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   ISSN (Online) 2076-2607
   Published by MDPI Homepage  [124 journals]
  • Microorganisms, Vol. 3, Pages 1-16: Identification of Multiple
           Bacteriocins in Enterococcus spp. Using an Enterococcus-Specific
           Bacteriocin PCR Array

    • Authors: Chris Henning, Dhiraj Gautam, Peter Muriana
      Pages: 1 - 16
      Abstract: Twenty-two bacteriocin-producing Enterococcus isolates obtained from food and animal sources, and demonstrating activity against Listeria monocytogenes, were screened for bacteriocin-related genes using a bacteriocin PCR array based on known enterococcal bacteriocin gene sequences in the NCBI GenBank database. The 22 bacteriocin-positive (Bac+) enterococci included En. durans (1), En. faecalis (4), En. faecium (12), En. hirae (3), and En. thailandicus (2). Enterocin A (entA), enterocins mr10A and mr10B (mr10AB), and bacteriocin T8 (bacA) were the most commonly found structural genes in order of decreasing prevalence. Forty-five bacteriocin genes were identified within the 22 Bac+ isolates, each containing at least one of the screened structural genes. Of the 22 Bac+ isolates, 15 possessed two bacteriocin genes, seven isolates contained three different bacteriocins, and three isolates contained as many as four different bacteriocin genes. These results may explain the high degree of bactericidal activity observed with various Bac+ Enterococcus spp. Antimicrobial activity against wild-type L. monocytogenes and a bacteriocin-resistant variant demonstrated bacteriocins having different modes-of-action. Mixtures of bacteriocins, especially those with different modes-of-action and having activity against foodborne pathogens, such as L. monocytogenes, may play a promising role in the preservation of food.
      PubDate: 2015-02-04
      DOI: 10.3390/microorganisms3010001
      Issue No: Vol. 3, No. 1 (2015)
  • Microorganisms, Vol. 3, Pages 17-33: Rapid Reactivation of Deep Subsurface
           Microbes in the Presence of C-1 Compounds

    • Authors: Pauliina Rajala, Malin Bomberg, Riikka Kietäväinen, Ilmo Kukkonen, Lasse Ahonen, Mari Nyyssönen, Merja Itävaara
      Pages: 17 - 33
      Abstract: Microorganisms in the deep biosphere are believed to conduct little metabolic activity due to low nutrient availability in these environments. However, destructive penetration to long-isolated bedrock environments during construction of underground waste repositories can lead to increased nutrient availability and potentially affect the long-term stability of the repository systems, Here, we studied how microorganisms present in fracture fluid from a depth of 500 m in Outokumpu, Finland, respond to simple carbon compounds (C-1 compounds) in the presence or absence of sulphate as an electron acceptor. C-1 compounds such as methane and methanol are important intermediates in the deep subsurface carbon cycle, and electron acceptors such as sulphate are critical components of oxidation processes. Fracture fluid samples were incubated in vitro with either methane or methanol in the presence or absence of sulphate as an electron acceptor. Metabolic response was measured by staining the microbial cells with fluorescent dyes that indicate metabolic activity and transcriptional response with RT-qPCR. Our results show that deep subsurface microbes exist in dormant states but rapidly reactivate their transcription and respiration systems in the presence of C-1 substrates, particularly methane. Microbial activity was further enhanced by the addition of sulphate as an electron acceptor. Sulphate- and nitrate-reducing microbes were particularly responsive to the addition of C-1 compounds and sulphate. These taxa are common in deep biosphere environments and may be affected by conditions disturbed by bedrock intrusion, as from drilling and excavation for long-term storage of hazardous waste.
      PubDate: 2015-02-05
      DOI: 10.3390/microorganisms3010017
      Issue No: Vol. 3, No. 1 (2015)
  • Microorganisms, Vol. 3, Pages 34-46: Fumaric Acid and Slightly Acidic
           Electrolyzed Water Inactivate Gram Positive and Gram Negative Foodborne

