Pooled multicolour tagging for visualizing subcellular protein dynamics

Imaging-based methods are widely used for studying the subcellular localization of proteins in living cells. While routine for individual proteins, global monitoring of protein dynamics following perturbation typically relies on arrayed panels of fluorescently tagged cell lines, limiting throughput and scalability. Here, we describe a strategy that combines high-throughput microscopy, computer vision and machine learning to detect perturbation-induced changes in multicolour tagged visual proteomics cell (vpCell) pools. We use genome-wide and cancer-focused intron-targeting sgRNA libraries to generate vpCell pools and a large, arrayed collection of clones each expressing two different endogenously tagged fluorescent proteins. Individual clones can be identified in vpCell pools by image analysis using the localization patterns and expression level of the tagged proteins as visual barcodes, enabling simultaneous live-cell monitoring of large sets of proteins. To demonstrate broad applicability and scale, we test the effects of antiproliferative compounds on a pool with cancer-related proteins, on which we identify widespread protein localization changes and new inhibitors of the nuclear import/export machinery. The time-resolved characterization of changes in subcellular localization and abundance of proteins upon perturbation in a pooled format highlights the power of the vpCell approach for drug discovery and mechanism-of-action studies.

Metagenome-derived virus-microbe ratios across ecosystems

It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa-200 µm size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by ~13 fold and in plankton from marine and saline waters by ~2-4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.

Machine Learning Differentiation of Autism Spectrum Sub-Classifications

PURPOSE

Disorders on the autism spectrum have characteristics that can manifest as difficulties with communication, executive functioning, daily living, and more. These challenges can be mitigated with early identification. However, diagnostic criteria has changed from DSM-IV to DSM-5, which can make diagnosing a disorder on the autism spectrum complex. We evaluated machine learning to classify individuals as having one of three disorders of the autism spectrum under DSM-IV, or as non-spectrum.

METHODS

We employed machine learning to analyze retrospective data from 38,560 individuals. Inputs encompassed clinical, demographic, and assessment data.

RESULTS

The algorithm achieved AUROCs ranging from 0.863 to 0.980. The model correctly classified 80.5% individuals; 12.6% of individuals from this dataset were misclassified with another disorder on the autism spectrum.

CONCLUSION

Machine learning can classify individuals as having a disorder on the autism spectrum or as non-spectrum using minimal data inputs.

Expanding the molecular and morphological diversity of Apusomonadida, a deep-branching group of gliding bacterivorous protists

Apusomonads are cosmopolitan bacterivorous biflagellate protists usually gliding on freshwater and marine sediment or wet soils. These nanoflagellates form a sister lineage to opisthokonts and may have retained ancestral features helpful to understanding the early evolution of this large supergroup. Although molecular environmental analyses indicate that apusomonads are genetically diverse, few species have been described. Here, we morphologically characterize 11 new apusomonad strains. Based on molecular phylogenetic analyses of the rRNA gene operon, we describe four new strains of the known species Multimonas media, Podomonas capensis, Apusomonas proboscidea, and Apusomonas australiensis, and rename Thecamonas oxoniensis as Mylnikovia oxoniensis n. gen., n. comb. Additionally, we describe four new genera and six new species: Catacumbia lutetiensis n. gen. n. sp., Cavaliersmithia chaoae n. gen. n. sp., Singekia montserratensis n. gen. n. sp., Singekia franciliensis n. gen. n. sp., Karpovia croatica n. gen. n. sp., and Chelonemonas dolani n. sp. Our comparative analysis suggests that apusomonad ancestor was a fusiform biflagellate with a dorsal pellicle, a plastic ventral surface, and a sleeve covering the anterior flagellum, that thrived in marine, possibly oxygen-poor, environments. It likely had a complex cell cycle with dormant and multiple fission stages, and sex. Our results extend known apusomonad diversity, allow updating their taxonomy, and provide elements to understand early eukaryotic evolution.

Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies

The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the 'Opisthosporidia hypothesis'). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium, suggested that the aphelids are sister to fungi (the 'Aphelida+Fungi hypothesis'). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (A. insulamus and A. tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida+Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid-fungal split and the remaining 12 likely evolved de novo, constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favour of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia.

