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Zhilin Xing, Tiantao Zhao, Weiyang Bai, Xu Yang, Shuai Liu, Lijie Zhang
The microbiome in artificial lake water and its impact on mercury (Hg) methylation remain largely unknown. We selected the largest artificial lake in southeastern china, Changshou Lake (CSL), which has high background levels of Hg, for our investigation of Hg transformation microorganisms. Five different sections of the water column of CSL were sampled during four seasons. The water samples were subjected to analysis of geochemical parameters, various Hg species and microbiome information. High concentrations of total mercury (THg) were detected in CSL in comparison with those found in natural lakes...
May 18, 2018: Ecotoxicology and Environmental Safety
Immacolata Antonucci, Giovanni Gallo, Danila Limauro, Patrizia Contursi, Ana Luisa Ribeiro, Alba Blesa, José Berenguer, Simonetta Bartolucci, Gabriella Fiorentino
BACKGROUND: The characterization of the molecular determinants of metal resistance has potential biotechnological application in biosensing and bioremediation. In this context, the bacterium Thermus thermophilus HB27 is a metal tolerant thermophile containing a set of genes involved in arsenic resistance which, differently from other microbes, are not organized into a single operon. They encode the proteins: arsenate reductase, TtArsC, arsenic efflux membrane transporter, TtArsX, and transcriptional repressor, TtSmtB...
May 18, 2018: Microbial Cell Factories
Deepthi KrishnanNair Geetha, Jayasudha Rajagopalaboopathi, Girish Rameshan Nair, Manikandan Palanisamy, Ram Rammohan, Narendran Venkatapathy, Prabagaran Solai Ramatchandirane
The conjunctival sac of healthy human harbours a variety of microorganisms. When the eye is compromised, an occasional inadvertent spread happens to the adjacent tissue, resulting in bacterial ocular infections. Microbiological investigation of the conjunctival swab is one of the broadly used modality to study the aetiological agent of conjunctiva. However, most of the time such methods yield unsatisfactory results. Hence, the present study intends to identify the bacterial community in human conjunctiva of pre-operative subjects through 16S rRNA gene libraries...
May 14, 2018: Experimental Eye Research
Daria Krefft, Aliaksei Papkov, Maciej Prusinowski, Agnieszka Zylicz-Stachula, Piotr M Skowron
BACKGROUND: Acoustic or hydrodynamic shearing, sonication and enzymatic digestion are used to fragment DNA. However, these methods have several disadvantages, such as DNA damage, difficulties in fragmentation control, irreproducibility and under-representation of some DNA segments. The DNA fragmentation tool would be a gentle enzymatic method, offering cleavage frequency high enough to eliminate DNA fragments distribution bias and allow for easy control of partial digests. Only three such frequently cleaving natural restriction endonucleases (REases) were discovered: CviJI, SetI and FaiI...
May 11, 2018: BMC Genomics
Ayako Yoshida, Saori Kosono, Makoto Nishiyama
2-Isopropylmalate synthase (IPMS) catalyzes the first step of leucine biosynthesis and is regulated via feedback inhibition by leucine. The thermophilic bacterium, Thermus thermophilus HB27, has two IPMS homologous genes: TTC0847 and TTC0849, both of which are in the branched-chain amino acid biosynthetic gene cluster. Since enzymes involved in the leucine biosynthetic pathway are evolutionarily related to those in isoleucine biosynthesis, TTC0847 and TTC0849 are expected to function as IPMS or citramalate synthase, which is the first enzyme in the isoleucine biosynthetic pathway from pyruvate...
May 5, 2018: Biochemical and Biophysical Research Communications
Jing Sun, Shizeng Wang, Wenna Li, Ruimin Li, Sheng Chen, Hyon Il Ri, Tae Mun Kim, Myong Su Kang, Lu Sun, Xinxiao Sun, Qipeng Yuan
Trehalose is a non-reducing disaccharide with a wide range of applications in the fields of food, cosmetics, and pharmaceuticals. In this study, trehalose synthase derived from Thermus thermophilus HB27 (TtTreS) was immobilized on silicalite-1-based material for trehalose production. The activity and the stability of TtTreS against pH and temperature were significantly improved by immobilization. Enzyme immobilization also led to a lower concentration of byproduct glucose, which reduces byproduct inhibition of TtTreS...
May 4, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Jennifer Kylie, J Scott Weese, Patricia V Turner
BACKGROUND: Rabbits are cecotrophic, hindgut-fermenters that rely heavily on their gastrointestinal microbiota for optimal digestion of plant-based diets. Dysbiosis, caused by disruption of the gastrointestinal microbiota, is known to predispose rabbits to rabbit enteritis complex (REC), a major cause of morbidity and mortality. The objectives of this study were to describe the fecal microbiota of domestic rabbits from a variety of settings (commercial meat, companion, laboratory, and shelter) and to identify how factors such as age, season, and routine antimicrobial use affect the fecal microbiota composition...