    • Authors: Charles Tango, Ahmad Mansur, Deog-Hwan Oh
      Pages: 34 - 46
      Abstract: Sanitizing effectiveness of slightly acidic electrolyzed water (SAEW) and fumaric acid (FA) at different dipping temperatures (25–60 °C), times (1–5 min), and concentrations (5–30 ppm for SAEW and 0.125%–0.5% for FA) on pure cultures of two Gram positive pathogens Staphylococcus aureus (SA) and Listeria monocytogenes (LM) and two Gram negative pathogens Escherichia coli O157:H7 (EC) and Salmonella Typhimurium (ST) was evaluated. FA (0.25%) showed the strongest sanitizing effect, demonstrating complete inactivation of EC, ST, and LM, while SA was reduced by 3.95–5.76 log CFU/mL at 25–60 °C, respectively, after 1 min of treatment. For SAEW, the complete inactivation was obtained when available chlorine concentration was increased to 20 ppm at 40 °C for 3 and 5 min. Moreover, Gram positive pathogens have been shown to resist to all treatment trends more than Gram negative pathogens throughout this experiment. Regardless of the different dipping temperatures, concentrations, and times, FA treatment was more effective than treatment with SAEW for reduction of foodborne pathogens. This study demonstrated that application of FA in food systems may be useful as a method for inactivation of foodborne pathogens.
      PubDate: 2015-02-12
      DOI: 10.3390/microorganisms3010034
      Issue No: Vol. 3, No. 1 (2015)
  • Microorganisms, Vol. 2, Pages 140-146: Microorganisms—A Journal and
           a Unifying Concept for the Science of Microbiology

    • Authors: John Fuerst
      Pages: 140 - 146
      Abstract: The MDPI journal Microorganisms is still very young, having been launched in 2013, but the concept of the microorganism has been in use for at least a century as a unifying principle for the discipline of microbiology, which was cemented firmly by the intellectual work of Roger Stanier and colleagues in their Microbial World and other general microbiology textbooks and related articles from the 1950s to the 1970s [1,2]. Merging the idea of the microscopic and the very small with the older idea of an organism as a living entity or cell, the concept of a microorganism enabled a real appreciation of the microbial world as one that is amenable to study using similar tools and approaches even though representing distinctly different types of reproductive units and cell organizations. In the late 20th century following the work of Carl Woese and other molecular evolutionists, biologists came to appreciate the commonality among all organisms, all being comprised of cells that bear a remarkable similarity to one another and that share a common evolutionary ancestry, and consequently with major features of a largely shared genetic code and molecular biology. In this sense microbiology and biology as a whole became unified as they never had been before.[...]
      PubDate: 2014-12-12
      DOI: 10.3390/microorganisms2040140
      Issue No: Vol. 2, No. 4 (2014)
  • Microorganisms, Vol. 2, Pages 128-139: Antibacterial and Antibiofilm
           Activities of Makaluvamine Analogs

    • Authors: Bhavitavya Nijampatnam, Dwayaja Nadkarni, Hui Wu, Sadanandan Velu
      Pages: 128 - 139
      Abstract: Streptococcus mutans is a key etiological agent in the formation of dental caries. The major virulence factor is its ability to form biofilms. Inhibition of S. mutans biofilms offers therapeutic prospects for the treatment and the prevention of dental caries. In this study, 14 analogs of makaluvamine, a marine alkaloid, were evaluated for their antibacterial activity against S. mutans and for their ability to inhibit S. mutans biofilm formation. All analogs contained the tricyclic pyrroloiminoquinone core of makaluvamines. The structural variations of the analogs are on the amino substituents at the 7-position of the ring and the inclusion of a tosyl group on the pyrrole ring N of the makaluvamine core. The makaluvamine analogs displayed biofilm inhibition with IC50 values ranging from 0.4 μM to 88 μM. Further, the observed bactericidal activity of the majority of the analogs was found to be consistent with the anti-biofilm activity, leading to the conclusion that the anti-biofilm activity of these analogs stems from their ability to kill S. mutans. However, three of the most potent N-tosyl analogs showed biofilm IC50 values at least an order of magnitude lower than that of bactericidal activity, indicating that the biofilm activity of these analogs is more selective and perhaps independent of bactericidal activity.
      PubDate: 2014-09-12
      DOI: 10.3390/microorganisms2030128
      Issue No: Vol. 2, No. 3 (2014)
  • Microorganisms, Vol. 2, Pages 92-110: The Science behind the Probiotic
           Strain Bifidobacterium animalis subsp. lactis BB-12®

