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https://www.readbyqxmd.com/read/28821183/improvement-of-the-threespine-stickleback-genome-using-a-hi-c-based-proximity-guided-assembly
#1
Catherine L Peichel, Shawn T Sullivan, Ivan Liachko, Michael A White
Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28820461/thermal-response-analysis-of-phospholipid-bilayers-using-ellipsometric-techniques
#2
Carmen M González-Henríquez, Vanessa A Villegas-Opazo, Dallits H Sagredo-Oyarce, Mauricio A Sarabia-Vallejos, Claudio A Terraza
Biomimetic planar artificial membranes have been widely studied due to their multiple applications in several research fields. Their humectation and thermal response are crucial for reaching stability; these characteristics are related to the molecular organization inside the bilayer, which is affected by the aliphatic chain length, saturations, and molecule polarity, among others. Bilayer stability becomes a fundamental factor when technological devices are developed-like biosensors-based on those systems...
August 18, 2017: Biosensors
https://www.readbyqxmd.com/read/28820423/-risk-factors-and-special-aspects-forgenital-tuberculosis-diagnostics
#3
G Lortkipanidze, N Kintraia, K Vacharadze, F Tsaava
Was examined 453 women, who applied to National Center for Tuberculosis and Lung Diseases for genital tuberculosis diagnostics. GTB was detected in 289 cases, in 164 cases GTB results was negative (control group). In 10 cases GTB was combined with pulmonary tuberculosis (OR-1,13). Risk factors are previous diseases of female reproductive organs- intracellular infection (OR-1,08), sexually transmitted diseases (OR-1,25), nonspecific inflammatory diseases (OR-1,009), interruption of pregnancy (OR-1,26), artificial abortions (OR-1,11), the most specific signs of Genital Tuberculosis is a pain in the stomach area (P-0,023), dysmenorrhoea (P-0,00001), intestinal obstruction (P-0,0006), heat (P-0,00001), liquid presence in posterior vault (P-0,007), hydrosalpinx (P-0,00001), Fallopian tubes deformation (P-0,000003), oophoritic cyst (P-0,067), adhesive process in small pelvis (P-0,0006)...
July 2017: Georgian Medical News
https://www.readbyqxmd.com/read/28820204/droplet-microfluidics-for-synthetic-biology
#4
REVIEW
Philip C Gach, Kosuke Iwai, Peter W Kim, Nathan J Hillson, Anup K Singh
Synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility...
August 18, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28820140/clarity-of-objectives-and-working-principles-enhances-the-success-of-biomimetic-programs
#5
Jonas Wolff, David Wells, Chris Reid, Sean John Blamires
Biomimetics, the transfer of functional principles from living systems into product designs, is increasingly being utilized by engineers. Nevertheless, recurring problems must be overcome if it is to avoid becoming a short-lived fad. Here we assess the efficiency and suitability of methods typically employed by examining three flagship examples of biomimetic design approaches from different disciplines: (1) the creation of gecko-inspired adhesives; (2) the synthesis of spider silk, and (3) the derivation of computer algorithms from natural self-organizing systems...
August 18, 2017: Bioinspiration & Biomimetics
https://www.readbyqxmd.com/read/28820023/use-of-oxalic-acid-as-inducer-in-photocatalytic-oxidation-of-cresol-red-in-aqueous-solution-under-natural-and-artificial-light
#6
N Seraghni, I Ghoul, I Lemmize, A Reguig, N Debbache, T Sehili
This work was carried out in the field of water treatment using advanced oxidation processes (AOPs), especially photolysis of carboxylic acid leads to the formation in situ of hydroxyl radical ((.)OH). Cresol red (CR) degradation induced by organic acids/UV system was investigated in aqueous solution. The preliminary study of CR-organic acid mixture in the dark and at room temperature allowed confirming the absence of interaction under our experimental conditions. However, up on irradiation at 365 nm the percentage of elimination of CR was 89% after 5 hours of irradiation...
August 18, 2017: Environmental Technology
https://www.readbyqxmd.com/read/28817256/tailorable-exciton-transport-in-doped-peptide-amphiphile-assemblies
#7
Lee A Solomon, Matthew E Sykes, Yimin A Wu, Richard D Schaller, Gary P Wiederrecht, Harry Christopher Fry
Light-harvesting biomaterials are an attractive target in photovoltaics, photocatalysis, and artificial photosynthesis. Through peptide self-assembly, complex nanostructures can be engineered to study the role of chromophore organization during light absorption and energy transport. To this end, we demonstrate the one-dimensional transport of excitons along naturally occurring, light-harvesting, Zn-protoporphyrin IX chromophores within self-assembled peptide-amphiphile nanofibers. The internal structure of the nanofibers induces packing of the porphyrins into linear chains...
