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Volume 2
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Biology, Volume 2, Issue 1 (March 2013) – 22 articles , Pages 1-480

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323 KiB  
Review
Climate Change and Intertidal Wetlands
by Pauline M. Ross and Paul Adam
Biology 2013, 2(1), 445-480; https://doi.org/10.3390/biology2010445 - 19 Mar 2013
Cited by 28 | Viewed by 12173
Abstract
Intertidal wetlands are recognised for the provision of a range of valued ecosystem services. The two major categories of intertidal wetlands discussed in this contribution are saltmarshes and mangrove forests. Intertidal wetlands are under threat from a range of anthropogenic causes, some site-specific, [...] Read more.
Intertidal wetlands are recognised for the provision of a range of valued ecosystem services. The two major categories of intertidal wetlands discussed in this contribution are saltmarshes and mangrove forests. Intertidal wetlands are under threat from a range of anthropogenic causes, some site-specific, others acting globally. Globally acting factors include climate change and its driving cause—the increasing atmospheric concentrations of greenhouse gases. One direct consequence of climate change will be global sea level rise due to thermal expansion of the oceans, and, in the longer term, the melting of ice caps and glaciers. The relative sea level rise experienced at any one locality will be affected by a range of factors, as will the response of intertidal wetlands to the change in sea level. If relative sea level is rising and sedimentation within intertidal wetlands does not keep pace, then there will be loss of intertidal wetlands from the seaward edge, with survival of the ecosystems only possible if they can retreat inland. When retreat is not possible, the wetland area will decline in response to the “squeeze” experienced. Any changes to intertidal wetland vegetation, as a consequence of climate change, will have flow on effects to biota, while changes to biota will affect intertidal vegetation. Wetland biota may respond to climate change by shifting in distribution and abundance landward, evolving or becoming extinct. In addition, impacts from ocean acidification and warming are predicted to affect the fertilisation, larval development, growth and survival of intertidal wetland biota including macroinvertebrates, such as molluscs and crabs, and vertebrates such as fish and potentially birds. The capacity of organisms to move and adapt will depend on their life history characteristics, phenotypic plasticity, genetic variability, inheritability of adaptive characteristics, and the predicted rates of environmental change. Full article
(This article belongs to the Special Issue Biological Implications of Climate Change)
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Article
Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals
by Tamaki Yuri, Rebecca T. Kimball, John Harshman, Rauri C. K. Bowie, Michael J. Braun, Jena L. Chojnowski, Kin-Lan Han, Shannon J. Hackett, Christopher J. Huddleston, William S. Moore, Sushma Reddy, Frederick H. Sheldon, David W. Steadman, Christopher C. Witt and Edward L. Braun
Biology 2013, 2(1), 419-444; https://doi.org/10.3390/biology2010419 - 13 Mar 2013
Cited by 92 | Viewed by 27951
Abstract
Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include [...] Read more.
Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions. Full article
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Review
Drought, Deluge and Declines: The Impact of Precipitation Extremes on Amphibians in a Changing Climate
by Susan C. Walls, William J. Barichivich and Mary E. Brown
Biology 2013, 2(1), 399-418; https://doi.org/10.3390/biology2010399 - 11 Mar 2013
Cited by 142 | Viewed by 23086
Abstract
The Class Amphibia is one of the most severely impacted taxa in an on-going global biodiversity crisis. Because amphibian reproduction is tightly associated with the presence of water, climatic changes that affect water availability pose a particularly menacing threat to both aquatic and [...] Read more.
The Class Amphibia is one of the most severely impacted taxa in an on-going global biodiversity crisis. Because amphibian reproduction is tightly associated with the presence of water, climatic changes that affect water availability pose a particularly menacing threat to both aquatic and terrestrial-breeding amphibians. We explore the impacts that one facet of climate change—that of extreme variation in precipitation—may have on amphibians. This variation is manifested principally as increases in the incidence and severity of both drought and major storm events. We stress the need to consider not only total precipitation amounts but also the pattern and timing of rainfall events. Such rainfall “pulses” are likely to become increasingly more influential on amphibians, especially in relation to seasonal reproduction. Changes in reproductive phenology can strongly influence the outcome of competitive and predatory interactions, thus potentially altering community dynamics in assemblages of co-existing species. We present a conceptual model to illustrate possible landscape and metapopulation consequences of alternative climate change scenarios for pond-breeding amphibians, using the Mole Salamander, Ambystoma talpoideum, as an example. Although amphibians have evolved a variety of life history strategies that enable them to cope with environmental uncertainty, it is unclear whether adaptations can keep pace with the escalating rate of climate change. Climate change, especially in combination with other stressors, is a daunting challenge for the persistence of amphibians and, thus, the conservation of global biodiversity. Full article
(This article belongs to the Special Issue Biological Implications of Climate Change)
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Review
Next-Generation Sequencing: From Understanding Biology to Personalized Medicine
by Karen S. Frese, Hugo A. Katus and Benjamin Meder
Biology 2013, 2(1), 378-398; https://doi.org/10.3390/biology2010378 - 1 Mar 2013
Cited by 36 | Viewed by 17628
Abstract
Within just a few years, the new methods for high-throughput next-generation sequencing have generated completely novel insights into the heritability and pathophysiology of human disease. In this review, we wish to highlight the benefits of the current state-of-the-art sequencing technologies for genetic and [...] Read more.