April 27, 2018: BMC Veterinary Research
Katarzyna Safianowicz, Tina L Bell, Michael A Kertesz
Mushrooms are an important food crop throughout the world. The most important edible mushroom is the button mushroom (Agaricus bisporus), which comprises about 30% of the global mushroom market. This species is cultivated commercially on a selective compost that is produced predominantly from wheat straw/stable bedding and chicken manure, at a moisture content of around 70% (w/w) and temperatures of up to 80 °C. Large volumes of water are required to achieve this moisture content, and many producers therefore collect leachate from the composting windrows and bunkers (known in the industry as "goody water") and reuse it to wet the raw ingredients...
April 25, 2018: Applied Microbiology and Biotechnology
Sudarson Sundarrajan, Sneha Rao, Sriram Padmanabhan
We studied the role of Thermus thermophilus Recombinase A (RecA) in enhancing the PCR signals of DNA viruses such as Hepatitis B virus (HBV). The RecA gene of a thermophilic eubacterial strain, T. thermophilus, was cloned and hyperexpressed in Escherichia coli. The recombinant RecA protein was purified using a single heat treatment step without the use of any chromatography steps, and the purified protein (>95%) was found to be active. The purified RecA could enhance the polymerase chain reaction (PCR) signals of HBV and improve the detection limit of the HBV diagnosis by real time PCR...
April 12, 2018: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
Christina M Ridley, Gerrit Voordouw
Little is known about the microbial ecology of the subsurface oil sands in Northern Alberta, Canada. Biodegradation of low molecular weight hydrocarbons by indigenous microbes has enriched high molecular weight hydrocarbons, resulting in highly viscous bitumen. This extreme subsurface environment is further characterized by low nutrient availability and limited access to water, thus resulting in low microbial biomass. Improved DNA isolation protocols and increasingly sensitive sequencing methods have allowed an in-depth investigation of the microbial ecology of this unique subsurface environmental niche...
April 24, 2018: FEMS Microbiology Ecology
Jen-Hao Cheng, Chien-Chih Huang, Yen-Hua Huang, Cheng-Yang Huang
Dihydropyrimidinase, a dimetalloenzyme containing a carboxylated lysine within the active site, is a member of the cyclic amidohydrolase family, which also includes allantoinase, dihydroorotase, hydantoinase, and imidase. Unlike all known dihydropyrimidinases, which are tetrameric, pseudomonal dihydropyrimidinase forms a dimer at neutral pH. In this paper, we report the crystal structure of P. aeruginosa dihydropyrimidinase at pH 5.9 (PDB entry 5YKD). The crystals of P. aeruginosa dihydropyrimidinase belonged to space group C 2221 with cell dimensions of a  = 108...
2018: Bioinorganic Chemistry and Applications
Santosh Kumar Chaudhary, Jeyaraman Jeyakanthan, Kanagaraj Sekar
Thymidylate kinase is an important enzyme in DNA synthesis. It catalyzes the conversion of thymidine monophosphate to thymidine diphosphate, with ATP as the preferred phosphoryl donor, in the presence of Mg2+ . In this study, the dynamics of the active site and the communication paths between the substrates, ATP and TMP, are reported for thymidylate kinase from Thermus thermophilus. Conformational changes upon ligand binding and the path for communication between the substrates and the protein are important in understanding the catalytic mechanism of the enzyme...
April 1, 2018: Acta Crystallographica. Section D, Structural Biology
Alba Blesa, Beate Averhoff, José Berenguer
The small amount of genetic content in thermophiles generally limits their adaptability to environmental changes. In Thermus spp., very active horizontal gene transfer (HGT) mechanisms allow the rapid spread of strain-specific adaptive gene modules among the entire population. Constitutive expression of a rather particular and highly efficient DNA transport apparatus (DTA) is at the center of this HGT-mediated enhanced adaptability. The function of the DTA is dependent on the integrity and longevity of the extracellular DNA (eDNA) being transformed, which can be improved by the production of extracellular vesicles (EV) through lysis of a fraction of the population...
April 12, 2018: Current Issues in Molecular Biology
John N Milligan, Raghav Shroff, Daniel J Garry, Andrew D Ellington
Strand-displacing polymerases are a crucial component of isothermal amplification (IA) reactions where the lack of thermal cycling reduces equipment needs and improves time-to-answer, especially for point of care applications. In order to improve the function of strand displacing polymerases, we have developed an emulsion-based directed evolution scheme, high temperature isothermal compartmentalized self-replication (HTI-CSR) that does not rely on thermal cycling. Starting from an algorithm-optimized shuffled library of exonuclease-deficient Family A polymerases from Geobacillus stearothermophilus (Bst LF) and Thermus aquaticus (Klentaq), we have applied HTI-CSR to generate a more thermostable strand displacing polymerase variant that performs well in Loop-mediated Isothermal Amplification (LAMP) and Rolling Circle Amplification (RCA), even after thermal challenges of up to 95°C that lead to better primer annealing...
