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https://www.readbyqxmd.com/read/28645185/soil-prokaryotic-communities-in-chernobyl-waste-disposal-trench-t22-are-modulated-by-organic-matter-and-radionuclide-contamination
#1
Nicolas Theodorakopoulos, Laureline Février, Mohamed Barakat, Philippe Ortet, Richard Christen, Laurie Piette, Sviatoslav Levchuk, Karine Beaugelin-Seiller, Claire Sergeant, Catherine Berthomieu, Virginie Chapon
After the Chernobyl nuclear power plant accident in 1986, contaminated soils, vegetation from the Red Forest, and other radioactive debris were buried within trenches. In this area, trench T22 has long been a pilot site for the study of radionuclide migration in soil. Here, we used 454 pyrosequencing of 16S rRNA genes to obtain a comprehensive view of the bacterial and archaeal diversity in soils collected inside and in the vicinity of the trench T22 and to investigate the impact of radioactive waste disposal on prokaryotic communities...
June 22, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28645159/genomic-characterization-of-two-novel-sar11-isolates-from-the-red-sea-including-the-first-strain-of-the-sar11-ib-clade
#2
Francy Jimenez-Infante, David Kamanda Ngugi, Manikandan Vinu, Jochen Blom, Intikhab Alam, Vladimir B Bajic, Ulrich Stingl
The SAR11 clade (Pelagibacterales) is a diverse group that forms a monophyletic clade within the Alphaproteobacteria, and constitutes up to one third of all prokaryotic cells in the photic zone of most oceans. Pelagibacterales are very abundant in the warm and highly saline surface waters of the Red Sea, raising the question of adaptive traits of SAR11 populations in this water body and warmer oceans through the world. In this study, two pure cultures were successfully obtained from surface waters on the Red Sea, one isolate of subgroup Ia and one of the previously uncultured SAR11 Ib lineage...
June 22, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28641927/from-prokaryotes-to-cancer-glutamine-flux-in-multicellular-units
#3
REVIEW
Ayelet Erez, Ilana Kolodkin-Gal
Bacteria in nature reside in organized communities, termed biofilms, which are composed of multiple individual cells adhering to each other. Similarly, tumors are a multicellular mass with distinct cellular phenotypes. Both tumors and biofilms are considered to be an active interphase between unicellular and multicellular life states. Because both of these units depend on glutamine for growth and survival, we review here glutamine flux within them as a readout for intra- and inter-commensal metabolism. We suggest that the difference between glutamine fluxes in these cellular communities lies mainly in their global multicellular metabolic organization...
June 19, 2017: Trends in Endocrinology and Metabolism: TEM
https://www.readbyqxmd.com/read/28641561/induction-of-humoral-and-cellular-immune-responses-in-mice-by-multiepitope-vaccines-composing-of-both-t-and-b-lymphocyte-epitopes-of-mage-a3which-are-recombined-into-hbcag
#4
Qingxin Chen, Wenshu Li, Pengfei Wang, Huanyi Shao, Yujie Ding, Wenhuan Wang, Danwei Cen, Yiqi Cai, Xiangyang Xue, Lifang Zhang, Guanbao Zhu
MAGE-A3 is highly expressed in many kinds of malignant diseases, and considered to be an ideal candidate for anti-tumor vaccine. To improve the immunogenicity of epitopes of MAGE-A3, hepatitis B virus core antigen (HBcAg) was used as an immune-carrier by insertion epitopes at HBcAg major immunodominant region (HBcAg(MIR)). In present study, we designed three kinds of MAGE-A3 multiepitopes containing T and B-cell dominant epitope-rich peptides, and constructed three recombinant chimeras of HBcAg(MIR)/MAGE-A3(EPI-1), HBcAg(MIR)/MAGE-A3(EPI-2), and HBcAg(MIR)/MAGE-A3(EPI-3) with prokaryotic codon optimization...
June 20, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28639622/growth-coupled-overproduction-is-feasible-for-almost-all-metabolites-in-five-major-production-organisms
#5
Axel von Kamp, Steffen Klamt
Computational modelling of metabolic networks has become an established procedure in the metabolic engineering of production strains. One key principle that is frequently used to guide the rational design of microbial cell factories is the stoichiometric coupling of growth and product synthesis, which makes production of the desired compound obligatory for growth. Here we show that the coupling of growth and production is feasible under appropriate conditions for almost all metabolites in genome-scale metabolic models of five major production organisms...
