FM-track: a fiducial marker tracking software for studying cell mechanics in a three-dimensional environment

Tracking the deformation of fiducial markers in the vicinity of living cells embedded in compliant synthetic or biological gels is a powerful means to study cell mechanics and mechanobiology in three-dimensional environments. However, current approaches to track and quantify three-dimensional (3D) fiducial marker displacements remain ad-hoc, can be difficult to implement, and may not produce reliable results. Herein, we present a compact software package entitled “FM-Track,” written in the popular Python language, to facilitate feature-based particle tracking tailored for 3D cell micromechanical environment studies. FM-Track contains functions for pre-processing images, running fiducial marker tracking, and post-processing and visualization. FM-Track can thus aid the study of cellular mechanics and mechanobiology by providing an extensible software platform to more reliably extract complex local 3D cell contractile information in transparent compliant gel systems.https://www.sciencedirect.com/science/article/pii/S2352711019303474Published versio

Ichnofacies of the Stairway Sandstone fish-fossil beds (Middle Ordovician, Northern Territory, Australia)

The Stairway Sandstone is a 30-560 m thick succession of Middle Ordovician siliciclastic sedimentary rocks within the Amadeus Basin of central Australia, deposited in the epeiric Larapintine Sea of northern peri-Gondwana. The Stairway Sandstone is significant as one of only two known Gondwanan successions to yield articulated arandaspid (pteraspidomorph agnathan) fish. Herein we use the ichnology of the Stairway Sandstone to reveal insights into the shallow marine habitat of these early vertebrates, and compare it with that of other known pteraspidomorph-bearing localities from across Gondwana. The Stairway Sandstone contains a diverse Ordovician ichnofauna including 22 ichnotaxa of Arenicolites, Arthrophycus, Asterosoma, Cruziana, Didymaulichnus, Diplichnites, Diplocraterion,? Gordia, Lockeia, Monocraterion, Monomorphichnus, Phycodes, Planolites, Rusophycus, Skolithos and Uchirites. These ichnofauna provide a well-preserved example of a typical Ordovician epeiric sea assemblage, recording the diverse ethologies of tracemakers in a very shallow marine environment of flashy sediment accumulation and regularly shifting sandy substrates. New conodont data refine the age of the Stairway Sandstone to the early Darriwilian, with ichnostratigraphic implications for the Cruziana rugosa group and Arthrophycus alleghaniensis

sMILES SSPs: A Library of Semi-Empirical MILES Stellar Population Models with Variable [α\alpha/Fe] Abundances

We present a new library of semi-empirical stellar population models that are based on the empirical MILES and semi-empirical sMILES stellar libraries. The models span a large range of age and metallicity, in addition to an [$\alpha$/Fe] coverage from $-$0.2 to $+$0.6 dex, at MILES resolution (FWHM=2.5$\mathring {\mathrm A}$) and wavelength coverage (3540.5-7409.6$\mathring {\mathrm A}$). These models are aimed at exploring abundance ratios in the integrated light from stellar populations in star clusters and galaxies. Our approach is to build SSPs from semi-empirical stars at particular [$\alpha$/Fe] values, thus producing new SSPs at a range of [$\alpha$/Fe] values from sub-solar to super-solar. We compare these new SSPs with previously published and well-used models and find similar abundance pattern predictions, but with some differences in age indicators. We illustrate a potential application of our new SSPs, by fitting them to the high signal-to-noise data of stacked SDSS galaxy spectra. Age, metallicity and [$\alpha$/Fe] trends were measured for galaxy stacks with different stellar velocity dispersions and show systematic changes, in agreement with previous analyses of subsets of those data. These new SSPs are made publicly available.Comment: 21 pages, 18 figures plus Supplementary Material. Accepted for publication in MNRA

ALDH1A3-acetaldehyde metabolism potentiates transcriptional heterogeneity in melanoma

