Modification of Seurat v4 for the Development of a Phase Assignment Tool Able to Distinguish between G2 and Mitotic Cells.

Single-cell RNA sequencing (scRNAseq) is a rapidly advancing field enabling the characterisation of heterogeneous gene expression profiles within a population. The cell cycle phase is a major contributor to gene expression variance between cells and computational analysis tools have been developed to assign cell cycle phases to cells within scRNAseq datasets. Whilst these tools can be extremely useful, all have the drawback that they classify cells as only G1, S or G2/M. Existing discrete cell phase assignment tools are unable to differentiate between G2 and M and continuous-phase-assignment tools are unable to identify a region corresponding specifically to mitosis in a pseudo-timeline for continuous assignment along the cell cycle. In this study, bulk RNA sequencing was used to identify differentially expressed genes between mitotic and interphase cells isolated based on phospho-histone H3 expression using fluorescence-activated cell sorting. These gene lists were used to develop a methodology which can distinguish G2 and M phase cells in scRNAseq datasets. The phase assignment tools present in Seurat were modified to allow for cell cycle phase assignment of all stages of the cell cycle to identify a mitotic-specific cell population.

An Inhibitor of PIDDosome Formation.

The PIDDosome-PIDD-RAIDD-caspase-2 complex-is a proapoptotic caspase-activation platform of elusive significance. DNA damage can initiate complex assembly via ATM phosphorylation of the PIDD death domain (DD), which enables RAIDD recruitment to PIDD. In contrast, the mechanisms limiting PIDDosome formation have remained unclear. We identify the mitotic checkpoint factor BubR1 as a direct PIDDosome inhibitor, acting in a noncanonical role independent of Mad2. Following its phosphorylation by ATM at DNA breaks, "primed" PIDD relocates to kinetochores via a direct interaction with BubR1. BubR1 binds the PIDD DD, competes with RAIDD recruitment, and negates PIDDosome-mediated apoptosis after ionizing radiation. The PIDDosome thus sequentially integrates DNA damage and mitotic checkpoint signals to decide cell fate in response to genotoxic stress. We further show that by sequestering PIDD at the kinetochore, BubR1 acts to delay PIDDosome formation until the next cycle, defining a new mechanism by which cells evade apoptosis during mitosis.

Human Melioidosis Caused by Novel Transmission of Burkholderia pseudomallei from Freshwater Home Aquarium, United States1.

Nearly all cases of melioidosis in the continental United States are related to international travel to areas to which Burkholderia pseudomallei, the bacterium that causes melioidosis, is endemic. We report the diagnosis and clinical course of melioidosis in a patient from the United States who had no international travel history and the public health investigation to determine the source of exposure. We tested environmental samples collected from the patient's home for B. pseudomallei by PCR and culture. Whole-genome sequencing was conducted on PCR-positive environmental samples, and results were compared with sequences from the patient's clinical specimen. Three PCR-positive environmental samples, all collected from a freshwater home aquarium that had contained imported tropical fish, were a genetic match to the clinical isolate from the patient. This finding suggests a novel route of exposure and a potential for importation of B. pseudomallei, a select agent, into the United States from disease-endemic areas.

Ethics and governance for internet-based conservation science research.

Internet-based research is increasingly important for conservation science and has wide-ranging applications and contexts, including culturomics, illegal wildlife trade, and citizen science. However, online research methods pose a range of ethical and legal challenges. Online data may be protected by copyright, database rights, or contract law. Privacy rights may also restrict the use and access of data, as well as ethical requirements from institutions. Online data have real-world meaning, and the ethical treatment of individuals and communities must not be marginalized when conducting internet-based research. As ethics frameworks originally developed for biomedical applications are inadequate for these methods, we propose that research activities involving the analysis of preexisting online data be treated analogous to offline social science methods, in particular, nondeceptive covert observation. By treating internet users and their data with respect and due consideration, conservationists can uphold the public trust needed to effectively address real-world issues.

