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Biology, Volume 4, Issue 3 (September 2015) – 8 articles , Pages 460-606

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1145 KiB  
Article
cAMP-Inhibits Cytoplasmic Phospholipase A2 and Protects Neurons against Amyloid-β-Induced Synapse Damage
by Clive Bate and Alun Williams
Biology 2015, 4(3), 591-606; https://doi.org/10.3390/biology4030591 - 16 Sep 2015
Cited by 28 | Viewed by 5265
Abstract
A key event in Alzheimer’s disease (AD) is the production of amyloid-β (Aβ) peptides and the loss of synapses. In cultured neurons Aβ triggered synapse damage as measured by the loss of synaptic proteins. α-synuclein (αSN), aggregates of which accumulate in Parkinson’s disease, [...] Read more.
A key event in Alzheimer’s disease (AD) is the production of amyloid-β (Aβ) peptides and the loss of synapses. In cultured neurons Aβ triggered synapse damage as measured by the loss of synaptic proteins. α-synuclein (αSN), aggregates of which accumulate in Parkinson’s disease, also caused synapse damage. Synapse damage was associated with activation of cytoplasmic phospholipase A2 (cPLA2), an enzyme that regulates synapse function and structure, and the production of prostaglandin (PG) E2. In synaptosomes PGE2 increased concentrations of cyclic adenosine monophosphate (cAMP) which suppressed the activation of cPLA2 demonstrating an inhibitory feedback system. Thus, Aβ/αSN-induced activated cPLA2 produces PGE2 which increases cAMP which in turn suppresses cPLA2 and, hence, its own production. Neurons pre-treated with pentoxifylline and caffeine (broad spectrum phosphodiesterase (PDE) inhibitors) or the PDE4 specific inhibitor rolipram significantly increased the Aβ/αSN-induced increase in cAMP and consequently protected neurons against synapse damage. The addition of cAMP analogues also inhibited cPLA2 and protected neurons against synapse damage. These results suggest that drugs that inhibit Aβ-induced activation of cPLA2 and cross the blood–brain barrier may reduce synapse damage in AD. Full article
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788 KiB  
Hypothesis
Homeostasis as the Mechanism of Evolution
by John S. Torday
Biology 2015, 4(3), 573-590; https://doi.org/10.3390/biology4030573 - 15 Sep 2015
Cited by 63 | Viewed by 27711
Abstract
Homeostasis is conventionally thought of merely as a synchronic (same time) servo-mechanism that maintains the status quo for organismal physiology. However, when seen from the perspective of developmental physiology, homeostasis is a robust, dynamic, intergenerational, diachronic (across-time) mechanism for the maintenance, perpetuation and [...] Read more.
Homeostasis is conventionally thought of merely as a synchronic (same time) servo-mechanism that maintains the status quo for organismal physiology. However, when seen from the perspective of developmental physiology, homeostasis is a robust, dynamic, intergenerational, diachronic (across-time) mechanism for the maintenance, perpetuation and modification of physiologic structure and function. The integral relationships generated by cell-cell signaling for the mechanisms of embryogenesis, physiology and repair provide the needed insight to the scale-free universality of the homeostatic principle, offering a novel opportunity for a Systems approach to Biology. Starting with the inception of life itself, with the advent of reproduction during meiosis and mitosis, moving forward both ontogenetically and phylogenetically through the evolutionary steps involved in adaptation to an ever-changing environment, Biology and Evolution Theory need no longer default to teleology. Full article
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1017 KiB  
Article
The Impact of Photobleaching on Microarray Analysis
by Marcel Von der Haar, John-Alexander Preuß, Kathrin Von der Haar, Patrick Lindner, Thomas Scheper and Frank Stahl
Biology 2015, 4(3), 556-572; https://doi.org/10.3390/biology4030556 - 11 Sep 2015
Cited by 38 | Viewed by 4766
Abstract
DNA-Microarrays have become a potent technology for high-throughput analysis of genetic regulation. However, the wide dynamic range of signal intensities of fluorophore-based microarrays exceeds the dynamic range of a single array scan by far, thus limiting the key benefit of microarray technology: parallelization. [...] Read more.
