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Intertidal seaweeds must cope with a suite of stressors imposed by aerial exposure at low tide, including nutrient limitation due to emersion. Seaweeds can access nutrients only when submerged, so individuals living higher compared to lower on the shore may have adaptations allowing them to acquire sufficient amounts of nutrients to survive and maintain growth. Using a combination of observations and experiments, we aimed to identify intraspecific variation in nitrate uptake rates across the intertidal distribution of F. vesiculosus, as well as test for acclimation in response to a change in tide height. We replicated our study at sites spanning nearly the entire Gulf of Maine coastline, to examine how local environmental variability may alter intraspecific variation in nitrate uptake. We found that average nitrate uptake rates were ~18% higher in upper compared to lower intertidal Fucus vesiculosus. Furthermore, we found evidence for both acclimation and adaptation to tide height during a transplant experiment. F. vesiculosus transplanted from the lower to the upper intertidal zone was characterized by increased nitrate uptake, but individuals transplanted from the upper to the lower intertidal zone retained high uptake rates. Our observations differed among Gulf of Maine regions and among time points of our study. Importantly, these differences may reflect associations between nitrate uptake rates and abiotic environmental conditions and seaweed nutrient status. Our study highlights the importance of long-term variation in ambient nutrient supply in driving intraspecific variation of seaweeds across the intertidal gradient and local and seasonal variation in ambient nutrient levels in mediating intraspecific differences.

UnlabelledIntrahepatic cholangiocarcinoma (ICC) is an aggressive liver bile duct malignancy exhibiting frequent isocitrate dehydrogenase (IDH1/IDH2) mutations. Through a high-throughput drug screen of a large panel of cancer cell lines, including 17 biliary tract cancers, we found that IDH mutant (IDHm) ICC cells demonstrate a striking response to the multikinase inhibitor dasatinib, with the highest sensitivity among 682 solid tumor cell lines. Using unbiased proteomics to capture the activated kinome and CRISPR/Cas9-based genome editing to introduce dasatinib-resistant "gatekeeper" mutant kinases, we identified SRC as a critical dasatinib target in IDHm ICC. Importantly, dasatinib-treated IDHm xenografts exhibited pronounced apoptosis and tumor regression. Our results show that IDHm ICC cells have a unique dependency on SRC and suggest that dasatinib may have therapeutic benefit against IDHm ICC. Moreover, these proteomic and genome-editing strategies provide a systematic and broadly applicable approach to define targets of kinase inhibitors underlying drug responsiveness.SignificanceIDH mutations define a distinct subtype of ICC, a malignancy that is largely refractory to current therapies. Our work demonstrates that IDHm ICC cells are hypersensitive to dasatinib and critically dependent on SRC activity for survival and proliferation, pointing to new therapeutic strategies against these cancers. Cancer Discov; 6(7); 727-39. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 681.

NAD (nicotinamide adenine dinucleotide) acts as a non-canonical RNA cap structure in bacteria and eukaryotes. Here the authors demonstrate the whole landscape of budding yeast NAD-RNAs which are subject to diverse surveillance pathways, suggesting that NAD caps in budding yeast are mostly dysfunctional.

Abstract We aimed at identifying the developmental stage at which leukemic cells of pediatric T‐ALLs are arrested and at defining leukemogenic mechanisms based on ATAC‐Seq. Chromatin accessibility maps of seven developmental stages of human healthy T cells revealed progressive chromatin condensation during T‐cell maturation. Developmental stages were distinguished by 2,823 signature chromatin regions with 95% accuracy. Open chromatin surrounding SAE1 was identified to best distinguish thymic developmental stages suggesting a potential role of SUMOylation in T‐cell development. Deconvolution using signature regions revealed that T‐ALLs, including those with mature immunophenotypes, resemble the most immature populations, which was confirmed by TF‐binding motif profiles. We integrated ATAC‐Seq and RNA‐Seq and found DAB1, a gene not related to leukemia previously, to be overexpressed, abnormally spliced and hyper‐accessible in T‐ALLs. DAB1‐negative patients formed a distinct subgroup with particularly immature chromatin profiles and hyper‐accessible binding sites for SPI1 (PU.1), a TF crucial for normal T‐cell maturation. In conclusion, our analyses of chromatin accessibility and TF‐binding motifs showed that pediatric T‐ALL cells are most similar to immature thymic precursors, indicating an early developmental arrest.

Predicting an individual's response to therapy is an important goal for precision medicine. Here, the authors use an algorithm that takes into account the interaction type and directionality of signalling pathways in protein–protein interactions and find that their pathway analysis can predict essential genes, which may be a target for therapy.