Within just a few years, the new methods for high-throughput next-generation sequencing have generated completely novel insights into the heritability and pathophysiology of human disease. In this review, we wish to highlight the benefits of the current state-of-the-art sequencing technologies for genetic and epigenetic research. We illustrate how these technologies help to constantly improve our understanding of genetic mechanisms in biological systems and summarize the progress made so far. This can be exemplified by the case of heritable heart muscle diseases, so-called cardiomyopathies. Here, next-generation sequencing is able to identify novel disease genes, and first clinical applications demonstrate the successful translation of this technology into personalized patient care. Full article
(This article belongs to the Special Issue Next Generation Sequencing Approaches in Biology)
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Article
The Effect of Freeze-Thaw Conditions on Arctic Soil Bacterial Communities
by Niraj Kumar, Paul Grogan, Haiyan Chu, Casper T. Christiansen and Virginia K. Walker
Biology 2013, 2(1), 356-377; https://doi.org/10.3390/biology2010356 - 28 Feb 2013
Cited by 39 | Viewed by 9819
Abstract
Climate change is already altering the landscape at high latitudes. Permafrost is thawing, the growing season is starting earlier, and, as a result, certain regions in the Arctic may be subjected to an increased incidence of freeze-thaw events. The potential release of carbon [...] Read more.
Climate change is already altering the landscape at high latitudes. Permafrost is thawing, the growing season is starting earlier, and, as a result, certain regions in the Arctic may be subjected to an increased incidence of freeze-thaw events. The potential release of carbon and nutrients from soil microbial cells that have been lysed by freeze-thaw transitions could have significant impacts on the overall carbon balance of arctic ecosystems, and therefore on atmospheric CO2 concentrations. However, the impact of repeated freezing and thawing with the consequent growth and recrystallization of ice on microbial communities is still not well understood. Soil samples from three distinct sites, representing Canadian geographical low arctic, mid-arctic and high arctic soils were collected from Daring Lake, Alexandra Fjord and Cambridge Bay sampling sites, respectively. Laboratory-based experiments subjected the soils to multiple freeze-thaw cycles for 14 days based on field observations (0 °C to −10 °C for 12 h and −10 °C to 0 °C for 12 h) and the impact on the communities was assessed by phospholipid fatty acid (PLFA) methyl ester analysis and 16S ribosomal RNA gene sequencing. Both data sets indicated differences in composition and relative abundance between the three sites, as expected. However, there was also a strong variation within the two high latitude sites in the effects of the freeze-thaw treatment on individual PLFA and 16S-based phylotypes. These site-based heterogeneities suggest that the impact of climate change on soil microbial communities may not be predictable a priori; minor differential susceptibilities to freeze-thaw stress could lead to a “butterfly effect” as described by chaos theory, resulting in subsequent substantive differences in microbial assemblages. This perspectives article suggests that this is an unwelcome finding since it will make future predictions for the impact of on-going climate change on soil microbial communities in arctic regions all but impossible. Full article
(This article belongs to the Special Issue Polar Microbiology: Recent Advances and Future Perspectives)
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Article
Targeted Toxin-Based Selectable Drug-Free Enrichment of Mammalian Cells with High Transgene Expression
by Masahiro Sato, Eri Akasaka, Issei Saitoh, Masato Ohtsuka, Shingo Nakamura, Takayuki Sakurai and Satoshi Watanabe
Biology 2013, 2(1), 341-355; https://doi.org/10.3390/biology2010341 - 28 Feb 2013
Cited by 10 | Viewed by 7106
Abstract
Almost all transfection protocols for mammalian cells use a drug resistance gene for the selection of transfected cells. However, it always requires the characterization of each isolated clone regarding transgene expression, which is time-consuming and labor-intensive. In the current study, we developed a [...] Read more.
