bluuebunny/crossref_metadata_2025 huggingface dataset:
Sarcosporidiosis
Authors: Mehlhorn Heinz
Published: April 2013

Sarcosporidiosis is a disease that occurs worldwide in many animals and human beings as a result of oral infections with developmental stages of several
Sarcocystis
species, the life cycle of which includes two types of hosts: a prey and a predator. Humans may be involved in both groups. The prey hosts are herbi‐ or omnivores, which are infected by oral uptake of oocysts and sporocysts from the feces of the predator hosts, which are carnivorous beings including man. The specimens of the latter group are infected by eating raw or undercooked meat of the prey animals containing so‐called cyst merozoites (cystozoites) inside tissue cyst in muscle cells or in brain cells. The final hosts (=carnivores with the sexual development inside their intestinal cells) may suffer from diarrhoea in case of severe infections. The intermediate hosts (=prey hosts) may severely suffer from bleeding of inner blood vessels (where the schizonts and merozoites develop within the first month after infection) and by destruction of brain and muscle cells, where the cysts are formed. After about 3 months the cyst merozoites inside the tissue cysts are infectious for the final host.

Key Concepts:

Human intestinal infections with
Sarcocystis
species are completely prohibited by noneating raw or undercooked meat.

Strict separation of human, dog and cat feces from food of farm animals prohibits their infections with
Sarcocystis
species.

Sarcosporidiosis is completey avoidable on farms by strict hygienic measurements.

Deep freezing or cooking of meat will kill sarcosporidians.
Protozoan Pathogens: Identification
Authors: Walochnik Julia , Aspöck Horst
Published: April 2013

The identification of protozoan pathogens is based upon direct detection of the respective causative agent in clinical specimens and/or upon detection of specific immune reactions of the host. A considerable part of protozoan diagnostics still mainly relies on microscopy, however, in the past years molecular methods, particularly polymerase chain reaction (PCR)‐based techniques, have gained more and more importance. One of the big advantages of molecular techniques is that they usually allow identification below the genus level, which is often impossible by light microscopy. Serological tests are of great value in all tissue parasites and generally in most extra‐intestinal infections, whereas they only have limited importance in acute infections with short incubation times and in immunocompromised patients. Rapid card tests detecting parasite antigens and host antibodies are available for several important protozoan parasites and serve particularly well in the field setting.

Key Concepts:

Of the around 100 protozoan species that can infect humans, some are of prime importance for human health, including the causative agents of
malaria, amebiasis, leishmaniasis
and
sleeping sickness
.

Several protozoan infections show a more severe progression in the
immunocompromised host
, important examples are toxoplasmosis, pneumocystosis, cryptosporidiosis and visceral leishmaniasis.

The size of protozoan pathogens varies from
∼2 μm
(amastigote
Leishmania
spp.) to
∼150 μm
(

Balantidium coli

).

As parasite density in stool or body fluids may not be constant, the collection of repeated samples is often essential.

Proper collection, storage and transport of clinical specimens are of crucial importance for reliable laboratory diagnostics.

Accurate diagnosis includes both parasite
detection
and species (in some cases: genotype/serotype)
identification
.

Although numerous protocols for molecular detection of protozoan pathogens have been established in the past years, consent on the most reliable technique is missing for most protozoan taxa, thus demonstration of the causative agent in native material or stained smears is still the
gold standard
for detection.

Good
microscopic expertise
is essential: low parasite density and/or morphologic variability can result in false negative results, pseudo‐parasites and artefacts are common causes of false positive results.

In many protozoan taxa, morphology alone does not provide enough information for identification on or below the species level, this is today mainly based on
molecular biological methods
.
Euglena
Authors: Buetow Dennis E
Published: April 2013

Euglena
is a genus of single‐celled, free‐living, mainly freshwater‐dwelling organisms that contain chloroplasts and show both plant‐ and animal‐like characteristics.
Euglena
Authors: Buetow Dennis E
Published: April 2013

Euglena

is a genus of single‐celled, free‐living microorganisms that show both plant‐ and animal‐like characteristics. Members of the genus are found widely in nature and mainly in fresh waters. Most are aerobic and use photosynthesis or many organic compounds as interchangeable sources of carbon and energy. The most studied species is the easily grown

E. gracilis

which, in spite of its relatively rigid surface, can be subfractionated to yield nuclei, mitochondria, chloroplasts, flagella and pellicles. Subfractions show some unusual characteristics: The nuclear envelope remains intact throughout mitosis and chromosomes are permanently condensed at all phases of the cell cycle, the mitochondrial respiratory chain has two terminal oxidases, and chloroplasts have three membranes reflecting their endosymbiotic evolutionary history. Various

Euglena

and some of their constituent molecules are useful for environmental biomediation and potentially useful biomedically.

Key Concepts:

Euglena
is a genus of single‐celled, free living microorganisms that show both plant‐ and animal‐like characteristics.

More than 250
Euglena
species have been described, though the actual number is not known.

The majority of
Euglena
species are green due to the presence of chloroplasts containing chlorophylls
a
and
b
.

