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BRCA1 mutations are associated with increased breast and ovarian cancer risk. BRCA1-mutant tumors are high-grade, recurrent, and often become resistant to standard therapies. Herein, we performed a targeted CRISPR-Cas9 screen and identified MEPCE, a methylphosphate capping enzyme, as a synthetic lethal interactor of BRCA1. Mechanistically, we demonstrate that depletion of MEPCE in a BRCA1-deficient setting led to dysregulated RNA polymerase II (RNAPII) promoter-proximal pausing, R-loop accumulation, and replication stress, contributing to transcription-replication collisions. These collisions compromise genomic integrity resulting in loss of viability of BRCA1-deficient cells. We also extend these findings to another RNAPII-regulating factor, PAF1. This study identifies a new class of synthetic lethal partners of BRCA1 that exploit the RNAPII pausing regulation and highlight the untapped potential of transcription-replication collision-inducing factors as unique potential therapeutic targets for treating cancers associated with BRCA1 mutations.

With $n$-body simulations we investigate the stability of tilted circumbinary planetary systems consisting of two nonzero mass planets. The planets are initially in circular orbits that are coplanar to each other, as would be expected if they form in a flat but tilted circumbinary gas disc and decouple from the disc within a time difference that is much less than the disc nodal precession period. We constrain the parameters of stable multiple planet circumbinary systems. Both planet-planet and planet-binary interactions can cause complex planet tilt oscillations which can destabilise the orbits of one or both planets. The system is considerably more unstable than the effects of these individual interactions would suggest, due to the interplay between these two interactions. The stability of the system is sensitive to the binary eccentricity, the orbital tilt and the semi-major axes of the two circumbinary planets. With an inner planet semi-major axis of $5\,a_{\rm b}$, where $a_{\rm b}$ is semi-major axis of the binary, the system is generally stable if the outer planet is located at $\gtrsim 8\,a_{\rm b}$, beyond the 2:1 mean motion resonance with the inner planet. For larger inner planet semi-major axis the system is less stable because the von-Zeipel--Kozai--Lidov mechanism plays a significant role, particularly for low binary-eccentricity cases. For the unstable cases, the most likely outcome is that one planet is ejected and the other remains bound on a highly eccentric orbit. Therefore we suggest that this instability is an efficient mechanism for producing free-floating planets., Comment: 13 pages, 10 figures

Pan-cancer analysis of TCGA and CPTAC (proteomics) data shows that SULF1 and SULF2 are oncogenic in a number of human malignancies and associated with poor survival outcomes. Our studies document a consistent upregulation of SULF1 and SULF2 in HNSC which is associated with poor survival outcomes. These heparan sulfate editing enzymes were considered largely functional redundant but single-cell RNAseq (scRNAseq) shows that SULF1 is secreted by cancer-associated fibroblasts in contrast to the SULF2 derived from tumor cells. Our RNAScope and patient-derived xenograft (PDX) analysis of the HNSC tissues fully confirm the stromal source of SULF1 and explain the uniform impact of this enzyme on the biology of multiple malignancies. In summary, SULF2 expression increases in multiple malignancies but less consistently than SULF1, which uniformly increases in the tumor tissues and negatively impacts survival in several types of cancer even though its expression in cancer cells is low. This paradigm is common to multiple malignancies and suggests a potential for diagnostic and therapeutic targeting of the heparan sulfatases in cancer diseases.

Pan-cancer analysis of TCGA and CPTAC (proteomics) data shows that SULF1 and SULF2 are oncogenic in a number of human malignancies and associated with poor survival outcomes. Our studies document a consistent upregulation of SULF1 and SULF2 in HNSC which is associated with poor survival outcomes. These heparan sulfate editing enzymes were considered largely functional redundant but single-cell RNAseq (scRNAseq) shows that SULF1 is secreted by cancer-associated fibroblasts in contrast to the SULF2 derived from tumor cells. Our RNAScope and patient-derived xenograft (PDX) analysis of the HNSC tissues fully confirm the stromal source of SULF1 and explain the uniform impact of this enzyme on the biology of multiple malignancies. In summary, SULF2 expression increases in multiple malignancies but less consistently than SULF1, which uniformly increases in the tumor tissues and negatively impacts survival in several types of cancer even though its expression in cancer cells is low. This paradigm is common to multiple malignancies and suggests a potential for diagnostic and therapeutic targeting of the heparan sulfatases in cancer diseases.