Almost all transfection protocols for mammalian cells use a drug resistance gene for the selection of transfected cells. However, it always requires the characterization of each isolated clone regarding transgene expression, which is time-consuming and labor-intensive. In the current study, we developed a novel method to selectively isolate clones with high transgene expression without drug selection. Porcine embryonic fibroblasts were transfected with pCEIEnd, an expression vector that simultaneously expresses enhanced green fluorescent protein (EGFP) and endo-b-galactosidase C(EndoGalC; an enzyme capable of digesting cell surface a-Gal epitope) upon transfection. After transfection, the surviving cells were briefly treated with IB4SAP (a-Gal epitope-specific BS-I-B4 lectin conjugated with a toxin saporin). The treated cells were then allowed to grow in normal medium, during which only cells strongly expressing EndoGalC and EGFP would survive because of the absence of a-Gal epitopes on their cell surface. Almost all the surviving colonies after IB4SAP treatment were in fact negative for BS-I-B4 staining, and also strongly expressed EGFP. This system would be particularly valuable for researchers who wish to perform large-scale production of therapeutically important recombinant proteins. Full article
(This article belongs to the Special Issue Gene Expression and Regulation)
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Communication
Micro-Eukaryotic Diversity in Hypolithons from Miers Valley, Antarctica
by Jarishma K. Gokul, Angel Valverde, Marla Tuffin, Stephen Craig Cary and Don A. Cowan
Biology 2013, 2(1), 331-340; https://doi.org/10.3390/biology2010331 - 22 Feb 2013
Cited by 10 | Viewed by 7649
Abstract
The discovery of extensive and complex hypolithic communities in both cold and hot deserts has raised many questions regarding their ecology, biodiversity and relevance in terms of regional productivity. However, most hypolithic research has focused on the bacterial elements of the community. This [...] Read more.
The discovery of extensive and complex hypolithic communities in both cold and hot deserts has raised many questions regarding their ecology, biodiversity and relevance in terms of regional productivity. However, most hypolithic research has focused on the bacterial elements of the community. This study represents the first investigation of micro-eukaryotic communities in all three hypolith types. Here we show that Antarctic hypoliths support extensive populations of novel uncharacterized bryophyta, fungi and protists and suggest that well known producer-decomposer-predator interactions may create the necessary conditions for hypolithic productivity in Antarctic deserts. Full article
(This article belongs to the Special Issue Polar Microbiology: Recent Advances and Future Perspectives)
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Review
The Dynamic Arctic Snow Pack: An Unexplored Environment for Microbial Diversity and Activity
by Catherine Larose, Aurélien Dommergue and Timothy M. Vogel
Biology 2013, 2(1), 317-330; https://doi.org/10.3390/biology2010317 - 5 Feb 2013
Cited by 50 | Viewed by 9339
Abstract
The Arctic environment is undergoing changes due to climate shifts, receiving contaminants from distant sources and experiencing increased human activity. Climate change may alter microbial functioning by increasing growth rates and substrate use due to increased temperature. This may lead to changes of [...] Read more.
The Arctic environment is undergoing changes due to climate shifts, receiving contaminants from distant sources and experiencing increased human activity. Climate change may alter microbial functioning by increasing growth rates and substrate use due to increased temperature. This may lead to changes of process rates and shifts in the structure of microbial communities. Biodiversity may increase as the Arctic warms and population shifts occur as psychrophilic/psychrotolerant species disappear in favor of more mesophylic ones. In order to predict how ecological processes will evolve as a function of global change, it is essential to identify which populations participate in each process, how they vary physiologically, and how the relative abundance, activity and community structure will change under altered environmental conditions. This review covers aspects of the importance and implication of snowpack in microbial ecology emphasizing the diversity and activity of these critical members of cold zone ecosystems. Full article
(This article belongs to the Special Issue Polar Microbiology: Recent Advances and Future Perspectives)
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Review
Hepatitis C Virus and Hepatocellular Carcinoma
by Tatsuo Kanda, Osamu Yokosuka and Masao Omata
Biology 2013, 2(1), 304-316; https://doi.org/10.3390/biology2010304 - 30 Jan 2013
Cited by 16 | Viewed by 9800
Abstract
Hepatitis C virus (HCV), a hepatotropic virus, is a single stranded-positive RNA virus of ~9,600 nt. length belonging to the Flaviviridae family. HCV infection causes acute hepatitis, chronic hepatitis, cirrhosis and hepatocellular carcinoma (HCC). It has been reported that HCV-coding proteins interact with [...] Read more.