Abstract Background The castor bean tick Ixodes ricinus is an important vector of several clinically important diseases, whose prevalence increases with accelerating global climate changes. Characterization of a tick life-cycle is thus of great importance. However, researchers mainly focus on specific organs of fed life stages, while early development of this tick species is largely neglected. Methods In an attempt to better understand the life-cycle of this widespread arthropod parasite, we sequenced the transcriptomes of four life stages (egg, larva, nymph and adult female), including unfed and partially blood-fed individuals. To enable a more reliable identification of transcripts and their comparison in all five transcriptome libraries, we validated an improved-fit set of five I. ricinus-specific reference genes for internal standard normalization of our transcriptomes. Then, we mapped biological functions to transcripts identified in different life stages (clusters) to elucidate life stage-specific processes. Finally, we drew conclusions from the functional enrichment of these clusters specifically assigned to each transcriptome, also in the context of recently published transcriptomic studies in ticks. Results We found that reproduction-related transcripts are present in both fed nymphs and fed females, underlining the poorly documented importance of ovaries as moulting regulators in ticks. Additionally, we identified transposase transcripts in tick eggs suggesting elevated transposition during embryogenesis, co-activated with factors driving developmental regulation of gene expression. Our findings also highlight the importance of the regulation of energetic metabolism in tick eggs during embryonic development and glutamate metabolism in nymphs. Conclusions Our study presents novel insights into stage-specific transcriptomes of I. ricinus and extends the current knowledge of this medically important pathogen, especially in the early phases of its development.

In this work we prove the existence of global weak solutions to a degenerate and strongly coupled parabolic system arising from the transport processes through partially saturated deformable porous materials. The hygro-thermal model is coupled with quasi-static evolution equations modeling elastic and inelastic mechanical deformations. Physically relevant Newton boundary conditions are considered for water pressure and temperature of the porous system. The traction boundary condition is imposed on the deformable solid skeleton of the porous material. Degeneration occurs in both elliptic and parabolic part of the balance equation for mass of water. The coupling between water pressure, temperature, stress tensor and internal variables occurs in transport coefficients, constitutive functions and the decomposition of the total strain tensor into elastic and plastic parts due to mechanical effect and strain tensor due to thermal expansion.

N-Glycanase 1 (NGLY1) deficiency is an ultra-rare, complex and devastating neuromuscular disease. Patients display multi-organ symptoms including developmental delays, movement disorders, seizures, constipation and lack of tear production. NGLY1 is a deglycosylating protein involved in the degradation of misfolded proteins retrotranslocated from the endoplasmic reticulum (ER). NGLY1-deficient cells have been reported to exhibit decreased deglycosylation activity and an increased sensitivity to proteasome inhibitors. We show that the loss of NGLY1 causes substantial changes in the RNA and protein landscape of K562 cells and results in downregulation of proteasomal subunits, consistent with its processing of the transcription factor NFE2L1. We employed the CMap database to predict compounds that can modulate NGLY1 activity. Utilizing our robust K562 screening system, we demonstrate that the compound NVP-BEZ235 (Dactosilib) promotes degradation of NGLY1-dependent substrates, concurrent with increased autophagic flux, suggesting that stimulating autophagy may assist in clearing aberrant substrates during NGLY1 deficiency.

Abstract Background DNA sequencing is at the core of many molecular biology laboratories. Despite its long history, there is a lack of user-friendly Sanger sequencing data analysis tools that can be run interactively as a web application or at large-scale in batch from the command-line. Results We present Tracy, an efficient and versatile command-line application that enables basecalling, alignment, assembly and deconvolution of sequencing chromatogram files. Its companion web applications make all functionality of Tracy easily accessible using standard web browser technologies and interactive graphical user interfaces. Tracy can be easily integrated in large-scale pipelines and high-throughput settings, and it uses state-of-the-art file formats such as JSON and BCF for reporting chromatogram sequencing results and variant calls. The software is open-source and freely available at https://github.com/gear-genomics/tracy, the companion web applications are hosted at https://www.gear-genomics.com. Conclusions Tracy can be routinely applied in large-scale validation efforts conducted in clinical genomics studies as well as for high-throughput genome editing techniques that require a fast and rapid method to confirm discovered variants or engineered mutations. Molecular biologists benefit from the companion web applications that enable installation-free Sanger chromatogram analyses using intuitive, graphical user interfaces.