Cancer cellular heterogeneity and therapy resistance arise substantially from metabolic and transcriptional adaptations, but how these are interconnected is poorly understood. Here, we show that, in melanoma, the cancer stem cell marker aldehyde dehydrogenase 1A3 (ALDH1A3) forms an enzymatic partnership with acetyl-coenzyme A (CoA) synthetase 2 (ACSS2) in the nucleus to couple high glucose metabolic flux with acetyl-histone H3 modification of neural crest (NC) lineage and glucose metabolism genes. Importantly, we show that acetaldehyde is a metabolite source for acetyl-histone H3 modification in an ALDH1A3-dependent manner, providing a physiologic function for this highly volatile and toxic metabolite. In a zebrafish melanoma residual disease model, an ALDH1-high subpopulation emerges following BRAF inhibitor treatment, and targeting these with an ALDH1 suicide inhibitor, nifuroxazide, delays or prevents BRAF inhibitor drug-resistant relapse. Our work reveals that the ALDH1A3-ACSS2 couple directly coordinates nuclear acetaldehyde-acetyl-CoA metabolism with specific chromatin-based gene regulation and represents a potential therapeutic vulnerability in melanoma.</p

Therapeutic gene editing of T cells to correct CTLA-4 insufficiency

Heterozygous mutations in CTLA-4 result in an inborn error of immunity with an autoimmune and frequently severe clinical phenotype. Autologous T cell gene therapy may offer a cure without the immunological complications of allogeneic hematopoietic stem cell transplantation. Here, we designed a homology-directed repair (HDR) gene editing strategy that inserts the CTLA-4 cDNA into the first intron of the CTLA-4 genomic locus in primary human T cells. This resulted in regulated expression of CTLA-4 in CD4+ T cells, and functional studies demonstrated CD80 and CD86 transendocytosis. Gene editing of T cells isolated from three patients with CTLA-4 insufficiency also restored CTLA-4 protein expression and rescued transendocytosis of CD80 and CD86 in vitro. Last, gene-corrected T cells from CTLA-4-/- mice engrafted and prevented lymphoproliferation in an in vivo murine model of CTLA-4 insufficiency. These results demonstrate the feasibility of a therapeutic approach using T cell gene therapy for CTLA-4 insufficiency

<i>HUWE1</i> is a critical colonic tumour suppressor gene that prevents MYC signalling, DNA damage accumulation and tumour initiation

Cancer genome sequencing projects have identified hundreds of genetic alterations, often at low frequencies, raising questions as to their functional relevance. One exemplar gene is HUWE1, which has been found to be mutated in numerous studies. However, due to the large size of this gene and a lack of functional analysis of identified mutations, their significance to carcinogenesis is unclear. To determine the importance of HUWE1, we chose to examine its function in colorectal cancer, where it is mutated in up to 15 per cent of tumours. Modelling of identified mutations showed that they inactivate the E3 ubiquitin ligase activity of HUWE1. Genetic deletion of Huwe1 rapidly accelerated tumourigenic in mice carrying loss of the intestinal tumour suppressor gene Apc, with a dramatic increase in tumour initiation. Mechanistically, this phenotype was driven by increased MYC and rapid DNA damage accumulation leading to loss of the second copy of Apc. The increased levels of DNA damage sensitised Huwe1-deficient tumours to DNA-damaging agents and to deletion of the anti-apoptotic protein MCL1. Taken together, these data identify HUWE1 as a bona fide tumour suppressor gene in the intestinal epithelium and suggest a potential vulnerability of HUWE1-mutated tumours to DNA-damaging agents and inhibitors of anti-apoptotic proteins

RAC1B modulates intestinal tumourigenesis via modulation of WNT and EGFR signalling pathways.