June 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28638074/geochemical-constraints-on-the-hadean-environment-from-mineral-fingerprints-of-prokaryotes
#6
Alexey A Novoselov, Dailto Silva, Jerusa Schneider, Ximena Celeste Abrevaya, Michael S Chaffin, Paloma Serrano, Margareth Sugano Navarro, Maria Josiane Conti, Carlos Roberto de Souza Filho
The environmental conditions on the Earth before 4 billion years ago are highly uncertain, largely because of the lack of a substantial rock record from this period. During this time interval, known as the Hadean, the young planet transformed from an uninhabited world to the one capable of supporting, and inhabited by the first living cells. These cells formed in a fluid environment they could not at first control, with homeostatic mechanisms developing only later. It is therefore possible that present-day organisms retain some record of the primordial fluid in which the first cells formed...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28637850/hierarchical-complexity-and-the-size-limits-of-life
#7
Noel A Heim, Jonathan L Payne, Seth Finnegan, Matthew L Knope, Michał Kowalewski, S Kathleen Lyons, Daniel W McShea, Philip M Novack-Gottshall, Felisa A Smith, Steve C Wang
Over the past 3.8 billion years, the maximum size of life has increased by approximately 18 orders of magnitude. Much of this increase is associated with two major evolutionary innovations: the evolution of eukaryotes from prokaryotic cells approximately 1.9 billion years ago (Ga), and multicellular life diversifying from unicellular ancestors approximately 0.6 Ga. However, the quantitative relationship between organismal size and structural complexity remains poorly documented. We assessed this relationship using a comprehensive dataset that includes organismal size and level of biological complexity for 11 172 extant genera...
June 28, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28636788/role-of-positively-charged-residues-on-the-polar-and-non-polar-faces-of-amphipathic-%C3%AE-helical-antimicrobial-peptides-amps-on-specificity-and-selectivity-for-gram-negative-pathogens
#8
Ziqing Jiang, Colin T Mant, Michael Vasil, Robert S Hodges
We have designed de novo and synthesized eight 26-residue all D-conformation amphipathic α-helical cationic antimicrobial peptides (AMPs), four with "specificity determinants" which provide specificity for prokaryotic cells over eukaryotic cells and four AMPs without specificity determinants. The eight AMPs contain six positively charged Lys residues on the polar face in four different arrangements to understand the role of these residues have on antimicrobial activity against 14 Acinetobacter baumannii strains, 7 of which were resistant to polymyxin B and colistin; 6 diverse Pseudomonas aeruginosa strains and 17 Staphylococcus aureus strains, 9 of which were Methicillin-sensitive (MSSA) and 8 of which were Methicillin-resistant (MRSA)...
June 21, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28634302/structure-of-human-fe-s-assembly-subcomplex-reveals-unexpected-cysteine-desulfurase-architecture-and-acyl-acp-isd11-interactions
#9
Seth A Cory, Jonathan G Van Vranken, Edward J Brignole, Shachin Patra, Dennis R Winge, Catherine L Drennan, Jared Rutter, David P Barondeau
In eukaryotes, sulfur is mobilized for incorporation into multiple biosynthetic pathways by a cysteine desulfurase complex that consists of a catalytic subunit (NFS1), LYR protein (ISD11), and acyl carrier protein (ACP). This NFS1-ISD11-ACP (SDA) complex forms the core of the iron-sulfur (Fe-S) assembly complex and associates with assembly proteins ISCU2, frataxin (FXN), and ferredoxin to synthesize Fe-S clusters. Here we present crystallographic and electron microscopic structures of the SDA complex coupled to enzyme kinetic and cell-based studies to provide structure-function properties of a mitochondrial cysteine desulfurase...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28633563/mammalian-synthetic-biology-engineering-biological-systems
#10
Joshua B Black, Pablo Perez-Pinera, Charles A Gersbach
The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution...
