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Biology, Volume 5, Issue 1 (March 2016)

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Open AccessReview Biochemical and Functional Insights into the Integrated Regulation of Innate Immune Cell Responses by Teleost Leukocyte Immune-Type Receptors
Received: 18 December 2015 / Revised: 1 March 2016 / Accepted: 1 March 2016 / Published: 8 March 2016
Cited by 4 | Viewed by 2062 | PDF Full-text (1086 KB) | HTML Full-text | XML Full-text
Abstract
Across vertebrates, innate immunity consists of a complex assortment of highly specialized cells capable of unleashing potent effector responses designed to destroy or mitigate foreign pathogens. The execution of various innate cellular behaviors such as phagocytosis, degranulation, or cell-mediated cytotoxicity are functionally indistinguishable [...] Read more.
Across vertebrates, innate immunity consists of a complex assortment of highly specialized cells capable of unleashing potent effector responses designed to destroy or mitigate foreign pathogens. The execution of various innate cellular behaviors such as phagocytosis, degranulation, or cell-mediated cytotoxicity are functionally indistinguishable when being performed by immune cells isolated from humans or teleost fishes; vertebrates that diverged from one another more than 450 million years ago. This suggests that vital components of the vertebrate innate defense machinery are conserved and investigating such processes in a range of model systems provides an important opportunity to identify fundamental features of vertebrate immunity. One characteristic that is highly conserved across vertebrate systems is that cellular immune responses are dependent on specialized immunoregulatory receptors that sense environmental stimuli and initiate intracellular cascades that can elicit appropriate effector responses. A wide variety of immunoregulatory receptor families have been extensively studied in mammals, and many have been identified as cell- and function-specific regulators of a range of innate responses. Although much less is known in fish, the growing database of genomic information has recently allowed for the identification of several immunoregulatory receptor gene families in teleosts. Many of these putative immunoregulatory receptors have yet to be assigned any specific role(s), and much of what is known has been based solely on structural and/or phylogenetic relationships with mammalian receptor families. As an attempt to address some of these shortcomings, this review will focus on our growing understanding of the functional roles played by specific members of the channel catfish (Ictalurus punctatus) leukocyte immune-type receptors (IpLITRs), which appear to be important regulators of several innate cellular responses via classical as well as unique biochemical signaling networks. Full article
(This article belongs to the Special Issue Current Topics in Fish Immunity)
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Open AccessArticle Melatonin and Sleep-Wake Rhythms before and after Ocular Lens Replacement in Elderly Humans
Received: 11 November 2015 / Revised: 19 January 2016 / Accepted: 2 February 2016 / Published: 15 February 2016
Cited by 4 | Viewed by 2393 | PDF Full-text (1922 KB) | HTML Full-text | XML Full-text
Abstract
Light of short wavelengths has been shown to play a key role in non-image forming responses. Due to aging, the ocular lens becomes more yellow reducing the transmission of short wavelengths in the elderly. In the present study, we make use of cataract [...] Read more.
Light of short wavelengths has been shown to play a key role in non-image forming responses. Due to aging, the ocular lens becomes more yellow reducing the transmission of short wavelengths in the elderly. In the present study, we make use of cataract surgery to investigate the effects of a relative increase of short wavelength transmission on melatonin- and sleep-wake rhythms (N = 14). We observed, on average, a delay of the sleep-wake and the nocturnal melatonin rhythms after cataract surgery. This delay is tentatively attributed to a relatively large increase of light transmittance in the evening hours more than an increase of the already relatively high light intensities found in the daytime. The later phase that we observed after cataract surgery (clear lens) as compared to the earlier phase observed before cataract (yellowish lens) is in agreement with the general later phase reported in the young (clear lens) population. Full article
(This article belongs to the Special Issue Circadian Rhythms from Bench to Bedside)
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Open AccessReview Sleep-Wake Regulation and Its Impact on Working Memory Performance: The Role of Adenosine
Received: 28 November 2015 / Revised: 15 January 2016 / Accepted: 19 January 2016 / Published: 5 February 2016
Cited by 8 | Viewed by 3997 | PDF Full-text (2215 KB) | HTML Full-text | XML Full-text
Abstract
The sleep-wake cycle is regulated by a fine-tuned interplay between sleep-homeostatic and circadian mechanisms. Compelling evidence suggests that adenosine plays an important role in mediating the increase of homeostatic sleep pressure during time spent awake and its decrease during sleep. Here, we summarize [...] Read more.
