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https://www.readbyqxmd.com/read/28331319/humanized-cd7-nanobody-based-immunotoxins-exhibit-promising-anti-t-cell-acute-lymphoblastic-leukemia-potential
#1
Yuan Yu, Jialu Li, Xuejun Zhu, Xiaowen Tang, Yangyi Bao, Xiang Sun, Yuhui Huang, Fang Tian, Xiaomei Liu, Lin Yang
BACKGROUND: Nanobodies, named as VHHs (variable domain of heavy chain of HCAb [heavy-chain antibodies]), are derived from heavy-chain-only antibodies that circulate in sera of camelids. Their exceptional physicochemical properties, possibility of humanization, and unique antigen recognition properties make them excellent candidates for targeted delivery of biologically active components, including immunotoxins. In our previous efforts, we have successfully generated the monovalent and bivalent CD7 nanobody-based immunotoxins, which can effectively trigger the apoptosis of CD7-positive malignant cells...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/28323872/expression-maturation-and-turnover-of-drrs-an-unusually-stable-dosr-regulated-small-rna-in-mycobacterium-tuberculosis
#2
Alexandra Moores, Ana B Riesco, Stefan Schwenk, Kristine B Arnvig
Mycobacterium tuberculosis depends on the ability to adjust to stresses encountered in a range of host environments, adjustments that require significant changes in gene expression. Small RNAs (sRNAs) play an important role as post-transcriptional regulators of prokaryotic gene expression, where they are associated with stress responses and, in the case of pathogens, adaptation to the host environment. In spite of this, the understanding of M. tuberculosis RNA biology remains limited. Here we have used a DosR-associated sRNA as an example to investigate multiple aspects of mycobacterial RNA biology that are likely to apply to other M...
2017: PloS One
https://www.readbyqxmd.com/read/28323299/cyanobacterial-nitrogenases-phylogenetic-diversity-regulation-and-functional-predictions
#3
Alberto A Esteves-Ferreira, João Henrique Frota Cavalcanti, Marcelo Gomes Marçal Vieira Vaz, Luna V Alvarenga, Adriano Nunes-Nesi, Wagner L Araújo
Cyanobacteria is a remarkable group of prokaryotic photosynthetic microorganisms, with several genera capable of fixing atmospheric nitrogen (N2) and presenting a wide range of morphologies. Although the nitrogenase complex is not present in all cyanobacterial taxa, it is spread across several cyanobacterial strains. The nitrogenase complex has also a high theoretical potential for biofuel production, since H2 is a by-product produced during N2 fixation. In this review we discuss the significance of a relatively wide variety of cell morphologies and metabolic strategies that allow spatial and temporal separation of N2 fixation from photosynthesis in cyanobacteria...
March 20, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28315746/optimized-protocol-for-soluble-prokaryotic-expression-purification-and-structural-analysis-of-human-placenta-specific-1-plac1
#4
Mahboobeh Nazari, Amir-Hassan Zarnani, Roya Ghods, Rahman Emamzadeh, Somayeh Najafzadeh, Arash Minai-Tehrani, Jafar Mahmoudian, Maryam Yousefi, Sedigheh Vafaei, Sam Massahi, Mohammad-Reza Nejadmoghaddam
Placenta specific -1 (PLAC1) has been recently introduced as a small membrane-associated protein mainly involved in placental development. Expression of PLAC1 transcript has been documented in almost one hundred cancer cell lines standing for fourteen distinct cancer types. The presence of two disulfide bridges makes difficult to produce functional recombinant PLAC1 in soluble form with high yield. This limitation also complicates the structural studies of PLAC1, which is important for prediction of its physiological roles...