This paper presents a detailed analysis of various approaches to hardware implemented compression algorithm dictionaries, including our optimized method. To obtain comprehensive and detailed results, we introduced a method for the fair comparison of programmable hardware architectures to show the benefits of our approach from the perspective of logic resources, frequency, and latency. We compared two generally used methods with our optimized method, which was found to be more suitable for maintaining the memory content via (in)valid bits in any mid-density memory structures, which are implemented in programmable hardware such as FPGAs (Field Programmable Gate Array). The benefits of our new method based on a “Distributed Memory” technique are shown on a particular example of compression dictionary but the method is also suitable for another use cases requiring a fast (re-)initialization of the used memory structures before each run of an algorithm with minimum time and logic resources consumption. The performance evaluation of the respective approaches has been made in Xilinx ISE and Xilinx Vivado toolkits for the Virtex-7 FPGA family. However the proposed approach is compatible with 99% of modern FPGAs.

The endothelial to haematopoietic transition (EHT) is the process where haemogenic endothelium differentiates into haematopoietic stem and progenitor cells (HSPCs). Here the authors use single cell transcriptomics and antibody screening to identify CD44 as a marker of EHT that is required for EHT and HSPC development.

The aim of the present study is to summarize new results concerning the capacity of the Roman aqueduct of Brigetio (Komárom/Szőny). Hydrological formulae used for calculations on the capacity of aqueducts are described and used to determine the daily discharge of the Roman aqueduct of Brigetio. The results presented are hypothetical, but it is hoped that they reflect the performance of the aqueduct. Calculations on per capita daily water supply and related problems are also addressed.

Caspase-8 is the key component of the receptor-mediated (extrinsic) apoptotic pathway. Immunological localization of active caspase-8 showed its presence in osteoblasts, including non-apoptotic ones. Further in vivo exploration of caspase-8 functions in the bone is hindered by the fact that the caspase-8 knock-out is lethal prenatally. Examinations were thus performed using individual cell populations in vitro. In this study, caspase-8 was eliminated by the CRISPR/cas9 technology in MC3T3-E1 cells, the most common in vitro model of osteoblastic populations. The aim of the work was to specify the consequences of caspase-8 deficiency on non-apoptotic pathways. The impact on the osteogenic gene expression of the osteoblastic cells along with alterations in proliferation, caspase cascades and rapamycin induced autophagy response were evaluated. Osteogenic differentiation of caspase-8 deficient cells was inhibited as these cells displayed a decreased level of mineralization and lower activity of alkaline phosphatase. Among affected osteogenic genes, based on the PCR Array, major changes were observed for Ctsk, as down-regulated, and Gdf10, as up-regulated. Other significantly down-regulated genes included those coding osteocalcin, bone morphogenetic proteins (-3, -4 and -7), collagens (-1a1, -14a1) or Phex. The formation of autophagosomes was not altered in rapamycin-treated caspase-8 deficient cells, but expression of some autophagy-related genes, including Tnfsf10, Cxcr4, Dapk1 and Igf1, was significantly downregulated. These data provide new insight into the effects of caspase-8 on non-apoptotic osteogenic pathways.

Insects are gaining more and more space in food and feed sectors, creating an intense scientific interest towards insects as food ingredients. Several papers deal with cereal-based products complemented by insect powder in the past few years. However, adulteration and quality control of such products present some hot topics for researchers, e.g., how can we justify the amounts and/or species of the insects used in the given products? Our paper aims to answer such questions by analysing seven edible insect powders of different species independently. The mixtures with wheat flour were analysed using near infrared spectroscopy and chemometric methods. Not only powders of different species were clearly differentiated, but also mixtures created by different amounts of wheat flour. Prediction of insect content showed 0.65% cross-validated error. The proposed methodology gives an excellent tool for quality control of insect-based cereal food products.

BackgroundSepsis is associated with high platelet turnover and elevated levels of immature platelets. Changes in the platelet transcriptome and the specific impact of immature platelets on the platelet transcriptome remain unclear. Thus, this study sought to address whether and how elevated levels of immature platelets affect the platelet transcriptome in patients with sepsis.MethodsBlood samples were obtained from patients with sepsis requiring vasopressor therapy (n = 8) and from a control group of patients with stable coronary artery disease and otherwise similar demographic characteristics (n = 8). Immature platelet fraction (IPF) was determined on a Sysmex XE 2100 analyser and platelet function was tested by impedance aggregometry. RNA from leukocyte-depleted platelets was used for transcriptome analysis by Next Generation Sequencing integrating the use of unique molecular identifiers.ResultsIPF (median [interquartile range]) was significantly elevated in sepsis patients (6.4 [5.3-8.7] % vs. 3.6 [2.6-4.6] %, p = 0.005). Platelet function testing revealed no differences in adenosine diphosphate- or thrombin receptor activating peptide-induced platelet aggregation between control and sepsis patients. Putative circular RNA transcripts were decreased in platelets from septic patients. Leukocyte contamination defined by CD45 abundance levels in RNA-sequencing was absent in both groups. Principal component analysis of transcripts showed only partial overlap of clustering with IPF levels. RNA sequencing showed up-regulation of 524 and down-regulation of 118 genes in platelets from sepsis patients compared to controls. Upregulated genes were mostly related to catabolic processes and protein translation. Comparison to published platelet transcriptomes showed a large overlap of changes observed in sepsis and COVID-19 but not with reticulated platelets from healthy donors.ConclusionsPatients with sepsis appear to have a less degraded platelet transcriptome as indicated by increased levels of immature platelets and decreased levels of putative circular RNA transcripts. The present data suggests that increased protein translation is a characteristic mechanism of systemic inflammation.