August 17, 2017: ACS Nano
https://www.readbyqxmd.com/read/28813413/polylox-barcoding-reveals-haematopoietic-stem-cell-fates-realized-in-vivo
#8
Weike Pei, Thorsten B Feyerabend, Jens Rössler, Xi Wang, Daniel Postrach, Katrin Busch, Immanuel Rode, Kay Klapproth, Nikolaus Dietlein, Claudia Quedenau, Wei Chen, Sascha Sauer, Stephan Wolf, Thomas Höfer, Hans-Reimer Rodewald
Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system...
August 16, 2017: Nature
https://www.readbyqxmd.com/read/28811818/prototype-generation-using-self-organizing-maps-for-informativeness-based-classifier
#9
Leandro Juvêncio Moreira, Leandro A Silva
The k nearest neighbor is one of the most important and simple procedures for data classification task. The kNN, as it is called, requires only two parameters: the number of k and a similarity measure. However, the algorithm has some weaknesses that make it impossible to be used in real problems. Since the algorithm has no model, an exhaustive comparison of the object in classification analysis and all training dataset is necessary. Another weakness is the optimal choice of k parameter when the object analyzed is in an overlap region...
2017: Computational Intelligence and Neuroscience
https://www.readbyqxmd.com/read/28809953/monitoring-health-and-reproductive-status-of-olms-proteus-anguinus-by-ultrasound
#10
Susanne Holtze, Maja Lukač, Ivan Cizelj, Frank Mutschmann, Claudia Anita Szentiks, Dušan Jelić, Robert Hermes, Frank Göritz, Stanton Braude, Thomas Bernd Hildebrandt
The olm (Proteus anguinus) is a troglomorphic, neotenous amphibian with extraordinary life expectancy and unique adaptations that deserve further investigation. A low reproductive rate and habitat decline render it threatened by extinction. Establishing captive populations for maintenance and artificial breeding may one day become crucial to the species. Longitudinal, in-vivo assessment of inner organs is invaluable to our understanding of reproductive physiology, health, and behavior. Using ultrasound, we measured heart rate and assessed health and reproductive status of 13 captive olms at Zagreb Zoo...
2017: PloS One
https://www.readbyqxmd.com/read/28808741/stable-isotope-raman-microspectroscopy-for-the-analysis-of-soil-organic-matter
#11
Alexandra C Wiesheu, Ramona Brejcha, Carsten W Mueller, Ingrid Kögel-Knabner, Martin Elsner, Reinhard Niessner, Natalia P Ivleva
We examined the potential of stable-isotope Raman microspectroscopy (SIRM) for the evaluation of differently enriched (13)C-labeled humic acids as model substances for soil organic matter (SOM). The SOM itself can be linked to the soil water holding capacity. Therefore, artificial humic acids (HA) with known isotopic compositions were synthesized and analyzed by means of SIRM. By performing a pregraphitization, a suitable analysis method was developed to cope with the high fluorescence background. Results were verified against isotope ratio mass spectrometry (IRMS)...
August 14, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28808674/in-situ-generated-tribomaterial-in-metal-metal-contacts-current-understanding-and-future-implications-for-implants
#12
N Espallargas, A Fischer, A Igual Muñoz, S Mischler, M A Wimmer
Artificial hip joints operate in aqueous biofluids that are highly reactive towards metallic surfaces. The reactivity at the metal interface is enhanced by mechanical interaction due to friction, which can change the near-surface structure of the metal and surface chemistry. There are now several reports in the literature about the in-situ generation of reaction films and tribo-metallurgical transformations on metal-on-metal hip joints. This paper summarizes current knowledge and provides a mechanistic interpretation of the surface chemical and metallurgical phenomena...
June 2017: Biotribology (Oxf)
https://www.readbyqxmd.com/read/28808555/phenotypic-convergence-of-artificially-reared-and-wild-trout-is-mediated-by-shape-plasticity
#13
Jorge Ruben Sánchez-González, Alfredo G Nicieza
Phenotypic plasticity can be viewed as the first level of defense of organism homeostasis against environmental stress and therefore represents the potential to deal with rapid environmental changes. Transitions between low complexity, artificial environments and complex, natural habitats can promote phenotypic plasticity. Here, we conducted an experimental introduction with juvenile brown trout to evaluate the plasticity of shape in response to a transition between contrasting environments. We released 202 juvenile trout reared under hatchery conditions in a natural stream and analyzed changes in shape and morphological variability after 5 months...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28808546/characterization-of-measurement-errors-using-structure-from-motion-and-photogrammetry-to-measure-marine-habitat-structural-complexity
#14
Mitch Bryson, Renata Ferrari, Will Figueira, Oscar Pizarro, Josh Madin, Stefan Williams, Maria Byrne
Habitat structural complexity is one of the most important factors in determining the makeup of biological communities. Recent advances in structure-from-motion and photogrammetry have resulted in a proliferation of 3D digital representations of habitats from which structural complexity can be measured. Little attention has been paid to quantifying the measurement errors associated with these techniques, including the variability of results under different surveying and environmental conditions. Such errors have the potential to confound studies that compare habitat complexity over space and time...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28803237/atf3-dependent-regulation-of-egr1-in-vitro-and-in-vivo
#15
Ilona Schoen, Sabine Koitzsch
BACKGROUND/AIMS: Activating transcription factor 3 (ATF3) and early growth response protein 1 (EGR1) are reported to interact, but their use as prognostic factors in cancer is discussed controversially. METHODS: We measured ATF3 and EGR1 gene expression changes in human mini-organ cultures (MOCs) of healthy nasal epithelia, UM-SCC-22B, and FADUDD cells after acid reflux exposure. Next, ATF3 and EGR1 gene expression was analysed in tumour tissues and related to the median expression of autologous reference tissue samples...