Ética y Gestión para la Investigación Científica de la Conservación Basada en Internet Resumen La investigación basada en internet es cada vez más importante para las ciencias de la conservación, además de tener contextos y aplicaciones de gran alcance como el análisis de textos, el mercado ilegal de fauna y la ciencia ciudadana. Sin embargo, los métodos de investigación en línea representan una gama de retos éticos y legales pues los datos virtuales pueden estar protegidos por derechos de autor, derechos de base de datos o leyes contractuales. Además, los derechos de privacidad pueden restringir el uso y el acceso a los datos, así como también los requerimientos éticos impuestos por las instituciones. Los datos virtuales tienen valor en el mundo real y el tratamiento ético de los individuos y de las comunidades no se debe marginalizar cuando se realiza una investigación por internet. Ya que los marcos éticos desarrollados originalmente para aplicarse en temas biomédicos son inadecuados para estos métodos, proponemos que las actividades de investigación que involucran el análisis de los datos virtuales preexistentes sean tratadas como análogas a los métodos no virtuales de las ciencias sociales, especialmente la observación encubierta no engañosa. Si se trata a los usuarios del internet y a sus datos con respeto y la consideración debida, los conservacionistas pueden mantener la confianza pública necesaria para tratar efectivamente los asuntos del mundo real.

Impact of proximal and distal cuff inflation on brachial artery endothelial function in healthy individuals.

PURPOSE: In this study, we examined whether the decrease in endothelial function associated with short-term exposure to elevated retrograde shear rate (SR), could be prevented when combined with a concurrent drop in transmural pressure in humans. METHODS: Twenty-five healthy individuals reported to our laboratory on three occasions to complete 30-min experimental conditions, preceded and followed by assessment of endothelial function using flow-mediated dilation (FMD). We used cuff inflation for 30-min to manipulate retrograde SR and transmural pressure in the brachial artery. Subjects underwent, in randomised order: (1) forearm cuff inflation to 60 mmHg (distal cuff; causing increase in retrograde SR), (2) upper arm cuff inflation to 60 mmHg (proximal cuff; causing increase in retrograde SR + decrease in transmural pressure), and (3) no cuff inflation (Control). RESULTS: The distal and proximal cuff conditions both increased brachial artery retrograde SR (p < 0.001) and oscillatory shear index (p < 0.001). The Control intervention did not alter SR patterns or FMD (p > 0.05). A significant interaction-effect was found for FMD (p < 0.05), with the decrease during distal cuff (from 6.9 ± 2.3% to 6.1 ± 2.5%), being reversed to an increase with proximal cuff (from 6.3 ± 2.0 to 6.9 ± 2.0%). The proximal cuff-related increase in FMD could not be explained by the decrease in antegrade or increase in retrograde shear. CONCLUSION: This study suggests that a decrease in transmural pressure may ameliorate the decline in endothelial function that occurs following exposure to elevated retrograde shear in healthy individuals.

Degenerate four-wave mixing in a silica hollow bottle-like microresonator.

A hollow, bottle-like microresonator (BLMR) was fabricated from a microcapillary with a nearly parabolic profile. From simulations at 1.55 µm the fundamental bottle mode is shown to be in the anomalous dispersion regime, while the conventional whispering gallery mode, confined to the center of the BLMR, is in the normal dispersion regime. Therefore, we have experimentally shown that, for a BLMR with a diameter of 102 um, degenerate four-wave mixing can only be observed by judicious selection of the tapered fiber coupling position. Dispersion tuning in such a system is also briefly discussed theoretically. BLMRs are promising devices for the implementation of sparsely distributed, widely spanned frequency combs at the telecommunications C-band.

Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy.

Based on soft-touch atomic force microscopy, a method is described to reconstruct the secondary structure of single extended biomolecules, without the need for crystallization. The method is tested by accurately reproducing the dimensions of the B-DNA crystal structure. Importantly, intramolecular variations in groove depth of the DNA double helix are resolved, which would be inaccessible for methods that rely on ensemble-averaging.

Sensitization of human cancer cells to gemcitabine by the Chk1 inhibitor MK-8776: cell cycle perturbation and impact of administration schedule in vitro and in vivo.