Hepatitis C virus (HCV), a hepatotropic virus, is a single stranded-positive RNA virus of ~9,600 nt. length belonging to the Flaviviridae family. HCV infection causes acute hepatitis, chronic hepatitis, cirrhosis and hepatocellular carcinoma (HCC). It has been reported that HCV-coding proteins interact with host-cell factors that are involved in cell cycle regulation, transcriptional regulation, cell proliferation and apoptosis. Severe inflammation and advanced liver fibrosis in the liver background are also associated with the incidence of HCV-related HCC. In this review, we discuss the mechanism of hepatocarcinogenesis in HCV-related liver diseases. Full article
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359 KiB  
Review
Transcriptional Regulation of the Mitochondrial Citrate and Carnitine/Acylcarnitine Transporters: Two Genes Involved in Fatty Acid Biosynthesis and β-oxidation
by Vito Iacobazzi, Vittoria Infantino and Ferdinando Palmieri
Biology 2013, 2(1), 284-303; https://doi.org/10.3390/biology2010284 - 29 Jan 2013
Cited by 20 | Viewed by 8662
Abstract
Transcriptional regulation of genes involved in fatty acid metabolism is considered the major long-term regulatory mechanism controlling lipid homeostasis. By means of this mechanism, transcription factors, nutrients, hormones and epigenetics control not only fatty acid metabolism, but also many metabolic pathways and cellular [...] Read more.
Transcriptional regulation of genes involved in fatty acid metabolism is considered the major long-term regulatory mechanism controlling lipid homeostasis. By means of this mechanism, transcription factors, nutrients, hormones and epigenetics control not only fatty acid metabolism, but also many metabolic pathways and cellular functions at the molecular level. The regulation of the expression of many genes at the level of their transcription has already been analyzed. This review focuses on the transcriptional control of two genes involved in fatty acid biosynthesis and oxidation: the citrate carrier (CIC) and the carnitine/ acylcarnitine/carrier (CAC), which are members of the mitochondrial carrier gene family, SLC25. The contribution of tissue-specific and less tissue-specific transcription factors in activating or repressing CIC and CAC gene expression is discussed. The interaction with drugs of some transcription factors, such as PPAR and FOXA1, and how this interaction can be an attractive therapeutic approach, has also been evaluated. Moreover, the mechanism by which the expression of the CIC and CAC genes is modulated by coordinated responses to hormonal and nutritional changes and to epigenetics is highlighted. Full article
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Article
Cell-Type Specific Determinants of NRAMP1 Expression in Professional Phagocytes
by Mathieu F. M. Cellier
Biology 2013, 2(1), 233-283; https://doi.org/10.3390/biology2010233 - 25 Jan 2013
Cited by 12 | Viewed by 10292
Abstract
The Natural resistance-associated macrophage protein 1 (Nramp1 or Solute carrier 11 member 1, Slc11a1) transports divalent metals across the membrane of late endosomes and lysosomes in professional phagocytes. Nramp1 represents an ancient eukaryotic cell-autonomous defense whereas the gene duplication that yielded Nramp1 and [...] Read more.
The Natural resistance-associated macrophage protein 1 (Nramp1 or Solute carrier 11 member 1, Slc11a1) transports divalent metals across the membrane of late endosomes and lysosomes in professional phagocytes. Nramp1 represents an ancient eukaryotic cell-autonomous defense whereas the gene duplication that yielded Nramp1 and Nramp2 predated the origin of Sarcopterygians (lobe-finned fishes and tetrapods). SLC11A1 genetic polymorphisms associated with human resistance to tuberculosis consist of potential regulatory variants. Herein, current knowledge of the regulation of SLC11A1 gene expression is reviewed and comprehensive analysis of ENCODE data available for hematopoietic cell-types suggests a hypothesis for the regulation of SLC11A1 expression during myeloid development and phagocyte functional polarization. SLC11A1 is part of a 34.6 kb CTCF-insulated locus scattered with predicted regulatory elements: a 3' enhancer, a large 5' enhancer domain and four elements spread around the transcription start site (TSS), including several C/EBP and PU.1 sites. SLC11A1 locus ends appear mobilized by ETS-related factors early during myelopoiesis; activation of both 5' and 3' enhancers in myelo-monocytic cells correlate with transcription factor binding at the TSS. Characterizing the corresponding cis/trans determinants functionally will establish the mechanisms involved and possibly reveal genetic variation that impacts susceptibility to infectious or immune diseases. Full article
(This article belongs to the Special Issue Gene Expression and Regulation)
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Article
Microbial Analyses of Ancient Ice Core Sections from Greenland and Antarctica
by Caitlin Knowlton, Ram Veerapaneni, Tom D'Elia and Scott O. Rogers
Biology 2013, 2(1), 206-232; https://doi.org/10.3390/biology2010206 - 25 Jan 2013
Cited by 47 | Viewed by 16508
Abstract
Ice deposited in Greenland and Antarctica entraps viable and nonviable microbes, as well as biomolecules, that become temporal atmospheric records. Five sections (estimated to be 500, 10,500, 57,000, 105,000 and 157,000 years before present, ybp) from the GISP2D (Greenland) ice core, three sections [...] Read more.