Members of the genus
Euglena
are found widely in nature, inhabiting freshwater pools, ponds and lakes.

Euglena
are able to use photosynthesis and heterotrophic oxidative assimilation as interchangeable and apparently equivalent sources of carbon and energy.

How to classify
Euglena
has been a long‐standing problem; the genus has been claimed as photosynthetic protozoa by zoologists and as algae by botanists.

Studies on the genus
Euglena
, and especially

E. gracilis

, have been significant for understanding the biochemistry and molecular biology of nuclei and subcellular organisms.
Ciliophora
Authors: Lynn Denis H
Published: April 2013

Ciliophora is the name for a phylum of protists commonly called the ciliates. Ciliates are the most complex of cells, having an elaborate cytoskeleton, cilia and two different kinds of nuclei. Free‐living ciliates can be found in almost any habitat that has water – in soils, hot springs and Antarctic sea ice. Symbiotic species live as commensals in sea urchins or as parasites of lobsters and fish. Ciliate life histories can have specialised forms for dispersal and for resisting desiccation. Their cell cortex is supported by a complex framework of basal bodies or kinetosomes, microtubules and microfilaments. The kinetosomes form the central unit in an organellar structure called the kinetid, which is important to understanding phylogenetic relationships among ciliates. The pattern of fibres and microtubules in the kinetid identifies a ciliate to a major clade, along with the sequences of genes. These two features together identify 12 major clades or classes of ciliates.

Key Concepts:

Ciliates are characterised by three main features: they exhibit nuclear dimorphism; undergo conjugation as a sexual process; and typically have cilia at some stage in their life cycle.

Ciliates are the ‘top’ predators in microbial food webs, and were likely the major predatory group before the evolution of animals.

Parasitic ciliates can cause morbidity and death of animals, and are becoming particularly important in aquaculture operations.

Ciliates can have complex life cycles, including macrostome or cannibalistic stages, swarmers or dispersal stages and cyst or desiccation‐resistant stages.

The kinetid, an organellar complex in the cell cortex, is composed of at least one kinetosome and its cilium associated with two microtubular ribbons and a striated kinetodesmal fibril, whose patterned arrangement identifies a ciliate to a particular major clade or class.

Ciliate macronuclei divide in two ways, which suggest that macronuclear division evolved independently twice in the phylum: heterotrich ciliates divide their macronucleus principally using extramacronuclear microtubules while intramacronucleate ciliates divide their macronucleus with intramacronuclear microtubules.

Ciliates are divided into two major clades or subphyla and 12 classes based on features of the kinetid and sequences of genes.
Haptophyta
Authors: Jordan Richard W
Published: April 2013

The haptophytes are a group of microalgae, mostly marine, usually phototrophic, that possess a unique organelle, the haptonema, situated close to the flagella. Species identification traditionally relies on the morphology of the unmineralised or mineralised scales, although some recent advances have been made using molecular genetics. A number of taxa form blooms, some of which are toxic to marine life. The haptophytes include the calcified scale‐producing coccolithophorids, whose ancestors are partly responsible for the vast chalk deposits found in northern Europe.

Key Concepts:

The haptophytes are a monophyletic group that possess a haptonema.

Species identification is based almost entirely on scale morphology and the combination of scale types.

Blooms can sometimes cover vast areas of the ocean, contributing significantly to the global carbon and sulphur cycles, and may be toxic.

Species‐specific viruses may be involved in the termination of haptophyte blooms.

The majority of the chalk and limestone deposits of the Mesozoic and Cenozoic eras were produced by continual coccolith accumulation in the sediments.
Antimycobacterial Drugs
Authors: Gillespie Stephen H , Murphy Michael E
Published: April 2013

Antimycobacterial drugs are used in the treatment of diseases caused by members of theMycobacteriumgenus, including tuberculosis (TB) and leprosy, which have affected man since antiquity, and the nontuberculous mycobacterioses (NTM) that are increasingly recognised. Combination chemotherapy is essential to kill heterogeneous populations of bacterial cells located in different conditions within the host, and to prevent drug resistance. Although combination therapy has been effective in controlling leprosy, the global HIV epidemic and the emergence drug resistance are undermining efforts to control TB. Currently available chemotherapeutic agents are highly effective in managing drug‐sensitive TB, however, the development of new antimycobacterial drugs to manage both drug‐sensitive and drug‐resistant disease is a global health priority. These drugs must be safe, effective and affordable in resource‐limited countries most burdened by TB disease. NTMs are increasingly being identified as human pathogens in both non‐ and immunocompromised patients; more evidence for the most efficacious treatments is required.

Key Concepts:

Tuberculosis is global health priority with 9 million active cases, and 1.7 million deaths each year, of whom 0.5 million are coinfected with HIV; with 1 in 3 people latently infected globally, there is a huge pool of potential future infection.

Mycobacteria are unusual; they are slow growing with a thick waxy cell wall made of lipid rich material which makes penetration by drugs problematic.

