bluuebunny/crossref_metadata_2025_split huggingface dataset:
Opiates and Opioids
Authors: Dickenson Tony 
Published: April 2013

Abstract

Morphine and the opiates, drugs found in the opium poppy or their chemical derivatives, are some of the most valuable drugs in medicine due to their ability to suppress pain. They act on systems in the brain, spinal cord and body that are more weakly regulated by endogenous opioids, natural transmitters. The effects of opioids can now be explained in terms of their acting as agonists at one of the four opiate receptors found in the brain, spinal cord and peripheral nervous system. All four receptors are inhibitory but the major one is the μ‐opioid receptor which mediates the wanted (analgesia and relief of anxiety) and unwanted effects of opioids (respiratory depression, nausea, constipation and the potential for dependence). These receptor events underlie the medical and nonmedical use of opioid drugs.

Key Concepts:

Opiates and opioids refer to drugs that are based on the structure or actions of morphine and codeine found naturally in the opium poppy.

These exogenous agents modulate the function of the central nervous system and body systems through activation of inhibitory opioid receptors, of which there are four.

The most important is the μ‐opioid receptor, named after morphine.

The receptors are not present just in case we wander into a poppy field but because there are endogenous opioid peptides that function as inhibitory neurotransmitters through activation of these receptors.

Opioids are valuable medical drugs – the analgesia and relief of anxiety are important effects but there are side‐effects that include respiratory depression, nausea, constipation, sedation and the potential for dependence.

Drugs such as heroin have dangers due to these side‐effects.
Bacterial and Archaeal Inclusions
Authors: Shively Jessup M , Cannon Gordon C , Heinhorst Sabine , Bryant Donald A , DasSarma Shiladitya , Bazylinski Dennis , Preiss Jack , Steinbüchel Alexander , Docampo Roberto , Dahl Christiane 
Published: April 2013

AbstractBacterial inclusions can be defined as discrete structures seen within the confines of prokaryotic cells, generally intracytoplasmic, but in some instances in the periplasmic region of the cell. Inclusions function as metabolic reserves, cell positioners, or as metabolic organelles. Some inclusions may contribute to more than one of these functions. Those that function as metabolic reserves are glycogen, polyhydroxyalkanoate, wax ester, triacylglycerol, cyanophycin, and polyphosphate granules, and sulfur globules. These reserves are commonly accumulated in response to a nutrient imbalance, for example, under conditions of excess carbon/energy. Magnetosomes and gas vesicles contribute to cell mobility thereby assisting the cells in attaining nutrient and/or redox needs. Carboxysomes, containing the enzyme ribulose bisphosphate carboxylase/oxygenase, and chlorosomes, sacs of self‐aggregated bacterriochlorophyll are carbon‐fixing and light‐harvesting organelles, respectively.Key Concepts:The cytoplasmic region of prokaryotic cells can be much more complex than originally thought.In addition to flagella, many prokaryotes have developed mechanisms whereby they are capable of positioning/orienting themselves in an aqueous environment.Although not as complex as the well‐known eukaryotic organelles, many prokaryotes possess simple organelles.Many of the inclusions may have useful properties for applications in biotechnology
Ultramicrobacteria
Authors: Duda Vitaly I 
Published: April 2013

Abstract

Ultramicrobacteria (UMB) are species of the domain Bacteria, whose cells possess a volume of less than 0.1 μm
3
and a small size of genome (from 3.2 to 0.58 Mb). UMB feature a combination of such determining characters as ultrasmall size of proliferating cells and small size of genome. As a synonym for UMB, some authors use the term ‘nanobacteria’ (NB). Several dozens of UMB species have been isolated from various habitats, such as aquatic and soil environments, sediments, silts, Greenland ice, permafrost, human intestines and insects; and are cultured under laboratory conditions on various nutritive media. The term ‘nan(n)obacteria’ is also used to designate ultrasmall bacterium‐like particles occurring in rocks, sands, soils, in deep subsurface, meteorite and clinical samples. UMB include species of free‐living and parasitic bacteria. They are characterised by a great diversity of morphology, ultrastructural organisation, physiology, biochemistry and ecology. Unique processes UMB perform are dehalorespiration, epibiont obligate and facultative parasitism, synthesis of organic compounds in oceanic waters involving bacteriorhodopsin. UMB have been found among organisms of six large phylogenetic branches of prokaryotes, where their nearest relatives are organisms with larger, typical‐of‐bacteria, cells; this is indicative of the polyphyletic origin of the currently known UMB species by reductive evolution.