    • Authors: Mikkel Jungersen, Anette Wind, Eric Johansen, Jeffrey Christensen, Birgitte Stuer-Lauridsen, Dorte Eskesen
      Pages: 92 - 110
      Abstract: This review presents selected data on the probiotic strain Bifidobacterium animalis subsp. lactis BB-12® (BB-12®), which is the world’s most documented probiotic Bifidobacterium. It is described in more than 300 scientific publications out of which more than 130 are publications of human clinical studies. The complete genome sequence of BB-12® has been determined and published. BB-12® originates from Chr. Hansen’s collection of dairy cultures and has high stability in foods and as freeze dried powders. Strain characteristics and mechanisms of BB-12® have been established through extensive in vitro testing. BB-12® exhibits excellent gastric acid and bile tolerance; it contains bile salt hydrolase, and has strong mucus adherence properties, all valuable probiotic characteristics. Pathogen inhibition, barrier function enhancement, and immune interactions are mechanisms that all have been demonstrated for BB-12®. BB-12® has proven its beneficial health effect in numerous clinical studies within gastrointestinal health and immune function. Clinical studies have demonstrated survival of BB-12® through the gastrointestinal tract and BB-12® has been shown to support a healthy gastrointestinal microbiota. Furthermore, BB-12® has been shown to improve bowel function, to have a protective effect against diarrhea, and to reduce side effects of antibiotic treatment, such as antibiotic-associated diarrhea. In terms of immune function, clinical studies have shown that BB-12® increases the body’s resistance to common respiratory infections as well as reduces the incidence of acute respiratory tract infections.
      PubDate: 2014-03-28
      DOI: 10.3390/microorganisms2020092
      Issue No: Vol. 2, No. 2 (2014)
  • Microorganisms, Vol. 2, Pages 111-127: Butyrolactone I Quantification from
           Lovastatin Producing Aspergillus terreus Using Tandem Mass
           Spectrometry—Evidence of Signalling Functions

    • Authors: Elina Palonen, Milla-Riina Neffling, Sheetal Raina, Annika Brandt, Tajalli Keshavarz, Jussi Meriluoto, Juhani Soini
      Pages: 111 - 127
      Abstract: Aspergillus terreus is an industrially important filamentous fungus producing a wide spectrum of secondary metabolites, including lovastatin and itaconic acid. It also produces butyrolactone I which has shown potential as an antitumour agent. Additionally, butyrolactone I has been implicated to have a regulating role in the secondary metabolism and morphology of A. terreus. In this study, a quantitative time-course liquid chromatography—electrospray ionisation—tandem mass spectrometry (LC-ESI-MS-MS) analysis of butyrolactone I is reported for the first time in nine-day long submerged cultures of A. terreus. Butyrolactone I was fragmented in the mass analysis producing a reproducible fragmentation pattern of four main daughter ions (m/z 307, 331, 363 and 393) in all the samples tested. Supplementing the cultures with 100 nM butyrolactone I caused a statistically significant increase (up to two-fold) in its production, regardless of the growth stage but was constitutive when butyrolactone I was added at high cell density during the stationary phase. Furthermore, the extracellular butyrolactone I concentration peaked at 48 h post inoculation, showing a similar profile as has been reported for bacterial quorum sensing molecules. Taken together, the results support the idea of butyrolactone I as a quorum sensing molecule in A. terreus.
      PubDate: 2014-06-04
      DOI: 10.3390/microorganisms2020111
      Issue No: Vol. 2, No. 2 (2014)
  • Microorganisms, Vol. 2, Pages 11-32: Towards an Ecological Understanding
           of Dinoflagellate Cyst Functions

    • Authors: Isabel Bravo, Rosa Figueroa
      Pages: 11 - 32
      Abstract: The life cycle of many dinoflagellates includes at least one nonflagellated benthic stage (cyst). In the literature, the different types of dinoflagellate cysts are mainly defined based on morphological (number and type of layers in the cell wall) and functional (long- or short-term endurance) differences. These characteristics were initially thought to clearly distinguish pellicle (thin-walled) cysts from resting (double-walled) dinoflagellate cysts. The former were considered short-term (temporal) and the latter long-term (resting) cysts. However, during the last two decades further knowledge has highlighted the great intricacy of dinoflagellate life histories, the ecological significance of cyst stages, and the need to clarify the functional and morphological complexities of the different cyst types. Here we review and, when necessary, redefine the concepts of resting and pellicle cysts, examining both their structural and their functional characteristics in the context of the life cycle strategies of several dinoflagellate species.
      PubDate: 2014-01-03
      DOI: 10.3390/microorganisms2010011
      Issue No: Vol. 2, No. 1 (2014)
  • Microorganisms, Vol. 2, Pages 33-57: Emergence of Algal Blooms: The
           Effects of Short-Term Variability in Water Quality on Phytoplankton
           Abundance, Diversity, and Community Composition in a Tidal Estuary

