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Abstract A remarkable observation emerging from recent cancer genome analyses is the identification of chromothripsis as a one‐off genomic catastrophe, resulting in massive somatic DNA structural rearrangements (SRs). Largely due to lack of suitable model systems, the mechanistic basis of chromothripsis has remained elusive. We developed an integrative method termed “complex alterations after selection and transformation (CAST),” enabling efficient in vitro generation of complex DNA rearrangements including chromothripsis, using cell perturbations coupled with a strong selection barrier followed by massively parallel sequencing. We employed this methodology to characterize catastrophic SR formation processes, their temporal sequence, and their impact on gene expression and cell division. Our in vitro system uncovered a propensity of chromothripsis to occur in cells with damaged telomeres, and in particular in hyperploid cells. Analysis of primary medulloblastoma cancer genomes verified the link between hyperploidy and chromothripsis in vivo. CAST provides the foundation for mechanistic dissection of complex DNA rearrangement processes.

Many cellular processes involve the recruitment of proteins to specific membranes, which are decorated with distinctive lipids that act as docking sites. The phosphoinositides form signaling hubs, and we examine mechanisms underlying recruitment. We applied a physiological, quantitative, liposome microarray-based assay to measure the membrane-binding properties of 91 pleckstrin homology (PH) domains, the most common phosphoinositide-binding target. 10,514 experiments quantified the role of phosphoinositides in membrane recruitment. For most domains examined, the observed binding specificity implied cooperativity with additional signaling lipids. Analyses of PH domains with similar lipid-binding profiles identified a conserved motif, mutations in which—including some found in human cancers—induced discrete changes in binding affinities in vitro and protein mislocalization in vivo. The data set reveals cooperativity as a key mechanism for membrane recruitment and, by enabling the interpretation of disease-associated mutations, suggests avenues for the design of small molecules targeting PH domains.

Sumsets as unions of sumsets of subsets, Discrete Analysis 2017:14, 5 pp. In May 2016 there was a remarkable development in additive combinatorics. First, Croot, Lev and Pach managed to use the so-called polynomial method to obtain an exponentially small upper bound for a problem closely related to the cap-set problem, a major open problem in the area. Then within a couple of weeks, Jordan Ellenberg and Dion Gijswijt independently saw how to adapt the Croot-Lev-Pach argument to solve the cap-set problem itself. This was reported on in several places, including [a blog post on this website](http://discreteanalysisjournal.com/post/45-an-exponential-upper-bound-for-the-cap-set-problem). Soon after that, Terence Tao found [a beautiful way of expressing the argument](https://terrytao.wordpress.com/2016/05/18/a-symmetric-formulation-of-the-croot-lev-pach-ellenberg-gijswijt-capset-bound/) in terms of a concept that came to be called slice rank, which clarified the previous proofs and led quickly to further results. The theorem of Ellenberg and Gijswijt implies that there is a constant $c

Climate change is a global issue with effects that are difficult to manage at a regional scale. Yet more often than not climate factors are just some of multiple stressors affecting species on a population level. Non-climatic factors—especially those of anthropogenic origins—may play equally important roles with regard to impacts on species and are often more feasible to address. Here we assess the influence of climate change on population trends of the endangered Yellow-eyed penguin (Megadyptes antipodes) over the last 30 years, using a Bayesian model. Sea surface temperature (SST) proved to be the dominating factor influencing survival of both adult birds and fledglings. Increasing SST since the mid-1990s was accompanied by a reduction in survival rates and population decline. The population model showed that 33% of the variation in population numbers could be explained by SST alone, significantly increasing pressure on the penguin population. Consequently, the population becomes less resilient to non-climate related impacts, such as fisheries interactions, habitat degradation and human disturbance. However, the extent of the contribution of these factors to declining population trends is extremely difficult to assess principally due to the absence of quantifiable data, creating a discussion bias towards climate variables, and effectively distracting from non-climate factors that can be managed on a regional scale to ensure the viability of the population.

