bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fungal Xerophiles (Osmophiles)
Authors: Vinnere Pettersson Olga , Leong Su‐lin L 
Published: April 2013

Abstract

Xerophilic fungi are yeasts and moulds that are capable of growth at or below a water activity (
a
w
) of 0.85. These microorganisms have developed physiological mechanisms that enable their biochemical pathways to function in environments where little water is available. External conditions of low
a
w
are sensed by membrane osmosensors, and xerophiles then accumulate glycerol as a compatible solute to balance the internal and external osmotic pressure. They also modify their membranes to retain this glycerol within the cell. As a group, xerophiles are extremely important in the spoilage of many processed foods and stored commodities, and in indoor environments. Moderate xerophiles include species within
Aspergillus
,
Penicillium
and
Eurotium
. Extreme xerophiles compete poorly at high
a
w
, because they require decreased
a
w
for growth. Some xerophiles have a preference for salt or sugar substrates, whereas other species can be isolated from both jam and salterns. Xerophiles are widely spread on the fungal tree of life.

Key Concepts:

Xerophiles have requirement for reduced water activity; fungi are the most successful xerophilic organisms, and the most extreme xerophiles are found among fungi.

Compatible solutes are accumulated intracellularly to maintain the osmotic balance in response to decreased water availability.

Glycerol is the primary compatible solute among xerophilic fungi.

Membrane composition plays an important role in retaining glycerol within the cells of xerophiles.

Moderate xerophiles of the genera
Aspergillus
,
Eurotium
and
Penicillium
are economically important spoilage organisms.

Some xerophiles are isolated from both high‐salt and high‐sugar environments; others have a preference for either salt or sugar.

Xerophiles can cause spoilage of food and feed: stored commodities, sugary products and salted foods.

Xerophilic species are widely spread on the fungal tree of life.
Fungal Spores
Authors: Moore‐Landecker Elizabeth 
Published: April 2013

Abstract

Many heterotrophic eukaryotic organisms belong to the monophyletic kingdom Fungi. Because of their stationary life style, fungi reproduce by forming spores, cells that are specialised for dispersal to new locations by air, water or animals. Flagellated zoospores are produced by simple aquatic fungi. Most fungi are terrestrial, growing as hyphae and producing thick‐walled nonmotile spores. Asexual spores include sporangiospores and conidia, whereas sexual spores include zygospores, ascospores and basidiospores. Ascospores and basidiospores often are forcibly ejected into the air. Sporulation requires favourable nutritional and environmental conditions such as light and temperature, and involves cellular signalling and metabolic responses. As spores mature, their walls thicken, energy reserves such as lipid are acccumulated, and their metabolism decreases as they prepare for dormancy. Mature spores may undergo either exogenous or constitutive dormancy before germination. Upon germination, metabolic acitivity increases and a germ tube emerges from the spore.

Key Concepts:

Fungal spores have a unique role in fungal life cycles as they provide the genetic link between one generation and another.

Spores can be part of asexual or sexual reproductive cycles, and are sometimes borne by multicellular sporocarps.

Spores in part owe their success to their thick walls, reserve energy source, low metabolic rate and ability to withstand environmental stress that enables them to survive during dispersal.

Some fungi coevolved with insects, establishing mutualistic symbiotic relationships, and depend upon them for spore dispersal.

Sporulation occurs within a narrow range of special nutritional and environmental conditions, and involves signal transduction, gene activation and metabolic turnover.

Sporulation and spore germination of some fungi are coordinated with light and temperature changes marking day and night cycles, the seasons or with life cycles of their hosts.

Conditions required for germination reflect the particular biological adaptations and requirements of the fungus, and ensure that further somatic growth will be successful.