Current therapeutic options for treating colorectal cancer have little clinical efficacy and acquired resistance during treatment is common, even following patient stratification. Understanding the mechanisms that promote therapy resistance may lead to the development of novel therapeutic options that complement existing treatments and improve patient outcome. Here, we identify RAC1B as an important mediator of colorectal tumourigenesis and a potential target for enhancing the efficacy of EGFR inhibitor treatment. We find that high RAC1B expression in human colorectal cancer is associated with aggressive disease and poor prognosis and deletion of Rac1b in a mouse colorectal cancer model reduces tumourigenesis. We demonstrate that RAC1B interacts with, and is required for efficient activation of the EGFR signalling pathway. Moreover, RAC1B inhibition sensitises cetuximab resistant human tumour organoids to the effects of EGFR inhibition, outlining a potential therapeutic target for improving the clinical efficacy of EGFR inhibitors in colorectal cancer

Male circumcision for HIV prevention: current evidence and implementation in sub-Saharan Africa

Heterosexual exposure accounts for most HIV transmission in sub-Saharan Africa, and this mode, as a proportion of new infections, is escalating globally. The scientific evidence accumulated over more than 20 years shows that among the strategies advocated during this period for HIV prevention, male circumcision is one of, if not, the most efficacious epidemiologically, as well as cost-wise. Despite this, and recommendation of the procedure by global policy makers, national implementation has been slow. Additionally, some are not convinced of the protective effect of male circumcision and there are also reports, unsupported by evidence, that non-sex-related drivers play a major role in HIV transmission in sub-Saharan Africa. Here, we provide a critical evaluation of the state of the current evidence for male circumcision in reducing HIV infection in light of established transmission drivers, provide an update on programmes now in place in this region, and explain why policies based on established scientific evidence should be prioritized. We conclude that the evidence supports the need to accelerate the implementation of medical male circumcision programmes for HIV prevention in generalized heterosexual epidemics, as well as in countering the growing heterosexual transmission in countries where HIV prevalence is presently low

Neocortical Axon Arbors Trade-off Material and Conduction Delay Conservation

The brain contains a complex network of axons rapidly communicating information between billions of synaptically connected neurons. The morphology of individual axons, therefore, defines the course of information flow within the brain. More than a century ago, Ramón y Cajal proposed that conservation laws to save material (wire) length and limit conduction delay regulate the design of individual axon arbors in cerebral cortex. Yet the spatial and temporal communication costs of single neocortical axons remain undefined. Here, using reconstructions of in vivo labelled excitatory spiny cell and inhibitory basket cell intracortical axons combined with a variety of graph optimization algorithms, we empirically investigated Cajal's conservation laws in cerebral cortex for whole three-dimensional (3D) axon arbors, to our knowledge the first study of its kind. We found intracortical axons were significantly longer than optimal. The temporal cost of cortical axons was also suboptimal though far superior to wire-minimized arbors. We discovered that cortical axon branching appears to promote a low temporal dispersion of axonal latencies and a tight relationship between cortical distance and axonal latency. In addition, inhibitory basket cell axonal latencies may occur within a much narrower temporal window than excitatory spiny cell axons, which may help boost signal detection. Thus, to optimize neuronal network communication we find that a modest excess of axonal wire is traded-off to enhance arbor temporal economy and precision. Our results offer insight into the principles of brain organization and communication in and development of grey matter, where temporal precision is a crucial prerequisite for coincidence detection, synchronization and rapid network oscillations

Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

Background and aims: Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress and novel therapeutic response in PC to develop a biomarker driven therapeutic strategy targeting DDR and replication stress in PC. Methods: We interrogated the transcriptome, genome, proteome and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient derived xenografts and human PC organoids. Results: Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, co-segregates with response to platinum (P &lt; 0.001) and PARP inhibitor therapy (P &lt; 0.001) in vitro and in vivo. We generated a novel signature of replication stress with which predicts response to ATR (P &lt; 0.018) and WEE1 inhibitor (P &lt; 0.029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P &lt; 0.001) but not associated with DDR deficiency. Conclusions: Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR proficient PC, and post-platinum therapy