BACKGROUND: Chk1 inhibitors have emerged as promising anticancer therapeutic agents particularly when combined with antimetabolites such as gemcitabine, cytarabine or hydroxyurea. Here, we address the importance of appropriate drug scheduling when gemcitabine is combined with the Chk1 inhibitor MK-8776, and the mechanisms involved in the schedule dependence. METHODS: Growth inhibition induced by gemcitabine plus MK-8776 was assessed across multiple cancer cell lines. Experiments used clinically relevant "bolus" administration of both drugs rather than continuous drug exposures. We assessed the effect of different treatment schedules on cell cycle perturbation and tumor cell growth in vitro and in xenograft tumor models. RESULTS: MK-8776 induced an average 7-fold sensitization to gemcitabine in 16 cancer cell lines. The time of MK-8776 administration significantly affected the response of tumor cells to gemcitabine. Although gemcitabine induced rapid cell cycle arrest, the stalled replication forks were not initially dependent on Chk1 for stability. By 18 h, RAD51 was loaded onto DNA indicative of homologous recombination. Inhibition of Chk1 at 18 h rapidly dissociated RAD51 leading to the collapse of replication forks and cell death. Addition of MK-8776 from 18-24 h after a 6-h incubation with gemcitabine induced much greater sensitization than if the two drugs were incubated concurrently for 6 h. The ability of this short incubation with MK-8776 to sensitize cells is critical because of the short half-life of MK-8776 in patients' plasma. Cell cycle perturbation was also assessed in human pancreas tumor xenografts in mice. There was a dramatic accumulation of cells in S/G2 phase 18 h after gemcitabine administration, but cells had started to recover by 42 h. Administration of MK-8776 18 h after gemcitabine caused significantly delayed tumor growth compared to either drug alone, or when the two drugs were administered with only a 30 min interval. CONCLUSIONS: There are two reasons why delayed addition of MK-8776 enhances sensitivity to gemcitabine: first, there is an increased number of cells arrested in S phase; and second, the arrested cells have adequate time to initiate recombination and thereby become Chk1 dependent. These results have important implications for the design of clinical trials using this drug combination.

The cancer therapeutic potential of Chk1 inhibitors: how mechanistic studies impact on clinical trial design.

Many anticancer agents damage DNA and activate cell cycle checkpoints that permit time for the cells to repair their DNA and recover. These checkpoints have undergone intense investigation as potential therapeutic targets and Chk1 inhibitors have emerged as promising novel therapeutic agents. Chk1 was initially recognized as a regulator of the G2/M checkpoint, but has since been demonstrated to have additional roles in replication fork stability, replication origin firing and homologous recombination. Inhibition of these pathways can dramatically sensitize cells to some antimetabolites. Current clinical trials with Chk1 inhibitors are primarily focusing on their combination with gemcitabine. Here, we discuss the mechanisms of, and emerging uses for Chk1 inhibitors as single agents and in combination with antimetabolites. We also discuss the pharmacodynamic issues that need to be addressed in attaining maximum efficacy in vivo. Following administration of gemcitabine to mice and humans, tumour cells accumulate in S phase for at least 24 h before recovering. In addition, stalled replication forks evolve over time to become more Chk1 dependent. We emphasize the need to assess cell cycle perturbation and Chk1 dependence of tumours in patients administered gemcitabine. These assessments will define the optimum dose and schedule for administration of these drug combinations.

Availability and use of web-based interventions for patients with head and neck cancer: a scoping review.

PURPOSE: To identify and review the nature, scope and use of web-based interventions for patients with head and neck cancer (HNC). METHOD: A scoping review guided by the methodological framework described by the Joanna Briggs Institute was performed to review empirical studies and websites. Seven electronic databases (CINAHL, Medline, Scopus, Embase, Cochrane, PubMed and PsycInfo) were searched from 2010 to 2020, data extracted and synthesised using thematic analysis. The Google search engine was employed, identifying the first 100 websites, using the search term head and neck cancer. Websites meeting eligibility criteria were assessed using the QUEST analysis tool, and descriptively summarised. RESULTS: Thirteen empirical studies and 32 websites were included. As identified by empirical studies, web-based interventions were developed to provide (1) patient information on HNC and related treatments, (2) advice and support during treatment and (3) management strategies promoting adjustment to life with and beyond HNC. The reviewed websites provided minimal information to aid shared decision-making and facilitate preparedness for treatment, with few utilising patient narratives. Web-based interventions for HNC patients were mainly text based and focused on survivorship. CONCLUSIONS: There is a paucity of theory-based, co-designed web-based interventions using patient narratives. IMPLICATIONS FOR CANCER SURVIVORS: As patients increasingly look to the internet for advice and support, healthcare professionals are in a position to provide high-quality web-based interventions. There is an opportunity to rigorously develop a web-based intervention, containing narratives of peoples' lives before and after HNC treatment, aiding decision-making, preparedness for treatment and self-management.