At any one time, there may be heterogeneous populations of mycobacterial cells in different metabolic states; these may be targeted by different antimycobacterial drugs.

Antimycobacterial drugs are used for the treatment of mycobacterial infections, including tuberculosis, leprosy and nontuberculous mycobacateria; the greatest burden of disease is borne by developing countries with limited resources.

Combination treatment is required for prolonged periods, usually 6 months or more, to kill heterogeneous mycobacterial cells in different locations within the host, and to prevent resistance developing.

Drug resistance develops through spontaneous mutations in the chromosomal DNA. Exposing mycobacteria to monotherapy selects out these resistant strains, as may happen when patients are nonadherent with prescribed therapy.

Drug resistance is a major problem in the control of tuberculosis globally; 5% resistant to both rifampicin and isoniazid (MDRTB) the backbones of currently recommended chemotherapy, with around 10% of those also resistant to fluoroquiniolones and second line agents (XDR TB).

Leprosy elimination programmes have successfully reduced the prevalence of the disease; patients are rendered noninfectious after the first dose of medication.

Nontuberculous mycobacteria are emerging as important human pathogens; there is a pacuity of robust evidence for their optimal management.

A large number of new agents with novel mechanisms of action are being trialled to assess their efficacy in treating mycobacterial disease.
Alcoholism
Authors: Wallace Melisa J , Newton Philip M
Published: April 2013

Alcohol has been consumed by humans for thousands of years, but its biological effects are complex and poorly understood. Similarly, alcoholism is a common and extremely debilitating condition for which there are no truly effective treatments, in part due to our incomplete understanding of the underlying biology of the condition. This chapter describes current understanding of the biology of alcohol intoxication and alcoholism, with a focus on the neurological and molecular bases for these phenomena. We explain what is known about how alcohol produces intoxication, tolerance and physical dependence, and how these relate to alcoholism. We describe risk factors for the development of alcoholism and how these relate to the acute and chronic effects of alcohol. We also outline the current treatments for alcoholism and some common co‐morbid disorders.

Key Concepts:

Alcoholism, like all addictions, is a disease.

Alcoholism is defined by repeated alcohol consumption despite known adverse consequences. The urge to drink is uncontrollable.

Alcoholism is distinct from the related phenomena of tolerance to alcohol and withdrawal from chronic alcohol exposure.

Alcohol is a weak and nonspecific drug, which acts through multiple molecular mechanisms.

There are few treatment options for alcoholism and those available have only limited success.
Pharmacogenetics
Authors: Novelli Giuseppe , Biancolella Michela
Published: April 2013

Pharmacogenetics (PGt) is the study of the influence of individual variations in
deoxyribonucleic acid
sequence on drug response. Drug response includes drug disposition (pharmacokinetics) and drug effect (pharmacodynamics). PGt is applicable to activities such as drug discovery, drug development and clinical practise. Currently, there are more than 200 drugs whose labelling includes pharmacogenetic information. ‘Test required’ examples: Cetuximab, Trastuzumab, Maraviroc, Abacavir, Dasatinib, Glivec, Tasigna, Gefitinib and Herceptin; ‘Test recommended’ examples: Carbamazepine, warfarin, azathioprine, etc. In the coming years, evaluation by regulatory authorities of new medicines may involve increasingly PGt components in pre‐ and post‐approval development, and may therefore depend on reliable PGt information. PGt is a rapidly and continuously evolving field; therefore, PGt studies should reflect on the ‘principles’ or necessary qualities of developing well‐controlled, rigorous and reproducible sample handling and testing procedures.

Key Concepts:

Pharmacogenetics define populations that can have most benefit from a drug.

Pharmacogenetics improve drug development.

Pharmacogenetics predict disease course (to justify more intense or prolonged treatments) (diagnostics and prognostics).

Pharmacogenetics can be used to monitor the effects of the therapy (pharmacodynamics).

Genomic biomarkers predict clinical outcomes (surrogate endpoints).

Pharmacogenetics can be useful to identify new biological pathways involved in drug metabolism and therefore new treatment opportunities.

Pharmacogenetics is applicable to activities such as drug discovery, drug development and clinical practise.

Pharmacogenetics is applicable also in drug disposition (PK) and drug effect (PD).

Pharmacogenetics is necessary to define individual dose adaptation of chemotherapeutics and in general for personalised medicine.

Pharmacogenetics is crucial in genomic biomarkers identification.
Chloroplast Genome
Authors: Howe Christopher J
Published: April 2013

Chloroplasts contain a genome that is a relic of the endosymbiont that gave rise to the organelle. These genomes typically contain 100–200 genes and encode proteins important for photosynthesis and other chloroplast functions, although dinoflagellate algae have a greatly reduced and fragmented chloroplast genome. Many nonphotosynthetic taxa retain a remnant chloroplast genome. In some organisms the chloroplast genome may be retained to allow redox‐mediated control of gene expression, whereas in others it may continue to exist because transfer of essential genes to the nucleus is no longer possible. Multiple
ribonucleic acid (RNA)
polymerases are involved in chloroplast transcription in land plants, and post‐transcriptional processing involving nuclear‐encoded RNA‐binding proteins also plays an important part in the expression of the chloroplast genome. Gene expression may be regulated at a number of levels, and redox poise in the organelle may be particularly important for this.