Ice deposited in Greenland and Antarctica entraps viable and nonviable microbes, as well as biomolecules, that become temporal atmospheric records. Five sections (estimated to be 500, 10,500, 57,000, 105,000 and 157,000 years before present, ybp) from the GISP2D (Greenland) ice core, three sections (500, 30,000 and 70,000 ybp) from the Byrd ice core, and four sections from the Vostok 5G (Antarctica) ice core (10,500, 57,000, 105,000 and 105,000 ybp) were studied by scanning electron microscopy, cultivation and rRNA gene sequencing. Bacterial and fungal isolates were recovered from 10 of the 12 sections. The highest numbers of isolates were found in ice core sections that were deposited during times of low atmospheric CO2, low global temperatures and low levels of atmospheric dust. Two of the sections (GISP2D at 10,500 and 157,000 ybp) also were examined using metagenomic/metatranscriptomic methods. These results indicated that sequences from microbes common to arid and saline soils were deposited in the ice during a time of low temperature, low atmospheric CO2 and high dust levels. Members of Firmicutes and Cyanobacteria were the most prevalent bacteria, while Rhodotorula species were the most common eukaryotic representatives. Isolates of Bacillus, Rhodotorula, Alternaria and members of the Davidiellaceae were isolated from both Greenland and Antarctica sections of the same age, although the sequences differed between the two polar regions. Full article
(This article belongs to the Special Issue Polar Microbiology: Recent Advances and Future Perspectives)
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198 KiB  
Review
MicroRNA Target Identification—Experimental Approaches
by Aida Martinez-Sanchez and Chris L. Murphy
Biology 2013, 2(1), 189-205; https://doi.org/10.3390/biology2010189 - 25 Jan 2013
Cited by 34 | Viewed by 9085
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules of 21–23 nucleotides that control gene expression at the post-transcriptional level. They have been shown to play a vital role in a wide variety of biological processes and dysregulated expression of miRNAs is observed in many [...] Read more.
MicroRNAs (miRNAs) are small non-coding RNA molecules of 21–23 nucleotides that control gene expression at the post-transcriptional level. They have been shown to play a vital role in a wide variety of biological processes and dysregulated expression of miRNAs is observed in many pathologies. Understanding the mechanism of action and identifying functionally important mRNA targets of a specific miRNA are essential to unravelling its biological function and to assist miRNA-based drug development. This review summarizes the current understanding of the mechanistic aspects of miRNA-mediated gene repression and focuses on the different approaches for miRNA target identification that have been proposed in recent years. Full article
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Article
Novel Cold-Adapted Esterase MHlip from an Antarctic Soil Metagenome
by Renaud Berlemont, Olivier Jacquin, Maud Delsaute, Marcello La Salla, Jacques Georis, Fabienne Verté, Moreno Galleni and Pablo Power
Biology 2013, 2(1), 177-188; https://doi.org/10.3390/biology2010177 - 25 Jan 2013
Cited by 16 | Viewed by 7652
Abstract
An Antarctic soil metagenomic library was screened for lipolytic enzymes and allowed for the isolation of a new cytosolic esterase from the a/b hydrolase family 6, named MHlip. This enzyme is related to hypothetical genes coding esterases, aryl-esterases and peroxydases, among others. MHlip [...] Read more.
An Antarctic soil metagenomic library was screened for lipolytic enzymes and allowed for the isolation of a new cytosolic esterase from the a/b hydrolase family 6, named MHlip. This enzyme is related to hypothetical genes coding esterases, aryl-esterases and peroxydases, among others. MHlip was produced, purified and its activity was determined. The substrate profile of MHlip reveals a high specificity for short p-nitrophenyl-esters. The apparent optimal activity of MHlip was measured for p-nitrophenyl-acetate, at 33 °C, in the pH range of 6–9. The MHlip thermal unfolding was investigated by spectrophotometric methods, highlighting a transition (Tm) at 50 °C. The biochemical characterization of this enzyme showed its adaptation to cold temperatures, even when it did not present evident signatures associated with cold-adapted proteins. Thus, MHlip adaptation to cold probably results from many discrete structural modifications, allowing the protein to remain active at low temperatures. Functional metagenomics is a powerful approach to isolate new enzymes with tailored biophysical properties (e.g., cold adaptation). In addition, beside the ever growing amount of sequenced DNA, the functional characterization of new catalysts derived from environment is still required, especially for poorly characterized protein families like α/b hydrolases. Full article
(This article belongs to the Special Issue Polar Microbiology: Recent Advances and Future Perspectives)
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Article
Timescales of Growth Response of Microbial Mats to Environmental Change in an Ice-Covered Antarctic Lake
by Ian Hawes, Dawn Y. Sumner, Dale T. Andersen, Anne D. Jungblut and Tyler J. Mackey
Biology 2013, 2(1), 151-176; https://doi.org/10.3390/biology2010151 - 25 Jan 2013
Cited by 32 | Viewed by 10134
Abstract
Lake Vanda is a perennially ice-covered, closed-basin lake in the McMurdo Dry Valleys, Antarctica. Laminated photosynthetic microbial mats cover the floor of the lake from below the ice cover to >40 m depth. In recent decades, the water level of Lake Vanda has [...] Read more.