In recent years, radio frequency identification (RFID) technology has been utilized to monitor product movements within a supply chain in real time. By utilizing RFID technology, the products can be tracked automatically in real-time. However, the RFID cannot detect the movement and direction of the tag. This study investigates the performance of machine learning (ML) algorithms to detect the movement and direction of passive RFID tags. The dataset utilized in this study was created by considering a variety of conceivable tag motions and directions that may occur in actual warehouse settings, such as going inside and out of the gate, moving close to the gate, turning around, and static tags. The statistical features are derived from the received signal strength (RSS) and the timestamp of tags. Our proposed model combined Isolation Forest (iForest) outlier detection, Synthetic Minority Over Sampling Technique (SMOTE) and Random Forest (RF) has shown the highest accuracy up to 94.251% as compared to other ML models in detecting the movement and direction of RFID tags. In addition, we demonstrated the proposed classification model could be applied to a web-based monitoring system, so that tagged products that move in or out through a gate can be correctly identified. This study is expected to improve the RFID gate on detecting the status of products (being received or delivered) automatically.

The main request for roof exposed to fire is the classification Broof (t3), which prevents the transfer and spread of flame on the surface, this is not required for green roof according to Czech fire standards and regulations. A fire can spread in three ways: direct contact, flying burning particles and thermal radiation. In most cases, the spread of fire between objects occurs with the help of radiation. The article deals with the difference in flame spread over the surface of a green roof during a normal fire without the influence of radiant heat and the Broof (t3) test, where the surface is exposed to radiant heat. The aim was to determine the dependence of flame spread on a flat green roof due to the effect of radiation during a fire and the possibility of endangering neighboring buildings.

This updated review aims to describe the current status in the development of liposome-based systems for the targeted delivery of phthalocyanines for photodynamic therapy (PDT). Although a number of other drug delivery systems (DDS) can be found in the literature and have been studied for phthalocyanines or similar photosensitizers (PSs), liposomes are by far the closest to clinical practice. PDT itself finds application not only in the selective destruction of tumour tissues or the treatment of microbial infections, but above all in aesthetic medicine. From the point of view of administration, some PSs can advantageously be delivered through the skin, but for phthalocyanines, systemic administration is more suitable. However, systemic administration places higher demands on advanced DDS, active tissue targeting and reduction of side effects. This review focuses on the already described liposomal DDS for phthalocyanines, but also describes examples of DDS used for structurally related PSs, which can be assumed to be applicable to phthalocyanines as well.

Viruses contribute significantly to the global decline of honey bee populations. One way to limit the impact of such viruses is the introduction of natural antiviral compounds from fungi as a component of honey bee diets. Therefore, we examined the effect of crude organic extracts from seven strains of the fungal genus Talaromyces in honey bee diets under laboratory conditions. The strains were isolated from bee bread prepared by honey bees infected with chronic bee paralysis virus (CBPV). The antiviral effect of the extracts was also quantified in vitro using mammalian cells as a model system. We found that three extracts (from strains B13, B18 and B30) mitigated CBPV infections and increased the survival rate of bees, whereas other extracts had no effect (B11 and B49) or were independently toxic (B69 and B195). Extract B18 inhibited the replication of feline calicivirus and feline coronavirus (FCoV) in mammalian cells, whereas extracts B18 and B195 reduced the infectivity of FCoV by ~90% and 99%, respectively. Our results show that nonpathogenic fungi (and their products in food stores) offer an underexplored source of compounds that promote disease resistance in honey bees.