OUP accepted manuscript

Proliferation of selfish genetic elements has led to significant genome size expansion in plastid and mitochondrial genomes of various eukaryotic lineages. Within the red algae, such expansion events are only known in the plastid genomes of the Proteorhodophytina, a highly diverse group of mesophilic microalgae. By contrast, they have never been described in the much understudied red algal mitochondrial genomes. Therefore, it remains unclear how widespread such organellar genome expansion events are in this eukaryotic phylum. Here, we describe new mitochondrial and plastid genomes from 25 red algal species, thereby substantially expanding the amount of organellar sequence data available, especially for Proteorhodophytina, and show that genome expansions are common in this group. We confirm that large plastid genomes are limited to the classes Rhodellophyceae and Porphyridiophyceae, which, in part, are caused by lineage-specific expansion events. Independently expanded mitochondrial genomes—up to three times larger than typical red algal mitogenomes—occur across Proteorhodophytina classes and a large shift toward high GC content occurred in the Stylonematophyceae. Although intron proliferation is the main cause of plastid and mitochondrial genome expansion in red algae, we do not observe recent intron transfer between different organelles. Phylogenomic analyses of mitochondrial and plastid genes from our expanded taxon sampling yielded well-resolved phylogenies of red algae with strong support for the monophyly of Proteorhodophytina. Our work shows that organellar genomes followed different evolutionary dynamics across red algal lineages.

Chemical-vapor deposited ultra-fast diamond detectors for temporal measurements of ion bunches

This article reports on the development of thin diamond detectors and their characterization for their application in temporal profile measurements of subnanosecond ion bunches. Two types of diamonds were used: a 20 μm thin polycrystalline chemical vapor deposited (CVD) diamond and a membrane with a thickness of (5 ± 1) μm etched out of a single crystal (sc) CVD diamond. The combination of a small detector electrode and an impedance matched signal outlet leads to excellent time response properties with a signal pulse resolution (FWHM) of τ = (113 ± 11) ps. Such a fast diamond detector is a perfect device for the time of flight measurements of MeV ions with bunch durations in the subnanosecond regime. The scCVD diamond membrane detector was successfully implemented within the framework of the laser ion generation handling and transport project, in which ion beams are accelerated via a laser-driven source and shaped with conventional accelerator technology. The detector was used to measure subnanosecond proton bunches with an intensity of 10⁸ protons per bunch.

DNA display of fragment pairs as a tool for the discovery of novel biologically active small molecules

A focused library for Hsp70 was prepared from fragments identified from an array combinatorially pairing two libraries of small molecule fragments. Screening of the focus library yielded high affinity ligand to Hsp70.

Fragment-based lead discovery has proven to be a powerful method in the drug discovery process. The combinatorial output that is accessible by combining fragments is very attractive; however, identifying fragment pairs that bind synergistically and linking them productively can be challenging. Several technologies have now been established to prepare and screen nucleic acid-encoded libraries (ssDNA, dsDNA, PNA), and it has been shown that pairs of molecules combined by hybridization can bind synergistically to a target. Herein we apply this concept to combinatorially pair two libraries of small molecule fragments, use the fittest fragments supplemented with closely related analogs to build a focused library covalently linking the fragments with different spacers, and apply this strategy to the discovery of a potent ligand for Hsp70.

Lymphatic microvessels density, VEGF-C, and VEGFR-3 expression in 25 cases of breast invasive lobular carcinoma

Invasive lobular carcinoma (ILC) is the second most common type of invasive breast cancer, having distinct morphologically but also prognostic and therapeutic features. This type of breast cancer shows a higher rate of multiple metastases with a more frequent axillary-lymph-node involvement. Related to these dissemination and metastatic features, we aimed to study the immunohistochemical expression of D2-40, VEGF-C and VEGFR-3 in 25 cases of ILCs stratified according to the histopathological and molecular classification. Regardless of histopathological or molecular subtype, the statistical tests proved that for ILC, the highest D2-40 lymphatic microvessels density (LMVD) was in the peritumoral areas. In classical subtype, the LMVD values were positively correlated with the degree of tumor differentiation and pTNM clinical stages and when these cases were classified based on the molecular criteria the highest recorded values were found in the luminal B subtype. In addition, regardless of the histopathological and molecular subtypes, the D2-40 LMVD varied in the same direction for both VEGF-C and VEGFR-3 categories, with the highest LMVD values recorded in those cases with the highest VEGF-C and VEGFR-3 reactivity, especially in the peritumoral areas. Considering only the molecular luminal A and B subtypes, we have noted that VEGF-C and VEGFR-3 expression was significantly higher in luminal A subtype compared to luminal B. This immunoprofile suggests the existence of a tumor type-specific lymphangiogenesis that may have certain prognostic and therapeutic implications.

Breast-conserving surgery in breast cancer

The breast cancer treatment is based nowadays on new surgical options: breast-conserving surgery, which applies at least for the first and second stage cancer, with radical intention. We have been practicing breast-conserving surgery for the last 16 years and we have performed 303 breast conserving operations from a total of 673. We recorded 12 local recurrences (3,96%) and 2 deaths due to cancer progression. Our protocol includes removal of the primary tumor with enough surrounding tissue to ensure negative margins of the resectable specimen, associated with axillary lymph-node dissection and postoperative breast irradiation. Our oncologist indicated chemotherapy on different postoperative conditions: tumor size, axillary lymph node involvement, patient's age, etc. The purpose of this paper is to emphasize our modest experience, nevertheless to draw the attention on important results, obtained by long-term monitoring of the patients who underwent breast-conserving surgery, in a two prospective protocols, and demonstrate the importance and applicability of breast conserving therapy. The conclusion of this study is that breast-conserving surgery followed by breast irradiation is reliable, as the results are similar with radical mastectomies; the main objective is to obtain a good cosmetic result, which depends on tumor size / breast size.

