Project description:Transcription is a complex process that integrates the state of the cell and its environment to generate adequate responses for cell fitness and survival. Recent microscopy experiments have been able to monitor transcription from single genes in individual cells. These observations have revealed two striking features: transcriptional activity can vary markedly from one cell to another, and is subject to large changes over time, sometimes within minutes. How the chromatin structure, transcription machinery assembly and signalling networks generate such patterns is still unclear. In this review, we present the techniques used to investigate transcription from single genes, introduce quantitative modelling tools, and discuss transcription mechanisms and their implications for gene expression regulation.
Project description:As an alternative to thermionic X-ray generators, cold-cathode X-ray tubes are being developed for portable and multichannel tomography. Field emission propagating from needle structures such as carbon nanotubes or Si tips currently dominates related research and development, but various obstacles prevent the widespread of this technology. An old but simple electron emission design is the planar tunnelling cathode using a metal-oxide-semiconductor (MOS) structure, which achieves narrow beam dispersion and low supplying voltage. Directly grown vertical graphene (VG) is employed as the gate electrode of MOS and tests its potential as a new emission source. The emission efficiency of the device is initially ≈1% because of unavoidable fabrication damage during the patterning processes; it drastically improves to >40% after ozone treatment. The resulting emission current obeys the Fowler-Nordheim tunnelling model, and the enhanced emission is attributed to the effective gate thickness reduction by ozone treatment. As a proof-of-concept experiment, a clustered array of 2140 cells is integrated into a system that provides mA-class emission current for X-ray generation. With pulsed digital excitations, X-ray imaging of a chest phantom, demonstrating the feasibility of using a VG MOS electron emission source as a new and innovative X-ray generator is realized.
Project description:BackgroundGlobal Biodiversity Information Facility (GBIF) has uneven data coverage across taxonomic, spatial and temporal dimensions. Temporal imbalances in the data coverage are particularly dramatic. Thus, 188.3M GBIF records were made in 2020, more than the whole lot of the currently available pre-1986 electronic data. This underscores the importance of reliable and precise biodiversity spatial data collected in early times. Biological collections certainly play a key role in our knowledge of biodiversity in the past. However, digitisation of historical literature is underway, being a modern trend in biodiversity data mining. The grid dataset for the flora of Vladimir Oblast, Russia, includes many historical records borrowed from the "Flora des Gouvernements Wladimir" by Alexander F. Fleroff (also known as Flerov or Flerow). Intensive study of Fleroff's collections and field surveys exactly in the same localities where he worked, showed that the quality of his data is superb. Species lists collected across hundreds of localities form a unique source of reliable information on the floristic diversity of Vladimir Oblast and adjacent areas for the period from 1894 to 1901. Since the grid dataset holds generalised data, we made precise georeferencing of Fleroff's literature records and published them in the form of a GBIF-mediated dataset.New informationA dataset, based on "Flora des Gouvernements Wladimir. I. Pflanzengeographische Beschreibung des Gouvernements Wladimir" by Fleroff (1902), includes 8,889 records of 654 taxa (mainly species) from 366 localities. The majority of records originate from Vladimir Oblast (4,611 records of 534 taxa from 195 localities) and Yaroslavl Oblast (2,013 records of 409 taxa from 66 localities), but also from Nizhny Novgorod Oblast (942 records), Ivanovo Oblast (667 records) and Moscow Oblast (656 records). The leading second-level administrative units by the number of records are Pereslavsky District (2,013 records), Aleksandrovsky District (1,318 records) and Sergievo-Posadsky District (599 records). Georeferencing was carried out, based on the expert knowledge of the area, analysis of modern satellite images and old topographic maps. For 2,460 records, the georeferencing accuracy is 1,000 m or less (28%), whereas for 6,070 records it is 2,000 m or less (68%). The mean accuracy of records of the entire dataset is 2,447 m. That accuracy is unattainable for most herbarium collections of the late 19th century. Some localities of rare plants discovered by Fleroff and included into the dataset were completely lost in the 20th century due to either peat mining or development of urban areas.