    • Authors: Todd Egerton, Ryan Morse, Harold Marshall, Margaret Mulholland
      Pages: 33 - 57
      Abstract: Algal blooms are dynamic phenomena, often attributed to environmental parameters that vary on short timescales (e.g., hours to days). Phytoplankton monitoring programs are largely designed to examine long-term trends and interannual variability. In order to better understand and evaluate the relationships between water quality variables and the genesis of algal blooms, daily samples were collected over a 34 day period in the eutrophic Lafayette River, a tidal tributary within Chesapeake Bay’s estuarine complex, during spring 2006. During this period two distinct algal blooms occurred; the first was a cryptomonad bloom and this was followed by a bloom of the mixotrophic dinoflagellate, Gymnodinium instriatum. Chlorophyll a, nutrient concentrations, and physical and chemical parameters were measured daily along with phytoplankton abundance and community composition. While 65 phytoplankton species from eight major taxonomic groups were identified in samples and total micro- and nano-phytoplankton cell densities ranged from 5.8 × 106 to 7.8 × 107 cells L−1, during blooms, cryptomonads and G. instriatum were 91.6% and 99.0%, respectively, of the total phytoplankton biomass during blooms. The cryptomonad bloom developed following a period of rainfall and concomitant increases in inorganic nitrogen concentrations. Nitrate, nitrite and ammonium concentrations 0 to 5 days prior were positively lag-correlated with cryptomonad abundance. In contrast, the G. insriatum bloom developed during periods of low dissolved nitrogen concentrations and their abundance was negatively correlated with inorganic nitrogen concentrations.
      PubDate: 2014-01-08
      DOI: 10.3390/microorganisms2010033
      Issue No: Vol. 2, No. 1 (2014)
  • Microorganisms, Vol. 2, Pages 58-72: Effect of Electrical Stimulation on
           Fruit Body Formation in Cultivating Mushrooms

    • Authors: Koichi Takaki, Kohei Yoshida, Tatsuya Saito, Tomohiro Kusaka, Ryo Yamaguchi, Kyusuke Takahashi, Yuichi Sakamoto
      Pages: 58 - 72
      Abstract: The effect of high-voltage electrical stimulation on fruit body formation in cultivating mushrooms was evaluated using a compact pulsed power generator designed and based on an inductive energy storage system. An output voltage from 50 to 130 kV with a 100 ns pulse width was used as the electrical stimulation to determine the optimum amplitude. The pulsed high voltage was applied to a sawdust-based substrate of Lyophyllum decastes and natural logs hosting Lentinula edodes, Pholiota nameko, and Naematoloma sublateritium. The experimental results showed that the fruit body formation of mushrooms increased 1.3–2.0 times in terms of the total weight. The accumulated yield of Lentinula edodes for four cultivation seasons was improved from 160 to 320 g by applying voltages of 50 or 100 kV. However, the yield was decreased from 320 to 240 g upon increasing the applied voltage from 100 to 130 kV. The yield of the other types of mushrooms showed tendencies similar to those of Lentinula edodes when voltage was applied. An optimal voltage was confirmed for efficient fruit body induction. The hypha activity was evaluated by the amount of hydrophobin release, which was mainly observed before the fruit body formation. The hydrophobin release decreased for three hours after stimulation. However, the hydrophobin release from the vegetative hyphae increased 2.3 times one day after the stimulation.
      PubDate: 2014-02-12
      DOI: 10.3390/microorganisms2010058
      Issue No: Vol. 2, No. 1 (2014)
  • Microorganisms, Vol. 2, Pages 73-91: A Comparative Overview of the
           Flagellar Apparatus of Dinoflagellate, Perkinsids and Colpodellids

    • Authors: Noriko Okamoto, Patrick Keeling
      Pages: 73 - 91
      Abstract: Dinoflagellates are a member of the Alveolata, and elucidation of the early evolution of alveolates is important for our understanding of dinoflagellates, and vice versa. The ultrastructure of the flagellar apparatus has been described from several dinoflagellates in the last few decades, and the basic components appear to be well conserved. The typical dinoflagellate apparatus is composed of two basal bodies surrounded by striated collars attached to a connective fiber. The longitudinal basal body is connected to a longitudinal microtubular root (LMR; equivalent of R1) and single microtubular root (R2), whereas the transverse basal body is connected to a transverse microtubular root (TMR; R3) and transverse striated root (TSR) with a microtubule (R4). Some of these components, especially the connective fibers and collars, are dinoflagellate specific characteristics that make their flagellar apparatus relatively complex. We also compare these structures with the flagellar apparatus from a number of close relatives of dinoflagellates and their sister, the apicomplexans, including colpodellids, perkinsids, and Psammosa. Though the ultrastructural knowledge of these lineages is still relatively modest, it provides us with an interesting viewpoint of the character evolution of the flagellar apparatus among those lineages.
      PubDate: 2014-03-10
      DOI: 10.3390/microorganisms2010073
      Issue No: Vol. 2, No. 1 (2014)
  • Microorganisms, Vol. 2, Pages 1-10: Sad State of Phage Electron
           Microscopy. Please Shoot the Messenger