The sleep-wake cycle is regulated by a fine-tuned interplay between sleep-homeostatic and circadian mechanisms. Compelling evidence suggests that adenosine plays an important role in mediating the increase of homeostatic sleep pressure during time spent awake and its decrease during sleep. Here, we summarize evidence that adenosinergic mechanisms regulate not only the dynamic of sleep pressure, but are also implicated in the interaction of homeostatic and circadian processes. We review how this interaction becomes evident at several levels, including electrophysiological data, neuroimaging studies and behavioral observations. Regarding complex human behavior, we particularly focus on sleep-wake regulatory influences on working memory performance and underlying brain activity, with a specific emphasis on the role of adenosine in this interplay. We conclude that a change in adenosinergic mechanisms, whether exogenous or endogenous, does not only impact on sleep-homeostatic processes, but also interferes with the circadian timing system. Full article
(This article belongs to the Special Issue Circadian Rhythms from Bench to Bedside)
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Open AccessArticle Aboveground Net Primary Productivity in a Riparian Wetland Following Restoration of Hydrology
Received: 1 September 2015 / Revised: 15 January 2016 / Accepted: 18 January 2016 / Published: 4 February 2016
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Abstract
This research presents the initial results of the effects of hydrological restoration on forested wetlands in the Mississippi alluvial plain near Memphis, Tennessee. Measurements were carried out in a secondary channel, the Loosahatchie Chute, in which rock dikes were constructed in the 1960s [...] Read more.
This research presents the initial results of the effects of hydrological restoration on forested wetlands in the Mississippi alluvial plain near Memphis, Tennessee. Measurements were carried out in a secondary channel, the Loosahatchie Chute, in which rock dikes were constructed in the 1960s to keep most flow in the main navigation channel. In 2008–2009, the dikes were notched to allow more flow into the secondary channel. Study sites were established based on relative distance downstream of the notched dikes. Additionally, a reference site was established north of the Loosahatchie Chute where the dikes remained unnotched. We compared various components of vegetation composition and productivity at sites in the riparian wetlands for two years. Salix nigra had the highest Importance Value at every site. Species with minor Importance Values were Celtis laevigata, Acer rubrum, and Plantanus occidentalis. Productivity increased more following the introduction of river water in affected sites compared to the reference. Aboveground net primary productivity was highest at the reference site (2926 ± 458.1 g·m−2·year−1), the intact site; however, there were greater increase at the sites in the Loosahatchie Chute, where measurements ranged from 1197.7 ± 160.0 g m−2·year−1·to 2874.2 ± 794.0 g·m−2·year−1. The site furthest from the notching was the most affected. Pulsed inputs into these wetlands may enhance forested wetland productivity. Continued monitoring will quantify impacts of restored channel hydrology along the Mississippi River. Full article
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Open AccessReview Endocrine and Local IGF-I in the Bony Fish Immune System
Received: 24 November 2015 / Revised: 14 January 2016 / Accepted: 18 January 2016 / Published: 26 January 2016
Cited by 5 | Viewed by 2346 | PDF Full-text (680 KB) | HTML Full-text | XML Full-text
Abstract
A role for GH and IGF-I in the modulation of the immune system has been under discussion for decades. Generally, GH is considered a stimulator of innate immune parameters in mammals and teleost fish. The stimulatory effects in humans as well as in [...] Read more.