Scientists should understand spore biology so that they may better control animal, plant and human diseases; to better utilise fungi for industrial purposes, or to utilise them more effectively in the laboratory.
Yeasts
Authors: Lachance Marc‐André 
Published: April 2013

Abstract

Yeasts are a group of eukaryotic fungi with a well‐defined cell wall whose growth is either entirely unicellular or a combination of hyphal and unicellular reproduction. The approximately 1500 known yeast species belong to two distinct fungal phyla, the Ascomycota and the Basidiomycota. Within each these phyla, yeasts can be found in several subphyla or classes, reflecting the enormous diversity of their evolutionary origins and biochemical properties. In nature, yeasts are found mainly in association with plants or animals but are also present in soil and aquatic environments. Yeasts grow rapidly and have simple requirements, for which reason they have been used as model systems in biochemistry, genetics and molecular biology. They were the first microorganisms to be domesticated for the production of beer, bread or wine, and they continue to be used for the benefit of humanity in the production of recombinant proteins and other materials.

Key Concepts:

Yeasts share in common a primarily unicellular mode of reproduction.

Yeasts are phylogenetically diverse, being classified in several classes of two fungal phyla.

The concept of yeast is rooted in history and does not always follow logical biological lines.

Yeasts have a rigid cell wall primarily made up of β‐(1–3)‐glucan.

Sexual reproduction in yeasts involves the formation of internally formed ascospores or externally formed basidiospores.

Current yeast classification is based on phylogenetic relationships inferred by gene sequencing.

Yeasts grow in nature primarily in association with the plant–insect interface or with warm‐blooded animals, but also occur in soil and aquatic habitats.

Yeasts serve as important industrial model systems in research.

Yeasts are of great importance in biotechnology. The main products are alcohol, yeast biomass and recombinant proteins.

A few yeast species cause infections in humans and other animals, but most yeasts act in an opportunistic fashion, in individuals that are immunocompromised.
Circadian Programmes in Cyanobacteria
Authors: Johnson Carl Hirschie 
Published: April 2013

Abstract

Cyanobacteria are prokaryotes that express circadian (daily) rhythms. In rhythmic environments, the fitness of cyanobacteria is improved when this clock is operational and when its circadian period is similar to the period of the environmental cycle. In cyanobacteria, three key proteins (KaiA, KaiB and KaiC) form a core molecular clockwork that orchestrates global gene expression by modulating chromosomal topology. The three‐dimensional structures of these proteins have been determined. KaiA, KaiB and KaiC form a multiprotein nanomachine that can reconstitute a circadian oscillator

in vitro

, and this oscillator appears to function as a post‐translational oscillator (PTO)

in vivo

. Because this PTO regulates rhythmic transcription and translation, the entire circadian system comprises both the PTO and a transcriptional/translational feedback loop. Models of the complete

in vivo

system have important implications for our understanding of circadian clocks in higher organisms, including mammals.

Key Concepts:

Prokaryotic cyanobacteria have a circadian timekeeping system that enhances fitness.

These cells exhibit pervasive circadian regulation of gene expression, possibly mediated by cyclic changes of chromosomal topology.

A circadian rhythm of the phosphorylation of the central clock protein KaiC can be reconstituted
in vitro
with three proteins derived from cyanobacteria (KaiA, KaiB and KaiC) and ATP.

KaiA, KaiB and KaiC are the only circadian clock proteins for which the 3‐D structure of full‐length proteins is known.

Structural, biochemical and biophysical methods have been used to study the mechanism by which KaiC is rhythmically phosphorylated and dephosphorylated.