Key Concepts:

Chloroplasts originated in the ancestor of plants and red and green algae by endosymbiotic acquisition of a cyanobacterium, and then spread to many other eukaryotic lineages.

There are other examples of stable acquisition of a cyanobacterium by a nonphotosynthetic host.

Chloroplast genomes are typically 100–200 kbp in size, and include a set of genes for proteins essential to photosynthesis. Other genes present in the ancestral symbiont have been lost or relocated to the nucleus.

Many nonphotosynthetic organisms retain remnant chloroplasts, with genomes, reflecting the fact that photosynthesis is not the only biochemical process that takes place in the chloroplast.

In many organisms, gene transfer from chloroplast to nucleus can still take place, at an unexpectedly high frequency.

Establishment of the chloroplast has resulted in the development of nuclear‐encoded RNA‐binding protein families and, in land plants, additional RNA polymerases that play a central role in chloroplast gene expression.

Post‐transcriptional RNA processing plays an important role in chloroplast gene expression.

In photosynthetic organisms, chloroplast gene expression is closely linked to the organelle's redox poise.

The chloroplast can also influence the expression of nuclear genes.
Arabidopsis thaliana
as an Experimental Organism
Authors: Serino Giovanna , Gusmaroli Giuliana
Published: April 2013

In the recent years

Arabidopsis thaliana

has undoubtedly emerged as the model experimental organism for essentially all aspects of plant biology, due to its short generation time, its small genome size and the availability of its complete
deoxyribonucleic
acid sequence. In addition,
Arabidopsis
has proven to be an ideal organism for studying plant development at the molecular, cellular, organismal and ecological level. By concentrating their efforts on a single model system,
Arabidopsis
scientists have made outstanding advances in almost any field of plant research. Further, discoveries made in
Arabidopsis
have been translated to other plant species such as economically important crops, as well as to animal systems, including complex human disease processes.

Key Concepts

Arabidopsis
is a small flowering plant, which has emerged as the primary experimental organism for the study of all aspects of plant biology.

Arabidopsis genome has been fully sequenced in 2000 and contains approximately 27 000 genes.

Several molecular tools have been established to identify
Arabidopsis
transcription profiles, epigenetic landscape, protein and metabolite composition.

Gain of function and loss of function transgenic lines for specific
Arabidopsis
genes can be easily made or obtained from public collections.

Most of the information on
Arabidopsis
research is available from dedicated websites.

Discoveries made in
Arabidopsis
can be easily translated to other plant species, as well as to animal systems.
Shoots and Buds in
Arabidopsis
Authors: Truernit Elisabeth
Published: April 2013

The shoot is the above‐ground part of higher plants. To produce new shoot tissue, repetitive organ formation takes place at the tip of shoots and in floral buds by the activity of stem cell systems, called shoot and flower meristems. The shoot meristem is set up during embryogenesis and, after seedling germination, produces leaves, stems and eventually flowers. One of the key issues of the shoot meristem is to maintain a balance between cell proliferation and differentiation. A complex set of genetic and hormonal regulation ensures the maintenance of undifferentiated cells in the centre of the shoot meristem and the initiation of organ primordia at its flanks. While shoot meristems are indeterminate structures, in flower meristems stem cell maintenance ceases once the floral organs have been generated.

Key Concepts:

The shoot apical meristem produces the above‐ground organs of plants.

Stem cells located in the centre of the shoot meristem are maintained by a self‐regulatory gene expression network involving the
WUSCHEL
and
CLAVATA
genes.

Cytokinins play a role in meristem cell proliferation and in stem cell positioning.

Auxin is essential for organ primordia formation.

The shoot meristem is established during plant embryogenesis.

In floral meristems, stem cells are only maintained for a limited time.
Flowers
Authors: Hileman Lena C
Published: April 2013

Flowers are the reproductive structures of the flowering plants (angiosperms, class Magnoliopsida). The best evidence suggests that flowering plants arose in the Cretaceous, and that following their origin, rapid and expansive diversification in flower form ensued. Modern‐day flowers vary widely in size, symmetry, presence or absence and shape of floral organs, colour, colour patterning and arrangement of flowers in higher order inflorescence structures. This extensive diversity in flower form is strongly linked to the evolution of reproductive strategies, with many variations in flower form and colour representing adaptations that enhance reproductive success. These include adaptations that enhance cross‐pollination between individual plants, especially floral diversification that has resulted from an evolutionary history of plant–pollinator interaction.

Key Concepts:

A number of key characteristics distinguish the reproductive structures of flowering plants from reproductive structures of other seed plants.

Recent work in model flowering plant species has resulted in a deep understanding of the genetic mechanisms that control flowering and flower developmental patterning.

Following their origin in the Cretaceous, flowers diversified rapidly in size, shape and colour.