A role for GH and IGF-I in the modulation of the immune system has been under discussion for decades. Generally, GH is considered a stimulator of innate immune parameters in mammals and teleost fish. The stimulatory effects in humans as well as in bony fish often appear to be correlated with elevated endocrine IGF-I (liver-derived), which has also been shown to be suppressed during infection in some studies. Nevertheless, data are still fragmentary. Some studies point to an important role of GH and IGF-I particularly during immune organ development and constitution. Even less is known about the potential relevance of local (autocrine/paracrine) IGF-I within adult and developing immune organs, and the distinct localization of IGF-I in immune cells and tissues of mammals and fish has not been systematically defined. Thus far, IGF-I has been localized in different mammalian immune cell types, particularly macrophages and granulocytes, and in supporting cells, but not in T-lymphocytes. In the present study, we detected IGF-I in phagocytic cells isolated from rainbow trout head kidney and, in contrast to some findings in mammals, in T-cells of a channel catfish cell line. Thus, although numerous analogies among mammals and teleosts exist not only for the GH/IGF-system, but also for the immune system, there are differences that should be further investigated. For instance, it is unclear whether the primarily reported role of GH/IGF-I in the innate immune response is due to the lack of studies focusing on the adaptive immune system, or whether it truly preferentially concerns innate immune parameters. Infectious challenges in combination with GH/IGF-I manipulations are another important topic that has not been sufficiently addressed to date, particularly with respect to developmental and environmental influences on fish growth and health. Full article
(This article belongs to the Special Issue Current Topics in Fish Immunity)
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Open AccessEditorial Acknowledgement to Reviewers of Biology in 2015
Received: 22 January 2016 / Accepted: 22 January 2016 / Published: 22 January 2016
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Abstract
The editors of Biology would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2015. [...] Full article
Open AccessArticle Effects of Fiddler Crab Burrows on Sediment Properties in the Mangrove Mudflats of Sungai Sepang, Malaysia
Received: 5 November 2015 / Revised: 13 January 2016 / Accepted: 14 January 2016 / Published: 19 January 2016
Cited by 3 | Viewed by 2189 | PDF Full-text (2963 KB) | HTML Full-text | XML Full-text
Abstract
In mangrove ecosystems, litter fall accumulates as refractory organic carbon on the sediment surface and creates anoxic sediment layers. Fiddler crabs, through their burrowing activity, translocate oxygen into the anoxic layers and promote aerobic respiration, iron reduction and nitrification. In this study, the [...] Read more.
In mangrove ecosystems, litter fall accumulates as refractory organic carbon on the sediment surface and creates anoxic sediment layers. Fiddler crabs, through their burrowing activity, translocate oxygen into the anoxic layers and promote aerobic respiration, iron reduction and nitrification. In this study, the effects of four species of fiddler crabs (Uca triangularis, Uca rosea, Uca forcipata and Uca paradussumieri) on organic content, water content, porosity, redox potential and solid phase iron pools of mangrove sediments were investigated. In each crab’s habitat, six cores down to 30 cm depth were taken from burrowed and non-burrowed sampling plots. Redox potential and oxidized iron pools were highest in surface sediment, while porosity, water and organic content were higher in deeper sediment. Reduced iron (Fe (II)) and redox potential were significantly different between burrowed and non-burrowed plots. Crab burrows extend the oxidized surface layer down to 4 cm depth and through the oxidation effect, reduce the organic content of sediments. The effects of burrows varied between the four species based on their shore location. The oxidation effect of burrows enhance the decomposition rate and stimulate iron reduction, which are processes that are expected to play an important role in biogeochemical properties of mangrove sediments. Full article
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Open AccessReview MHC and Evolution in Teleosts
Received: 5 November 2015 / Revised: 12 January 2016 / Accepted: 13 January 2016 / Published: 19 January 2016
Cited by 12 | Viewed by 2953 | PDF Full-text (3167 KB) | HTML Full-text | XML Full-text
Abstract
Major histocompatibility complex (MHC) molecules are key players in initiating immune responses towards invading pathogens. Both MHC class I and class II genes are present in teleosts, and, using phylogenetic clustering, sequences from both classes have been classified into various lineages. The polymorphic [...] Read more.