Breast invasive lobular carcinoma: a retrospective clinicopathologic study of 25 cases

Invasive lobular carcinoma (ILC) is the second most common type of invasive breast cancer, having distinct prognostic and biologic implications. As an objective of the present work, we analyzed the clinicopathologic characteristics and prognostic factor of this invasive breast cancer variant. Clinical and morphological data of 25 cases of ILC collected during 2006-2011 were reviewed. Histopathologically, 11 cases were of classic type, and the others were non-classic with solid and histiocytoid subtypes being mostly encountered. Overall the non-classic ILC type was diagnosed in more aged patients (with a median age at onset of 59 years), with a predominance for a more advanced tumor degree differentiation (78.5% as grade 2 and 3), in advanced pTNM stages (50% in stage III and IV), with 50% lymph node involvement and with over 70% ER and Her2 reactivity. Statistically, we found that for the solid variant prevailed a PR+ and Her2- status while in histiocytoid subtype the PR- and Her2+ immunoprofile was most encountered. We conclude that non-classic ILC type represents a distinct entity of invasive breast carcinoma with a worsen prognostic than the conventional ILC type.

Products Derived from Catalytic Oxidation of Methylene Blue

It was established that the process of catalytic oxidation of methylene blue, at low concentrations (20 mg/L), i.e. in real solutions, gives sulfates and nitrates and new product, which can be categorized, in their vast majority, as impurities, probably got from the vacuum distillation unit, which make up for only ~ 10 % of methylene blue used in the experiment. Methylene blue adsorption at the interface occurs in real solutions. In case of performing the process at methylene blue concentration of 120 mg/L, hemi-micelles are adsorbed at the interface and the OH• radical acts more effectively due to the presence at the interface of a greater number of dye molecules.

Catalytic Oxidation of Methylene Blue

The intact activated carbon CAN-8, obtained from nutshells by activation with water vapours, in the presence of oxygen and at relatively low temperatures, possesses catalytic activity, caused by the presence of alkaline functional groups on its surface, as well as by the formation, in these experimental conditions, of the OH radical, which has a high oxidation potential. After 25 cycles of the process of methylene blue oxidation, the data of chromatographic analyses indicate the presence of three organic components in the solution.

Marinitoga litoralis sp. nov., a thermophilic, heterotrophic bacterium isolated from a coastal thermal spring on Île Saint-Paul, Southern Indian Ocean

A novel thermophilic, anaerobic and organotrophic bacterium, designated strain MC3T, was isolated from a coastal thermal spring on Île Saint-Paul in the Southern Indian Ocean. Cells of strain MC3T were motile rods, 0.8–1.0 μm wide and 1.0–2.4 μm long during exponential phase and up to 7.0 μm long during stationary phase. Strain MC3T was an anaerobic organotroph able to use diverse organic compounds. It was also able to reduce sulfur to sulfide. Growth was observed at temperatures ranging from 45 to 70 °C (optimum at 60 °C), between pH 5.5 and 7.5 (optimum at pH 6) and from 8 to 46 g NaCl l−1 (optimum at 26 g l−1). The total G+C content of the genomic DNA was 26.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain MC3T was affiliated with the genus Marinitoga within the order Thermotogales. It shared 94.4–95.7 % 16S rRNA gene sequence similarity with strains of other Marinitoga species; Marinitoga hydrogenitolerans was found to be the most closely related organism. Based on the data from the phylogenetic analysis and the physiological properties of the novel isolate, strain MC3T should be classified as a representative of a novel species, for which the name Marinitoga litoralis sp. nov. is proposed; the type strain is MC3T (=DSM 21709T =JCM 15581T).

Adsorption of Ammonia Ions and Ammonium from Aqueous Solutions on Modified Activated Carbons

The adsorption process of ammonia ions and ammonium from aqueous solutions on the intact activated carbon obtained from nutshells through activation with phosphoric acid and oxidized with H2O2 and later impregnated with salt containing Co2+, Ag+, Ni2+, Cu2+, has been investigated. The efficiency of ammonia ions and ammonium elimination from various water categories, using both activated carbon (the intact CAN-7 and CAN-7 oxidized with H2O2 and impregnated with Co2+, Ag+, Ni2+, Cu2+ ions) has been demonstrated.

