Homologous Expression of the Caldicellulosiruptor bescii CelA Reveals that the Extracellular Protein Is Glycosylated

Members of the bacterial genus Caldicellulosiruptor are the most thermophilic cellulolytic microbes described with ability to digest lignocellulosic biomass without conventional pretreatment. The cellulolytic ability of different species varies dramatically and correlates with the presence of the multimodular cellulase CelA, which contains both a glycoside hydrolase family 9 endoglucanase and a glycoside hydrolase family 48 exoglucanase known to be synergistic in their activity, connected by three cellulose-binding domains via linker peptides. This architecture exploits the cellulose surface ablation driven by its general cellulase processivity as well as excavates cavities into the surface of the substrate, revealing a novel paradigm for cellulase activity. We recently reported that a deletion of celA in C. bescii had a significant effect on its ability to utilize complex biomass. To analyze the structure and function of CelA and its role in biomass deconstruction, we constructed a new expression vector for C. bescii and were able, for the first time, to express significant quantities of full-length protein in vivo in the native host. The protein, which contains a Histidine tag, was active and excreted from the cell. Expression of CelA protein with and without its signal sequence allowed comparison of protein retained intracellularly to protein transported extracellularly. Analysis of protein in culture supernatants revealed that the extracellular CelA protein is glycosylated whereas the intracellular CelA is not, suggesting that either protein transport is required for this post-translational modification or that glycosylation is required for protein export. The mechanism and role of protein glycosylation in bacteria is poorly understood and the ability to express CelA in vivo in C. bescii will allow the study of the mechanism of protein glycosylation in this thermophile. It will also allow the study of glycosylation of CelA itself and its role in the structure and function of this important enzyme in biomass deconstruction.     

Dependency parsing of biomedical text with BERT

Background

Entity normalization is an important information extraction task which has gained renewed attention in the last decade, particularly in the biomedical and life science domains. In these domains, and more generally in all specialized domains, this task is still challenging for the latest machine learning-based approaches, which have difficulty handling highly multi-class and few-shot learning problems. To address this issue, we propose C-Norm, a new neural approach which synergistically combines standard and weak supervision, ontological knowledge integration and distributional semantics.

Results

Our approach greatly outperforms all methods evaluated on the Bacteria Biotope datasets of BioNLP Open Shared Tasks 2019, without integrating any manually-designed domain-specific rules.

Conclusions

Our results show that relatively shallow neural network methods can perform well in domains that present highly multi-class and few-shot learning problems.

     

Proteomic identification of glyceraldehyde 3-phosphate dehydrogenase as an inhibitory target of hydrogen peroxide in Arabidopsis.

Hydrogen peroxide (H2O2) is now recognised as a key signalling molecule in eukaryotes. In plants, H2O2 is involved in regulating stomatal closure, gravitropic responses, gene expression and programmed cell death. Although several kinases, such as oxidative signal-inducible 1 (OXI1) kinase and mitogen-activated protein kinases are known to be activated by exogenous H2O2, little is known about the proteins that directly react with H2O2. Here, we utilised a proteomic approach, using iodoacetamide-based fluorescence tagging of proteins in conjunction with mass spectrometric analysis, to identify several proteins that might be potential targets of H2O2 in the cytosolic fraction of Arabidopsis thaliana, the most prominent of which was cytosolic glyceraldehyde 3-phosphate dehydrogenase (cGAPDH; EC 1.2.1.12). cGAPDH from Arabidopsis is inactivated by H2O2 in vitro, and this inhibition is reversible by the subsequent addition of reductants such as reduced glutathione (GSH). It has been suggested recently that Arabidopsis GAPDH has roles outside of its catalysis as part of glycolysis, while in other systems this includes that of mediating reactive oxygen species (ROS) signalling. Here, we suggest that cGAPDH in Arabidopsis might also have such a role in mediating ROS signalling in plants.     

Reproductive ecology of three rare North American Pinguicula species

Pinguicula (Lentibulariaceae) is a genus of more than 100 carnivorous plant species. A handful of comprehensive studies have examined the reproductive ecology of these species, mostly in Europe and none in the USA. During 2013–2016 different aspects of the reproductive ecology of P. ionantha, P. lutea and P. planifolia were studied at multiple locations in the Florida Panhandle, USA. All three species are of conservation concern within the study region and some aspects of their reproductive ecology may be contributing to their rarity. For all species, we conducted breeding system studies investigating xenogamy vs. autogamy, self‐incompatibility vs. self‐compatibility, pollen:ovule ratios, flower phenology and longevity, and pollinator visitation, as well as fruit and seed set differences among populations. All three Pinguicula species were determined to be xenogamous and self‐compatible, although the pollen:ovule ratios were extremely low. In addition, these species have floral nastic movements and flower longevity that ranges from 2 to 3 weeks depending on the species. Hymenoptera was identified as the primary group of pollinators visiting all species, although observed visitation events were low. All three Pinguicula species had extremely high levels of fruit set and seed set. Worldwide, Pinguicula species share similar breeding system and reproductive patterns. The rare status of P. ionantha, P. lutea and P. planifolia is more likely due to their ecological requirements, demographics and/or patterns of genetic diversity, than reproduction. This work is among the first and most comprehensive associated with the reproductive ecology of North American Pinguicula.     