Mathematical modelling that has been applied to the
in vitro
and
in vivo
systems indicate the existence of a core biochemical post‐translational oscillator (PTO) that controls a larger transcription/translation feedback loop (TTFL).
Endosymbionts
Authors: Jeon Kwang W 
Published: April 2013

AbstractEndosymbionts are smaller symbiotic partners living inside a host organism, establishing endosymbiosis. The symbionts may live within the host's cells (intracellular) or outside cells (extracellular) in multicellular hosts. A symbiotic relationship may be parasitic (one partner harming the other), commensal (usually not affecting each other) or beneficial (unilaterally or mutually). Examples of intracellular endosymbionts include bacteria and single‐celled algae living inside free‐living cells or cells of various multicellular organisms. It is believed that cellular organelles such as mitochondria and chloroplasts arose within eukaryotic cells by a series of intracellular endosymbioses. Some bacteria live in various marine invertebrates and in insects as extracellular endosymbionts. Many of both intracellular and extracellular endosymbionts form obligate endosymbioses, in which neither the endosymbionts nor their hosts can live without the other. Recent genetic studies have shown that lateral gene transfers occur between symbionts and hosts. In some cases, the transferred symbionts’ genes are expressed in the progeny of multicellular hosts.Key Concepts:Endosymbiosis is a wide‐spread phenomenon in nature.Endosymbionts may live inside host cells or outside cells in multicellular hosts.Hosts provide suitable habitat to established endosymbionts.Cellular organelles arose within eukaryotic cells by a series of intracellular endosymbioses.Genes are transferred laterally between endosymbionts and hosts.Transferred endosymbionts’ genes may be expressed in the hosts and their progenies.
Halophiles
Authors: DasSarma Shiladitya , DasSarma Priya 
Published: April 2013

AbstractHalophiles are salt‐loving organisms that flourish in saline environments and can be classified as slightly, moderately or extremely halophilic, depending on their requirement for sodium chloride. Although most marine organisms are slight halophiles, moderate and extreme halophiles are generally more specialised microbes, which inhabit hypersaline environments with salinity higher than in the sea. Hypersaline environments are found all over the world, in arid, coastal, and deep‐sea locations, underground salt mines, and artificial salterns. Halophilic microorganisms include a variety of heterotrophic, phototrophic, and methanogenic archaea, photosynthetic, lithotrophic, and heterotrophic bacteria, and photosynthetic and heterotrophic eukaryotes. Examples of well‐adapted and widely distributed extremely halophilic microorganisms include archaea for example,Halobacteriumsp. NRC‐1, cyanobacteria such asAphanothece halophytica, and the green algaDunaliella salina. Multicellular halophilic eukaryotic organisms include brine shrimp and the larvae of brine flies. Halophilic organisms either accumulate internal organic compatible solutes to balance the osmotic stress of the environment or produce acidic proteins to increase solvation and improve function in high salinity.Key Concepts:Halophiles are salt‐loving organisms that inhabit saline and hypersaline environments and include prokaryotic (archaeal and bacterial) and eukaryotic organisms.Many halophiles accumulate compatible solutes in cells to balance the osmotic stress in their environment.Some halophiles produce acidic proteins that are able to function in high salinity by increasing solvation and preventing aggregation, precipitation and denaturation.
Measles Virus
Authors: Rima Bertus K , Duprex W Paul 
Published: April 2013

AbstractMeasles virus(MV) is responsible for a childhood infection characterised by a maculopapular rash, dry cough, coryza, conjunctivitis and photophobia. Although mild in developed countries, the infection is associated with significant morbidity in developing countries and still kills more than 200 000 children per annum even though it is a vaccine preventable disease. The virus replication cycle is well understood and the molecular description of the virus has progressed to a stage where the main emphasis of research has reverted towards understanding the pathogenesis and molecular basis of virus attenuation. Such knowledge will assist in the development of new vaccines and serve to increase our understanding of epidemiology and transmission. Our ability to make recombinant viruses that express autofluorescent proteins from additional transcription units within the genome has created a paradigm shift in changing our view of MV from simply a ’respiratory infection‘ causing agent to one that affects the immune system in a serious and potentially dangerous manner. Identification of the early target cells as alveolar macrophages and/or dendritic cells in the deep lung alongside understanding the early events in viral pathogenesis helps shed light on how this highly infectious agent establishes such a profoundly immunosuppressive disease in the host.Key Concepts:Measles is a relatively simple enveloped, negative‐sensed RNA virus which contains only six genes.Measles virus is a highly infectious agent, which causes a profound immunosuppression and a severe disease in susceptible individuals.The molecular basis of the immunosuppression is unknown.A highly efficacious vaccine has been developed, although the molecular basis of the attenuation remains an enigma.It is essential to vaccinate 95% of the birth cohort as the virus is so infectious and when vaccine uptake levels decrease in disease‐free regions importations from endemic parts of the world often occur.The vaccine is exceptionally thermolabile and this is challenging for those involved in delivering the product to remote areas of the developing world and in areas where conflict is rife.Recombinant measles viruses have helped to define the early steps in the establishment of an infection.Measles has been considered for eradication although the potential for cross‐species infection is being considered due to the cross‐protective morbillivirus antibodies which are elicited.
Prion Diseases
Authors: Ryou Chongsuk 
Published: April 2013