April 9, 2018: Biochemistry
Dong-Xu Jia, Teng Wang, Zi-Jian Liu, Li-Qun Jin, Jia-Jia Li, Cheng-Jun Liao, De-Shui Chen, Yu-Guo Zheng
Glucose isomerase (GI) responsible for catalyzing the isomerization from d-glucose to d-fructose, was an important enzyme for producing high fructose corn syrup (HFCS). In a quest to prepare HFCS at elevated temperature and facilitate enzymatic recovery, an effective procedure for whole cell immobilization of refractory Thermus oshimai glucose isomerase (ToGI) onto Celite 545 using tris(hydroxymethyl)phosphine (THP) as crosslinker was established. The immobilized biocatalyst showed an activity of approximate 127...
April 4, 2018: Journal of Bioscience and Bioengineering
S Palikša, G Alzbutas, R Skirgaila
Personalized medicine and advanced diagnostic tools based on RNA analysis are focusing on fast and direct One-Step RT-PCR assays. First strand complementary DNA (cDNA) synthesized by the reverse transcriptase (RT) is exponentially amplified in the end-point or real-time PCR. Even a minor discrepancy in PCR conditions would result in big deviations during the data analysis. Thus, One-Step RT-PCR composition is typically based on the PCR buffer. In this study, we have used compartmentalized ribosome display technique for in vitro evolution of the Moloney Murine Leukemia Virus reverse transcriptase (M-MuLV RT) that would be able to perform efficient full-length cDNA synthesis in PCR buffer optimized for Thermus aquaticus DNA polymerase...
March 1, 2018: Protein Engineering, Design & Selection: PEDS
Andrew K Leight, Byron C Crump, Raleigh R Hood
Routine monitoring of shellfish growing waters for bacteria indicative of human sewage pollution reveals little about the bacterial communities that co-occur with these indicators. This study investigated the bacterial community, potential pathogens, and fecal indicator bacteria in 40 water samples from a shellfish growing area in the Chesapeake Bay, USA. Bacterial community composition was quantified with deep sequencing of 16S rRNA gene amplicons, and absolute gene abundances were estimated with an internal standard ( Thermus thermophilus genomes)...
2018: Frontiers in Microbiology
Megan Sjodt, Kelly Brock, Genevieve Dobihal, Patricia D A Rohs, Anna G Green, Thomas A Hopf, Alexander J Meeske, Veerasak Srisuknimit, Daniel Kahne, Suzanne Walker, Debora S Marks, Thomas G Bernhardt, David Z Rudner, Andrew C Kruse
The shape, elongation, division and sporulation (SEDS) proteins are a large family of ubiquitous and essential transmembrane enzymes with critical roles in bacterial cell wall biology. The exact function of SEDS proteins was for a long time poorly understood, but recent work has revealed that the prototypical SEDS family member RodA is a peptidoglycan polymerase-a role previously attributed exclusively to members of the penicillin-binding protein family. This discovery has made RodA and other SEDS proteins promising targets for the development of next-generation antibiotics...
April 5, 2018: Nature
Guangtao Song, Hui Chen, Gang Sheng, Yanli Wang, Jizhong Lou
Argonaute (AGO) proteins play central roles in nucleic acid-guided interferences that regulate gene expression and defend against foreign genetic elements in all life. Although much progress has been made on the function of argonaute proteins in target recognition and cleavage, the detailed mechanism of their biological functions is not fully under-stood. Here, using AFM-based single-molecule force spectroscopy, we studied the target-guide dissociation in the absence or presence of Thermus thermophiles AGO (TtAGO)...
March 28, 2018: Biochemistry
Zhichang Qiu, Ningyang Li, Xiaoming Lu, Zhenjia Zheng, Mingjie Zhang, Xuguang Qiao
Black garlic is a distinctive garlic deep-processed product made from fresh garlic at high temperature and controlled humidity. To explore microbial community structure, diversity and metabolic potential during the 12days of the black garlic processing, Illumina MiSeq sequencing technology was performed to sequence the 16S rRNA V3-V4 hypervariable region of bacteria. A total of 677,917 high quality reads were yielded with an average read length of 416bp. Operational taxonomic units (OTU) clustering analysis showed that the number of species OTUs ranged from 148 to 1974, with alpha diversity increasing remarkably, indicating the high microbial community abundance and diversity...
April 2018: Food Research International
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