Project description:ObjectiveTo identify the core components of digital behaviour change interventions for weight loss maintenance targeting physical activity, in terms of: (i) behaviour change techniques, (ii) mechanisms of action, (iii) modes of delivery, (iv) dose and (v) tailoring/personalization. In addition, the links between these components were investigated.MethodsA literature search was performed in five electronic databases: PubMed, Embase, CINHAL, PsycINFO and Web of Science. Two reviewers independently screened the identified articles and extracted data related with the study characteristics and behaviour change techniques, mechanism of action, mode of delivery, dose, and tailoring, using standardized classifications whenever available (e.g. behaviour change techniques taxonomy).ResultsSeventeen articles reporting 11 original studies were selected. Two studies were protocols, 9 studies presented results for weight change and all but one showed no significant differences between the intervention and control groups. Eight studies (73%) provided adequate information on behaviour change techniques. Five studies (45%) provided partial information about how the behaviour change techniques were linked to mechanisms of action, and only one study (0.9%) described these links for all the techniques. Around half of the studies reported the modes through which behaviour change techniques were delivered. Descriptions of dose were present in most studies, but with minimal information. The use of tailoring or personalization approaches was mentioned in eight studies (73%), but descriptions of what was tailored and how were minimal.ConclusionsThe compilation of information regarding intervention components was difficult due to the lack of information and systematization in reporting across papers. This is particularly true for the reporting of the links between behaviour change techniques and the other core intervention components. This information is crucial to help us understand in the context of behaviour change interventions what works or does not work, how it works and why.
Project description:Laboratory cultivation of viruses is critical for determining requirements for viral replication, developing detection methods, identifying drug targets, and developing antivirals. Several viruses have a history of recalcitrance towards robust replication in laboratory cell lines, including human noroviruses and hepatitis B and C viruses. These viruses have tropism for tissue components of the enterohepatic circulation system: the intestine and liver, respectively. The purpose of this review is to discuss how key enterohepatic signaling molecules, bile acids (BAs), and BA receptors are involved in the replication of these viruses and how manipulation of these factors was useful in the development and/or optimization of culture systems for these viruses. BAs have replication-promoting activities through several key mechanisms: (1) affecting cellular uptake, membrane lipid composition, and endocytic acidification; (2) directly interacting with viral capsids to influence binding to cells; and (3) modulating the innate immune response. Additionally, expression of the Na+-taurocholate cotransporting polypeptide BA receptor in continuous liver cell lines is critical for hepatitis B virus entry and robust replication in laboratory culture. Viruses are capable of hijacking normal cellular functions, and understanding the role of BAs and BA receptors, components of the enterohepatic system, is valuable for expanding our knowledge on the mechanisms of norovirus and hepatitis B and C virus replication.
Project description:The human microbiome is predominantly composed of facultative and obligate anaerobic bacteria that live in hypoxic/anoxic polymicrobial biofilm communities. Given the oxidative sensitivity of large fractions of the human microbiota, green fluorescent protein (GFP) and related genetically-encoded fluorophores only offer limited utility for live cell imaging due the oxygen requirement for chromophore maturation. Consequently, new fluorescent imaging modalities are needed to study polymicrobial interactions and microbiome-host interactions within anaerobic environments. The fluorescence-activating and absorption shifting tag (FAST) is a rapidly developing genetically-encoded fluorescent imaging technology that exhibits tremendous potential to address this need. In the FAST system, fluorescence only occurs when the FAST protein is complexed with one of a suite of cognate small molecule fluorogens. To expand the utility of FAST imaging, we sought to develop a modular platform (Click-FAST) to democratize fluorogen engineering for personalized use cases. Using Click-FAST, investigators can quickly and affordably sample a vast chemical space of compounds, potentially imparting a broad range of desired functionalities to the parental fluorogen. In this work, we demonstrate the utility of the Click-FAST platform using a novel fluorogen, PLBlaze-alkyne, which incorporates the widely available small molecule ethylvanillin as the hydroxybenzylidine head group. Different azido reagents were clicked onto PLBlaze-alkyne and shown to impart useful characteristics to the fluorogen, such as selective bacterial labeling in mixed populations as well as fluorescent signal enhancement. Conjugation of an 80 Å PEG molecule to PLBlaze-alkyne illustrates the broad size range of functional fluorogen chimeras that can be employed. This PEGylated fluorogen also functions as an exquisitely selective membrane permeability marker capable of outperforming propidium iodide as a fluorescent marker of cell viability.