Abstract

Prion diseases, also known as transmissible spongiform encephalopathies (TSEs), are transmissible degenerative disorders of the central nervous system in mammals. TSEs are fatal and are caused by the proteinaceous infectious particles, termed prions that lack informational nucleic acids. TSEs include Creutzfeldt–Jakob disease in humans, scrapie in sheep, bovine spongiform encephalopathy or ‘mad cow disease’ in cattle and chronic wasting disease in deer and elk. These diseases manifest spongiform degeneration, reactive gliosis, and deposition of prion aggregates in the brain. The aetiology of TSEs is sporadic, genetic, or acquired. The primary structure of PrP
C
, conformational diversity of PrP
Sc
, and their interplay influence intra‐ and inter‐species prion transmission. The role of lymphoreticular system is pivotal in early prion pathogenesis and neuroinvasion, whereas neuronal damage caused by prion infection could be achieved by several different mechanisms. Despite the potential risk for public health, diagnosis and therapy for prion diseases are currently unavailable.

Key Concepts:

Prion diseases represent a group of human and animal diseases that include sporadic, inherited, and acquired Creutzfeldt–Jakob disease (CJD), Gerstmann–Sträussler–Scheinker syndrome (GSS), and fatal familial insomnia (FFI) in humans, bovine spongiform encephalopathy (BSE) in cattle, scrapie in sheep, chronic wasting disease (CWD) in cervids, transmissible mink encephalopathy (TME) in mink, feline spongiform encephalopathy (FSE) in cats, and exotic ungluate encephalopathy (EUE) in exotic ungulates.

Prion diseases are fatal neurological disorders and caused by the unconventional proteinaceous pathogen, termed prion.

Prion diseases manifest characteristic clinical and neuropathological features.

Prion diseases are transmissible within and between the species.

Transmission of prion diseases is determined by the amino acid sequence variability of PrP
C
and prion strains conferred by conformational diversity of PrP
Sc
.

The lymphoreticular system is crucial in prion pathogenesis and neuroinvasion.

Gain of pathologic PrP
Sc
function and/or loss of neuroprotective PrP
C
function facilitate neuronal damages in the central nervous system by direct or indirect mechanism associated with astrocyte and microglial cells.

Atypical TSEs and human‐to‐human transmission of vCJD have been identified.

Diagnosis and therapy for prion disease are not available.
Respiratory Syncytial Virus
Authors: Rawling Joanna , Melero José A 
Published: April 2013

Abstract

Human respiratory syncytial virus (HRSV) is a ubiquitous
ribonucleic acid
(RNA) virus that represents the leading cause of acute lower respiratory infections (mainly bronchiolitis and pneumonia) in infants and young children worldwide. HRSV belongs to the
Pneumovirinae
subfamily within the
Paramyxoviridae
family of enveloped, negative‐strand RNA viruses. Epithelial cells lining the nasal passages and respiratory tract are the primary target of HRSV infection, although alveolar macrophages and dendritic cells are also infected. Infected cells respond by producing a variety of cytokines, chemokines and interferons that are involved in the inflammatory response to HRSV. Although primary HRSV infection occurs at an early age, immunity is short‐lived or incomplete and re‐infections occur throughout life. Initial efforts to develop a vaccine based on formalin‐inactivated HRSV resulted in vaccine‐enhanced disease, and there is still no licensed prophylactic HRSV vaccine available.