Lake Vanda is a perennially ice-covered, closed-basin lake in the McMurdo Dry Valleys, Antarctica. Laminated photosynthetic microbial mats cover the floor of the lake from below the ice cover to >40 m depth. In recent decades, the water level of Lake Vanda has been rising, creating a “natural experiment” on development of mat communities on newly flooded substrates and the response of deeper mats to declining irradiance. Mats in recently flooded depths accumulate one lamina (~0.3 mm) per year and accrue ~0.18 µg chlorophyll-a cm−2 y−1. As they increase in thickness, vertical zonation becomes evident, with the upper 2-4 laminae forming an orange-brown zone, rich in myxoxanthophyll and dominated by intertwined Leptolyngbya trichomes. Below this, up to six phycobilin-rich green/pink-pigmented laminae form a subsurface zone, inhabited by Leptolyngbya, Oscillatoria and Phormidium morphotypes. Laminae continued to increase in thickness for several years after burial, and PAM fluorometry indicated photosynthetic potential in all pigmented laminae. At depths that have been submerged for >40 years, mats showed similar internal zonation and formed complex pinnacle structures that were only beginning to appear in shallower mats. Chlorophyll-a did not change over time and these mats appear to represent resource-limited “climax” communities. Acclimation of microbial mats to changing environmental conditions is a slow process, and our data show how legacy effects of past change persist into the modern community structure. Full article
(This article belongs to the Special Issue Polar Microbiology: Recent Advances and Future Perspectives)
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Article
Thermodynamic Stability of Psychrophilic and Mesophilic Pheromones of the Protozoan Ciliate Euplotes
by Michael Geralt, Claudio Alimenti, Adriana Vallesi, Pierangelo Luporini and Kurt Wüthrich
Biology 2013, 2(1), 142-150; https://doi.org/10.3390/biology2010142 - 14 Jan 2013
Cited by 15 | Viewed by 7545
Abstract
Three psychrophilic protein pheromones (En-1, En-2 and En-6) from the polar ciliate, Euplotes nobilii, and six mesophilic pheromones (Er-1, Er-2, Er-10, Er-11, Er-22 and Er [...] Read more.
Three psychrophilic protein pheromones (En-1, En-2 and En-6) from the polar ciliate, Euplotes nobilii, and six mesophilic pheromones (Er-1, Er-2, Er-10, Er-11, Er-22 and Er-23) from the temperate-water sister species, Euplotes raikovi, were studied in aqueous solution for their thermal unfolding and refolding based on the temperature dependence of their circular dichroism (CD) spectra. The three psychrophilic proteins showed thermal unfolding with mid points in the temperature range 55–70 °C. In contrast, no unfolding was observed for any of the six mesophilic proteins and their regular secondary structures were maintained up to 95 °C. Possible causes of these differences are discussed based on comparisons of the NMR structures of the nine proteins. Full article
(This article belongs to the Special Issue Polar Microbiology: Recent Advances and Future Perspectives)
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Review
PRDM Proteins: Molecular Mechanisms in Signal Transduction and Transcriptional Regulation
by Erika Di Zazzo, Caterina De Rosa, Ciro Abbondanza and Bruno Moncharmont
Biology 2013, 2(1), 107-141; https://doi.org/10.3390/biology2010107 - 14 Jan 2013
Cited by 54 | Viewed by 13873
Abstract
PRDM (PRDI-BF1 and RIZ homology domain containing) protein family members are characterized by the presence of a PR domain and a variable number of Zn-finger repeats. Experimental evidence has shown that the PRDM proteins play an important role in gene expression regulation, modifying [...] Read more.