Project description:Increases in X-ray brightness from synchrotron light sources lead to a requirement for higher frame rates from hybrid pixel array detectors (HPADs), while also favoring charge integration over photon counting. However, transfer of the full uncompressed data will begin to constrain detector design, as well as limit the achievable continuous frame rate. Here a data compression scheme that is easy to implement in a HPAD's application-specific integrated circuit (ASIC) is described, and how different degrees of compression affect image quality in ptychography, a commonly employed coherent imaging method, is examined. Using adaptive encoding quantization, it is shown in simulations that one can digitize signals up to 16383 photons per pixel (corresponding to 14 bits of information) using only 8 or 9 bits for data transfer, with negligible effect on the reconstructed image.
Project description:The ability to map and estimate the activity of radiological source distributions in unknown three-dimensional environments has applications in the prevention and response to radiological accidents or threats as well as the enforcement and verification of international nuclear non-proliferation agreements. Such a capability requires well-characterized detector response functions, accurate time-dependent detector position and orientation data, a digitized representation of the surrounding 3D environment, and appropriate image reconstruction and uncertainty quantification methods. We have previously demonstrated 3D mapping of gamma-ray emitters with free-moving detector systems on a relative intensity scale using a technique called Scene Data Fusion (SDF). Here we characterize the detector response of a multi-element gamma-ray imaging system using experimentally benchmarked Monte Carlo simulations and perform 3D mapping on an absolute intensity scale. We present experimental reconstruction results from hand-carried and airborne measurements with point-like and distributed sources in known configurations, demonstrating quantitative SDF in complex 3D environments.
Project description:MotivationThe use of experimental information has been demonstrated to increase the success rate of computational macromolecular docking. Many methods use information to post-filter the simulation output while others drive the simulation based on experimental restraints, which can become problematic for more complex scenarios such as multiple binding interfaces.ResultsWe present a novel method for including interface information into protein docking simulations within the LightDock framework. Prior to the simulation, irrelevant regions from the receptor are excluded for sampling (filter of initial swarms) and initial ligand poses are pre-oriented based on ligand input information. We demonstrate the applicability of this approach on the new 55 cases of the Protein-Protein Docking Benchmark 5, using different amounts of information. Even with incomplete or incorrect information, a significant improvement in performance is obtained compared to blind ab initio docking.Availability and implementationThe software is supported and freely available from https://github.com/brianjimenez/lightdock and analysis data from https://github.com/brianjimenez/lightdock_bm5.Supplementary informationSupplementary data are available at Bioinformatics online.
Project description:Positive transcription elongation factor b (P-TEFb), which comprises cyclin-dependent kinase 9 (CDK9) kinase and cyclin T subunits, is an essential kinase complex in human cells. Phosphorylation of the negative elongation factors by P-TEFb is required for productive elongation of transcription of protein-coding genes by RNA polymerase II (pol II). In addition, P-TEFb-mediated phosphorylation of the carboxyl-terminal domain (CTD) of the largest subunit of pol II mediates the recruitment of transcription and RNA processing factors during the transcription cycle. CDK9 also phosphorylates p53, a tumor suppressor that plays a central role in cellular responses to a range of stress factors. Many viral factors affect transcription by recruiting or modulating the activity of CDK9. In this review, we will focus on how the function of CDK9 is regulated by viral gene products. The central role of CDK9 in viral life cycles suggests that drugs targeting the interaction between viral products and P-TEFb could be effective anti-viral agents.