Flower diversification is largely the result of natural selection favouring modifications that enhance reproductive success through either self‐fertilisation or cross‐pollination.
Endodermis and Exodermis in Roots
Authors: Schreiber Lukas , Franke Rochus B
Published: April 2013

Roots of terrestrial plants are designed to take up water and nutrients. At the same time, uptake of unwanted compounds, for example toxic, and infection by soil borne pathogens must be avoided. Specific unicellular tissues, the endodermis and the exodermis, allow roots to establish and maintain this selectivity. The endodermis represents an unicellular cell layer separating the central cylinder of the root from the cortex. The exodermis represents an unicellular cell layer located at the outer surface of the root directly below the root epidermis. Both tissues are characterised by specific cell wall modifications. In early developmental stages the anticlinal radial walls exhibit Casparian bands, composed of the polymers suberin and lignin. In a subsequent developmental state a suberin lamella is deposited on the inner surface of endo‐ and exodermal cell walls. These apoplastic barriers, mainly composed of suberin, significantly affect radial uptake of water and dissolved nutrients and radial loss of oxygen.

Key Concepts:

Casparian bands, composed of lignin and suberin, form characteristic cell wall modifications in radial walls of endodermal and exodermal cells.

Suberin lamellae are deposited onto the inner surface of endodermal and exodermal cell walls.

Apoplastic barriers in roots are established by the deposition of suberin into and onto the cell wall.

Suberised apoplastic barriers in roots help to establish root selectivity in nutrient uptake.

The endodermis, forming an ‘inner’ apoplastic barrier in the root, is important in preventing nutrients actively concentrated in the xylem from passively diffusing back to the soil.

The exodermis, forming an ‘outer’ apoplastic barrier at the root surface, mainly establishes the root/soil interface between the root and the soil environment surrounding the root.

As an adaptation to various environmental stress factors (e.g. drought, salt, heavy metal stress, oxygen deficiency, etc.) suberisation of apoplastic barriers is significantly modified.

Fatty acid elongases and cytochrome P450 hydroxylases represent important key enzymes in suberin biosynthesis.
Enteroviruses in Humans
Authors: Romero José R
Published: April 2013

Enteroviruses are significantribonucleic acid (RNA)viral pathogens of humans with a worldwide distribution. Humans are the only known hosts for the enteroviruses. Their major route of infection is that of the faecal–oral route. In temperate climates enteroviral infection occurs primarily in the summer and early fall. Infants represent the majority of cases. Enteroviral infection results in viremia and prolonged gastrointestinal shedding of the virus. Enteroviral syndromes involve almost every organ system. Although the majority of infections are asymptomatic or result in a self‐limited infection, fatalities do occur. Especially in neonates or individuals with B‐cell immunodeficiencies. Advances in technology are providing improved understanding of their taxonomy, epidemiology and means of detection.

Key Concepts:

Enteroviruses have RNA genomes. The 5′NTR of the enteroviruses contain areas of conserved nucleotide identity.

Originally five species were described within the genus: polioviruses, the group A and B coxsackievirus, the echoviruses and the numbered enteroviruses. Using modern molecular virologic methods the species have been redefined and novel members of the genus have been identified.

Enteroviruses have a worldwide distribution and exhibit strong seasonality. The coding sequence of VP1 is used for the detailed analysis of enteroviruses.

Humans are the sole reservoir for the enteroviruses. Infections by enteroviruses are significantly higher in infants.

Faecal–oral transmission is the major mode of transmission of the enteroviruses. Infection results in prolonged shedding of the enteroviruses.

Understanding the pathophysiology of the enteroviruses is based on the study of prototypic members of the genus: the polioviruses.

The major determinant of susceptibility to the enteroviruses is the presence of the receptor required for viral attachment.

Reverse transcription‐polymerase chain reaction (RT‐PCR) has replaced tissue culture and mouse inoculation for detection of the enteroviruses. RT‐PCR is more sensitive and faster for the detection of the enteroviruses than tissue culture or mouse inoculation.

RT‐PCR diagnosis of enteroviral infections can significantly impact on patient care.

Management of enteroviral infections is supportive in nature.
Fungal Infections in Humans
Authors: Jain Neena , Fries Bettina C
Published: April 2013

Fungi are pathogenic to humans and cause a variety of diseases in normal and immunocompromised hosts. Fungi can exist as filamentous/mould or yeast form, both forms are able to cause infections in human host. Dimorphic fungi, that is,

Histoplasma capsulatum

also exist and can grow as a filamentous form at room temperature and yeast at body temperature. Fungi can infect any part of the human body including hairs and nails and depending upon their level of penetration is divided into four groups, superficial mycoses, cutaneous mycoses, subcutaneous mycoses and systemic/deep mycoses. Systemic mycoses are often fatal without treatment. Ability to maintain constant body temperature is the natural defence against pathogenic fungi. In the event of infection, accurate diagnosis and often the combination of different treatment modalities are required for a successful treatment.

