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Suymara Toledo Miranda, Antonio Teixeira de Matos, Gheila Corrêa Ferres Baptestini, Alisson Carraro Borges
In horizontal subsurface flow constructed wetlands (HSSF-CWs), the main operational problem is clogging of the porous medium. In this study, the unclogging of HSSF-CWs was evaluated, at rest, by adding a nitrogen-based nutrient solution to the influent. For this, six HSSF-CWs were used, consisting of two uncultivated (CW-C), two cultivated with Tifton 85-grass (Cynodon spp.) (CW-T) and two cultivated with alligator weed (Alternanthera philoxeroides) (CW-A), which were fully clogged after being used for the treatment of swine wastewater...
October 2016: Water Science and Technology: a Journal of the International Association on Water Pollution Research
Miguel Pinto, Vítor Borges, Minia Antelo, Miguel Pinheiro, Alexandra Nunes, Jacinta Azevedo, Maria José Borrego, Joana Mendonça, Dina Carpinteiro, Luís Vieira, João Paulo Gomes
Insights into the genomic adaptive traits of Treponema pallidum, the causative bacterium of syphilis, have long been hampered due to the absence of in vitro culture models and the constraints associated with its propagation in rabbits. Here, we have bypassed the culture bottleneck by means of a targeted strategy never applied to uncultivable bacterial human pathogens to directly capture whole-genome T. pallidum data in the context of human infection. This strategy has unveiled a scenario of discreet T. pallidum interstrain single-nucleotide-polymorphism-based microevolution, contrasting with a rampant within-patient genetic heterogeneity mainly targeting multiple phase-variable loci and a major antigen-coding gene (tprK)...
October 17, 2016: Nature Microbiology
Letícia Maria Menezes Nóbrega, Francisco Montagner, Adriana Costa Ribeiro, Márcia Alves Pinto Mayer, Brenda Paula Figueiredo de Almeida Gomes
The aim of this study was to explore the bacterial diversity of 10 root canals with acute apical abscess using clonal analysis. Samples were collected from 10 patients and submitted to bacterial DNA isolation, 16S rRNA gene amplification, cloning, and sequencing. A bacterial genomic library was constructed and bacterial diversity was estimated. The mean number of taxa per canal was 15, ranging from 11 to 21. A total of 689 clones were analyzed and 76 phylotypes identified, of which 47 (61.84%) were different species and 29 (38...
October 10, 2016: Brazilian Oral Research
Nikolaus Leisch, Nika Pende, Philipp M Weber, Harald R Gruber-Vodicka, Jolanda Verheul, Norbert O E Vischer, Sophie S Abby, Benedikt Geier, Tanneke den Blaauwen, Silvia Bulgheresi
The reproduction mode of uncultivable microorganisms deserves investigation as it can largely diverge from conventional transverse binary fission. Here, we show that the rod-shaped gammaproteobacterium thriving on the surface of the Robbea hypermnestra nematode divides by FtsZ-based, non-synchronous invagination of its poles-that is, the host-attached and fimbriae-rich pole invaginates earlier than the distal one. We conclude that, in a naturally occurring animal symbiont, binary fission is host-oriented and does not require native FtsZ to polymerize into a ring at any septation stage...
October 10, 2016: Nature Microbiology
L Furlan, B Contiero, F Chiarini, M Colauzzi, E Sartori, I Benvegnù, F Fracasso, P Giandon
A survey of maize fields was conducted in northeast Italy from 1986 to 2014, resulting in a dataset of 1296 records including information on wireworm damage to maize, plant-attacking species, agronomic characteristics, landscape and climate. Three wireworm species, Agriotes brevis Candeze, A. sordidus Illiger and A. ustulatus Schäller, were identified as the dominant pest species in maize fields. Over the 29-year period surveyed, no yield reduction was observed when wireworm plant damage was below 15 % of the stand...
October 6, 2016: Environmental Science and Pollution Research International
Jaime Iranzo, Eugene V Koonin, David Prangishvili, Mart Krupovic
: Archaea and particularly hyperthermophilic crenarchaea are hosts to many unusual viruses with diverse virion shapes and distinct gene compositions. As is typical of viruses in general, there are no universal genes in the archaeal virosphere. Therefore, to obtain a comprehensive picture of the evolutionary relationships between viruses, network analysis methods are more productive than traditional phylogenetic approaches. Here we present a comprehensive comparative analysis of genomes and proteomes from all currently known taxonomically classified and unclassified, cultivated and uncultivated archaeal viruses...