Major histocompatibility complex (MHC) molecules are key players in initiating immune responses towards invading pathogens. Both MHC class I and class II genes are present in teleosts, and, using phylogenetic clustering, sequences from both classes have been classified into various lineages. The polymorphic and classical MHC class I and class II gene sequences belong to the U and A lineages, respectively. The remaining class I and class II lineages contain nonclassical gene sequences that, despite their non-orthologous nature, may still hold functions similar to their mammalian nonclassical counterparts. However, the fact that several of these nonclassical lineages are only present in some teleost species is puzzling and questions their functional importance. The number of genes within each lineage greatly varies between teleost species. At least some gene expansions seem reasonable, such as the huge MHC class I expansion in Atlantic cod that most likely compensates for the lack of MHC class II and CD4. The evolutionary trigger for similar MHC class I expansions in tilapia, for example, which has a functional MHC class II, is not so apparent. Future studies will provide us with a more detailed understanding in particular of nonclassical MHC gene functions. Full article
(This article belongs to the Special Issue Current Topics in Fish Immunity)
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Open AccessReview Notch-Mediated Cell Adhesion
Received: 26 October 2015 / Revised: 12 January 2016 / Accepted: 13 January 2016 / Published: 16 January 2016
Cited by 1 | Viewed by 3439 | PDF Full-text (2230 KB) | HTML Full-text | XML Full-text
Abstract
Notch family members are generally recognized as signaling molecules that control various cellular responses in metazoan organisms. Early fly studies and our mammalian studies demonstrated that Notch family members are also cell adhesion molecules; however, information on the physiological roles of this function [...] Read more.
Notch family members are generally recognized as signaling molecules that control various cellular responses in metazoan organisms. Early fly studies and our mammalian studies demonstrated that Notch family members are also cell adhesion molecules; however, information on the physiological roles of this function and its origin is limited. In this review, we discuss the potential present and ancestral roles of Notch-mediated cell adhesion in order to explore its origin and the initial roles of Notch family members dating back to metazoan evolution. We hypothesize that Notch family members may have initially emerged as cell adhesion molecules in order to mediate multicellularity in the last common ancestor of metazoan organisms. Full article
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Open AccessConcept Paper Heterochrony as Diachronically Modified Cell-Cell Interactions
Received: 29 September 2015 / Revised: 29 December 2015 / Accepted: 31 December 2015 / Published: 14 January 2016
Cited by 5 | Viewed by 1711 | PDF Full-text (1039 KB) | HTML Full-text | XML Full-text
Abstract
Heterochrony is an enabling concept in evolution theory that metaphorically captures the mechanism of biologic change due to mechanisms of growth and development. The spatio-temporal patterns of morphogenesis are determined by cell-to-cell signaling mediated by specific soluble growth factors and their cognate receptors [...] Read more.
Heterochrony is an enabling concept in evolution theory that metaphorically captures the mechanism of biologic change due to mechanisms of growth and development. The spatio-temporal patterns of morphogenesis are determined by cell-to-cell signaling mediated by specific soluble growth factors and their cognate receptors on nearby cells of different germline origins. Subsequently, down-stream production of second messengers generates patterns of form and function. Environmental upheavals such as Romer’s hypothesized drying up of bodies of water globally caused the vertebrate water-land transition. That transition caused physiologic stress, modifying cell-cell signaling to generate terrestrial adaptations of the skeleton, lung, skin, kidney and brain. These tissue-specific remodeling events occurred as a result of the duplication of the Parathyroid Hormone-related Protein Receptor (PTHrPR) gene, expressed in mesodermal fibroblasts in close proximity to ubiquitously expressed endodermal PTHrP, amplifying this signaling pathway. Examples of how and why PTHrPR amplification affected the ontogeny, phylogeny, physiology and pathophysiology of the lung are used to substantiate and further our understanding through insights to the heterochronic mechanisms of evolution, such as the fish swim bladder evolving into the vertebrate lung, interrelated by such functional homologies as surfactant and mechanotransduction. Instead of the conventional description of this phenomenon, lung evolution can now be understood as adaptive changes in the cellular-molecular signaling mechanisms underlying its ontogeny and phylogeny. Full article
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Open AccessReview DNA Methylation Analysis: Choosing the Right Method
Received: 8 July 2015 / Revised: 16 December 2015 / Accepted: 22 December 2015 / Published: 6 January 2016
Cited by 82 | Viewed by 7187 | PDF Full-text (1848 KB) | HTML Full-text | XML Full-text
Abstract
In the burgeoning field of epigenetics, there are several methods available to determine the methylation status of DNA samples. However, choosing the method that is best suited to answering a particular biological question still proves to be a difficult task. This review aims [...] Read more.