Key Concepts:

Formation of a minimal autoreplicating microbial cell is the prerogative of the prokaryotes.

Ultrasmall size of cells enables parasitism (predation) of UMB on ‘large‐cell’ species of prokaryotes.

UMB are important model objects for studies of genome evolution in prokaryotes.

UMB studies are of vital importance for solving issues of the origin and evolution of primeval living objects.

UMB research opens new vistas for biotechnology.

Use of UMB representatives, mycoplasms, played a crucial role in epochal works by J Craig Venter and collaborators for experimentally creating a new living being (cells with chemically synthesised genome) and a new bacterial species.

Description of new UMB cell structures expands the diversity pattern of the ultrastructural and molecular organisation of the prokaryotic cell.

Gram‐negative, Gram‐positive or archaeal type of cell organisation are not the prohibitive factors for UMB or UMA to form.
Algal Carbon Dioxide Concentrating Mechanisms
Authors: Mukherjee Bratati , Moroney James V 
Published: April 2013

Abstract

Photosynthetic microorganisms like cyanobacteria and many eukaryotic algae acclimate to a limited availability of carbon dioxide (CO
2
) in their environment by inducing a process called the carbon dioxide concentrating mechanism. This process uses an active inorganic carbon (C
i
; CO
2
and/or HCO
3
−
) uptake system that leads to the internal accumulation of C
i
to levels significantly higher than extracellular levels. Carbonic anhydrase activity converts much of the accumulated hydrogen carbonate to CO
2
, concentrating this substrate around Rubisco and thereby optimising photosynthetic efficiency even under low CO
2
conditions. The efficiency of the process is further improved by the sequestration of Rubisco into specialised structures like the cyanobacterial carboxysome or the pyrenoid in eukaryotic algae. The carbon dioxide concentrating mechanism enhances carbon dioxide fixation and growth in algae. With the increasing demands for sustainable energy sources, algae with efficient carbon dioxide concentrating mechanisms are attractive models for biotechnological and transgenic applications for biofuel and biomass production.

Key Concepts:

The carbon dioxide concentrating mechanism helps photosynthetic algae optimise photosynthesis under limiting CO
2
conditions.

Rubisco uses both carbon dioxide and oxygen as substrates.

Rubisco is localised in the carboxysome in cyanobacteria and the pyrenoid in the green alga,
Chlamydomonas reinhardtii.

The charged hydrogen carbonate needs transporters to enter the cell and cross organellar membranes.

Carbonic anhydrase is an efficient enzyme that carries out the reversible interconversion of carbon dioxide and hydrogen carbonate and this reaction proceeds at a much faster rate than the uncatalysed reaction.

At higher pH levels most of the inorganic carbon is in the form of hydrogen carbonate.

Most algae with carbon dioxide concentrating mechanisms can take up both carbon dioxide and hydrogen carbonate.

Carbon dioxide can diffuse out of the cell so algae trap carbon dioxide in the form of the charged hydrogen carbonate anion.

Algae are used for large‐scale biomass production and are currently being explored as sources of bio‐fuel.
Algal Cell Walls
Authors: Domozych David S 
Published: April 2013

