Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another

Distribution and Demography of Antarctic Krill and Salps in the Atlantic Sector of the Southern Ocean during Austral Summer 2021–2022

The study aimed to investigate krill (Euphausia superba) and salp (Salpa thompsoni) populations in the Atlantic sector of the Southern Ocean in January and February 2022. Samples were obtained to measure the abundance, biomass and distribution patterns of krill and salp. Sex differences and feeding habits of the Antarctic krill were determined. The dependence of the physiological state of the studied aquatic organisms on changes in environmental parameters was analyzed. Current data on the association of the dynamics of hydrometeorological parameters and processes with the distribution of chlorophyll a, krill, and salp were obtained. It was established that, at numerous stations, the biomass of salps prevailed over krill. The result indicates the replacement of the Antarctic krill populations by gelatinous zooplankton. The obtained results allow assessment of the biological resource potential in the studied region based on the analysis of the samples collected

Oligohexamethylene Guanidine Derivative as a Means to Prevent Biological Fouling of a Polymer-Based Composite Optical Oxygen Sensor

The use of biocidal agents is a common practice for protection against biofouling in biomass-rich environments. In this paper, oligohexamethyleneguanidine (OHMG) polymer, known for its biocidal properties, was further modified with para-aminosalicylic acid (PAS) to enhance its properties against microorganisms coated with a lipid membrane. The structure of the product was confirmed by 1H NMR, 13C NMR, and FTIR spectroscopy. The values of the minimum inhibitory concentration (MIC) against Mycobacterium smegmatis ATCC 607 and Pseudomonas chlororaphis 449 were found to be 1.40 and 1.05 μg/mL, respectively. The synthesized substance was used as an additive to the polymer matrix of the composite optical oxygen sensor material. A series of samples with different contents of OHMG-PAS was prepared using a co-dissolution method implying the fabrication of a coating from a solution containing both polymers. It turned out that the mutual influence of the components significantly affects the distribution of the indicator in the matrix, surface morphology, and contact angle. The optimal polymer content turned out to be wt.3%, at which point the water contact angle reaches almost 122°, and the fouling rate decreases by almost five times, which is confirmed by both the respiratory MTT assay and confocal microscopy with staining. This opens up prospects for creating stable and biofouling-resistant sensor elements for use in air tanks or seawater

A Two-Mediator System Based on a Nanocomposite of Redox-Active Polymer Poly(thionine) and SWCNT as an Effective Electron Carrier for Eukaryotic Microorganisms in Biosensor Analyzers

Electropolymerized thionine was used as a redox-active polymer to create a two-mediated microbial biosensor for determining biochemical oxygen demand (BOD). The electrochemical characteristics of the conducting system were studied by cyclic voltammetry and electrochemical impedance spectroscopy. It has been shown that the most promising in terms of the rate of interaction with the yeast B. adeninivorans is the system based on poly(thionine), single-walled carbon nanotubes (SWCNT), and neutral red (kint = 0.071 dm3/(g·s)). The biosensor based on this system is characterized by high sensitivity (the lower limit of determined BOD concentrations is 0.4 mgO2/dm3). Sample analysis by means of the developed analytical system showed that the results of the standard dilution method and those using the biosensor differed insignificantly. Thus, for the first time, the fundamental possibility of effectively using nanocomposite materials based on SWCNT and the redox-active polymer poly(thionine) as one of the components of two-mediator systems for electron transfer from yeast microorganisms to the electrode has been shown. It opens up prospects for creating stable and highly sensitive electrochemical systems based on eukaryotes

Coordination to Imidazole Ring Switches on Phosphorescence of Platinum Cyclometalated Complexes: The Route to Selective Labeling of Peptides and Proteins via Histidine Residues