CD9 co-operation with syndecan-1 is required for a major staphylococcal adhesion pathway.

Epithelial colonization is a critical first step in bacterial pathogenesis. Staphylococcus aureus can utilize several host factors to associate with cells, including α5ß1 integrin and heparan sulfate proteoglycans, such as the syndecans. Here, we demonstrate that a partner protein of both integrins and syndecans, the host membrane adapter protein tetraspanin CD9, is essential for syndecan-mediated staphylococcal adhesion. Fibronectin is also essential in this process, while integrins are only critical for post-adhesion entry into human epithelial cells. Treatment of epithelial cells with CD9-derived peptide or heparin caused significant reductions in staphylococcal adherence, dependent on both CD9 and syndecan-1. Exogenous fibronectin caused a CD9-dependent increase in staphylococcal adhesion, whereas blockade of ß1 integrins did not affect adhesion but did reduce the subsequent internalization of adhered bacteria. CD9 disruption or deletion increased ß1 integrin-mediated internalization, suggesting that CD9 coordinates sequential staphylococcal adhesion and internalization. CD9 controls staphylococcal adhesion through syndecan-1, using a mechanism that likely requires CD9-mediated syndecan organization to correctly display fibronectin at the host cell surface. We propose that CD9-derived peptides or heparin analogs could be developed as anti-adhesion treatments to inhibit the initial stages of staphylococcal pathogenesis. IMPORTANCE Staphylococcus aureus infection is a significant cause of disease and morbidity. Staphylococci utilize multiple adhesion pathways to associate with epithelial cells, including interactions with proteoglycans or ß1 integrins through a fibronectin bridge. Interference with another host protein, tetraspanin CD9, halves staphylococcal adherence to epithelial cells, although CD9 does not interact directly with bacteria. Here, we define the role of CD9 in staphylococcal adherence and uptake, observing that CD9 coordinates syndecan-1, fibronectin, and ß1 integrins to allow efficient staphylococcal infection. Two treatments that disrupt this action are effective and may provide an alternative to antibiotics. We provide insights into the mechanisms that underlie staphylococcal infection of host cells, linking two known adhesion pathways together through CD9 for the first time.

Myeloproliferative neoplasms: diagnosis, management and treatment.

This article provides an overview of myeloproliferative neoplasms for nurses who do not specialise in haematology. Diagnosis, management and treatment of patients with these conditions is discussed, as well as long-term nursing implications.

FANCI functions as a repair/apoptosis switch in response to DNA crosslinks.

Cells counter DNA damage through repair or apoptosis, yet a direct mechanism for this choice has remained elusive. When facing interstrand crosslinks (ICLs), the ICL-repair protein FANCI heterodimerizes with FANCD2 to initiate ICL excision. We found that FANCI alternatively interacts with a pro-apoptotic factor, PIDD1, to enable PIDDosome (PIDD1-RAIDD-caspase-2) formation and apoptotic death. FANCI switches from FANCD2/repair to PIDD1/apoptosis signaling in the event of ICL-repair failure. Specifically, removing key endonucleases downstream of FANCI/FANCD2, increasing ICL levels, or allowing damaged cells into mitosis (when repair is suppressed) all suffice for switching. Reciprocally, apoptosis-committed FANCI reverts from PIDD1 to FANCD2 after a failed attempt to assemble the PIDDosome. Monoubiquitination and deubiquitination at FANCI K523 impact interactor selection. These data unveil a repair-or-apoptosis switch in eukaryotes. Beyond ensuring the removal of unrepaired genomes, the switch's bidirectionality reveals that damaged cells can offset apoptotic defects via de novo attempts at lesion repair.

Poly(ADP-Ribose) Glycohydrolase (PARG) vs. Poly(ADP-Ribose) Polymerase (PARP) - Function in Genome Maintenance and Relevance of Inhibitors for Anti-cancer Therapy.