Key Concepts:

Human respiratory syncytial virus (HRSV) is the leading cause of serious respiratory tract disease in children and infants worldwide.

HRSV belongs to the
Pneumovirinae
subfamily within the
Paramyxoviridae
family of negative‐strand RNA viruses.

The HRSV genome comprises 10 genes that encode 11 viral proteins.

HRSV derives its name from the formation of multinucleated, fused cells (syncytia), which are the hallmark of infection of cultured cells or lung tissue.

Following attachment to the target cell, entry by HRSV is mediated by fusion of the viral envelope with the host cell plasma membrane at neutral pH.

The entire replication cycle of HRSV takes place in the cytoplasm of the infected cell.

Reverse genetics has permitted the recovery of infectious HRSV from complementary DNA.

HRSV strains disseminate rapidly worldwide, accumulating mutations predominantly in the attachment protein, probably as a consequence of immune selection.

Pathology associated with HRSV infections is not only the result of direct virus injury, but largely the consequence of an aberrant immune/inflammatory response.

Palivizumab, a neutralising monoclonal antibody directed against HRSV fusion protein, is the only product available on the market for prophylactic treatment of children at high risk of severe infection.
Retroviral Replication
Authors: Pedersen Finn Skou , Pyrz Magdalena , Duch Mogens 
Published: April 2013

Abstract

Retroviruses are enveloped animal
ribonucleic acid
(RNA) viruses that replicate via a
deoxyribonucleic acid
(DNA) intermediate, which is integrated into the host genome as a provirus. Interaction of the viral envelope protein with a target cell receptor triggers entry of the viral nucleoprotein core by fusion of viral and cellular membranes. After entry, the viral enzymes
reverse transcriptase
and
integrase
mediate reverse transcription of viral RNA and integration of the resulting double‐stranded DNA copy of the viral genome, respectively. Expression of viral RNA and proteins from proviral DNA utilises the transcription and translation machinery of the host. Retrovirus particles are assembled through protein–protein and protein–lipid interactions, released from the cell by budding, and subsequently matured by a
viral protease
. A provirus can be transmitted through the germline from parents to offspring as an endogenous retrovirus. Host cell restriction factors target multiple steps of retroviral replication in a complex interplay of virus–host interactions.

Key Concepts:

Reverse transcription and integration into the host genome are hallmarks of retroviral replication.

The viral RNA genome contains a packaging signal for selective encapsidation into viral particles and a binding site for a tRNA primer for initiation of reverse transcription.

The integrated virus contains long‐terminal repeats harbouring signals for transciptional initiation and polyadenylation, which define the retroviral transcription unit.

Open reading frames for Gag, Pol and Env are found in all retroviruses, but some retroviruses encode additional proteins such as Tat and Rev of HIV‐1.

A stop‐codon between gag and pol can be bypassed by read‐through or frame‐shifting during translation of retroviral mRNA to make the Gag–Pol polyprotein.

Retroviruses have specialised strategies for export of unspliced genomic‐length viral RNA from the nucleus.

The metastable retroviral envelope protein drives the fusion of viral and cellular membranes by a type I fusion mechanism to allow retroviral entry in a receptor‐dependent manner.

The retroviral protease is required for maturation of viral particles after their release from producer cells by budding.

A retrovirus can integrate into the genome of germ cells and become part of the genetic material transmitted from parents to offspring.

A provirus can be maintained through species diversification as an endogenous retrovirus that may serve as a marker of phylogenetic relationship and evolutionary distance.