DNA-Microarrays have become a potent technology for high-throughput analysis of genetic regulation. However, the wide dynamic range of signal intensities of fluorophore-based microarrays exceeds the dynamic range of a single array scan by far, thus limiting the key benefit of microarray technology: parallelization. The implementation of multi-scan techniques represents a promising approach to overcome these limitations. These techniques are, in turn, limited by the fluorophores’ susceptibility to photobleaching when exposed to the scanner’s laser light. In this paper the photobleaching characteristics of cyanine-3 and cyanine-5 as part of solid state DNA microarrays are studied. The effects of initial fluorophore intensity as well as laser scanner dependent variables such as the photomultiplier tube’s voltage on bleaching and imaging are investigated. The resulting data is used to develop a model capable of simulating the expected degree of signal intensity reduction caused by photobleaching for each fluorophore individually, allowing for the removal of photobleaching-induced, systematic bias in multi-scan procedures. Single-scan applications also benefit as they rely on pre-scans to determine the optimal scanner settings. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the lab-to-lab comparability of microarray experiment results. Full article
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924 KiB  
Review
Multi-Facial, Non-Peptidic α-Helix Mimetics
by Maryanna E. Lanning and Steven Fletcher
Biology 2015, 4(3), 540-555; https://doi.org/10.3390/biology4030540 - 31 Aug 2015
Cited by 13 | Viewed by 5995
Abstract
α-Helices often recognize their target proteins at protein–protein interfaces through more than one recognition face. This review describes the state-of-the-art in the design of non-peptidic α-helix mimetics that reproduce functionality from multiple faces of an α-helix. Full article
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181 KiB  
Review
The Mucosal Immune System of Teleost Fish
by Irene Salinas
Biology 2015, 4(3), 525-539; https://doi.org/10.3390/biology4030525 - 12 Aug 2015
Cited by 310 | Viewed by 15298
Abstract
Teleost fish possess an adaptive immune system associated with each of their mucosal body surfaces. Evidence obtained from mucosal vaccination and mucosal infection studies reveal that adaptive immune responses take place at the different mucosal surfaces of teleost. The main mucosa-associated lymphoid tissues [...] Read more.
Teleost fish possess an adaptive immune system associated with each of their mucosal body surfaces. Evidence obtained from mucosal vaccination and mucosal infection studies reveal that adaptive immune responses take place at the different mucosal surfaces of teleost. The main mucosa-associated lymphoid tissues (MALT) of teleosts are the gut-associated lymphoid tissue (GALT), skin-associated lymphoid tissue (SALT), the gill-associated lymphoid tissue (GIALT) and the recently discovered nasopharynx-associated lymphoid tissue (NALT). Teleost MALT includes diffuse B cells and T cells with specific phenotypes different from their systemic counterparts that have co-evolved to defend the microbe-rich mucosal environment. Both B and T cells respond to mucosal infection or vaccination. Specific antibody responses can be measured in the gills, gut and skin mucosal secretions of teleost fish following mucosal infection or vaccination. Rainbow trout studies have shown that IgT antibodies and IgT+ B cells are the predominant B cell subset in all MALT and respond in a compartmentalized manner to mucosal infection. Our current knowledge on adaptive immunity in teleosts is limited compared to the mammalian literature. New research tools and in vivo models are currently being developed in order to help reveal the great intricacy of teleost mucosal adaptive immunity and help improve mucosal vaccination protocols for use in aquaculture. Full article
(This article belongs to the Special Issue Current Understanding of Fish Immune Systems)
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378 KiB  
Review
Antibody Affinity Maturation in Fishes—Our Current Understanding
by Brad G. Magor
Biology 2015, 4(3), 512-524; https://doi.org/10.3390/biology4030512 - 31 Jul 2015
Cited by 29 | Viewed by 6830
Abstract
It has long been believed that fish lack antibody affinity maturation, in part because they were thought to lack germinal centers. Recent research done on sharks and bony fishes indicates that these early vertebrates are able to affinity mature their antibodies. This article [...] Read more.