Operation Warp Speed was a partnership created to accelerate the development of Covid-19 vaccines. The National Institutes of Health oversaw one data and safety monitoring board to review/monitor all Operation Warp Speed trials. This article describes the challenges faced in monitoring these trials and provides ideas for future similar endeavors. [ABSTRACT FROM AUTHOR]

Objective: To assess the reliability of a BMI-based Silhouette Matching Test (BMI-SMT). Methods: The perceptions of ideal and current body images of 215 ninth through twelfth graders' were assessed at 5 different schools within a mid-Atlantic state public school system. Results: Findings provided quantifiable data and discriminating measurements of community and population-based body image perceptions. Conclusion: The BMI-SMT technique provided reliable information to help community and individual-based programs track and measure body-image perception data among individuals and populations.

New bounds on curve tangencies and orthogonalities, Discrete Analysis 2016:18, 22 pp. An important subfield of combinatorial geometry is that of _incidence problems_. Typically with such a problem one has two collections $A$ and $B$ of geometrical objects and some notion of incidence concerning them, and one wants to know how many incidences there can be. A fundamental theorem of this kind is the Szemerédi-Trotter theorem, which asserts that given $n$ points and $m$ lines in the plane, the number of incidences between them (that is, the number of pairs $(p,\ell)$ where $p$ is one of the points, $\ell$ is one of the lines, and $p$ is contained in $\ell$) is at most $C(n+m+(mn)^{2/3})$. Another important problem in the area is the _joints problem_, which is now a theorem of Larry Guth and Nets Katz. Given a set $L$ of lines in $\mathbb R^3$, define a _joint_ to be a point $p\in\mathbb R^3$ such that there are three lines $\ell_1,\ell_2$ and $\ell_3$ that meet at $p$ and have linearly independent directions. Guth and Katz proved that $n$ lines can give rise to at most $O(n^{3/2})$ joints, which is best possible, as one can see by taking all axis parallel lines in $\mathbb R^3$ that intersect the grid $\{1,2,\dots,m\}^3$, with $m\sim\sqrt n$. This was part of the proof of their remarkable solution to the Erdős distance problem [2]. This paper is about incidences of a special kind between algebraic curves in the plane. Given a set $C$ of such curves, a _tangency_ is a point $p$ in the plane and a line $\ell$ through $p$ such that at least two curves in $C$ go through $p$ in direction $l$. An _orthogonality_ is a point $p$ and a line $l$ through $p$ such that at least one curve in $C$ goes through $p$ in the direction of $\ell$ and at least one curve in $C$ goes through $p$ in the direction orthogonal to $\ell$. (Throughout, we are assuming that the curves are not singular at $p$.) The first main result of the paper roughly speaking states that a set $\mathcal L$ of $n$ algebraic curves of degree at most $D$ can give rise to at most $C_Dn^{3/2}$ tangencies. A more precise statement is that if you define the _multiplicity_ of a tangency $(p,\ell)$ to be the number of curves in $\mathcal L$ that go through $p$ in direction $\ell$, then the sum of the multiplicities over all the tangencies is at most $C_Dn^{3/2}$. Like Guth and Katz's proof of the joints problem, and Zeev Dvir's famous solution of the finite-field Kakeya problem [1], the proof uses the polynomial method. They also prove the result in arbitrary fields, provided that $|\mathcal L|\leq c_D\chi^2$, where $\chi$ is the characteristic of the field (where this should be interpreted as meaning that there is no restriction if the characteristic is zero). The theorem about orthogonalities is a little more complicated to state. One would like to say that $n$ plane curves of degree $D$ can give rise to at most $C_Dn^{3/2}$ orthogonalities, but that is false: for example, one can take $n/2$ parallel lines and another $n/2$ parallel lines that are orthogonal to the first ones. However, in a certain sense this is the only kind of counterexample. A precise statement can be found as Theorem 2 in the paper, but the rough idea is as follows. We say that $X$ is a _family of curves_ if it can be defined in a polynomial manner. Then if $k$ is a field and $X$ is a family of curves in $k^2$ of degree at most $D$, then one of the following two situations occurs. Either every set $\mathcal L$ of $n$ curves from $X$ gives rise to at most $C_{D,X}n^{3/2}$ orthogonalities or for every $n\leq c_D\chi^2$ one can find $n$ curves in $X$ that give rise to $n^2(1/4-o_{D,X}(1))$ orthogonalities (where $o_{D,X}(1)$ denotes a term that tends to zero as $n$, and hence also the characteristic, tend to infinity while $D$ and the equations that define the family $X$ remain fixed). Both results are proved by first transforming the set of curves into a set of curves in $k^3$ such that tangencies/orthogonalities in the original set correspond to intersections in the new set. A simple example (given in the paper at the end of Section 1.3) shows that the condition that the curves should be algebraic of bounded degree is essential. [1] Zeev Dvir, _On the size of Kakeya sets in finite fields_, JAMS 22 (2009), 1093–1097; [preprint available online](https://www.cs.princeton.edu/~zdvir/papers/Dvir09.pdf) [2] Larry Guth and Nets. Katz, On the Erdo ̋s distinct distance problem in the plane., Ann. of Math. 181 (2015), 155–190; or see [arxiv:1011.4105](https://arxiv.org/abs/1011.4105)