Accretion discs appear in many astrophysical systems. In most cases, these discs are probably not completely axisymmetric. Discs in binary systems are often found to be misaligned with respect to the binary orbit. In this case, the gravitational torque from a companion induces nodal precession in misaligned rings of gas. We first calculate whether this precession is strong enough to overcome the internal disc torques communicating angular momentum. For typical parameters, precession torque wins. To check this result, we perform numerical simulations using the Smoothed Particle Hydrodynamics code, PHANTOM, and confirm that sufficiently thin and sufficiently inclined discs can break into distinct planes that precess effectively independently. Disc tearing is widespread and severely changes the disc structure. It enhances dissipation and promotes stronger accretion onto the central object. We also perform a stability analysis on isolated warped discs to understand the physics of disc breaking and tearing observed in numerical simulations. The instability appears in the form of viscous anti-diffusion of the warp amplitude and the surface density. The discovery of disc breaking and tearing has revealed new physical processes that dramatically change the evolution of accretion discs, with obvious implications for observed systems.

The distribution of orbital energies imparted into stellar debris following the close encounter of a star with a supermassive black hole is the principal factor in determining the rate of return of debris to the black hole, and thus in determining the properties of the resulting lightcurves from such events. We present simulations of tidal disruption events for a range of $\beta\equiv r_{\rm t}/r_{\rm p}$ where $r_{\rm p}$ is the pericentre distance and $r_{\rm t}$ the tidal radius. We perform these simulations at different spatial resolutions to determine the numerical convergence of our models. We compare simulations in which the heating due to shocks is included or excluded from the dynamics. For $\beta \lesssim 8$ the simulation results are well-converged at sufficiently moderate-to-high spatial resolution, while for $\beta \gtrsim 8$ the breadth of the energy distribution can be grossly exaggerated by insufficient spatial resolution. We find that shock heating plays a non-negligible role only for $\beta \gtrsim 4$, and that typically the effect of shock heating is mild. We show that self-gravity can modify the energy distribution over time after the debris has receded to large distances for all $\beta$. Primarily, our results show that across a range of impact parameters, while the shape of the energy distribution varies with $\beta$, the width of the energy spread imparted to the bulk of the debris is closely matched to the canonical spread, $\Delta E = GM_\bullet R_\star/r_{\rm t}^2$, for the range of $\beta$ we have simulated., Comment: 17 pages, 7 figures, accepted for publication in ApJ

Mutations in several genes encoding components of the SWI/SNF chromatin remodeling complex cause neurodevelopmental disorders (NDDs). Here, we report on 5 individuals with mutations in SMARCD1, presenting with developmental delay, intellectual disability, hypotonia, feeding difficulties, and small hands and feet. The mutations were proven to be de novo in 4 of the 5 individuals, by trio exome sequencing. Mutations in other SWI/SNF components cause Coffin-Siris syndrome and Nicolaides-Baraitser syndrome, or other syndromic and non-syndromic NDDs. Although the individuals presented here have dysmorphisms and some clinical overlap with these syndromes, they lack the typical facial dysmorphisms. To gain insight into the function of SMARCD1 in neurons, we investigated the Drosophila ortholog, Bap60, in postmitotic memory-forming neurons of the adult Drosophila mushroom body (MB). Targeted knockdown of Bap60 in the MB of adult flies causes defects in long-term memory. Mushroom body specific transcriptome analysis revealed that Bap60 is required for context-dependent expression of genes involved in neuron function and development in juvenile flies when synaptic connections are actively being formed in response to experience. Taken together, we identify a NDD caused by SMARCD1 mutations and establish a role for the SMARCD1 ortholog Bap60 in regulation of neurodevelopmental genes during a critical time window of juvenile adult brain development that is essential in establishing neuronal circuits that are required for learning and memory.