March 16, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28315239/-14-c-acetyl-coenzyme-a-based-in-vitro-n-terminal-acetylation-assay
#5
Adrian Drazic, Thomas Arnesen
N-terminal acetylation is one of the most abundant co- and posttranslational protein modifications, conserved from prokaryotes to eukaryotes. The functional consequences of this modification are manifold, ranging from protein folding, stability, and interaction to subcellular localization. We describe here an isotope-labeled [(14)C]-acetyl-Coenzyme A-based acetylation assay, allowing the determination of weak catalytic activities of NATs in vitro. It allows the use of purified recombinant enzymes from Escherichia coli, or co-immunoprecipitated enzymes from various organisms, as well as the determination of the in vitro activity of various cell lysates...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28303296/sortase-a-aided-escherichia-coli-expression-system-for-functional-osteoprotegerin-cysteine-rich-domain
#6
Mengmeng Jin, Yuan Chen, Yunfeng Zhao, Luyang Che, Yanyan Ma, Jingzhe Li, Yi Wang, Hua Tao, Juan Ma, Bing Pan, Changzhen Liu, Peng Huang
As a natural inhibitor of the receptor activator of nuclear factor-кB ligand (RANKL), osteprotegerin (OPG) is considered a promising treatment for metabolic bone diseases. Typical approaches for preparing recombinant OPG or its derivatives employ eukaryotic expression systems. Due to the advantages of a prokaryotic expression system, which include its convenience, low cost, and abundant production, in this study, we establish a strategy for preparing functional OPG using the Escherichia coli expression system...
March 16, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28303150/development-of-synebrick-vectors-as-a-synthetic-biology-platform-for-gene-expression-in-synechococcus-elongatus-pcc-7942
#7
Wook Jin Kim, Sun-Mi Lee, Youngsoon Um, Sang Jun Sim, Han Min Woo
Cyanobacteria are oxygenic photosynthetic prokaryotes that are able to assimilate CO2 using solar energy and water. Metabolic engineering of cyanobacteria has suggested the possibility of direct CO2 conversion to value-added chemicals. However, engineering of cyanobacteria has been limited due to the lack of various genetic tools for expression and control of multiple genes to reconstruct metabolic pathways for biochemicals from CO2. Thus, we developed SyneBrick vectors as a synthetic biology platform for gene expression in Synechococcus elongatus PCC 7942 as a model cyanobacterium...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28303119/viruses-and-protists-induced-mortality-of-prokaryotes-around-the-antarctic-peninsula-during-the-austral-summer
#8
Dolors Vaqué, Julia A Boras, Francesc Torrent-Llagostera, Susana Agustí, Jesús M Arrieta, Elena Lara, Yaiza M Castillo, Carlos M Duarte, Maria M Sala
During the Austral summer 2009 we studied three areas surrounding the Antarctic Peninsula: the Bellingshausen Sea, the Bransfield Strait and the Weddell Sea. We aimed to investigate, whether viruses or protists were the main agents inducing prokaryotic mortality rates, and the sensitivity to temperature of prokaryotic heterotrophic production and mortality based on the activation energy (Ea) for each process. Seawater samples were taken at seven depths (0.1-100 m) to quantify viruses, prokaryotes and protists abundances, and heterotrophic prokaryotic production (PHP)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28300533/membranes-energetics-and-evolution-across-the-prokaryote-eukaryote-divide
#9
Michael Lynch, Georgi K Marinov
The evolution of the eukaryotic cell marked a profound moment in Earth's history, with most of the visible biota coming to rely on intracellular membrane-bound organelles. It has been suggested that this evolutionary transition was critically dependent on the movement of ATP synthesis from the cell surface to mitochondrial membranes and the resultant boost to the energetic capacity of eukaryotic cells. However, contrary to this hypothesis, numerous lines of evidence suggest that eukaryotes are no more bioenergetically efficient than prokaryotes...
March 16, 2017: ELife
https://www.readbyqxmd.com/read/28298336/moonlighting-glycolytic-protein-glyceraldehyde-3-phosphate-dehydrogenase-gapdh-an-evolutionarily-conserved-plasminogen-receptor-on-mammalian-cells
#10
Anoop Singh Chauhan, Manoj Kumar, Surbhi Chaudhary, Anil Patidar, Asmita Dhiman, Navdeep Sheokand, Himanshu Malhotra, Chaaya Iyengar Raje, Manoj Raje
Prokaryotic pathogens establish infection in mammals by capturing the proteolytic enzyme plasminogen (Plg) onto their surface to digest host extracellular matrix (ECM). One of the bacterial surface Plg receptors is the multifunctional glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). In a defensive response, the host mounts an inflammatory response, which involves infiltration of leukocytes to sites of inflammation. This requires macrophage exit from the blood and migration across basement membranes, a phenomenon dependent on proteolytic remodeling of the ECM utilizing Plg...