The nuclear pore complex (NPC) mediates nucleocytoplasmic transport through the nuclear envelope. How the NPC assembles into this double membrane boundary has remained enigmatic. Here, we captured temporally staged assembly intermediates by correlating live cell imaging with high-resolution electron tomography and super-resolution microscopy. Intermediates were dome-shaped evaginations of the inner nuclear membrane (INM), that grew in diameter and depth until they fused with the flat outer nuclear membrane. Live and super-resolved fluorescence microscopy revealed the molecular maturation of the intermediates, which initially contained the nuclear and cytoplasmic ring component Nup107, and only later the cytoplasmic filament component Nup358. EM particle averaging showed that the evagination base was surrounded by an 8-fold rotationally symmetric ring structure from the beginning and that a growing mushroom-shaped density was continuously associated with the deforming membrane. Quantitative structural analysis revealed that interphase NPC assembly proceeds by an asymmetric inside-out extrusion of the INM.

In this note we generalize a recent theorem of Guth and Katz on incidences between points and lines in 3-space from characteristic 0 to characteristic $p$ , and we explain how some of the special features of algebraic geometry in characteristic $p$ manifest themselves in problems of incidence geometry.

Abstract The generation of mathematical models of biological processes, the simulation of these processes under different conditions, and the comparison and integration of multiple data sets are explicit goals of systems biology that require the knowledge of the absolute quantity of the system's components. To date, systematic estimates of cellular protein concentrations have been exceptionally scarce. Here, we provide a quantitative description of the proteome of a commonly used human cell line in two functional states, interphase and mitosis. We show that these human cultured cells express at least ∼10 000 proteins and that the quantified proteins span a concentration range of seven orders of magnitude up to 20 000 000 copies per cell. We discuss how protein abundance is linked to function and evolution.

Polo-like kinase 1 (PLK1) orchestrates multiple events of cell division. Although PLK1 function has been intensively studied in centriole-containing and rapidly cycling somatic cells, much less is known about its function in the meiotic divisions of mammalian oocytes, which arrest for a long period of time in prophase before meiotic resumption and lack centrioles for spindle assembly. Here, using specific small molecule inhibition combined with live mouse oocyte imaging, we comprehensively characterize meiotic PLK1's functions. We show that PLK1 becomes activated at meiotic resumption on microtubule organizing centers (MTOCs) and later at kinetochores. PLK1 is required for efficient meiotic resumption by promoting nuclear envelope breakdown. PLK1 is also needed to recruit centrosomal proteins to acentriolar MTOCs to promote normal spindle formation, as well as for stable kinetochore-microtubule attachment. Consequently, PLK1 inhibition leads to metaphase I arrest with misaligned chromosomes activating the spindle assembly checkpoint (SAC). Unlike in mitosis, the metaphase I arrest is not bypassed by the inactivation of the SAC. We show that PLK1 is required for the full activation of the anaphase promoting complex/cyclosome (APC/C) by promoting the degradation of the APC/C inhibitor EMI1 and is therefore essential for entry into anaphase I. Moreover, our data suggest that PLK1 is required for proper chromosome segregation and the maintenance of chromosome condensation during the meiosis I-II transition, independently of the APC/C. Thus, our results define the meiotic roles of PLK1 in oocytes and reveal interesting differential requirements of PLK1 between mitosis and oocyte meiosis in mammals.

