle on plant's surfaces provide an important control on uptake by vascular plants.

Bryophytes and lichens are vulnerable to air pollution as they lack a protective cuticle.

Acid rain, ozone, SO
2
and other pollutants can directly injure the physiology of above ground plant tissues such as leaf gas exchange, carbon transport or flowering.

Soils are affected by increased acidity and nitrogen deposition which have long term effects on plant nutrient uptake, root system health and species competition.

Biodiversity and structure of plant communities appears to be damaged by long term nitrogen deposition.

Air pollution increases plant attack from pests and pathogens and increases vulnerability to cold and drought stress.

More understanding is needed of damage mechanisms to inform air quality guidelines to protect plants and their ecosystems.
Ecology of Vertebrate Nutrition
Authors: McWilliams Scott R 
Published: April 2013

AbstractVertebrate nutritional ecology is the study of the interrelationships between food resources in the environment and the consumptive use of these food resources by vertebrate animals. Consumptive use includes how vertebrate animals procure, digest, absorb and metabolise available foods in the environment to satisfy their requirements for health, growth and reproduction. The challenge for wild vertebrates is to satisfy their nutritional requirements in an environment that often varies in food availability and quality. Vertebrate animals have evolved a diverse and interesting suite of solutions to the problem(s) of acquiring necessary nutrients and energy in a world where food often does not want to be eaten.Key Concepts:Vertebrates require certain amounts of energy, protein, as well as about 38 micronutrients including 10 essential amino acids, 1–3 essential fatty acids, 13 vitamins and at least 14 essential minerals.Energy requirements (kJ day−1) of vertebrates increase with body mass of the animal in a predictable allometric manner (slope≈0.72), although birds on average have higher energy requirements for a given body size than mammals.Protein requirements of vertebrates depend on protein quality (i.e. amino acid composition of dietary protein) because animals require a balanced profile of essential amino acids relative to their needs so that normal rates of protein synthesis are maintained.Vertebrate animals can grow normally on a diet without carbohydrates provided they consume adequate fats that include the few essential fatty acids.Bill morphology in birds, and tooth and jaw structure in all other vertebrate classes are impressively diverse and provide excellent examples of evolutionary design in relation to procuring food.The chemical breakdown of ingested food involves specific enzymes that digest each of the three major types of macronutrients: proteases for digestion of protein, carbohydrases for digestion of carbohydrates and lipases for digestion of fats.Absorption of digested macronutrients and micronutrients by the intestine involves several processes including passive diffusion, facilitated diffusion and active transport.Changes in specific activity of digestive enzymes and the absorption rate of digested nutrients by the intestine in response to diet changes provide strong evidence for adaptive modulation of digestive features.The evolution of enlarged portions of the gut to house symbiotic microbes was crucial in the radiation of herbivorous vertebrates because it provided the appropriate conditions for microbial fermentation to have significant nutritional benefits.Contemporary research is providing new insights into the importance of phenotypic plasticity and flexibility in the metabolism, physiology and behaviour of wild animals and how this influences an animal's ability to satisfy its nutritional needs in their natural environment.
Urban Ecology: Patterns of Population Growth and Ecological Effects
Authors: Zipperer Wayne C , Pickett Steward TA 
Published: April 2013

Abstract

Currently, over 50% of the world's population lives in urban areas. By 2050, this estimate is expected to be 70%. This urban growth, however, is not uniformly distributed around the world. The majority of it will occur in developing nations and create megacities whose populations exceed at least 10 million people. Not all urban areas, however, are growing. Some are actually losing populations because of changing economic conditions and population demographics. Whether a city is growing or losing population, governances face unique challenges with respect to infrastructural, water and transportation needs. To meet these challenges, agencies within city government are cooperating by pooling resources and removing conflicting policies, partnering with the private sector to offset costs of infrastructure, and taking new approaches to design infrastructure. By linking ecological theory with urban design, a more integrative approach to create liveable spaces, which are sustainable, can be achieved in rapidly expanding and shrinking urban areas.

Key Concepts:

Megacities and shrinking cities are our future. In the nineteenth and twentieth centuries, most of the world's population lived in rural areas. With economic shifts people moved into cities to find employment, better health services, and improved education opportunities.

Future cities represent major ecological, social and economic challenges and opportunities. Rapid urban growth creates economic incentives but can fragment, destroy or degrade existing natural ecosystems. Similarly, population losses create economic and ecological opportunities for expansion and growth.

Integrating ecological theory in urban design can create a framework for sustainable cities that are adaptive and resilient. Often, infrastructure is designed to meet engineering specifications but do not incorporate ecological functionality. By integrating ecological with the engineering, infrastructure can meet regulations at the same time enhancing the environment.
Eutrophication of Lakes and Rivers
Authors: Duncan Emily , Kleinman Peter JA , Sharpley Andrew N 
Published: April 2013

Abstract

Eutrophication is an ecological process, akin to aging, in which a water body is increasingly enriched with organic matter. Although the most obvious signs of eutrophication in lakes and rivers involve algal blooms and fish kills, the systemic of eutrophication, although profound, are often not as noticeable to the casual observer. Eutrophication of lakes and rivers is accelerated by nutrient pollution, one of the most pervasive water quality problems in the world. Increases in populations and intensification of land use have accelerated eutrophication of water bodies from the Great Lakes of North America, to Lake Tai of China to Lake Victoria in Africa. Because nutrients can come from many sources, point as well as nonpoint, comprehensive strategies are required to curb eutrophication. A variety of watershed programs have yielded success, but they are outnumbered by the ever‐expanding number of lakes and rivers that are undergoing eutrophication.

Key Concepts:

Eutrophication of lakes and rivers is caused primarily by inputs of phosphorus and nitrogen.

Accelerated eutrophication can render a water body unusable for many uses, from fishing to swimming to drinking water.

Point source pollution comes predominately from industrial sources and wastewater treatment plants.

Nonpoint source pollution, or diffuse pollution, derives from urban and rural land uses, ranging from lawns and golf courses to agricultural fields.

Watershed management is required to successfully control eutrophication, involving comprehensive programs that tackle the many sources of nutrients in a watershed.

Nonpoint sources of nutrients, such as soils, sediments and groundwater, are extremely difficult to combat, requiring decades to reverse.
Agricultural Production
Authors: Pimentel David 
Published: April 2013

Abstract

World food security is threatened because agricultural production is unable to keep up with the increasing demand for food to feed a rapidly growing human population. Soil erosion due to agricultural production occurs much faster than soil formation. Water is fundamental to food production requiring 1000 L to produce 1 kg of biomass. Plants only collect less than 0.1% of energy reaching them per year. Approximately 10 kcal of fossil energy are required to produce 1 kcal of food. Finite natural resources, such as land, water and energy, limit what most technological advances in agricultural production can accomplish. If projected human population growth comes to pass, additional malnutrition and even further starvation will occur. Severe social and political disorder will also occur because agricultural production will fail to keep pace with population growth.

Key Concepts:

Malnutrition is more than simply not enough food or even being hungry or not but whether adequate absorption of food nutrients occurs and how successfully disease and parasitic organisms compete for nutrients with the human organism they may come to inhabit.