    • Authors: Hans-W. Ackermann
      Pages: 1 - 10
      Abstract: Two hundred and sixty publications from 2007 to 2012 were classified according to the quality of electron micrographs; namely as good (71); mediocre (21); or poor (168). Publications were from 37 countries; appeared in 77 journals; and included micrographs produced with about 60 models of electron microscopes. The quality of the micrographs was not linked to any country; journal; or electron microscope. Main problems were poor contrast; positive staining; low magnification; and small image size. Unsharp images were frequent. Many phage descriptions were silent on virus purification; magnification control; even the type of electron microscope and stain used. The deterioration in phage electron microscopy can be attributed to the absence of working instructions and electron microscopy courses; incompetent authors and reviewers; and lenient journals. All these factors are able to cause a gradual lowering of standards.
      PubDate: 2013-12-24
      DOI: 10.3390/microorganisms2010001
      Issue No: Vol. 2, No. 1 (2013)
  • Microorganisms, Vol. 1, Pages 1-2: Microorganisms—A Forum for
           Understanding Microbial Life in All Its Forms

    • Authors: John Fuerst
      Pages: 1 - 2
      Abstract: It is my great pleasure to welcome you to Microorganisms, a new open access journal, which is dedicated to microorganisms in all their forms and via any approach to their study.
      PubDate: 2013-02-19
      DOI: 10.3390/microorganisms1010001
      Issue No: Vol. 1, No. 1 (2013)
  • Microorganisms, Vol. 1, Pages 3-25: Understanding Bioluminescence in
           Dinoflagellates—How Far Have We Come'

    • Authors: Martha Valiadi, Debora Iglesias-Rodriguez
      Pages: 3 - 25
      Abstract: Some dinoflagellates possess the remarkable genetic, biochemical, and cellular machinery to produce bioluminescence. Bioluminescent species appear to be ubiquitous in surface waters globally and include numerous cosmopolitan and harmful taxa. Nevertheless, bioluminescence remains an enigmatic topic in biology, particularly with regard to the organisms’ lifestyle. In this paper, we review the literature on the cellular mechanisms, molecular evolution, diversity, and ecology of bioluminescence in dinoflagellates, highlighting significant discoveries of the last quarter of a century. We identify significant gaps in our knowledge and conflicting information and propose some important research questions that need to be addressed to advance this research field.
      PubDate: 2013-09-05
      DOI: 10.3390/microorganisms1010003
      Issue No: Vol. 1, No. 1 (2013)
  • Microorganisms, Vol. 1, Pages 26-32: Circadian Rhythms in Dinoflagellates:
           What Is the Purpose of Synthesis and Destruction of Proteins'

    • Authors: J. Hastings
      Pages: 26 - 32
      Abstract: There is a prominent circadian rhythm of bioluminescence in many species of light-emitting dinoflagellates. In Lingulodinium polyedrum a daily synthesis and destruction of proteins is used to regulate activity. Experiments indicate that the amino acids from the degradation are conserved and incorporated into the resynthesized protein in the subsequent cycle. A different species, Pyrocystis lunula, also exhibits a rhythm of bioluminescence, but the luciferase is not destroyed and resynthesized each cycle. This paper posits that synthesis and destruction constitutes a cellular mechanism to conserve nitrogen in an environment where the resource is limiting.
      PubDate: 2013-09-18
      DOI: 10.3390/microorganisms1010026
      Issue No: Vol. 1, No. 1 (2013)
  • Microorganisms, Vol. 1, Pages 33-57: Biology of the Marine Heterotrophic
           Dinoflagellate Oxyrrhis marina: Current Status and Future Directions