Human sera from the United States, Thailand, and sub-Saharan Africa and chimpanzee sera were tested for neutralizing antibodies to 3 chimpanzee adenoviruses. Antibodies were more common in humans residing in sub-Saharan Africa than in humans living in the United States or Thailand. This finding suggests cross-species transmission of chimpanzee adenoviruses.

O6-alkylguanine-DNA alkyltransferase (AGT) fusion proteins can be specifically and covalently labeled with fluorescent O6-benzylguanine (O6-BG) derivatives for multicolor live cell imaging approaches. Here, we characterize several new BG fluorophores suitable for in vivo AGT labeling that display fluorescence emission maxima covering the visible spectrum from 472 to 673 nm, thereby extending the spectral limits set by fluorescent proteins. We show that the photostability of the cell-permeable dyes BG Rhodamine Green (BG505) and CP tetra-methylrhodamine (CP-TMR) is in the range of enhanced green fluorescent protein (EGFP) and monomeric red fluorescent protein (mRFP), and that BG diethylaminomethyl coumarin (BGDEAC), a derivative of coumarin, is even more stable than enhanced cyan fluorescent protein (ECFP). Due to the increasing number of new BG derivatives with interesting fluorescence properties, such as far-red emission, fluorescence labeling of AGT fusion proteins is becoming a versatile alternative to existing live cell imaging approaches.

Between 1999 and 2003 we collected information on the breeding distribution and abundance of 12 seabird species occurring on nine islands off the coasts of north and central Chile (27°-33°S). The Peruvian booby Sula variegata was the most abundant seabird with a breeding population of ca. 18,000 pairs concentrated in two islands, followed by the Humboldt penguin Spheniscus humboldti with ca. 9,000 pairs, the largest colony being at Chañaral Island with ca. 7,000 pairs. Kelp gulls Larus dominicanus bred at all the surveyed sites in colonies of variable size, ranging from 40 to 2,000 pairs. Peruvian diving-petrels Pelecanoides garnotii and Peruvian pelicans Pelecanus occidentalis bred at restricted sites, but generally in large colonies. Magellanic penguins Spheniscus magellanicus, wedge-rumped storm-petrels Oceanodroma tethys, Neotropical cormorants Hypoleucos brasiliensis, guanay cormorants Leucocarbo bougainvillii, red-legged cormorants Stictocarbo gairmardi, band-tailed gulls Larus belcheri and Inca terns Larosterna inca nested at few sites forming small colonies (from a few to 150 pairs). Two new breeding sites are reported for the Peruvian diving-petrel and nesting of the wedge-rumped storm-petrel is confirmed on the Chilean coast for the first time. Despite protective status, most of the islands showed human disturbance, derived mainly from guano harvesting, egging and tourism. On at least five of these islands we were able to confirm introduced mammals including rats, rabbits and cats. These factors are likely to be detrimental to seabirds and thus demand detailed assessment. Further comprehensive ornithological surveys in other areas are needed so as to improve the scarce knowledge that we currently have on the seabird populations along the Chilean coast