Poly(ADP-ribose) polymerases (PARPs) are a family of enzymes that catalyze the addition of poly(ADP-ribose) (PAR) subunits onto themselves and other acceptor proteins. PARPs are known to function in a large range of cellular processes including DNA repair, DNA replication, transcription and modulation of chromatin structure. Inhibition of PARP holds great potential for therapy, especially in cancer. Several PARP1/2/3 inhibitors (PARPi) have had success in treating ovarian, breast and prostate tumors harboring defects in the homologous recombination (HR) DNA repair pathway, especially BRCA1/2 mutated tumors. However, treatment is limited to specific sub-groups of patients and resistance can occur, limiting the use of PARPi. Poly(ADP-ribose) glycohydrolase (PARG) reverses the action of PARP enzymes, hydrolysing the ribose-ribose bonds present in poly(ADP-ribose). Like PARPs, PARG is involved in DNA replication and repair and PARG depleted/inhibited cells show increased sensitivity to DNA damaging agents. They also display an accumulation of perturbed replication intermediates which can lead to synthetic lethality in certain contexts. In addition, PARG is thought to play an important role in preventing the accumulation of cytoplasmic PAR and therefore parthanatos, a caspase-independent PAR-mediated type of cell death. In contrast to PARP, the therapeutic potential of PARG has been largely ignored. However, several recent papers have demonstrated the exciting possibilities that inhibitors of this enzyme may have for cancer treatment, both as single agents and in combination with cytotoxic drugs and radiotherapy. This article discusses what is known about the functions of PARP and PARG and the potential future implications of pharmacological inhibition in anti-cancer therapy.

How Cells Handle DNA Breaks during Mitosis: Detection, Signaling, Repair, and Fate Choice.

Mitosis is controlled by a complex series of signaling pathways but mitotic control following DNA damage remains poorly understood. Effective DNA damage sensing and repair is integral to survival but is largely thought to occur primarily in interphase and be repressed during mitosis due to the risk of telomere fusion. There is, however, increasing evidence to suggest tight control of mitotic progression in the incidence of DNA damage, whether induced in mitotic cells or having progressed from failed interphase checkpoints. Here we will discuss what is known to date about signaling pathways controlling mitotic progression and resulting cell fate in the incidence of mitotic DNA damage.

An Ex Vivo Evaluation of Tomographic 3-D Ultrasound, B-Mode Ultrasound, CT And MR Imaging to Measure Artery Diameter, Length and Wall Volume.

Precise measurement of luminal diameter in arteries is important when planning interventional vascular procedures in patients. Measuring wall volume may be important in detecting early artery disease and in the assessment of treatments to prevent atherosclerosis. An ex vivo phantom using porcine arteries was used to evaluate the accuracy with which (i) B-mode ultrasound, (ii) 3-D tomographic ultrasound (tUS), (iii) computed tomography (CT) and (iv) magnetic resonance imaging (MRI) measured length, diameters and volume. The mean error in inner-to-inner diameter measurements by B mode, tUS, CT and MRI were 0.08 ± 0.26, -0.73 ± 0.96 mm, 0.09 ± 0.55 and 0.60 ± 1.01 mm, respectively. The mean error in outer-to-outer diameter measurements by B mode, tUS, CT and MRI were -1.33 ± 0.61, -1.03 ± 0.35, 0.02 ± 1.00 and -0.47 ± 1.32 mm, respectively. The mean error in volume measurements by B mode, tUS, CT and MRI were -0.54 ± 0.62, -0.06 ± 0.09, 0.01 ± 0.18 and -0.20 ± 0.32 cm3, respectively. Errors in length and diameters remain within clinically acceptable thresholds where MRI was the least accurate. tUS was the most accurate method of volume measurement.

An IRAK1-PIN1 signalling axis drives intrinsic tumour resistance to radiation therapy.