    • Authors: Zhiling Guo, Huan Zhang, Sheng Liu, Senjie Lin
      Pages: 33 - 57
      Abstract: Heterotrophic dinoflagellates are prevalent protists in marine environments, which play an important role in the carbon cycling and energy flow in the marine planktonic community. Oxyrrhis marina (Dinophyceae), a widespread heterotrophic dinoflagellate, is a model species used for a broad range of ecological, biogeographic, and evolutionary studies. Despite the increasing research effort on this species, there lacks a synthesis of the existing data and a coherent picture of this organism. Here we reviewed the literature to provide an overview of what is known regarding the biology of O. marina, and identify areas where further studies are needed. As an early branch of the dinoflagellate lineage, O. marina shares similarity with typical dinoflagellates in permanent condensed chromosomes, less abundant nucleosome proteins compared to other eukaryotes, multiple gene copies, the occurrence of trans-splicing in nucleus-encoded mRNAs, highly fragmented mitochondrial genome, and disuse of ATG as a start codon for mitochondrial genes. On the other hand, O. marina also exhibits some distinct cytological features (e.g., different flagellar structure, absence of girdle and sulcus or pustules, use of intranuclear spindle in mitosis, presence of nuclear plaque, and absence of birefringent periodic banded chromosomal structure) and genetic features (e.g., a single histone-like DNA-associated protein, cob-cox3 gene fusion, 5′ oligo-U cap in the mitochondrial transcripts of protein-coding genes, the absence of mRNA editing, the presence of stop codon in the fused cob-cox3 mRNA produced by post-transcriptional oligoadenylation, and vestigial plastid genes). The best-studied biology of this dinoflagellate is probably the prey and predators types, which include a wide range of organisms. On the other hand, the abundance of this species in the natural waters and its controlling factors, genome organization and gene expression regulation that underlie the unusual cytological and ecological characteristics are among the areas that urgently need study.
      PubDate: 2013-10-21
      DOI: 10.3390/microorganisms1010033
      Issue No: Vol. 1, No. 1 (2013)
  • Microorganisms, Vol. 1, Pages 58-70: The Genus Neoceratium (Planktonic
           Dinoflagellates) as a Potential Indicator of Ocean Warming

    • Authors: Alina Tunin-Ley, Rodolphe Lemée
      Pages: 58 - 70
      Abstract: Among the planktonic dinoflagellates, the species-rich genus Neoceratium has particularly remarkable features that include its easily recognizable outline and large size. This ubiquitous genus shows consistent presence in all plankton samples and has been a model for numerous studies since the end of the 19th century. It has already been described as a good candidate to monitor water masses and describe ocean circulation. We argue that the sensitivity displayed by Neoceratium to water temperature also makes it relevant as an indicator of ocean warming. The advantages and interests of using Neoceratium species to monitor climate change on a large scale are reassessed in view of recent advances in understanding their biology and ecology.
      PubDate: 2013-10-25
      DOI: 10.3390/microorganisms1010058
      Issue No: Vol. 1, No. 1 (2013)
  • Microorganisms, Vol. 1, Pages 71-99: Transcription and Maturation of mRNA
           in Dinoflagellates

    • Authors: Sougata Roy, David Morse
      Pages: 71 - 99
      Abstract: Dinoflagellates are of great importance to the marine ecosystem, yet scant details of how gene expression is regulated at the transcriptional level are available. Transcription is of interest in the context of the chromatin structure in the dinoflagellates as it shows many differences from more typical eukaryotic cells. Here we canvas recent transcriptome profiles to identify the molecular building blocks available for the construction of the transcriptional machinery and contrast these with those used by other systems. Dinoflagellates display a clear paucity of specific transcription factors, although surprisingly, the rest of the basic transcriptional machinery is not markedly different from what is found in the close relatives to the dinoflagellates.
      PubDate: 2013-11-01
      DOI: 10.3390/microorganisms1010071
      Issue No: Vol. 1, No. 1 (2013)
  • Microorganisms, Vol. 1, Pages 100-121: Elements in the Development of a
           Production Process for Modified Vaccinia Virus Ankara

    • Authors: Ingo Jordan, Verena Lohr, Yvonne Genzel, Udo Reichl, Volker Sandig
      Pages: 100 - 121
      Abstract: The production of several viral vaccines depends on chicken embryo fibroblasts or embryonated chicken eggs. To replace this logistically demanding substrate, we created continuous anatine suspension cell lines (CR and CR.pIX), developed chemically-defined media, and established production processes for different vaccine viruses. One of the processes investigated in greater detail was developed for modified vaccinia virus Ankara (MVA). MVA is highly attenuated for human recipients and an efficient vector for reactogenic expression of foreign genes. Because direct cell-to-cell spread is one important mechanism for vaccinia virus replication, cultivation of MVA in bioreactors is facilitated if cell aggregates are induced after infection. This dependency may be the mechanism behind our observation that a novel viral genotype (MVA-CR) accumulates with serial passage in suspension cultures. Sequencing of a major part of the genomic DNA of the new strain revealed point mutations in three genes. We hypothesize that these changes confer an advantage because they may allow a greater fraction of MVA-CR viruses to escape the host cells for infection of distant targets. Production and purification of MVA-based vaccines may be simplified by this combination of designed avian cell line, chemically defined media and the novel virus strain.
      PubDate: 2013-11-01
      DOI: 10.3390/microorganisms1010100
      Issue No: Vol. 1, No. 1 (2013)
  • Microorganisms, Vol. 1, Pages 122-136: An Updated List of Generic Names in
           the Thoracosphaeraceae