CDK1 Is a Synthetic Lethal Target for KRAS Mutant Tumours

Activating KRAS mutations are found in approximately 20% of human cancers but no RAS-directed therapies are currently available. Here we describe a novel, robust, KRAS synthetic lethal interaction with the cyclin dependent kinase, CDK1. This was discovered using parallel siRNA screens in KRAS mutant and wild type colorectal isogenic tumour cells and subsequently validated in a genetically diverse panel of 26 colorectal and pancreatic tumour cell models. This established that the KRAS/CDK1 synthetic lethality applies in tumour cells with either amino acid position 12 (p.G12V, pG12D, p.G12S) or amino acid position 13 (p.G13D) KRAS mutations and can also be replicated in vivo in a xenograft model using a small molecule CDK1 inhibitor. Mechanistically, CDK1 inhibition caused a reduction in the S-phase fraction of KRAS mutant cells, an effect also characterised by modulation of Rb, a master control of the G₁/S checkpoint. Taken together, these observations suggest that the KRAS/CDK1 interaction is a robust synthetic lethal effect worthy of further investigation.     

Twelve Weeks of Sprint Interval Training Improves Indices of Cardiometabolic Health Similar to Traditional Endurance Training despite a Five-Fold Lower Exercise Volume and Time Commitment

AimsWe investigated whether sprint interval training (SIT) was a time-efficient exercise strategy to improve insulin sensitivity and other indices of cardiometabolic health to the same extent as traditional moderate-intensity continuous training (MICT). SIT involved 1 minute of intense exercise within a 10-minute time commitment, whereas MICT involved 50 minutes of continuous exercise per session.MethodsSedentary men (27±8y; BMI = 26±6kg/m²) performed three weekly sessions of SIT (n = 9) or MICT (n = 10) for 12 weeks or served as non-training controls (n = 6). SIT involved 3x20-second ‘all-out’ cycle sprints (~500W) interspersed with 2 minutes of cycling at 50W, whereas MICT involved 45 minutes of continuous cycling at ~70% maximal heart rate (~110W). Both protocols involved a 2-minute warm-up and 3-minute cool-down at 50W.ResultsPeak oxygen uptake increased after training by 19% in both groups (SIT: 32±7 to 38±8; MICT: 34±6 to 40±8ml/kg/min; p<0.001 for both). Insulin sensitivity index (CS_I), determined by intravenous glucose tolerance tests performed before and 72 hours after training, increased similarly after SIT (4.9±2.5 to 7.5±4.7, p = 0.002) and MICT (5.0±3.3 to 6.7±5.0 x 10⁻⁴ min^-1 [μU/mL]^-1, p = 0.013) (p<0.05). Skeletal muscle mitochondrial content also increased similarly after SIT and MICT, as primarily reflected by the maximal activity of citrate synthase (CS; P<0.001). The corresponding changes in the control group were small for VO₂peak (p = 0.99), CS_I (p = 0.63) and CS (p = 0.97).ConclusionsTwelve weeks of brief intense interval exercise improved indices of cardiometabolic health to the same extent as traditional endurance training in sedentary men, despite a five-fold lower exercise volume and time commitment.     

Characterization of the co‐elution of host cell proteins with monoclonal antibodies during protein A purification

Protein A chromatography is commonly used as the initial step for purifying monoclonal antibody biotherapeutics expressed in mammalian tissue culture cells. The purpose of this step, as well as later chromatography steps, is, in part, to remove host cell proteins (HCPs) and other related impurities. Understanding the retention mechanism for the subset of HCPs retained during this step is of great interest to monoclonal antibody (mAb) process developers because it allows formation of a guided HCP clearance strategy. However, only limited information is available about the specific HCPs that co‐purify with mAbs at this step. In this study, a comprehensive comparison of HCP subpopulations that associated with 15 different mAbs during protein A chromatography was conducted by a 2D‐LC‐HDMS^E approach. We found that a majority of CHO HCPs binding to and eluting with the mAbs were common among the mAbs studied, with only a small percentage (～10% on average) of a mAb's total HCP content in the protein A (PrA) eluate specific for a particular antibody. The abundance of these HCPs in cell culture fluids and their ability to interact with mAbs were the two main factors determining their prevalence in protein A eluates. Potential binding segments for HCPs to associate with mAbs were also studied through their co‐purification with individual Fc and (Fab′)₂ antibody fragments. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:708–717, 2016     

The anatomy of Lepetella sierrai (Vetigastropoda,Lepetelloidea): implications for reproduction,feeding, and symbiosis in lepetellid limpets

The Lepetelloidea, a clade of small limpet‐shaped gastropods, can be used as a case study in continental margin and deep‐sea diversification. Lineages in this clade have been found associated with a combination of different substrates, including hydrothermal vents, seeps, wood, whale carcasses, polychaete tubes, chondrichthyan egg cases, seagrass rhizomes, algal holdfasts, crab carapaces, and sponges. Members of one lepetelloidean family, Lepetellidae, live on or inside empty tubes of members of the polychaete genus Hyalinoecia. The detailed morphology of a Mediterranean species, Lepetella sierrai Dantart & Luque 1944, was reconstructed in three dimensions from serial semi‐thin sections and compared with that of eleven other members of Lepetellidae. The hermaphroditic lepetellid limpets possessed a ciliated seminal groove, distinct testis and ovary with a common distal gonoduct, and a seminal receptacle containing mature sperm. A unique alimentary tract, with huge esophageal pouches, no true stomach, an extensive multilobed midgut, and short intestine, was present. Additionally, a bacteriocyte system throughout the entire mantle rim was revealed via light and transmission electron microscopy. This is the first recognized evidence for intracellular microbial symbiosis in lepetelloidean limpets. Semi‐thin sections showed evidence of a parasite, potentially a chitonophilid copepod, penetrating the body wall of the limpet. Hypotheses about reproductive biology, feeding, and symbiosis are presented based on anatomical features and knowledge of the habitat described herein.