June 21, 2017: Annual Review of Biomedical Engineering
https://www.readbyqxmd.com/read/28630381/antibody-response-to-human-extracellular-her2-subdomain-proteins-in-mice
#11
Fateme Sadri-Ardalani, Moslem Ahmadi, Azam Hemmati, Shaghayegh Emami, Samira Farid, Mohammad Mehdi Amiri, Mahmood Jeddi-Tehrani, Mahdi Shabani, Fazel Shokri
BACKGROUND: In addition to passive immunotherapy using anti-HER2 monoclonal antibodies, active immunotherapy via HER2 targeting is an interesting approach to inducing specific anti-tumor immune responses. We have recently reported the immunogenicity of HER2 subdomains following DNA immunization and HER2 protein boosting. In the present study, we evaluated the immunogenicity of different HER2 extracellular subdomains for the induction of anti-HER2 antibody response in BALB/c mice. OBJECTIVE: To investigate and characterize antibody responses to human recombinant proteins of HER2 extracellular subdomains in immunized mice...
June 2017: Iranian Journal of Immunology: IJI
https://www.readbyqxmd.com/read/28630311/a-prokaryotic-viral-sequence-is-expressed-and-conserved-in-mammalian-brain
#12
Yang-Hui Yeh, Vignesh Gunasekharan, Laura Manuelidis
A natural and permanent transfer of prokaryotic viral sequences to mammals has not been reported by others. Circular "SPHINX" DNAs <5 kb were previously isolated from nuclease-protected cytoplasmic particles in rodent neuronal cell lines and brain. Two of these DNAs were sequenced after Φ29 polymerase amplification, and they revealed significant but imperfect homology to segments of commensal Acinetobacter phage viruses. These findings were surprising because the brain is isolated from environmental microorganisms...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28629143/nutrients-and-other-environmental-factors-influence-virus-abundances-across-oxic-and-hypoxic-marine-environments
#13
Jan F Finke, Brian P V Hunt, Christian Winter, Eddy C Carmack, Curtis A Suttle
Virus particles are highly abundant in seawater and, on average, outnumber microbial cells approximately 10-fold at the surface and 16-fold in deeper waters; yet, this relationship varies across environments. Here, we examine the influence of a suite of environmental variables, including nutrient concentrations, salinity and temperature, on the relationship between the abundances of viruses and prokaryotes over a broad range of spatial and temporal scales, including along a track from the Northwest Atlantic to the Northeast Pacific via the Arctic Ocean, and in the coastal waters of British Columbia, Canada...
June 17, 2017: Viruses
https://www.readbyqxmd.com/read/28629018/the-bone-building-blues-self-hardening-copper-doped-calcium-phosphate-cement-and-its-in-vitro-assessment-against-mammalian-cells-and-bacteria
#14
Julietta V Rau, Victoria M Wu, Valerio Graziani, Inna V Fadeeva, Alexander S Fomin, Marco Fosca, Vuk Uskoković
A blue calcium phosphate cement with optimal self-hardening properties was synthesized by doping whitlockite (β-TCP) with copper ions. The mechanism and the kinetics of the cement solidification process were studied using energy dispersive X-ray diffraction and it was found out that hardening was accompanied by the phase transition from TCP to brushite. Reduced lattice parameters in all crystallographic directions resulting from the rather low (1:180) substitution rate of copper for calcium was consistent with the higher ionic radius of the latter...
October 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28624506/cellular-gauge-symmetry-and-the-li-organization-principle-general-considerations
#15
REVIEW
Arturo Tozzi, James F Peters, Jorge Navarro, Wu Kun, Bi Lin, Pedro C Marijuán
Based on novel topological considerations, we postulate a gauge symmetry for living cells and proceed to interpret it from a consistent Eastern perspective: the li organization principle. In our framework, the reference system is the living cell, equipped with general symmetries and energetic constraints standing for the intertwined biochemical, metabolic and signaling pathways that allow the global homeostasis of the system. Environmental stimuli stand for forces able to locally break the symmetry of metabolic/signaling pathways, while the species-specific DNA is the gauge field that restores the global homeostasis after external perturbations...