PRDM (PRDI-BF1 and RIZ homology domain containing) protein family members are characterized by the presence of a PR domain and a variable number of Zn-finger repeats. Experimental evidence has shown that the PRDM proteins play an important role in gene expression regulation, modifying the chromatin structure either directly, through the intrinsic methyltransferase activity, or indirectly through the recruitment of chromatin remodeling complexes. PRDM proteins have a dual action: they mediate the effect induced by different cell signals like steroid hormones and control the expression of growth factors. PRDM proteins therefore have a pivotal role in the transduction of signals that control cell proliferation and differentiation and consequently neoplastic transformation. In this review, we describe pathways in which PRDM proteins are involved and the molecular mechanism of their transcriptional regulation. Full article
(This article belongs to the Special Issue Gene Expression and Regulation)
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Article
Isolation and Characterization of Bacteria from Ancient Siberian Permafrost Sediment
by De-Chao Zhang, Anatoli Brouchkov, Gennady Griva, Franz Schinner and Rosa Margesin
Biology 2013, 2(1), 85-106; https://doi.org/10.3390/biology2010085 - 10 Jan 2013
Cited by 52 | Viewed by 16036
Abstract
In this study, we isolated and characterized bacterial strains from ancient (Neogene) permafrost sediment that was permanently frozen for 3.5 million years. The sampling site was located at Mammoth Mountain in the Aldan river valley in Central Yakutia in Eastern Siberia. Analysis of [...] Read more.
In this study, we isolated and characterized bacterial strains from ancient (Neogene) permafrost sediment that was permanently frozen for 3.5 million years. The sampling site was located at Mammoth Mountain in the Aldan river valley in Central Yakutia in Eastern Siberia. Analysis of phospolipid fatty acids (PLFA) demonstrated the dominance of bacteria over fungi; the analysis of fatty acids specific for Gram-positive and Gram-negative bacteria revealed an approximately twofold higher amount of Gram-negative bacteria compared to Gram-positive bacteria. Direct microbial counts after natural permafrost enrichment showed the presence of (4.7 ± 1.5) × 108 cells g−1 sediment dry mass. Viable heterotrophic bacteria were found at 0 °C, 10 °C and 25 °C, but not at 37 °C. Spore-forming bacteria were not detected. Numbers of viable fungi were low and were only detected at 0 °C and 10 °C. Selected culturable bacterial isolates were identified as representatives of Arthrobacter phenanthrenivorans, Subtercola frigoramans and Glaciimonas immobilis. Representatives of each of these species were characterized with regard to their growth temperature range, their ability to grow on different media, to produce enzymes, to grow in the presence of NaCl, antibiotics, and heavy metals, and to degrade hydrocarbons. All strains could grow at −5 °C; the upper temperature limit for growth in liquid culture was 25 °C or 30 °C. Sensitivity to rich media, antibiotics, heavy metals, and salt increased when temperature decreased (20 °C > 10 °C > 1 °C). In spite of the ligninolytic activity of some strains, no biodegradation activity was detected. Full article
(This article belongs to the Special Issue Polar Microbiology: Recent Advances and Future Perspectives)
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938 KiB  
Review
Understanding the Dynamics of Gene Regulatory Systems; Characterisation and Clinical Relevance of cis-Regulatory Polymorphisms
by Philip Cowie, Ruth Ross and Alasdair MacKenzie
Biology 2013, 2(1), 64-84; https://doi.org/10.3390/biology2010064 - 9 Jan 2013
Cited by 8 | Viewed by 10622
Abstract
Modern genetic analysis has shown that most polymorphisms associated with human disease are non-coding. Much of the functional information contained in the non-coding genome consists of cis-regulatory sequences (CRSs) that are required to respond to signal transduction cues that direct cell specific [...] Read more.
Modern genetic analysis has shown that most polymorphisms associated with human disease are non-coding. Much of the functional information contained in the non-coding genome consists of cis-regulatory sequences (CRSs) that are required to respond to signal transduction cues that direct cell specific gene expression. It has been hypothesised that many diseases may be due to polymorphisms within CRSs that alter their responses to signal transduction cues. However, identification of CRSs, and the effects of allelic variation on their ability to respond to signal transduction cues, is still at an early stage. In the current review we describe the use of comparative genomics and experimental techniques that allow for the identification of CRSs building on recent advances by the ENCODE consortium. In addition we describe techniques that allow for the analysis of the effects of allelic variation and epigenetic modification on CRS responses to signal transduction cues. Using specific examples we show that the interactions driving these elements are highly complex and the effects of disease associated polymorphisms often subtle. It is clear that gaining an understanding of the functions of CRSs, and how they are affected by SNPs and epigenetic modification, is essential to understanding the genetic basis of human disease and stratification whilst providing novel directions for the development of personalised medicine. Full article
(This article belongs to the Special Issue Gene Expression and Regulation)
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767 KiB  
Review
BRCA1 and Its Network of Interacting Partners
by Charita M. Christou and Kyriacos Kyriacou
Biology 2013, 2(1), 40-63; https://doi.org/10.3390/biology2010040 - 2 Jan 2013
Cited by 47 | Viewed by 17514
Abstract
BRCA1 is a large multi-domain protein with a pivotal role in maintaining genome stability and cell cycle progression. Germline mutations in the BRCA1 gene confer an estimated lifetime risk of 60%–80% for breast cancer and 15%–60% for ovarian cancer. Many of the germline [...] Read more.