Drug-based strategies to overcome tumour resistance to radiotherapy (R-RT) remain limited by the single-agent toxicity of traditional radiosensitizers (for example, platinums) and a lack of targeted alternatives. In a screen for compounds that restore radiosensitivity in p53 mutant zebrafish while tolerated in non-irradiated wild-type animals, we identified the benzimidazole anthelmintic oxfendazole. Surprisingly, oxfendazole acts via the inhibition of IRAK1, a kinase thus far implicated in interleukin-1 receptor (IL-1R) and Toll-like receptor (TLR) immune responses. IRAK1 drives R-RT in a pathway involving IRAK4 and TRAF6 but not the IL-1R/TLR-IRAK adaptor MyD88. Rather than stimulating nuclear factor-κB, radiation-activated IRAK1 prevented apoptosis mediated by the PIDDosome complex (comprising PIDD, RAIDD and caspase-2). Countering this pathway with IRAK1 inhibitors suppressed R-RT in tumour models derived from cancers in which TP53 mutations predict R-RT. Moreover, IRAK1 inhibitors synergized with inhibitors of PIN1, a prolyl isomerase essential for IRAK1 activation in response to pathogens and, as shown here, in response to ionizing radiation. These data identify an IRAK1 radiation-response pathway as a rational chemoradiation therapy target.

Dry reagent-based polymerase chain reaction compared with other laboratory methods available for the diagnosis of Buruli ulcer disease.

BACKGROUND: Because of the multifaceted clinical presentation of Buruli ulcer disease, misclassification of clinically diagnosed cases may occur frequently. Laboratory tests for the confirmation of suspected cases include microscopic examination, culture, polymerase chain reaction (PCR), and histopathologic examination. However, microscopic examination, the only test usually available in areas of endemicity, has a low sensitivity. METHODS: To make a highly sensitive diagnostic method locally available, dry reagent-based PCR (DRB-PCR), which is well adapted to tropical conditions, was pilot-tested in Ghana. Subsequently, the assay was used for the routine diagnosis of Buruli ulcer disease over a period of 2 years. The method was compared with other diagnostic tests to evaluate its performance under field conditions. RESULTS: The interassay agreement rate between DRB-PCR and standard PCR was 91.7% for swab specimens and 95% for tissue specimens. Among all of the locally available tests, DRB-PCR revealed the highest overall positivity ratio. Sixty percent of patients with clinical diagnoses of Buruli ulcer disease had the diagnoses confirmed by DRB-PCR of swab or tissue specimens, compared with 30%-40% of patients who had diagnoses confirmed by microscopic examination of swab or tissue specimens. The positivity ratio of DRB-PCR varied considerably when analyzed per treatment center. Standardization of specimen collection resulted in a 30% increase in the positivity ratio of the assay, compared with that in the pilot-testing phase. CONCLUSIONS: DRB-PCR is a reliable tool for the diagnosis of Buruli ulcer disease. However, PCR assays are suitable for detection only during early stages of the disease, when samples still contain bacilli. The quality of clinical diagnosis and the quality of diagnostic specimens strongly influence the positivity ratio.

NPM1 directs PIDDosome-dependent caspase-2 activation in the nucleolus.

The PIDDosome (PIDD-RAIDD-caspase-2 complex) is considered to be the primary signaling platform for caspase-2 activation in response to genotoxic stress. Yet studies of PIDD-deficient mice show that caspase-2 activation can proceed in the absence of PIDD. Here we show that DNA damage induces the assembly of at least two distinct activation platforms for caspase-2: a cytoplasmic platform that is RAIDD dependent but PIDD independent, and a nucleolar platform that requires both PIDD and RAIDD. Furthermore, the nucleolar phosphoprotein nucleophosmin (NPM1) acts as a scaffold for PIDD and is essential for PIDDosome assembly in the nucleolus after DNA damage. Inhibition of NPM1 impairs caspase-2 processing, apoptosis, and caspase-2-dependent inhibition of cell growth, demonstrating that the NPM1-dependent nucleolar PIDDosome is a key initiator of the caspase-2 activation cascade. Thus we have identified the nucleolus as a novel site for caspase-2 activation and function.

A mitosis-sensing caspase activation platform? New insights into the PIDDosome.

In contrast to the apoptosome and death-inducing signaling complex, the PIDDosome remains an orphan caspase activation platform unassigned to a specific apoptotic pathway. We found that DNA damage-induced PIDDosome formation is blocked by the mitotic checkpoint factor BUBR1 (budding uninhibited by benzimidazole-related 1), via a direct interaction that disrupts the PIDDosome core scaffold. This inhibition occurs at the kinetochore, thus physically connecting the mitotic and apoptotic machineries.