In this study, we have shown that substitution of chloride ligand for imidazole (Im) ring in the cyclometalated platinum complex Pt­(phpy)­(PPh₃)Cl (<b>1</b>; phpy, 2-phenylpyridine; PPh₃, triphenylphosphine), which is nonemissive in solution, switches on phosphorescence of the resulting compound. Crystallographic and nuclear magnetic resonance (NMR) spectroscopic studies of the substitution product showed that the luminescence ignition is a result of Im coordination to give the [Pt­(phpy)­(Im)­(PPh₃)]Cl complex. The other imidazole-containing biomolecules, such as histidine and histidine-containing peptides and proteins, also trigger luminescence of the substitution products. The complex <b>1</b> proved to be highly selective toward the imidazole ring coordination that allows site-specific labeling of peptides and proteins with <b>1</b> using the route, which is orthogonal to the common bioconjugation schemes via lysine, aspartic and glutamic acids, or cysteine and does not require any preliminary modification of a biomolecule. The utility of this approach was demonstrated on (i) site-specific modification of the ubiquitin, a small protein that contains only one His residue in its sequence, and (ii) preparation of nonaggregated HSA-based Pt phosphorescent probe. The latter particles easily internalize into the live HeLa cells and display a high potential for live-cell phosphorescence lifetime imaging (PLIM) as well as for advanced correlation PLIM and FLIM experiments

Fast and simple tool for the quantification of biofilm-embedded cells sub-populations from fluorescent microscopic images

<div><p>Fluorescent staining is a common tool for both quantitative and qualitative assessment of pro- and eukaryotic cells sub-population fractions by using microscopy and flow cytometry. However, direct cell counting by flow cytometry is often limited, for example when working with cells rigidly adhered either to each other or to external surfaces like bacterial biofilms or adherent cell lines and tissue samples. An alternative approach is provided by using fluorescent microscopy and confocal laser scanning microscopy (CLSM), which enables the evaluation of fractions of cells subpopulations in a given sample. For the quantitative assessment of cell fractions in microphotographs, we suggest a simple two-step algorithm that combines single cells selection and the statistical analysis. To facilitate the first step, we suggest a simple procedure that supports finding the balance between the detection threshold and the typical size of single cells based on objective cell size distribution analysis. Based on a series of experimental measurements performed on bacterial and eukaryotic cells under various conditions, we show explicitly that the suggested approach effectively accounts for the fractions of different cell sub-populations (like the live/dead staining in our samples) in all studied cases that are in good agreement with manual cell counting on microphotographs and flow cytometry data. This algorithm is implemented as a simple software tool that includes an intuitive and user-friendly graphical interface for the initial adjustment of algorithm parameters to the microphotographs analysis as well as for the sequential analysis of homogeneous series of similar microscopic images without further user intervention. The software tool entitled <i>BioFilmAnalyzer</i> is freely available online at <a href="https://bitbucket.org/rogex/biofilmanalyzer/downloads/" target="_blank">https://bitbucket.org/rogex/biofilmanalyzer/downloads/</a>.</p></div

VEGF- and VEGFR2-Targeted Liposomes for Cisplatin Delivery to Glioma Cells

Targeted delivery of anticancer drugs to brain tumors, especially glioblastoma multiforme, which is the most frequent and aggressive type, is one of the important objectives in nanomedicine. Vascular endothelial growth factor (VEGF) and its receptor type II (VEGFR2) are promising targets because they are overexpressed by not only core tumor cells but also by migrated glioma cells, which are responsible for resistance and rapid progression of brain tumors. The purpose of the present study was to develop the liposomal drug delivery system combining enhanced loading capacity of cisplatin and high binding affinity to glioma cells. This was achieved by using of highly soluble cisplatin analogue, <i>cis</i>-diamminedinitratoplatinum­(II), and antibodies against the native form of VEGF or VEGFR2 conjugated to liposome surface. The developed drug delivery system revealed sustained drug release profile, high affinity to antigens, and increased uptake by glioma C6 and U-87 MG cells. Pharmacokinetic study on glioma C6-bearing rats revealed prolonged blood circulation time of the liposomal formulation. The above features enabled the present drug delivery system to overcome both poor pharmacokinetics typical for platinum formulations and low loading capacity typical for conventional liposomal cisplatin formulations

Evaluation of the Caco-2 non-viable cells fraction by using <i>BioFilmAnalyzer</i> software exemplified for 12 microscopic images.

<p>The percentage of red-stained cells quantified by the <i>BioFilmAnalyzer</i> software is shown in each panel.</p

<i>S</i>. <i>aureus</i> cells count and live/dead ratio dependence on the image analysis threshold <i>T</i>.

<p>Full lines show the linear regression lines, while dashed line shows the ideal counting line as determined by the manual analysis performed by several experts in visual microscopic image analysis. Panels A-C show data for the 12 images presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193267#pone.0193267.g002" target="_blank">Fig 2</a>. Panels D-F show data for the 115 microscopic images taken randomly from different experiments with various imaging conditions.</p