It has long been believed that fish lack antibody affinity maturation, in part because they were thought to lack germinal centers. Recent research done on sharks and bony fishes indicates that these early vertebrates are able to affinity mature their antibodies. This article reviews the functionality of the fish homologue of the immunoglobulin (Ig) mutator enzyme activation-induced cytidine deaminase (AID). We also consider the protein and molecular evidence for Ig somatic hypermutation and antibody affinity maturation. In the context of recent evidence for a putative proto-germinal center in fishes we propose some possible reasons that observed affinity maturation in fishes often seems lacking and propose future work that might shed further light on this process in fishes. Full article
(This article belongs to the Special Issue Current Understanding of Fish Immune Systems)
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388 KiB  
Review
The Regulation of Reverse Cholesterol Transport and Cellular Cholesterol Homeostasis by MicroRNAs
by Diana M. DiMarco and Maria Luz Fernandez
Biology 2015, 4(3), 494-511; https://doi.org/10.3390/biology4030494 - 28 Jul 2015
Cited by 34 | Viewed by 8805
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that have the ability to post-transcriptionally regulate gene expression. Hundreds of miRNAs have been identified in humans and they are involved in the regulation of almost every process, including cholesterol transport, metabolism, and maintenance of cholesterol homeostasis. [...] Read more.
MicroRNAs (miRNAs) are small, non-coding RNAs that have the ability to post-transcriptionally regulate gene expression. Hundreds of miRNAs have been identified in humans and they are involved in the regulation of almost every process, including cholesterol transport, metabolism, and maintenance of cholesterol homeostasis. Because of their small size and their ability to very specifically regulate gene expression, miRNAs are attractive targets for the regulation of dyslipidemias and other lipid-related disorders. However, the complex interactions between miRNAs, transcription factors, and gene expression raise great potential for side effects as a result of miRNA overexpression or inhibition. Many dietary components can also target specific miRNAs, altering the expression of downstream genes. Therefore, much more research is necessary to fully understand the role(s) of each miRNA in the body and how they may be impacted by diet and health. The present review aims to summarize the known roles of miRNAs in the regulation of reverse cholesterol transport and the maintenance of cholesterol homeostasis, as well as the potential clinical consequences of their manipulation. Full article
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603 KiB  
Review
Sensors of Infection: Viral Nucleic Acid PRRs in Fish
by Sarah Poynter, Graeme Lisser, Andrea Monjo and Stephanie DeWitte-Orr
Biology 2015, 4(3), 460-493; https://doi.org/10.3390/biology4030460 - 08 Jul 2015
Cited by 40 | Viewed by 8611
Abstract
Viruses produce nucleic acids during their replication, either during genomic replication or transcription. These nucleic acids are present in the cytoplasm or endosome of an infected cell, or in the extracellular space to be sensed by neighboring cells during lytic infections. Cells have [...] Read more.
Viruses produce nucleic acids during their replication, either during genomic replication or transcription. These nucleic acids are present in the cytoplasm or endosome of an infected cell, or in the extracellular space to be sensed by neighboring cells during lytic infections. Cells have mechanisms of sensing virus-generated nucleic acids; these nucleic acids act as flags to the cell, indicating an infection requiring defense mechanisms. The viral nucleic acids are called pathogen-associated molecular patterns (PAMPs) and the sensors that bind them are called pattern recognition receptors (PRRs). This review article focuses on the most recent findings regarding nucleic acids PRRs in fish, including: Toll-like receptors (TLRs), RIG-I-like receptors (RLRs), cytoplasmic DNA sensors (CDSs) and class A scavenger receptors (SR-As). It also discusses what is currently known of the downstream signaling molecules for each PRR family and the resulting antiviral response, either type I interferons (IFNs) or pro-inflammatory cytokine production. The review highlights what is known but also defines what still requires elucidation in this economically important animal. Understanding innate immune systems to virus infections will aid in the development of better antiviral therapies and vaccines for the future. Full article
(This article belongs to the Special Issue Current Understanding of Fish Immune Systems)
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