Key Concepts:

Fungal infections represent the invasion of fungi in tissue.

Only 200 fungal species are able to cause infection to human host, of these only 20–25 species commonly cause infection.

Fungi appearance is either hyphae (known as mould) or yeast. Few are dimorphic and change from one state to other depending on the temperature conditions.

Fungi can cause superficial to deeper infections to human host.

Most of the fungal infections are opportunistic and do not need the human host for survival.

Most fungal infections are airborne and acquired by inhalation or contact of air, soil or surfaces contaminated with spores.

Causes more damage to immune‐suppressed patients, that is, organ transplant recipients and AIDS patients.

Diagnosis is made usually by using simple tests that include microscopic stains, culture and Antibody/antigen tests, in some cases imaging can be helpful for deep‐seated infection diagnosis.

Fungal infection commonly caused by normal flora so the reoccurrence rate is higher than other infection

Allylamines, antimetabolites, azoles, glucan synthesis inhibitors, polyenes, echinocandins and others are the drugs used to cure fungal infections.
Implantable Pumps and Ports
Authors: Buchwald Henry , Rohde Thomas D
Published: April 2013

An implantable pump is a device that can be implanted within the body to deliver a drug or other substance to the same location or another site in the body. In addition to a reservoir and pumping mechanism, an implantable pump usually has a refill septum so that it can be refilled

in situ

and a catheter for remote delivery; an implantable port also has a refill septum and a delivery catheter but lacks a reservoir and an intrinsic pump.

Pumps and ports have been utilised for continuous heparin, chemotherapeutic agents, antibiotic, antispasmotic, analgesic and insulin infusions. The future use of this modality is only limited by the boundaries of imagination.

Key Concepts:

Implantable pumps and ports allow for intravenous, intrathecal and specific organ delivery of drugs and other agents.

They circumvent alimentary tract destruction or failure of absorption, and permit the bypassing of the blood–brain barrier.

These systems can provide constant circulating drug levels. Various continuous and programmable flow devices are available.

Pumps and ports have been utilised for continuous heparin, chemotherapeutic agents, antibiotic, antispasmotic, analgesic and insulin infusions.

The future use of this modality is only limited by the boundaries of imagination.
Fungi and the History of Mycology
Authors: Kendrick Bryce
Published: April 2013

Fungi, broadly defined, (1) are eukaryotic, (2) have no plastids or photosynthetic pigments, (3) are therefore heterotrophic (unable to make their own food from inorganic components), (4) are osmotrophic (absorb rather than ingest food), (5) are often opportunistic and capable of exploiting many different substrates, (6) are never amoeboid at any stage, (7) almost always live inside branching networks of microscopic, apically extending, tubular structures known as hyphae, (8) almost all reproduce by unicellular or multicellular spores, (9) generally have haploid somatic nuclei and (10) mostly do not produce flagellate cells. Mycology is the branch of science that studies these organisms.

Key Concepts:

The fungi are classified in two biological kingdoms, which are called Chromista and Eumycota (also known as Stramenopila and Fungi, respectively).

Fungi are composed of hyphae (germ tubes) that arise when a spore germinates. Hyphae have walls of chitin (in the eumycotan fungi) or cellulose (in the chromistan fungi).

The nuclei in somatic cells of chromistan fungi are diploid, whereas those in somatic cells of eumycotan fungi are haploid.

Almost all fungi eventually reproduce by means of spores, usually modified bits of hyphae, which vary greatly in size and appearance.

The ascomycetes and basidiomycetes are characterised by their sexual reproductive structures (teleomorphs), for example, cup fungi and mushrooms.

Many ascomycetes and basidiomycetes appear to have lost the ability to develop sexual structures, and survive happily as mitosporic fungi (anamorphs).

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

The current classification of the fungi and our understanding of their life cycles is to a large extent based on the work of Anton de Bary in the middle of the nineteenth century.
von
Behring, Emil Adolf
Authors: Parascandola John
Published: April 2013

Emil Adolf von Behring (1854–1917) was a German medical scientist who developed antitoxins against diphtheria and tetanus. For his work on the diphtheria antitoxin, he was elevated to the Prussian nobility (and thereafter known as von Behring) and also awarded the first Nobel Prize in Medicine or Physiology in 1901. In 1895, he assumed the chair of hygiene at the University of Marburg, where he remained until his death, working on tuberculosis and developing an active preventive vaccine against diphtheria.

Key Concepts:

Diphtheria and tetanus bacilli produce toxins which cause the symptoms of these diseases.

Using guinea‐pigs and then sheep, Behring worked to develop serum antitoxin into a useful therapeutic agent for the treatment of diphtheria.