AbstractAlgal cell walls are composed of a diverse array of fibrillar, matrix and crystalline polymers interacting with various ions and water. The diverse array of cell walls exhibited in the various algal groups is a manifestation of ancient evolutionary origins and ecological pressures of modern earth habitats. Cell walls often represent the dominant component of the extracellular matrix and represent the largest or a significant percentage of the photosynthetically fixed carbon of the algae. Walls are typically fibrous composites of microfibrillar polysaccharides embedded in matrix polysaccharides and proteoglycans. Scales and extracellular polymeric substances may also constitute the algal extracellular matrix. The production of the cell walls requires the highly coordinated interaction of several subcellular systems and is controlled by complex gene expression programmes. Modern technologies employed from immunology, molecular genetics, biochemistry and microscopy‐based imaging are transforming our understanding of the cell structure, functions and development.Key Concepts:Algae represent a diverse group of photosynthetic eukaryotes with a wide range of cell wall types.New technologies derived from immunology, microscopy‐based imaging, molecular genetics and biochemistry are greatly enhancing our understanding of algal cell walls.Primitive green algae of the Prasinophyceae produce layers of multishaped scales.The Charophycean green algae produce cell walls containing polymers similar to land plants.The red algae possess complex composite cell walls made of cellulose, xylan or mannan fibrils and extensive matrix polysaccharides including the economically important carrageenan and agar.Diatoms produce highly sculpted frustules made of silica‐based composites and often produce extensive stalks and other extracellular polymeric substances.Brown algae produce cell walls containing cellulose, matrix polysaccharides and in some cases, phenolics.
Algal Eyes
Authors: Hegemann Peter , Dieckmann Carol 
Published: April 2013

Abstract‘Vision’ is defined in a very general sense as recognition of the ambient light pattern by a motile organism and its use for orientation in a local environment. The ‘eye’ is the organ or organelle in which the light absorption and transformation into a transient intracellular signal occurs. The pigmented eyespot is functioning as the optical system that operates in most motile green algae as an interference reflecting device (quarter wave stack). In Chlorophyceae the light sensors are light‐gated ion channels (Channelrhodopsin (ChR)), whereas in Euglenoida photo‐activated adenylyl cyclases (PAC) fulfil this function. ChR is located within the eyespot overlaying part of the plasma membrane whereas PAC is found as a paraflagellar swelling at the basis of the long flagalla.Key Concepts:Motile green algae are able to detect the light direction by means of a pigmented eye.Algal eyes are designed for detection of defuse light.Chlorophyceae use light‐gated ion channels (Channelrhodopsins) for fast depolarisation of the plasma membrane.The depolarisation changes of the plasma membrane (PM) follow intensity changes recorded by the photoreceptor according to the orientation of the cells respective to the direction of the light source.Depolarisation of the PM is continued to the flagellar membrane.Flagallar membrane depolarisation causes activation of voltage gated Ca‐channel and influx of Ca2+.Intraflagellar Ca2+changes modulate the flagellar beating pattern resulting in directional changes of the swimming.As a sensor, Euglenoids use a photo‐activated adenylyl cyclases (PAC) that produces cAMP in the light.Since the PAC is attached to the long flagella, the produced cAMP is immediately sensed by the cAMP‐regulated ion channels at the flagaller base.The intraflagallar Ca2+changes alter the flagellar bending and the swimming direction accordingly.
Algal Flagella
Authors: Wirschell Maureen , Dutcher Susan K 
Published: April 2013

Abstract

Flagella are highly conserved organelles comprised of several hundred proteins that are assembled using the equally conserved mechanism called intraflagellar transport (IFT). The molecular motors dynein and kinesin drive IFT‐mediated flagellar assembly. In addition, flagellar movement is powered by the flagellar dynein motors. The outer and inner dynein arms function in generating flagellar beat frequency and flagellar waveform that are the two main features of flagellar bending. The biflagellate algae

Chlamydomonas reinhardtii

is a powerful model organism for the study of flagellar assembly and function. Recent advances have revealed that cilia and flagella play vital motile and sensory roles in the developing human embryo and in adult tissue function. Defects in assembly or function of mammalian cilia/flagella underlie an expanding set of human diseases and syndromes, collectively called ‘the ciliopathies’. Much of our current understanding of flagellar assembly, motility and the ciliopathies has come from studies in
Chlamydomonas
.

Key Concepts:

Cilia and flagella are highly conserved organelles.

Dynein motors drive flagellar movement.

Chlamydomonas reinhardtii
is a powerful model experimental system for studying flagella.