BRCA1 is a large multi-domain protein with a pivotal role in maintaining genome stability and cell cycle progression. Germline mutations in the BRCA1 gene confer an estimated lifetime risk of 60%–80% for breast cancer and 15%–60% for ovarian cancer. Many of the germline mutations associated with cancer development are concentrated in the amino terminal RING domain and the carboxyl terminal BRCT motifs of BRCA1, which are the most well-characterized regions of the protein. The function of BRCA1 in DNA repair, transcription and cell cycle control through the DNA damage response is orchestrated through its association with an impressive repertoire of protein complexes. The association of BRCA1 with ATM/ATR, CHK2 and Aurora A protein kinases regulates cell cycle progression, whilst its association with RAD51 has a direct impact on the repair of double strand DNA breaks (DSBs) by homologous recombination (HR). BRCA1 interactions with the MRN complex of proteins, with the BRCC complex of proteins that exhibit E3 ligase activity and with the phosphor proteins CtIP, BACH1 (BRIP1) and Abraxas (CCDC98) are also implicated in DNA repair mechanisms and cell cycle checkpoint control. BRCA1 through its association with specific proteins and multi-protein complexes is a sentinel of the normal cell cycle control and DNA repair. Full article
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Review
Gene Expression and Regulation in Adrenocortical Tumorigenesis
by Annabelle L. Fonseca, James Healy, John W. Kunstman, Reju Korah and Tobias Carling
Biology 2013, 2(1), 26-39; https://doi.org/10.3390/biology2010026 - 27 Dec 2012
Cited by 4 | Viewed by 6708
Abstract
Adrenocortical tumors are frequently found in the general population, and may be benign adrenocortical adenomas or malignant adrenocortical carcinomas. Unfortunately the clinical, biochemical and histopathological distinction between benign and malignant adrenocortical tumors may be difficult in the absence of widely invasive or metastatic [...] Read more.
Adrenocortical tumors are frequently found in the general population, and may be benign adrenocortical adenomas or malignant adrenocortical carcinomas. Unfortunately the clinical, biochemical and histopathological distinction between benign and malignant adrenocortical tumors may be difficult in the absence of widely invasive or metastatic disease, and hence attention has turned towards a search for molecular markers. The study of rare genetic diseases that are associated with the development of adrenocortical carcinomas has contributed to our understanding of adrenocortical tumorigenesis. In addition, comprehensive genomic hybridization, methylation profiling, and genome wide mRNA and miRNA profiling have led to improvements in our understanding, as well as demonstrated several genes and pathways that may serve as diagnostic or prognostic markers. Full article
(This article belongs to the Special Issue Gene Expression and Regulation)
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Article
Linking Eco-Energetics and Eco-Hydrology to Select Sites for the Assisted Colonization of Australia’s Rarest Reptile
by Nicola Mitchell, Matthew R. Hipsey, Sophie Arnall, Gavan McGrath, Hasnein Bin Tareque, Gerald Kuchling, Ryan Vogwill, Murugesu Sivapalan, Warren P. Porter and Michael R. Kearney
Biology 2013, 2(1), 1-25; https://doi.org/10.3390/biology2010001 - 27 Dec 2012
Cited by 49 | Viewed by 12906
Abstract
Assisted colonization—the deliberate translocation of species from unsuitable to suitable regions—is a controversial management tool that aims to prevent the extinction of populations that are unable to migrate in response to climate change or to survive in situ. The identification of suitable [...] Read more.
Assisted colonization—the deliberate translocation of species from unsuitable to suitable regions—is a controversial management tool that aims to prevent the extinction of populations that are unable to migrate in response to climate change or to survive in situ. The identification of suitable translocation sites is therefore a pressing issue. Correlative species distribution models, which are based on occurrence data, are of limited use for site selection for species with historically restricted distributions. In contrast, mechanistic species distribution models hold considerable promise in selecting translocation sites. Here we integrate ecoenergetic and hydrological models to assess the longer-term suitability of the current habitat of one of the world’s rarest chelonians, the Critically Endangered Western Swamp Tortoise (Psuedemydura umbrina). Our coupled model allows us to understand the interaction between thermal and hydric constraints on the foraging window of tortoises, based on hydrological projections of its current habitat. The process can then be repeated across a range of future climates to identify regions that would fall within the tortoise’s thermodynamic niche. The predictions indicate that climate change will result in reduced hydroperiods for the tortoises. However, under some climate change scenarios, habitat suitability may remain stable or even improve due to increases in the heat budget. We discuss how our predictions can be integrated with energy budget models that can capture the consequences of these biophysical constraints on growth, reproduction and body condition. Full article
(This article belongs to the Special Issue Biological Implications of Climate Change)
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