August 12, 2017: ORL; Journal for Oto-rhino-laryngology and its related Specialties
https://www.readbyqxmd.com/read/28802224/speciation-of-the-trivalent-f-elements-eu-iii-and-cm-iii-in-digestive-media
#16
Claudia Wilke, Astrid Barkleit, Thorsten Stumpf, Atsushi Ikeda-Ohno
In case radioactive materials are released into the environment, their incorporation into our digestive system would be a significant concern. Trivalent f-elements, i.e., trivalent actinides and lanthanides, could potentially represent a serious health risk due to their chemo- and radiotoxicity, nevertheless the biochemical behavior of these elements are mostly unknown even to date. This study, therefore, focuses on the chemical speciation of trivalent f-elements in the human gastrointestinal tract. To simulate the digestive system artificial digestive juices (saliva, gastric juice, pancreatic juice and bile fluid) were prepared...
August 4, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28800824/assessing-the-antimicrobial-potential-of-aerosolised-electrochemically-activated-solutions-ecas-for-reducing-the-microbial-bio-burden-on-fresh-food-produce-held-under-cooled-or-cold-storage-conditions
#17
R M S Thorn, J Pendred, D M Reynolds
The main aim of this study was to assess the antimicrobial efficacy of electrochemically activated fog (ECAF) for reducing the microbial bio-burden on artificially inoculated fresh produce held under cooled (cucumber and vine tomatoes) or cold (rocket and broccoli) storage conditions. The ECAF treatment (1100 ± 5 mV ORP; 50 ± 5 mg L(-1) free chlorine; 2.7 ± 0.1 pH) resulted in a significant log reduction in the potential pathogen E. coli recovered from rocket (2.644 Log10 CFU g(-1)), broccoli (4...
December 2017: Food Microbiology
https://www.readbyqxmd.com/read/28799694/patient-with-a-total-artificial-heart-maintained-on-outpatient-dialysis-while-listed-for-combined-organ-transplant-a-single-center-experience
#18
Ramy M Hanna, Huma Hasnain, Mohammad Kamgar, Mina Hanna, Raffi Minasian, James Wilson
Advanced mechanical circulatory support is increasingly being used with more sophisticated devices that can deliver pulsatile rather than continuous flow. These devices are more portable as well, allowing patients to await cardiac transplantation in an outpatient setting. It is known that patients with renal failure are at increased risk for developing worsening acute kidney injury during implantation of a ventricular assist device (VAD) or more advanced modalities like a total artificial heart (TAH). Dealing with patients who have an implanted TAH who develop renal failure has been a challenge with the majority of such patients having to await a combined cardiac and renal transplant prior to transition to outpatient care...
August 11, 2017: Hemodialysis International
https://www.readbyqxmd.com/read/28796509/predicting-thermal-behavior-of-secondary-organic-aerosols
#19
John H Offenberg, Michael Lewandowski, Tadeusz E Kleindienst, Kenneth S Docherty, Mohammed Jaoui, Jonathan Krug, Theran P Riedel, David A Olson
Volume concentrations of secondary organic aerosol (SOA) are measured in 139 steady-state, single precursor hydrocarbon oxidation experiments after passing through a temperature controlled inlet. The response to change in temperature is well predicted through a feedforward Artificial Neural Network. The most parsimonious model, as indicated by Akaike's Information Criterion, Corrected (AIC,C), utilizes 11 input variables, a single hidden layer of 4 tanh activation function nodes, and a single linear output function...
August 10, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28794937/label-free-direct-electrical-detection-of-a-histidine-rich-protein-with-sub-femtomolar-sensitivity-using-an-organic-field-effect-transistor
#20
Tsukuru Minamiki, Yui Sasaki, Shizuo Tokito, Tsuyoshi Minami
There is a growing interest in achieving sensor systems to enable on-site testing of biomarkers. Herein, a new strategy for highly sensitive protein detection at sub-femtomolar levels without any labelling has been demonstrated by using an organic field-effect transistor (OFET). An artificial histidine-rich protein receptor (Ni(II)-nitrilotriacetic acid complex, Ni(II)-nta) functionalizes a detection portion (i.e. an extended-gate electrode) of the fabricated OFET device. The OFET responds electrically and selectively to a target analyte (bovine serum albumin), meaning that the binding processes at the Ni(II)-nta on the extended-gate electrode for the analyte affect the field-effect properties of the device...
August 2017: ChemistryOpen
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