Defects in assembly or function of cilia/flagella result in multiple pathologies called ‘the ciliopathies’.
Green Algae
Authors: Lewis Louise A , Hall John D , Zechman Frederick W 
Published: April 2013

Abstract

The green algae are a large and diverse group of photosynthetic eukaryotes. They comprise many ancient and diverse lineages, including land plants. Through evolutionary time, green algae have formed a number of symbiotic associations with fungi and animals and their chloroplasts have been incorporated into other eukaryotic organisms through secondary endosymbioses. Green algae display many degrees of organismal complexity: from microscopic unicells to macroscopic, multicellular thalli more than a metre in length. They are critical components of almost all aquatic ecosystems and many terrestrial ecosystems as well. Green algae are commercially important as feed and as a source of many industrial and pharmaceutical chemicals. Available chloroplast, mitochondrial and nuclear genomic data have contributed greatly to our understanding of their biology and evolutionary history. Scientists are still discovering new species and lineages of green algae as well as novel biological and chemical characteristics.

Key Concepts:

Green algae are extraordinarily diverse morphologically and are separated taxonomically into two phyla, Chlorophyta and Charophyta.

Embryophyte land plants evolved from green algae in Charophyta.

Similar morphological forms of vegetative cells evolved in independent lineages of green algae.

As primary producers, green algae are important components of marine, freshwater and terrestrial ecosystems.

Green algae are important model organisms.

Green algae are important symbionts with fungi, bacteria, animals and plants.

Green algae are economically important as sources of industrial products, biofuels and food.

Most groups of green algae are poorly studied and many new species are being discovered.
Chytridiomycota
Authors: Longcore Joyce E , Simmons D Rabern 
Published: April 2013

AbstractThe Chytridiomycota is a phylum in the kingdom Fungi, whose members produce unwalled, asexual spores that swim by means of a single, posteriorly directed flagellum. Members are microscopic saprobes or parasites found in fresh and saline water and soils. The phylum contains two classes, the Monoblepharidomycetes with one order and the Chytridiomycetes with seven orders and several undescribed groups. Orders are based on molecular and ultrastructural characters. Many species of chytrids were described without these characters and need to be re‐examined to place them in the proper orders and genera. Chytrids are important as degraders of cellulose, keratin and chitin and also as algal pathogens, sometimes controlling algal blooms. A few are plant pathogens withSynchytrium endobioticumcausing black wart of potatoes. The rhizophydialean chytridBatrachochytrium dendrobatidisgrows in keratinised skin cells of amphibians and is pathogenic to many species, causing amphibian population declines on several continents and extirpation of some species.Key Concepts:Members of the Chytridiomycota are ubiquitous in aquatic and terrestrial habitats and can be found by microscopically examining baits placed with aquatic debris or with soil plus water.Chytridiomycota reproduce primarily by zoospores, which are mitotically produced, contained by a membrane and motile via a posteriorly directed flagellum.Because of convergent evolution of light microscopic characters, many genera described before the molecular era are polyphyletic and may not be placed in the correct order.Systematics in the Chytridiomycota relies on transmission electron microscopic features of zoospores and on DNA sequence information.Algal parasites are usually species specific and are capable of affecting population levels of planktonic algae.Batrachochytrium dendrobatidisis a chytrid pathogen of amphibians responsible for some amphibian population declines on at least five continents.
Fungal Metabolites
Authors: Moss Maurice O 
Published: April 2013

Abstract

The fungi are a kingdom of organisms as complex and diverse as plants and animals with an estimated 1.5 million species, of which only about 10% have been named and described. The diversity of fungi is reflected in the diversity of fungal metabolites which are the products of secondary metabolism. The biosynthetic pathways are also diverse including polyketides, sesquiterpenes and diterpenes, diketopiperazines, cyclic peptides, β‐lactams and combinations of these pathways. Many of these compounds have biological activity which may be harmful, such as mycotoxins and phytotoxins, or beneficial such as antibiotics and other pharmaceuticals. The structure of many of these relatively low molecular weight compounds has often been a challenge to the natural products chemist but the continuing development of mass spectroscopy, nuclear magnetic resonance spectrometry with increasingly sophisticated methods of chromatography have led to the continuing discovery of novel fungal metabolites.