The major success of Behring's later years was the development in 1913 of an active preventive vaccine against diphtheria, based on a toxin–antitoxin mixture rendered stable by formaldehyde.
Safety Considerations in the Tissue Culture Laboratory
Authors: Martin Bernice M
Published: April 2013

The routine work of cell maintenance and some experiments that affect cells in culture can potentially pose a hazard to the researcher. Hazards may be associated with equipment, sterilisation methods, tissue or whole animal sources used to obtain the cells, as well as experiments that are designed to be detrimental to or alter the normal cell function. Essentially, hazards can be of mechanical, chemical, ionising or biological origin. Regardless of the source, the culturist can still work effectively and be safe. To do so, the culturist should be armed with proper training for cell culture studies, adequate personal protection equipment, advanced knowledge of any potential hazard and sources of information for responding in an emergency. With these tools, the risk to the culturist is minimised. The approaches to some of these issues are discussed below.

Key Concepts:

Properly prepared cell culturists can work safely.

Sterilisation used to protect the cells can harm culturists.

Culturists should be fully aware of potential hazards during experiments designed to change or kill cells.
Membrane Targeting: Methods
Authors: Gorfe Alemayehu A , Hocker Harrison J
Published: April 2013

The responsiveness of cells to external signals, or cell signalling, involves highly regulated sequences of biochemical reactions at the plasma membrane. When receptor proteins in the outer surface of the plasma membrane are activated by environmental signals, they undergo shape change or chemical modification to assemble internal proteins into an organised complex on the inner surface. Specific protein domains and lipids (fats) that are physically attached to proteins tether key components of this complex to the lipid bilayer of the membrane. Scientists have developed cell‐based and chemical techniques that allow them to introduce specific membrane‐targeting motifs into proteins to produce and study how this may alter cell behaviour. As a result, a great deal has been learned about the molecular basis of membrane targeting by lipid‐modified proteins. This knowledge holds a promise for the rational design of new compounds to prevent defective membrane targeting that could lead to abnormal signalling and the development of diseases.

Key Concepts:

Lipid bilayers provide the fundamental architecture of biological membranes.

The two‐dimensional surface of membranes provides a structural framework to organise multiple signalling proteins.

Proteins target membranes using globular domains and lipids that are covalently attached to them.

The most common lipid‐based membrane‐targeting motifs in the interior of the cell include modification of cysteine and glycine amino acids by acyl and prenyl groups.

G‐proteins are the quintessential examples of membrane targeting by lipidation.

Modern cell biology and chemical biology techniques can be used to artificially attach lipids to proteins.

Prevention of defective membrane targeting is being pursued as a new therapeutic strategy.
Donné, Alfred
Authors: Hoquet Thierry
Published: April 2013

Alfred François Donné (1801–1878) was a French physician and hygienist. He is mostly celebrated today for his contributions to bacteriology, his use of microscopy and his contribution to the development of photography. Together with his student Léon Foucault, Donné devised a technique to project on screen micro‐daguerreotypes of excellent quality.
Gullstrand, Allvar
Authors: Ljungstrom Olof , Normark Daniel
Published: April 2013

Allvar Gullstrand (1862–1930) was a Swedish ophthalmologist and Nobel Prize laureate (1911), who worked out the mathematical basis of astigmatism, and used mathematical methods to solve a number of other complex problems in geometrical optics. Gullstrand presented his doctoral dissertation at the Karolinska Institutet in Stockholm, but spent the majority of his career at Uppsala University, becoming professor of ophthalmology there in 1894. From 1914 to 1927 he held a personal professorship in physical and physiological optics freed from all teaching duties.
Transmission Electron Microscopy: Preparation of Specimens
Authors: Böttcher Bettina
Published: April 2013

Sample preparation of biological specimens for electron microscopy aims at bringing the sample into a suitable size (<500 nm thick, accommodated on a 3 mm diameter, round sample carrier) and to strengthen these samples against the adverse conditions in the electron microscope (beam damage and vacuum). There are two types of samples, one are large cellular structures, which require further sectioning and the other are individual assemblies, which are small enough to be imaged in suspension. Any preparation method of these types of samples has to fulfil four basic requirements: (1) to avoid collapse of the structures in the vacuum of the electron microscope; (2) to provide a sample sufficiently thin to avoid multiple scattering of electrons; (3) to minimise structural alterations as a consequence of the damage by the electron beam; (4) to maximise the contrast in the resolution band of interest. The relative importance of each constraint varies with the type of specimen and with the level of resolution sought.

Key Concepts:

Fragile samples such as tissues, cells and some molecular machines are stabilised by cross‐linking with aldehydes (formaldehyde or glutaraldehyde) or Osmium tetroxide (lipids).

Vitrification by rapid freezing converts liquid water into amorphous solid water.

Vitrification perseveres ultra structures with the least artifacts (cryo fixation).

Vitrification is achieved by plunge freezing of thin objects (<1–2 μm) or by high pressure freezing of thicker objects (<600 μm).

Large samples such as cells and tissues are stabilised by embedding in plastic resins or by vitrification.

Thick objects are cut to appropriate thickness either with conventional ultramicrotomes (diamond knifes or glass knifes) or with a focused ion beam.