September 28, 2016: Journal of Virology
Sachin Goyal, Pratima Nangia-Makker, Lulu Farhana, Yingjie Yu, Adhip Pn Majumdar
Over the past two decades there has been remarkable progress in cancer diagnosis, treatment and screening. The basic mechanisms leading to pathogenesis of various types of cancers are also understood better and some patients, if diagnosed at a particular stage go on to lead a normal pre-diagnosis life. Despite these achievements, racial disparity in some cancers remains a mystery. The higher incidence, aggressiveness and mortality of breast, prostate and colorectal cancers (CRCs) in African-Americans as compared to Caucasian-Americans are now well documented...
September 26, 2016: World Journal of Stem Cells
Martina Cappelletti, Daniele Ghezzi, Davide Zannoni, Bruno Capaccioni, Stefano Fedi
"Terre Calde di Medolla" (TCM) (literally, "Hot Lands of Medolla") refers to a farming area in Italy with anomalously high temperatures and diffuse emissions of biogenic CO2, which has been linked to CH4 oxidation processes from a depth of 0.7 m to the surface. We herein assessed the composition of the total bacterial community and diversity of methane-oxidizing bacteria (MOB) in soil samples collected at a depth at which the peak temperature was detected (0.6 m). Cultivation-independent methods were used, such as: i) a clone library analysis of the 16S rRNA gene and pmoA (coding for the α-subunit of the particulate methane monooxygenase) gene, and ii) Terminal Restriction Fragment Length Polymorphism (T-RFLP) fingerprinting...
September 17, 2016: Microbes and Environments
Daizy Bharti, Santosh Kumar, Antonietta La Terza
The morphology of Rigidosticha italiensis n. gen., n. sp., which was found in a soil sample collected from an uncultivated field in Lombardia, Italy, was investigated using live observation and protargol staining. Rigidosticha n. gen. is characterised by a rigid body, undulating membranes resembling a Steinia pattern, oxytrichid frontal ciliature, distinct mid-ventral cirral pairs, transverse cirri, one right and one left row of marginal cirri, absence of dorsal kinety 3 fragmentation, more than two dorsomarginal rows, and caudal cirri...
August 25, 2016: European Journal of Protistology
Hidenori Matsui, Tetsufumi Takahashi, Somay Y Murayama, Ikuo Uchiyama, Katsushi Yamaguchi, Shuji Shigenobu, Masato Suzuki, Emiko Rimbara, Keigo Shibayama, Anders Øverby, Masahiko Nakamura
We present here the draft whole-genome shotgun sequence of an uncultivated strain SNTW101 of Helicobacter suis, which has been maintained in the stomachs of mice. This strain was originally isolated from gastric biopsy specimens of a urea breath test-negative Japanese patient suffering from nodular gastritis.
2016: Genome Announcements
Lilach Iasur-Kruh, Vered Naor, Tirtza Zahavi, Matthew J Ballinger, Rakefet Sharon, Wyatt E Robinson, Steve J Perlman, Einat Zchori-Fein
The planthopper Hyalesthes obsoletus (Hemiptera: Cixiidae) is an important vector of phytoplasma diseases in grapevine. In the current study, the bacterial community compositions of symbionts of this insect were examined. Two dominant bacterial lineages were identified by mass sequencing: the obligate symbiont Candidatus Sulcia, and a facultative symbiont that is closely related to Pectobacterium sp. and to BEV, a cultivable symbiont of another phytoplasma vector, the leafhopper Euscelidius variegatus. In addition, one bacterium was successfully isolated in this study - a member of the family Xanthomonadaceae that is most closely related to the genus Dyella...
September 4, 2016: Research in Microbiology
Ramona Marasco, Francesca Mapelli, Eleonora Rolli, Maria J Mosqueira, Marco Fusi, Paola Bariselli, Muppala Reddy, Ameur Cherif, George Tsiamis, Sara Borin, Daniele Daffonchio
Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities...
2016: Frontiers in Microbiology
Alyce Taylor-Brown, Nathan L Bachmann, Nicole Borel, Adam Polkinghorne
BACKGROUND: Recent molecular studies have revealed considerably more diversity in the phylum Chlamydiae than was previously thought. Evidence is growing that many of these novel chlamydiae may be important pathogens in humans and animals. A significant barrier to characterising these novel chlamydiae is the requirement for culturing. We recently identified a range of novel uncultured chlamydiae in captive snakes in Switzerland, however, nothing is known about their biology. Using a metagenomics approach, the aim of this study was to characterise the genome of a novel chlamydial taxon from the choana of a captive snake...