In the burgeoning field of epigenetics, there are several methods available to determine the methylation status of DNA samples. However, choosing the method that is best suited to answering a particular biological question still proves to be a difficult task. This review aims to provide biologists, particularly those new to the field of epigenetics, with a simple algorithm to help guide them in the selection of the most appropriate assay to meet their research needs. First of all, we have separated all methods into two categories: those that are used for: (1) the discovery of unknown epigenetic changes; and (2) the assessment of DNA methylation within particular regulatory regions/genes of interest. The techniques are then scrutinized and ranked according to their robustness, high throughput capabilities and cost. This review includes the majority of methods available to date, but with a particular focus on commercially available kits or other simple and straightforward solutions that have proven to be useful. Full article
(This article belongs to the Special Issue DNA Methylation)
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Open AccessReview Disease Transmission by Misfolded Prion-Protein Isoforms, Prion-Like Amyloids, Functional Amyloids and the Central Dogma
Received: 16 July 2015 / Revised: 22 October 2015 / Accepted: 28 December 2015 / Published: 4 January 2016
Cited by 3 | Viewed by 2239 | PDF Full-text (249 KB) | HTML Full-text | XML Full-text
Abstract
In 1982, the term “prions” (proteinaceous infectious particles) was coined to specify a new principle of infection. A misfolded isoform of a cellular protein has been described as the causative agent of a fatal neurodegenerative disease. At the beginning of prion research scientists [...] Read more.
In 1982, the term “prions” (proteinaceous infectious particles) was coined to specify a new principle of infection. A misfolded isoform of a cellular protein has been described as the causative agent of a fatal neurodegenerative disease. At the beginning of prion research scientists assumed that the infectious agent causing transmissible spongiform encephalopathy (TSE) was a virus, but some unconventional properties of these pathogens were difficult to bring in line with the prevailing viral model. The discovery that prions (obviously devoid of any coding nucleic acid) can store and transmit information similarly to DNA was initially even denoted as being “heretical” but is nowadays mainly accepted by the scientific community. This review describes, from a historical point of view, how the “protein-only hypothesis” expands the Central Dogma. Definition of both, the prion principle and the Central Dogma, have been essential steps to understand information storage and transfer within and among cells and organisms. Furthermore, the current understanding of the infectivity of prion-proteins after misfolding is summarized succinctly. Finally, prion-like amyloids and functional amyloids, as found in yeast and bacteria, will be discussed. Full article
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Open AccessReview Cell Adhesion Molecules and Ubiquitination—Functions and Significance
Received: 28 October 2015 / Revised: 2 December 2015 / Accepted: 15 December 2015 / Published: 23 December 2015
Cited by 5 | Viewed by 2560 | PDF Full-text (1120 KB) | HTML Full-text | XML Full-text
Abstract
Cell adhesion molecules of the immunoglobulin (Ig) superfamily represent the biggest group of cell adhesion molecules. They have been analyzed since approximately 40 years ago and most of them have been shown to play a role in tumor progression and in the nervous [...] Read more.
Cell adhesion molecules of the immunoglobulin (Ig) superfamily represent the biggest group of cell adhesion molecules. They have been analyzed since approximately 40 years ago and most of them have been shown to play a role in tumor progression and in the nervous system. All members of the Ig superfamily are intensively posttranslationally modified. However, many aspects of their cellular functions are not yet known. Since a few years ago it is known that some of the Ig superfamily members are modified by ubiquitin. Ubiquitination has classically been described as a proteasomal degradation signal but during the last years it became obvious that it can regulate many other processes including internalization of cell surface molecules and lysosomal sorting. The purpose of this review is to summarize the current knowledge about the ubiquitination of cell adhesion molecules of the Ig superfamily and to discuss its potential physiological roles in tumorigenesis and in the nervous system. Full article
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