Key Concepts:

Fungal secondary metabolism is both diverse and distinct.

Secondary metabolism is linked to primary metabolism by a common pool of intermediates such as acetyl‐CoA, mevalonate and amino acids.

Penicillins, cephalosporins and griseofulvin are widely used antibiotics.

Mycotoxins such as aflatoxin, ochratoxin and patulin are controlled in human foodstuffs by legislation.

The majority of plants have endophytic fungi some of which produce useful metabolites.
Fungi: Ecological Importance and Impact on Humans
Authors: Kendrick Bryce 
Published: April 2013

Abstract

Fungi play vital roles in the biosphere. They are essential to the recycling of nutrients in all terrestrial habitats because they are the dominant decomposers of the complex components of plant debris, such as cellulose and lignin. As opportunistic heterotrophs, they have evolved hyphae to penetrate solid substrates, and spores for long‐range dispersal. They cause many diseases of plants and animals, but they also have established mutualistic symbioses with a wide range of organisms: cyanobacteria and green algae (in lichens), bryophytes, pteridophytes, gymnosperms and angiosperms (in mycorrhizae), and coleopteran, dipteran, homopteran, hymenopteran and isopteran insects. As parasites or pathogens they are well equipped to penetrate host organisms and to liberate spores that will effectively transmit them from one host to the next, and many species produce toxic compounds (mycotoxins). Some fungi affect human health in various ways.

Key concepts:

Many fungi are opportunistic heterotrophs, disposers of, or recyclers of, organic substrates, especially those of plant origin.

Parasitic fungi attack almost all known taxa of plants and animals.

Fungi have established mutualistic symbioses with cyanobacteria and chlorophycota (green algae) to form lichens.

Fungi often form symbiotic associations with the roots of plants (bryophytes, pteridophytes, gymnosperms and angiosperms) in mycorrhizae.

Some fungi live as symbionts with coleoptera, diptera, homoptera and hymenoptera.

Some fungi cause diseases (mycoses) in humans or excrete toxic compounds (mycotoxins).

Fungal spores can cause severe allergies in humans.
Mycotoxins
Authors: Ehrlich Kenneth C , Chang Perng‐Kuang , Bhatnagar Deepak 
Published: April 2013

AbstractMycotoxins are a class of natural fungal metabolites that are specifically toxic to mammals and are frequent contaminants of foods and feeds. In this article we describe mycotoxins from Ascomycota or sac fungi, the largest phylum of fungi, which includes penicillia, aspergilli, fusaria, alternaria, claviceps and other non‐Basidiomycota (‘higher fungi’ or mushroom‐producing) genera. We discuss the toxicity and biosynthesis of the most agriculturally important mycotoxins, namely, polyketide toxins (fumonisins, aflatoxins, ochratoxins, patulin and zearalenone), nonribosomal peptide toxins (ergot alkaloids and tremorgenic toxins) and trichothecenes produced via the terpene biosynthesis pathway. The Ascomycota produce mycotoxins in crops both before harvest and during storage. The genes required for biosynthesis are usually clustered. Transcriptional regulation of biosynthesis involves a pathway‐specific Cys6Zn2type protein as well as a secondary metabolite‐specific methyltransferase, LaeA. Both of these transcription factors are unique to fungi. Hypotheses about the evolution of mycotoxin biosynthesis in fungi are discussed.Key Concepts:Mycotoxins are produced by ascomycete (‘lower’) fungi in certain agriculturally important crops.The most common mycotoxins exert a variety of generally nonlethal toxic effects in animals.Biosynthesis of mycotoxins usually involves a co‐regulated, clustered set of genes on one chromosome.Co‐regulation involves transcription factors of the Cys6Zn2type and a putative methyltransferase, LaeA.Mycotoxins can be of several types: polyketides, nonribosomal peptides or terpene‐derived metabolites.Mycotoxin biosynthesis has evolved in fungi in the absence of agriculture and is not strictly associated with fungal virulence in contaminated crops.