2016: BMC Genomics
J H L Lessa, A M Araujo, G N T Silva, L R G Guilherme, G Lopes
Soil management may affect selenium (Se) adsorption capacity. This study investigated adsorption and desorption of Se (VI) in selected Brazilian soils from the Cerrado biome, an area of ever increasing importance for agriculture expansion in Brazil. Soil samples were collected from cultivated and uncultivated soils, comprising clayed and sandy soils. Following chemical and mineralogical characterization, soil samples were subjected to Se adsorption and desorption tests. Adsorption was evaluated after a 72-h reaction with increasing concentrations of Se (0-2000 μg L(-1)) added as Na2SeO4 in a NaCl electrolyte solution (pH 5...
December 2016: Chemosphere
Jikai Lei, Yanni Sun
MOTIVATION: Clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) allows more specific and efficient gene editing than all previous genetic engineering systems. These exciting discoveries stem from the finding of the CRISPR system being an adaptive immune system that protects the prokaryotes against exogenous genetic elements such as phages. Despite the exciting discoveries, almost all knowledge about CRISPRs is based only on microorganisms that can be isolated, cultured and sequenced in labs...
September 1, 2016: Bioinformatics
Janetta R Hakovirta, Samantha Prezioso, David Hodge, Segaran P Pillai, Linda M Weigel
Analysis of 16S ribosomal RNA (rRNA) genes is important in phylogenetic classification of known and novel bacterial genera and species and for detection of uncultivable bacteria. PCR amplification of 16S rRNA genes with universal primers produces a mixture of amplicons from all rRNA operons in the genome, and the sequence data is generally a consensus sequence. We describe here valuable data that is missing from consensus sequences, variable effects on sequence data generated from non-identical 16S rRNA amplicons, and the appearance of data displayed by different sequence software...
August 31, 2016: Journal of Clinical Microbiology
Sumit Handa, Blair G Paul, Jeffery F Miller, David L Valentine, Partho Ghosh
BACKGROUND: Diversity-generating retroelements (DGRs) provide organisms with a unique means for adaptation to a dynamic environment through massive protein sequence variation. The potential scope of this variation exceeds that of the vertebrate adaptive immune system. DGRs were known to exist only in viruses and bacteria until their recent discovery in archaea belonging to the 'microbial dark matter', specifically in organisms closely related to Nanoarchaeota. However, Nanoarchaeota DGR variable proteins were unassignable to known protein folds and apparently unrelated to characterized DGR variable proteins...
2016: BMC Structural Biology
Alexandra S Tauzin, Elisabeth Laville, Yao Xiao, Sébastien Nouaille, Pascal Le Bourgeois, Stéphanie Heux, Jean-Charles Portais, Magali Remaud-Simeon, Pierre Monsan, Eric C Martens, Gabrielle Potocki-Veronese, Florence Bordes
In prominent gut Bacteroides strains, sophisticated strategies have been evolved to achieve the complete degradation of dietary polysaccharides such as xylan, which is one of the major components of the plant cell wall. Polysaccharide Utilization Loci (PULs) consist of gene clusters encoding different proteins with a vast arsenal of functions, including carbohydrate binding, transport and hydrolysis. Transport is often attributed to TonB-dependent transporters, although major facilitator superfamily (MFS) transporters have also been identified in some PULs...
August 30, 2016: Molecular Microbiology
Laura A Hug, Brett J Baker, Karthik Anantharaman, Christopher T Brown, Alexander J Probst, Cindy J Castelle, Cristina N Butterfield, Alex W Hernsdorf, Yuki Amano, Kotaro Ise, Yohey Suzuki, Natasha Dudek, David A Relman, Kari M Finstad, Ronald Amundson, Brian C Thomas, Jillian F Banfield
The tree of life is one of the most important organizing principles in biology(1). Gene surveys suggest the existence of an enormous number of branches(2), but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships(3-5) or on the known, well-classified diversity of life with an emphasis on eukaryotes(6). These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments...
2016: Nature Microbiology
Takahiro Hosokawa, Yoshiko Ishii, Naruo Nikoh, Manabu Fujie, Nori Satoh, Takema Fukatsu
Diverse organisms are associated with obligate microbial mutualists. How such essential symbionts have originated from free-living ancestors is of evolutionary interest. Here we report that, in natural populations of the stinkbug Plautia stali, obligate bacterial mutualists are evolving from environmental bacteria. Of six distinct bacterial lineages associated with insect populations, two are uncultivable with reduced genomes, four are cultivable with non-reduced genomes, one uncultivable symbiont is fixed in temperate populations, and the other uncultivable symbiont coexists with four cultivable symbionts in subtropical populations...
2016: Nature Microbiology
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