The formation and recall of long-term memory (LTM) requires neuron activity-induced gene expression. Transcriptome analysis has been used to identify genes that have altered expression after memory acquisition, however, we still have an incomplete picture of the transcriptional changes that are required for LTM formation. The complex spatial and temporal dynamics of memory formation creates significant challenges in defining memory-relevant gene expression changes. The Drosophila mushroom body (MB) is a signaling hub in the insect brain that integrates sensory information to form memories across several different experimental memory paradigms. Here, we performed transcriptome analysis in the MB at two time points after the acquisition of LTM: 1 hr and 24 hr. The MB transcriptome was compared to biologically paired whole head (WH) transcriptomes. In both, we identified more transcript level changes at 1 hr after memory acquisition (WH = 322, MB = 302) than at 24 hr (WH = 23, MB = 20). WH samples showed downregulation of developmental genes and upregulation of sensory response genes. In contrast, MB samples showed vastly different changes in transcripts involved in biological processes that are specifically related to LTM. MB-downregulated genes were highly enriched for metabolic function. MB-upregulated genes were highly enriched for known learning and memory processes, including calcium-mediated neurotransmitter release and cAMP signaling. The neuron activity inducible genes Hr38 and sr were also specifically induced in the MB. These results highlight the importance of sampling time and cell type in capturing biologically relevant transcript level changes involved in learning and memory. Our data suggests that MB cells transiently upregulate known memory-related pathways after memory acquisition and provides a critical frame of reference for further investigation into the role of MB-specific gene regulation in memory.

Proteinase-Activated Receptors (PARs) are a four-member family of G-protein coupled receptors that are activated via proteolysis. PAR4 is a member of this family that is cleaved and activated by the serine proteinases such as thrombin, trypsin and cathepsin-G. PAR4 is expressed in a variety of tissues and cell types including the platelets, vascular smooth muscle cells and neuronal cells. In studying PAR4 signaling and trafficking, we observed dynamic changes in the cell membrane with spherical membrane protrusions that resemble plasma membrane blebbing. Since non-apoptotic membrane blebbing is now recognized as an important regulator of cell migration, cancer cell invasion, and vesicular content release we sought to elucidate the signaling pathway downstream of PAR4 activation that leads to such events. Using a combination of pharmacological inhibition and CRISPR/Cas9 mediated gene editing approaches we establish that PAR4-dependent membrane blebbing occurs independently of the Gαq/11 and Gαi signaling pathways and is dependent on signaling via the β-arrestin-1/-2 pathway and RhoA signaling. In order to gain a more comprehensive understanding of β-arrestin mediated signaling downstream of PAR4 and to guide future studies, we undertook RNAseq analysis of PAR4 activated genes in control cells and in cells lacking β-arrestin-1/-2. A list of differentially expressed genes was generated followed by Gene Ontology (GO) and enrichment analysis revealing PAR4 regulation of genes involved in processes including blood coagulation and circulation, cell-cell adhesion, sensory perception and neuron-neuron synaptic transmission, terms that relates back to known function of PAR4 and that are consistent with our finding of membrane blebbing triggered by PAR4 activation. Together these studies provide further mechanistic insight into PAR4 regulation of cellular function. SIGNIFICANCE STATEMENT We find that the thrombin receptor PAR4 triggers cell membrane blebbing in a RhoA- and β-arrestin-dependent manner. In addition to identifying novel cellular responses mediated by PAR4, these data provide further evidence for biased signaling in PAR4 since membrane blebbing was dependent on some, but not all, signaling pathways activated by PAR4. Finally through CRISPR/Cas9-mediated targeting and RNA-seq analysis we catalogue here PAR4-dependent transcription that is dependent on β-arrestin.

Proteinase-Activated Receptors (PARs) are a four-member family of G-protein coupled receptors that are activated via proteolysis. PAR4 is a member of this family that is cleaved and activated by serine proteinases such as thrombin, trypsin and cathepsin-G. PAR4 is expressed in a variety of tissues and cell types including platelets, vascular smooth muscle cells and neuronal cells. In studying PAR4 signalling and trafficking, we observed dynamic changes in the cell membrane with spherical membrane protrusions that resemble plasma membrane blebbing. Since non-apoptotic membrane blebbing is now recognized as an important regulator of cell migration, cancer cell invasion, and vesicular content release we sought to elucidate the signalling pathway downstream of PAR4 activation that leads to such events. Using a combination of pharmacological inhibition and CRISPR/Cas9-mediated gene-editing approaches we establish that PAR4-dependent membrane blebbing occurs independently of the Gαq/11and Gαisignalling pathways and is dependent on signalling via the β-arrestin-1/-2 and RhoA signalling pathways. In order to gain a more comprehensive understanding of β-arrestin-mediated signalling downstream of PAR4 and to guide future studies, we undertook RNA-seq analysis of PAR4 activated genes in control cells and in cells lacking β-arrestin-1/-2. A list of differentially expressed genes was generated followed by Gene Ontology (GO) and enrichment analysis, revealing PAR4 regulation of genes involved in processes including blood coagulation and circulation, cell-cell adhesion, sensory perception and neuron-neuron synaptic transmission-terms that relate back to known functions of PAR4 and are consistent with our finding of membrane blebbing triggered by PAR4 activation. Together these studies provide further mechanistic insight into PAR4 regulation of cellular function.Significance StatementWe find that the thrombin receptor PAR4 triggers cell membrane blebbing in a RhoA- and β-arrestin-dependent manner. In addition to identifying novel cellular responses mediated by PAR4, these data provide further evidence for biased signaling in PAR4 since membrane blebbing was dependent on some, but not all, signaling pathways activated by PAR4. Finally through CRISPR/Cas9-mediated targeting and RNA-seq analysis we catalogue here PAR4-dependent transcription that is dependent on β-arrestin.