March 15, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28296967/the-combined-rapid-detection-and-species-level-identification-of-yeasts-in-simulated-blood-culture-using-a-colorimetric-sensor-array
#11
Nabin K Shrestha, Sung H Lim, Deborah A Wilson, Ana Victoria SalasVargas, Yair S Churi, Paul A Rhodes, Peter J Mazzone, Gary W Procop
BACKGROUND: A colorimetric sensor array (CSA) has been demonstrated to rapidly detect and identify bacteria growing in blood cultures by obtaining a species-specific "fingerprint" of the volatile organic compounds (VOCs) produced during growth. This capability has been demonstrated in prokaryotes, but has not been reported for eukaryotic cells growing in culture. The purpose of this study was to explore if a disposable CSA could differentially identify 7 species of pathogenic yeasts growing in blood culture...
2017: PloS One
https://www.readbyqxmd.com/read/28289838/a-stochastic-analysis-of-autoregulation-of-gene-expression
#12
Renaud Dessalles, Vincent Fromion, Philippe Robert
This paper analyzes, in the context of a prokaryotic cell, the stochastic variability of the number of proteins when there is a control of gene expression by an autoregulation scheme. The goal of this work is to estimate the efficiency of the regulation to limit the fluctuations of the number of copies of a given protein. The autoregulation considered in this paper relies mainly on a negative feedback: the proteins are repressors of their own gene expression. The efficiency of a production process without feedback control is compared to a production process with an autoregulation of the gene expression assuming that both of them produce the same average number of proteins...
March 13, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28289836/prokaryotic-abundance-and-activity-in-permafrost-of-the-northern-victoria-land-and-upper-victoria-valley-antarctica
#13
Rosabruna La Ferla, Maurizio Azzaro, Luigi Michaud, Gabriella Caruso, Angelina Lo Giudice, Rodolfo Paranhos, Anderson S Cabral, Antonella Conte, Alessandro Cosenza, Giovanna Maimone, Maria Papale, Alessandro Ciro Rappazzo, Mauro Guglielmin
Victoria Land permafrost harbours a potentially large pool of cold-affected microorganisms whose metabolic potential still remains underestimated. Three cores (BC-1, BC-2 and BC-3) drilled at different depths in Boulder Clay (Northern Victoria Land) and one sample (DY) collected from a core in the Dry Valleys (Upper Victoria Valley) were analysed to assess the prokaryotic abundance, viability, physiological profiles and potential metabolic rates. The cores drilled at Boulder Clay were a template of different ecological conditions (different temperature regime, ice content, exchanges with atmosphere and with liquid water) in the same small basin while the Dry Valleys site was very similar to BC-2 conditions but with a complete different geological history and ground ice type...
March 13, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28277897/high-throughput-sequencing-reveals-circular-substrates-for-an-archaeal-rna-ligase
#14
Hubert F Becker, Alice Heliou, Kamel Djaout, Roxane Lestini, Mireille Regnier, Hannu Myllykallio
It is only recently that the abundant presence of circular RNAs (circRNAs) in all kingdoms of Life, including the hyperthermophilic archaeon Pyrococcus abyssi, has emerged. This led us to investigate the physiological significance of a previously observed weak intramolecular ligation activity of Pab1020 RNA ligase. Here we demonstrate that this enzyme, despite sharing significant sequence similarity with DNA ligases, is indeed an RNA-specific polynucleotide ligase efficiently acting on physiologically significant substrates...
March 9, 2017: RNA Biology
https://www.readbyqxmd.com/read/28276199/new-insights-into-a-hot-environment-for-early-life
#15
REVIEW
Jianghong Dai
Investigating the physical-chemical setting of early life is a challenging task. In this contribution, I attempt to introduce a provocative concept from cosmology-cosmic microwave background (CMB), which is the residual thermal radiation from a hot early Universe-to the field. For this purpose, I revisit a recently deduced biomarker, the 1,6-anhydro bond of sugars in bacteria. In vitro, the 1,6-anhydro bond of sugars reflects and captures residual thermal radiation in thermochemical processes and therefore is somewhat analogous to CMB...