June 14, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28622586/outerwear-through-the-ages-evolutionary-cell-biology-of-vesicle-coats
#16
REVIEW
Joel B Dacks, Margaret S Robinson
Vesicular transport was key to the evolution of eukaryotes, and is essential for eukaryotic life today. All modern eukaryotes have a set of vesicle coat proteins, which couple cargo selection to vesicle budding in the secretory and endocytic pathways. Although these coats share common features (e.g. recruitment via small GTPases, β-propeller-α-solenoid proteins acting as scaffolds), the relationships between them are not always clear. Structural studies on the coats themselves, comparative genomics and cell biology in diverse eukaryotes, and the recent discovery of the Asgard archaea and their 'eukaryotic signature proteins' are helping us to piece together how coats may have evolved during the prokaryote-to-eukaryote transition...
June 13, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28622140/reactive-nitrogen-species-rns-resistant-microbes-adaptation-and-medical-implications
#17
Sujeenthar Tharmalingam, Azhar Alhasawi, Varun P Appanna, Joe Lemire, Vasu D Appanna
Nitrosative stress results from an increase in reactive nitrogen species (RNS) within the cell. Though the RNS - nitric oxide (NO) and peroxynitrite (ONOO-) - play pivotal physiological roles, at elevated concentrations, these moieties can be poisonous to both prokaryotic and eukaryotic cells alike due to their capacity to disrupt a variety of essential biological processes. Numerous microbes are known to adapt to nitrosative stress by elaborating intricate strategies aimed at neutralizing RNS. In this review, we will discuss both the enzymatic systems dedicated to the elimination of RNS as well as the metabolic networks that are tailored to generate RNS-detoxifying metabolites - α-keto-acids...
June 15, 2017: Biological Chemistry
https://www.readbyqxmd.com/read/28621807/cellular-compartmentation-follows-rules-the-schnepf-theorem-its-consequences-and-exceptions-a-biological-membrane-separates-a-plasmatic-from-a-non-plasmatic-phase
#18
REVIEW
Daniel Moog, Uwe G Maier
Is the spatial organization of membranes and compartments within cells subjected to any rules? Cellular compartmentation differs between prokaryotic and eukaryotic life, because it is present to a high degree only in eukaryotes. In 1964, Prof. Eberhard Schnepf formulated the compartmentation rule (Schnepf theorem), which posits that a biological membrane, the main physical structure responsible for cellular compartmentation, usually separates a plasmatic form a non-plasmatic phase. Here we review and re-investigate the Schnepf theorem by applying the theorem to different cellular structures, from bacterial cells to eukaryotes with their organelles and compartments...
June 16, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28620688/controlling-microbial-phb-synthesis-via-crispri
#19
Dan Li, Li Lv, Jin-Chun Chen, Guo-Qiang Chen
Microbial polyhydroxyalkanoates (PHA) are a family of biopolyesters with properties similar to petroleum plastics such as polyethylene (PE) or polypropylene (PP). Polyhydroxybutyrate (PHB) is the most common PHA known so far. Clustered regularly interspaced short palindromic repeats interference (CRISPRi), a technology recently developed to control gene expression levels in eukaryotic and prokaryotic genomes, was employed to regulate PHB synthase activity influencing PHB synthesis. Recombinant Escherichia coli harboring an operon of three PHB synthesis genes phaCAB cloned from Ralstonia eutropha, was transformed with various single guided RNA (sgRNA with its guide sequence of 20-23 bases) able to bind to various locations of the PHB synthase PhaC, respectively...
June 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28619109/type-ii-crispr-cas9-approach-in-the-oncological-therapy
#20
REVIEW
A Biagioni, A Chillà, E Andreucci, A Laurenzana, F Margheri, S Peppicelli, M Del Rosso, G Fibbi
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a prokaryotic adaptable immune mechanism used by many bacteria and archaea to protect themselves from foreign nucleic acids. This complex system can recognize and cut non-self DNA in order to provide the prokaryotic organisms a strong defense against foreign viral or plasmid attacks and make the cell immune from further assaults. Today, it has been adapted to be used in vitro and in vivo in eukaryotic cells to perform a complete and highly selective gene knockout or a specific gene editing...
June 15, 2017: Journal of Experimental & Clinical Cancer Research: CR
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