    • Authors: Marc Gottschling, Sylvia Soehner
      Pages: 122 - 136
      Abstract: Calcareous dinophytes produce exoskeletal calcified structures during their life history (a unique character among the alveolates) and are subsumed under the Thoracosphaeraceae as part of the Peridiniales. We provide a brief synopsis about the taxonomic history of the group, from the first descriptions of fossils in the 19th century through to the results of molecular phylogenetics studies undertaken during the past two decades. Delimitation and circumscription of the Thoracosphaeraceae are challenging, as they comprise both phototrophic (presumably including endosymbiotic) as well as heterotrophic (and even parasitic) dinophytes from marine and freshwater environments, respectively. However, calcareous structures are not known from all members of the Thoracosphaeraceae, and the corresponding species and groups are considered to have lost the capacity to calcify. Five years ago, a taxonomic list of 99 generic names assigned to the Thoracosphaeraceae was published, and we update this compendium with 19 additional names based on recent studies.
      PubDate: 2013-11-01
      DOI: 10.3390/microorganisms1010122
      Issue No: Vol. 1, No. 1 (2013)
  • Microorganisms, Vol. 1, Pages 137-157: A Novel Bioinformatics Strategy to
           Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery:
           Batch-Learning Self-Organizing Map (BLSOM)

    • Authors: Yuki Iwasaki, Takashi Abe, Kennosuke Wada, Yoshiko Wada, Toshimichi Ikemura
      Pages: 137 - 157
      Abstract: With the remarkable increase of genomic sequence data of microorganisms, novel tools are needed for comprehensive analyses of the big sequence data available. The self-organizing map (SOM) is an effective tool for clustering and visualizing high-dimensional data, such as oligonucleotide composition on one map. By modifying the conventional SOM, we developed batch-learning SOM (BLSOM), which allowed classification of sequence fragments (e.g., 1 kb) according to phylotypes, solely depending on oligonucleotide composition. Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes important in life sciences. BLSOM is most suitable for phylogenetic assignment of metagenomic sequences, because fragmental sequences can be clustered according to phylotypes, solely depending on oligonucleotide composition. We first constructed oligonucleotide BLSOMs for all available sequences from genomes of known species, and by mapping metagenomic sequences on these large-scale BLSOMs, we can predict phylotypes of individual metagenomic sequences, revealing a microbial community structure of uncultured microorganisms, including viruses. BLSOM has shown that influenza viruses isolated from humans and birds clearly differ in oligonucleotide composition. Based on this host-dependent oligonucleotide composition, we have proposed strategies for predicting directional changes of virus sequences and for surveilling potentially hazardous strains when introduced into humans from non-human sources.
      PubDate: 2013-11-20
      DOI: 10.3390/microorganisms1010137
      Issue No: Vol. 1, No. 1 (2013)
  • Microorganisms, Vol. 1, Pages 158-161: Control of a Multi-Drug-Resistant
           Acinetobacter baumannii Outbreak after Orthopedics Department Relocation

    • Authors: Vasiliki Gogou, Georgios Meletis, Dimosthenis Tsitouras
      Pages: 158 - 161
      Abstract: Acinetobacter baumannii clinical isolates have the ability to survive in the hospital niche for prolonged time periods and to develop resistance against multiple antimicrobial agents. Therefore, A. baumannii has emerged as an important cause of nosocomial outbreaks worldwide, especially in critical-care environments such as intensive care units. In the present communication, we report a multi-drug-resistant A. baumannii outbreak that occurred in an orthopedics department in Greece after the admission of a patient previously hospitalized in the intensive care unit of a Greek tertiary care hospital. Despite the implementation of infection control measures, 29 patients were infected, significantly raising their hospitalization periods and treatment costs. Interestingly, the outbreak was put under control after the department’s previously programmed relocation.
      PubDate: 2013-12-02
      DOI: 10.3390/microorganisms1010158
      Issue No: Vol. 1, No. 1 (2013)
  • Microorganisms, Vol. 1, Pages 162-174: Molecular Quantification and
           Genetic Diversity of Toxigenic Fusarium Species in Northern Europe as
           Compared to Those in Southern Europe