March 9, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28271476/%C3%AE-2-macroglobulins-structure-and-function
#16
Irene Garcia-Ferrer, Aniebrys Marrero, F Xavier Gomis-Rüth, Theodoros Goulas
α2-macroglobulins are broad-spectrum endopeptidase inhibitors, which have to date been characterised from metazoans (vertebrates and invertebrates) and Gram-negative bacteria. Their structural and biochemical properties reveal two related modes of action: the "Venus flytrap" and the "snap-trap" mechanisms. In both cases, peptidases trigger a massive conformational rearrangement of α2-macroglobulin after cutting in a highly flexible bait region, which results in their entrapment. In some homologs, a second action takes place that involves a highly reactive β-cysteinyl-γ-glutamyl thioester bond, which covalently binds cleaving peptidases and thus contributes to the further stabilization of the enzyme:inhibitor complex...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28270584/viruses-in-the-oceanic-basement
#17
Olivia D Nigro, Sean P Jungbluth, Huei-Ting Lin, Chih-Chiang Hsieh, Jaclyn A Miranda, Christopher R Schvarcz, Michael S Rappé, Grieg F Steward
Microbial life has been detected well into the igneous crust of the seafloor (i.e., the oceanic basement), but there have been no reports confirming the presence of viruses in this habitat. To detect and characterize an ocean basement virome, geothermally heated fluid samples (ca. 60 to 65°C) were collected from 117 to 292 m deep into the ocean basement using seafloor observatories installed in two boreholes (Integrated Ocean Drilling Program [IODP] U1362A and U1362B) drilled in the eastern sediment-covered flank of the Juan de Fuca Ridge...
March 7, 2017: MBio
https://www.readbyqxmd.com/read/28269158/detecting-cell-division-of-pseudomonas-aeruginosa-bacteria-from-bright-field-microscopy-images-with-hidden-conditional-random-fields
#18
Lee-Ling S Ong, Xinghua Zhang, Binu Kundukad, Justin Dauwels, Patrick Doyle, H Harry Asada
An approach to automatically detect bacteria division with temporal models is presented. To understand how bacteria migrate and proliferate to form complex multicellular behaviours such as biofilms, it is desirable to track individual bacteria and detect cell division events. Unlike eukaryotic cells, prokaryotic cells such as bacteria lack distinctive features, causing bacteria division difficult to detect in a single image frame. Furthermore, bacteria may detach, migrate close to other bacteria and may orientate themselves at an angle to the horizontal plane...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28263314/widespread-distribution-of-encapsulin-nanocompartments-reveals-functional-diversity
#19
Tobias W Giessen, Pamela A Silver
Cells organize and regulate their metabolism via membrane- or protein-bound organelles. In this way, incompatible processes can be spatially separated and controlled. In prokaryotes, protein-based compartments are used to sequester harmful reactions and store useful compounds. These protein compartments play key roles in various metabolic and ecological processes, ranging from iron homeostasis to carbon fixation. One of the newest types of protein organelle are encapsulin nanocompartments. They are able to encapsulate specific protein cargo and are proposed to be involved in redox-related processes...
March 6, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28260486/investigation-of-structure-of-the-ribosomal-l12-p-stalk
#20
REVIEW
I V Mitroshin, M B Garber, A G Gabdulkhakov
This review contains recent data on the structure of the functionally important ribosomal domain, L12/P stalk, of the large ribosomal subunit. It is the most mobile site of the ribosome; it has been found in ribosomes of all living cells, and it is involved in the interaction between ribosomes and translation factors. The difference between the structures of the ribosomal proteins forming this protuberance (despite their general resemblance) determines the specificity of interaction between eukaryotic and prokaryotic ribosomes and the respective protein factors of translation...
December 2016: Biochemistry. Biokhimii︠a︡
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