Morphology and adhesion of human fibroblast cells cultured on bioactive polymer grafted ligament prosthesis

The anterior cruciate ligament (ACL) is the most important ligament for the knee stabilization. Unfortunately, it is also the most commonly injured. Synthetic polymers such as polyethylene terephthalate (PET) are widely used to fabricate ligament prostheses. In this study, we reported how to graft poly(sodium styrene sulfonate) (pNaSS) onto PET fabrics used to prepare ligament at a rate of about 4.5 x 10(-6) mol/g. In this study, we analyzed the morphology of human fibroblast MacCoy adhering onto the pNaSS grafted fabrics. Cell adhesion strength onto grafted and non grafted fabrics previously adsorbed with serum proteins was also evaluated after the application of shear stresses. Results showed that human fibroblast MacCoy adhered more strongly on the pNaSS grafted fabric compared to the non grafted one. The cell spreading is well on the grafted fiber even after the shear stress application: about 65% of cells remained adhered on the pNaSS grafted fabric as compared to 32% on the non grafted one. We concluded that Mac Coy human fibroblast cells strongly adhered onto the pNaSS functionalized PET prosthesis surface and showed a better spread cell morphology as well as a more homogeneous distribution than on the non grafted sample surfaces.

Layersome: Development and optimization of stable liposomes as drug delivery system

This paper describes the development of stable drug delivery systems named layersomes. The layersomes are conventional liposomes coated with one or multiple layers of biocompatible polyelectrolytes in order to stabilise their structure. The formulation strategy is based on an alternative coating procedure of positive poly(lysine) (pLL) and negative poly(glutamic acid) (pGA) polypeptides on initially charged small unilamellar liposomes (SUVs). The size distribution and the zeta potential of the final entity depend on the number of polyelectrolyte layers and the charge of the last coating layer. Morphological studies were achieved by flux cytometry and cryo electron microscopy. Release studies of encapsulated hydrophilic 5(6)-carboxyfluorescein (5,6CF) in the presence of Triton or ethanol showed an increased membrane resistance of the layersomes compared to classical SUVs. Finally, encapsulation of piroxicam (PX) was performed with success.

Radical graft polymerization of styrene sulfonate on poly(ethylene terephthalate) films for ACL applications: "grafting from" and chemical characterization

The purpose of this study is to develop a reliable method of functionalizing poly(ethylene terephthalate) with bioactive polymers to produce a "biointegrable" artificial anterior cruciate ligament. Radical graft polymerization of the sodium salt of styrene sulfonate (NaSS) onto poly(ethylene terephthalate) (PET) films was performed using the "grafting from" technique. Prior to the grafting, the surfaces of poly(ethylene terephthalate) films were activated by ozonation to generate peroxide and hydroperoxide reactive species on the PET film surfaces. The radical polymerization of NaSS was initiated by thermal decomposition of the hydroperoxides. The grafted PET surfaces were characterized by a toluidin blue colorimetric method, X-ray photoelectron spectroscopy, contact angle measurements, and atomic force microscopy. The influence of ozonation time, monomer concentration, and temperature on NaSS grafting ratios was examined. A total of 30 min of ozonation followed by grafting from a 15% NaSS solution at 70 degrees C for 90 min or more resulted in attachment of poly(NaSS) chains to the PET film surfaces.

Pulsed Doppler echocardiography in the diagnosis and estimation of severity of aortic insufficiency

Detection and estimation of the degree of chronic aortic insufficiency with pulsed Doppler echocardiography was attempted in 27 patients documented to have aortic insufficiency on aortography. Twenty-five patients had associated aortic stenosis or mitral valve disease, or both. A disturbed diastolic flow within the left ventricular outflow tract was recorded in all but one patient (Doppler sensitivity 96 percent). Aortic insufficiency was clinically undetected in three patients (clinical sensitivity 89 percent). In a small number of patients Doppler echocardiography also appeared to be highly specific for this disorder. The Doppler technique estimated the degree of aortic insufficiency by assessing the distribution of diastolic flow within the outflow tract and the body of the left ventricle. A significant correlation between the Doppler method and the angiographic estimation of aortic insufficiency was found (r = 0.88, p less than 0.01).

[The dumping syndrome. Surgical treatment]

Data are presented, from the specialized literature, in connection with the frequency of the dumping syndrome, and the methods for its correction. An analysis is made of indications and of surgical methods used for the correction of this syndrome in a total of 74 patients of which 32 were operated. Preference was given to sub-diaphragmatic troncular vagotomy and to re-positioning of the duodenum with efferent loop, or by gastro-duodenal interpositioning of a segment of jejunal loop in an-iso-peristaltic position. The results of these interventions are, as a rule, favourable, but some disturbances may occur, dependent on the development of peri-visceritis, loop dysfunction, or duodenal dysfunction, as well as gastro-oestrophageal reflux.