Technology has led to rapid progress in the identification of genes involved in neurodevelopmental disorders such as intellectual disability (ID), but our functional understanding of the causative genes is lagging. Here, we show that the SWI/SNF chromatin remodelling complex is one of the most over-represented cellular components disrupted in ID. We investigated the role of individual subunits of this large protein complex using targeted RNA interference in post-mitotic memory-forming neurons of the Drosophila mushroom body (MB). Knockdown flies were tested for defects in MB morphology, short-term memory and long-term memory. Using this approach, we identified distinct roles for individual subunits of the Drosophila SWI/SNF complex. Bap60, Snr1 and E(y)3 are required for pruning of the MBγ neurons during pupal morphogenesis, while Brm and Osa are required for survival of MBγ axons during ageing. We used the courtship conditioning assay to test the effect of MB-specific SWI/SNF knockdown on short- and long-term memory. Several subunits, including Brm, Bap60, Snr1 and E(y)3, were required in the MB for both short- and long-term memory. In contrast, Osa knockdown only reduced long-term memory. Our results suggest that individual components of the SWI/SNF complex have different roles in the regulation of structural plasticity, survival and functionality of post-mitotic MB neurons. This study highlights the many possible processes that might be disrupted in SWI/SNF-related ID disorders. Our broad phenotypic characterization provides a starting point for understanding SWI/SNF-mediated gene regulatory mechanisms that are important for development and function of post-mitotic neurons., Summary: The SWI/SNF chromatin remodelling complex is the most over-represented protein complex in the intellectual disability. Different components of this complex have distinct roles in development and function of memory-forming neurons in the Drosophila mushroom body.

Mutations in several genes encoding components of the SWI/SNF chromatin remodeling complex cause syndromic intellectual disability (ID). Here, we report on 5 individuals with mutations in the SMARCD1 gene, presenting with ID, developmental delay, hypotonia, feeding difficulties, and small extremities. The mutations were proven to be de novo in 4 of the 5 individuals. Mutations in other SWI/SNF components cause Coffin-Siris, Nicolaides-Baraitser, or other syndromic ID disorders. Although the individuals presented here have some clinical overlap with these disorders, they lack the typical facial dysmorphisms. To gain insight into the function of SMARCD1 in neurons, we investigated the Drosophila ortholog, Bap60, in postmitotic memory-forming neurons of the adult Drosophila mushroom body (MB). Targeted knockdown of Bap60 in the MB of adult flies causes defects in long-term memory. Mushroom body specific transcriptome analysis revealed that Bap60 is required for context-dependent expression of genes involved in neuron function and development in juvenile flies when synaptic connections are actively being formed in response to experience. Taken together, we identify SMARCD1 mutations as a novel cause of ID, and establish a role for the SMARCD1 ortholog Bap60 in regulation of neurodevelopmental genes during a critical time window of juvenile adult brain development that is essential in establishing neuronal circuits that are required for learning and memory.

The formation and recall of long-term memory (LTM) requires neuron activity-induced gene expression. Transcriptome analysis has been used to identify genes that have altered expression after memory acquisition, however, we still have an incomplete picture of the transcriptional changes that are required for LTM formation. The complex spatial and temporal dynamics of memory formation creates significant challenges in defining memory-relevant gene expression changes. The mushroom body (MB) is a signaling hub in the insect brain that integrates sensory information to form memories. Here, we performed transcriptome analysis in theDrosophilaMB at two time points after the acquisition of LTM: 1 hour and 24 hours. The MB transcriptome was compared to biologically paired whole head (WH) transcriptomes. In both, we identified more transcriptional changes 1 hour after memory acquisition (WH = 322, MB = 302) than at 24 hours (WH = 23, MB = 20). WH samples showed downregulation of developmental genes and upregulation of sensory response genes. In contrast, MB samples showed vastly different gene expression changes affecting biological processes that are specifically related to LTM. MB-downregulated genes were highly enriched for metabolic function, consistent with the MB-specific energy influx that occurs during LTM formation. MB-upregulated genes were highly enriched for known learning and memory processes, including calcium-mediated neurotransmitter release and cAMP signalling. The neuron activity inducible geneshr38andsrwere also specifically induced in the MB. These results highlight the importance of sampling time and cell type in capturing biologically relevant transcriptional changes involved in learning and memory. Our data suggests that MB cells transiently upregulate known memory-related pathways after memory acquisition and provides a critical frame of reference for further investigation into the role of MB-specific gene regulation in memory.