Contrast can be enhanced by staining procedures, which use electron dense heavy atom derivates such as Uranyl acetate, Phosphotungstic acid, osmium tetroxide, ammonium molybdate.
Protein Structure: Unusual Covalent Bonds
Authors: Lecomte Juliette TJ , Falzone Christopher J
Published: April 2013

Proteins are linear polypeptides made out of a small set of amino acids. The chemical diversity of the building blocks is limited, but a protein's covalent structure can be amended

in vivo

so that unusual linkages are introduced and new functionalities are conveyed. These covalent modifications may occur during translation or after the protein is fully synthesised; they may be spontaneous or enzymatic and transient or long lived. They are generally consequential to cellular function and integrity of the organism. The broad array of modification includes common and frequent substitutions such as phosphorylation and rarer alterations such as formylglycine formation. A survey of long‐lived modifications is presented from a physicochemical perspective with attention to biological relevance.

Key Concepts:

Covalent bonds other than found in the standard set of amino acids expand the chemical properties of proteins.

Unusual bonds are found in protein‐derived prosthetic groups.

Unusual covalent bonds play functional roles.

Some unusual covalent bonds are irreversibly formed and are markers of aging.

Many unusual bonds are reversibly formed and participate in regulatory mechanisms.

Unusual bonds are often difficult to detect and identify, especially
in vivo
.

Technological advances have improved the ability to detect modifications in entire proteomes.
Chaperonins
Authors: Consalvi Valerio , Chiaraluce Roberta
Published: April 2013

The challenge in protein folding is the production of the native, active conformation from the primary sequence information.

In vivo

, in the cytosolic environment, acquisition of the native conformation is in competition with proteolytic degradation and/or intracellular precipitation. Chaperone proteins assist in finding the native fold in all cellular phases, and these key components of the cellular machinery occur ubiquitously through archaea, bacteria and eukarya. Chaperonins are complex polymeric proteins that form a closed environment, the ‘Anfinsen cage’, to allow correct protein folding triggered by
adenosine triphosphate
hydrolysis, avoiding intermolecular aspecific aggregation. The chaperonins prevent protein unfolding and misfolding, events responsible for several human diseases, such as cancer and amyloid diseases. The chaperonins are considered potential drug targets due to their role in protein misfolding, aggregation and denaturation and in cellular signalling.

Key Concepts:

Proteins must fold properly to acquire their native and functional conformation.

Protein misfolding is characterised by the exposure of buried hydrophobic residues.

Protein misfolding may be followed by protein aggregation.

The folding of many proteins need to be assisted by other proteins to prevent misfolding and/or aggregation.

The chaperonins prevent protein unfolding and misfolding, events responsible for several human diseases, such as cancer and amyloid diseases.

The ‘Anfinsen cage’ is a closed environment that encapsulates the nonnative protein and allows correct protein folding in the internal chaperonin compartment.
Protein Family Databases
Authors: Mulder Nicola J
Published: April 2013

As new protein sequences continue to flood into public databases with the advancement of sequencing technologies, the importance of protein family databases for automatic protein functional classification increases. These databases are developed independently and each has its own methods and areas of interest, as well as its own strengths and weaknesses. To simplify access to multiple databases by the user, many of these databases have also been amalgamated into integrated protein family resources, which vary in their level of manual curation. These protein family databases or integrated resources have a number of applications in modern biology or bioinformatics, including protein functional annotation, orthologue prediction, protein–protein interaction prediction, gene set enrichment analysis and providing datasets for evaluation of mathematic models of biological systems or networks.

Key Concepts:

Protein signatures are mathematical descriptions of the sequence characteristics of members of the same protein family or domain.

Profiles and hidden Markov models are tools for characterising protein families or domains.

Regular expressions or patterns are used for describing short highly conserved motifs.

Protein family data has a number of applications, notably for the functional classification of new protein sequences.
RNA
Structural Motifs
Authors: Zhang Ming , Perelson Alan S , Tung Chang‐Shung
Published: April 2013

Chemically,
ribonucleic acid
(RNA) is a close cousin of
deoxyribonucleic acid
(DNA). RNA is, however, involved in a wide range of cellular activities (e.g. translating genetic information, serving as a structural scaffold, catalysing biological reactions) that often require the molecule to fold into a specific structure in order to perform its targeted function. Structurally and functionally it is therefore more closely related to proteins than to DNA. An RNA structural motif is defined as a collection of residues that fold into a stable three‐dimensional (3D) structure and which can be found in naturally occurring RNAs in unexpected abundance. Owing to the fact that stable 3D structures are associated with RNA structural motifs, these motifs often served as nucleation sites for RNA folding.

Key Concepts:

RNA motifs can help stabilise a global RNA structure, as well as guide the RNA folding process.

Hairpins are essential in constituting RNA tertiary architecture and in forming binding sites for other molecules.

Owing to variation of the lengths of loops and stems, as well as the types of interactions between them, pseudoknots represent a structurally diverse group.

Triloops and tetraloops with specific sequences are stable and frequently observed hairpin loops.

Self‐folding RNA structures, including the adenosine platform, ribose zipper, bulge–helix–bulge motif and G‐bulge motif, can provide the nucleation sites for RNA folding.