Pyrolysis represents one of the most convenient technologies for the chemical transformation of waste. The exposure to corrosion products and high temperatures does, however, require chemically resistant construction materials. This study was carried out to analyze the corrosion behavior of 1.4571 (AISI 316Ti) and 1.4305 (AISI 303) stainless steels machined with wire electric discharge machining (WEDM) in a pyrolysis environment. Different machining parameters were used for both materials tested to examine the influence of WEDM machining. The total testing time in the pyrolysis environment was 28 days, with the testing chamber being refilled 12 times. The surface topography was analyzed following the WEDM, cleaning, and corrosion test. The surface morphology and cross-section analyses were carried out using electron microscopy at all three stages of the process. An analysis of the chemical composition of the surfaces was carried out as well as of the pyrolysis environment to which the samples were exposed. It was established that the organic acids found in the pyrolysis chamber did not degrade the tested stainless steels to a meaningful degree. Minor fissures, that is, fine precipitated carbides, were observed on the surface of both the steel types and in their subsurface layer, as well as a significant presence of carbon. This presence was directly connected to the impurities found on the surface after the removal from the test furnace that were probably of a protective or passivation nature.

The ATR-Chk1 pathway is critical for DNA damage responses and cell-cycle progression. Chk1 inhibition is more deleterious to cycling cells than ATR inhibition, raising questions about ATR and Chk1 functions in the absence of extrinsic replication stress. Here we show that a key role of ATR in S phase is to coordinate RRM2 accumulation and origin firing. ATR inhibitor (ATRi) induces massive ssDNA accumulation and replication catastrophe in a fraction of early S-phase cells. In other S-phase cells, however, ATRi induces moderate ssDNA and triggers a DNA-PK and Chk1-mediated backup pathway to suppress origin firing. The backup pathway creates a threshold such that ATRi selectively kills cells under high replication stress, whereas Chk1 inhibitor induces cell death at a lower threshold. The levels of ATRi-induced ssDNA correlate with ATRi sensitivity in a panel of cell lines, suggesting that ATRi-induced ssDNA could be predictive of ATRi sensitivity in cancer cells.

Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quantification of the angle of each leaf for each plant. The resulting measurements are both heritable and correlated with manually collected leaf angles. This automated and scaleable reconstruction approach was employed to measure leaf-by-leaf angles for a population of 366 sorghum plants at multiple time points, resulting in 971 successful reconstructions and 3,376 leaf angle measurements from individual leaves. A genome wide association study conducted using aggregated leaf angle data identified a known large effect leaf angle gene, several previously identified leaf angle QTL from a sorghum NAM population, and novel signals. Genome wide association studies conducted separately for three individual sorghum leaves identified a number of the same signals, a previously unreported signal shared across multiple leaves, and signals near the sorghum orthologs of two maize genes known to influence leaf angle. Automated measurement of individual leaves and mapping variants associated with leaf angle reduce the barriers to engineering ideal canopy architectures in sorghum and other grain crops.

Despite the development of high-end optical lithography systems, electron-beam lithography (EBL) remains the preferred solution for rapid fabrication of deep sub-micrometric features. Although poly-methylmethacrylate (PMMA), HSQ and ZEP remain the most popular resists on the market, a variety of alternatives have emerged, including chemically amplified resists like CSAR. Here, we investigate the use of two resists initially intended for deep ultraviolet (DUV) lithography, namely M108Y and M35G from JSR, as EBL resists. Their chemically amplified nature involves high sensitivity, de facto increasing the throughput. The critical dimensions of each resist are studied, as well as the pattern transfer into the underlying silicon substrate. They yield similar CD performance as ZEP or CSAR; at the same time, they are more resistant than those resists with respect to different dry etching recipes. Overall, the two analyzed DUV photoresists are proven to be valid solutions as alternatives to standard EBL resists.

Summary: Early embryogenesis depends on proper control of intracellular homeostasis of ions including Ca2+ and Mg2+. Deletion of the Ca2+ and Mg2+ conducting the TRPM7 channel is embryonically lethal in mice but leaves compaction, blastomere polarization, blastocoel formation, and correct specification of the lineages of the trophectoderm and inner cell mass unaltered despite that free cytoplasmic Ca2+ and Mg2+ is reduced at the two-cell stage. Although Trpm7−/− embryos are able to hatch from the zona pellucida, no expansion of Trpm7−/− trophoblast cells can be observed, and Trpm7−/− embryos are not identifiable in utero at E6.5 or later. Given the proliferation and adhesion defect of Trpm7−/− trophoblast stem cells and the ability of Trpm7−/− ESCs to develop to embryos in tetraploid embryo complementation assays, we postulate a critical role of TRPM7 in trophectoderm cells and their failure during implantation as the most likely explanation of the developmental arrest of Trpm7-deficient mouse embryos.