Defects in neuronal migration cause brain malformations, which are associated with intellectual disability (ID) and epilepsy. Using exome sequencing, we identified compound heterozygous variants (p.Arg71His and p. Leu729ThrfsTer6) in TMTC3, encoding transmembrane and tetratricopeptide repeat containing 3, in four siblings with nocturnal seizures and ID. Three of the four siblings have periventricular nodular heterotopia (PVNH), a common brain malformation caused by failure of neurons to migrate from the ventricular zone to the cortex. Expression analysis using patient-derived cells confirmed reduced TMTC3 transcript levels and loss of the TMTC3 protein compared to parental and control cells. As TMTC3 function is currently unexplored in the brain, we gathered support for a neurobiological role for TMTC3 by generating flies with post-mitotic neuron-specific knockdown of the highly conserved Drosophila melanogaster TMTC3 ortholog, CG4050/tmtc3. Neuron-specific knockdown of tmtc3 in flies resulted in increased susceptibility to induced seizures. Importantly, this phenotype was rescued by neuron-specific expression of human TMTC3, suggesting a role for TMTC3 in seizure biology. In addition, we observed co-localization of TMTC3 in the rat brain with vesicular GABA transporter (VGAT), a presynaptic marker for inhibitory synapses. TMTC3 is localized at VGAT positive pre-synaptic terminals and boutons in the rat hypothalamus and piriform cortex, suggesting a role for TMTC3 in the regulation of GABAergic inhibitory synapses. TMTC3 did not co-localize with Vglut2, a presynaptic marker for excitatory neurons. Our data identified TMTC3 as a synaptic protein that is involved in PVNH with ID and epilepsy, in addition to its previously described association with cobblestone lissencephaly.

A firm level simulation model (MARSIM) was developed to analyze the survival of different shrimp farm sizes in Texas. The model simulates the annual activities of a shrimp farm: production, finances, cash receipts, capital replacement and depreciation, cash flows, income taxes, balances, and growth. A firm is replicated 50 times over a 10-year planning horizon. Random values for shrimp growth and survival, temperature, hurricanes, and prices received in each of 10 years are generated from multivariate empirical probability density functions (pdf) for these variables. For the analysis summarized here, a shrimp farm was simulated using 3 different size systems and 4 different pond sizes. Results indicate that higher rates of return and faster payback are associated with larger total farm size and larger ponds. For large farms (400 surface hectares), pond size becomes less critical to obtaining an acceptable rate of return to investment. The amount of time taken to construct a facility significantly impacts the rate of return. Hurricanes, prices, production, and temperature variation are also critical factors affecting the firm's returns and survival.

The potential treeline in continental climates is controlled mainly by low temperature. In contrast, wind is the principal factor limiting tree growth in oceanic climates like that of Britain (Tranquillini, 1979). The natural treeline has recently been investigated in Britain and is higher than previously believed.

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Compact binaries such as double neutron stars or a neutron star paired with a black-hole, are strong sources of gravitational waves during coalescence and also the likely progenitors of various electromagnetic phenomena, notably short-duration gamma-ray bursts (SGRBs), and kilonovae. In this work, we generate populations of synthetic binaries and place them in galaxies from the large-scale hydrodynamical galaxy evolution simulation EAGLE. With our zELDA code, binaries are seeded in proportion to star formation rate, and we follow their evolution to merger using both the BPASS and COSMIC binary stellar evolution codes. We track their dynamical evolution within their host galaxy potential, to estimate the galactocentric distance at the time of the merger. Finally, we apply observational selection criteria to allow comparison of this model population with the legacy sample of SGRBs. We find a reasonable agreement with the redshift distribution (peaking at $0.526$)., Comment: Accepted for publication in MNRAS, 21 Pages (6 Tables, 14 Figures), 14 Pages Appendix (4 Tables, 16 Figures)

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