    • Authors: Tapani Yli-Mattila, Sari Rämö, Veli Hietaniemi, Taha Hussien, Ana Carlobos-Lopez, Christian Cumagun
      Pages: 162 - 174
      Abstract: Fusarium species produce important mycotoxins, such as deoxynivalenol (DON), nivalenol (NIV) and T-2/HT-2-toxins in cereals. The highest DON and T-2/HT-2 toxin levels in northern Europe have been found in oats. About 12%–24% of Finnish oat samples in 2012 contained >1.75 mg·kg−1 of DON, which belongs to type B trichothecenes. Fusarium graminearum is the most important DON producer in northern Europe and Asia and it has been displacing the closely related F. culmorum in northern Europe. The 3ADON chemotype of F. graminearum is dominant in most northern areas, while the 15ADON chemotype of F. graminearum is predominating in Central and southern Europe. We suggest that the northern population of F. graminearum may be more specialized to oats than the southern population. Only low levels of F. culmorum DNA were found in a few oat samples and no correlation was found between F. culmorum DNA and DON levels. DNA levels of F. graminearum were in all cases in agreement with DON levels in 2011 and 2012, when DON was measured by gas chromatography-mass spectrometry (GC-MS). When the RIDA® QUICK SCAN kit results (DON) were compared to DNA levels of F. graminearum, the variation was much higher. The homogenization of the oats flour by grinding oats with 1 mm sieve seems to be connected to this variation. There was a significant correlation between the combined T-2 and HT-2 and the combined DNA levels of F. langsethiae and F. sporotrichioides in Finland in 2010–2012.
      PubDate: 2013-12-03
      DOI: 10.3390/microorganisms1010162
      Issue No: Vol. 1, No. 1 (2013)
  • Microorganisms, Vol. 1, Pages 175-187: Macroalgal Endophytes from the
           Atlantic Coast of Canada: A Potential Source of Antibiotic Natural

    • Authors: Andrew Flewelling, Katelyn Ellsworth, Joseph Sanford, Erica Forward, John Johnson, Christopher Gray
      Pages: 175 - 187
      Abstract: As the need for new and more effective antibiotics increases, untapped sources of biodiversity are being explored in an effort to provide lead structures for drug discovery. Endophytic fungi from marine macroalgae have been identified as a potential source of biologically active natural products, although data to support this is limited. To assess the antibiotic potential of temperate macroalgal endophytes we isolated endophytic fungi from algae collected in the Bay of Fundy, Canada and screened fungal extracts for the presence of antimicrobial compounds. A total of 79 endophytes were isolated from 7 species of red, 4 species of brown, and 3 species of green algae. Twenty of the endophytes were identified to the genus or species level, with the remaining isolates designated codes according to their morphology. Bioactivity screening assays performed on extracts of the fermentation broths and mycelia of the isolates revealed that 43 endophytes exhibited antibacterial activity, with 32 displaying antifungal activity. Endophytic fungi from Bay of Fundy macroalgae therefore represent a significant source of antibiotic natural products and warrant further detailed investigation.
      PubDate: 2013-12-13
      DOI: 10.3390/microorganisms1010175
      Issue No: Vol. 1, No. 1 (2013)
  • Microorganisms, Vol. 1, Pages 188-198: Temporal Variation of Mycotoxin
           Producing Fungi in Norwegian Cereals

    • Authors: Leif Sundheim, Guro Brodal, Inger Hofgaard, Trond Rafoss
      Pages: 188 - 198
      Abstract: Spring barley is grown on about half of the Norwegian cereal area. The rest of the area is equally divided between wheat and oats. Most years the domestic production provides 70%–80% of the domestic market for bread wheat. Barley and oats are mainly grown for animal feed. During the years 2008–2012, severe epidemics of Fusarium head blight have led to increased mycotoxin contamination of cereals. During that period, precipitation was above normal during anthesis and grain maturation. The most important mycotoxin producers have been F. avenaceum, F. culmorum, F. graminearum and F. langsethiae. Increased deoxynivalenol contamination of Norwegian cereals during recent years is due to severe F. graminearum epidemics.
      PubDate: 2013-12-17
      DOI: 10.3390/microorganisms1010188
      Issue No: Vol. 1, No. 1 (2013)
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