Histone deacetylase inhibitors (HDACi) can induce human immunodeficiency virus (HIV) transcription from the HIV long terminal repeat (LTR). However, ex vivo and in vivo responses to HDACi are variable and the activity of HDACi in cells other than T-cells have not been well characterised. Here, we developed a novel assay to determine the activity of HDACi on patient-derived HIV LTRs in different cell types. HIV LTRs from integrated virus were amplified using triple-nested Alu-PCR from total memory CD4+ T-cells (CD45RO+) isolated from HIV-infected patients prior to and following suppressive antiretroviral therapy. NL4-3 or patient-derived HIV LTRs were cloned into the chromatin forming episomal vector pCEP4, and the effect of HDACi investigated in the astrocyte and epithelial cell lines SVG and HeLa, respectively. There were no significant differences in the sequence of the HIV LTRs isolated from CD4+ T-cells prior to and after 18 months of combination antiretroviral therapy (cART). We found that in both cell lines, the HDACi panobinostat, trichostatin A, vorinostat and entinostat activated patient-derived HIV LTRs to similar levels seen with NL4-3 and all patient derived isolates had similar sensitivity to maximum HDACi stimulation. We observed a marked difference in the maximum fold induction of luciferase by HDACi in HeLa and SVG, suggesting that the effect of HDACi may be influenced by the cellular environment. Finally, we observed significant synergy in activation of the LTR with vorinostat and the viral protein Tat. Together, our results suggest that the LTR sequence of integrated virus is not a major determinant of a functional response to an HDACi.

The Aequorea victoria green fluorescent protein (GFP) is widely recognized as a powerful tool in cell biology, serving as a vital reporter for monitoring localization and dynamics of intracellular proteins and organelles over time. GFP variants with shifted spectral characteristics have been described and offer enormous potential for double-labeling experiments and protein-protein interaction studies. However, most GFP variant combinations are not suitable for double-label, time-lapse imaging experiments because of either extremely rapid photobleaching of blue-shifted GFP variants or crossover of their excitation and emission spectra, which must then be computer corrected. Here, we describe the successful use of two photostable spectral GFP variants, W7 and 10C, in dual-color, timelapse imaging of fusion proteins in living cells using either wide-field or confocal microscopy. W7 and 10C were highly photostable during repetitive long-term imaging and were cleanly separated by their different excitation spectra alone with negligible crossover of fluorescence. We present time-lapse image sequences of COS-7 cells co-expressing both a marker of the Golgi complex (galactosyl transferase) fused to W7 and a marker of the nuclear envelope (lamin-B receptor) fused to 10C. To our knowledge, these image sequences provide the first simultaneous visualization of Golgi and nuclear envelope membranes in living cells.

Latently infected resting CD4(+) T cells are a major barrier to HIV cure. Understanding how latency is established, maintained and reversed is critical to identifying novel strategies to eliminate latently infected cells. We demonstrate here that co-culture of resting CD4(+) T cells and syngeneic myeloid dendritic cells (mDC) can dramatically increase the frequency of HIV DNA integration and latent HIV infection in non-proliferating memory, but not naïve, CD4(+) T cells. Latency was eliminated when cell-to-cell contact was prevented in the mDC-T cell co-cultures and reduced when clustering was minimised in the mDC-T cell co-cultures. Supernatants from infected mDC-T cell co-cultures did not facilitate the establishment of latency, consistent with cell-cell contact and not a soluble factor being critical for mediating latent infection of resting CD4(+) T cells. Gene expression in non-proliferating CD4(+) T cells, enriched for latent infection, showed significant changes in the expression of genes involved in cellular activation and interferon regulated pathways, including the down-regulation of genes controlling both NF-κB and cell cycle. We conclude that mDC play a key role in the establishment of HIV latency in resting memory CD4(+) T cells, which is predominantly mediated through signalling during DC-T cell contact.

Free-ranging marine predators rarely search for prey along straight lines because dynamic ocean processes usually require complex search strategies. If linear movement patterns occur they are usually associated with travelling events or migratory behaviour. However, recent fine scale tracking of flying seabirds has revealed straight-line movements while birds followed fishing vessels. Unlike flying seabirds, penguins are not known to target and follow fishing vessels. Yet yellow-eyed penguins from New Zealand often exhibit directed movement patterns while searching for prey at the seafloor, a behaviour that seems to contradict common movement ecology theories. While deploying GPS dive loggers on yellow-eyed penguins from the Otago Peninsula we found that the birds frequently followed straight lines for several kilometres with little horizontal deviation. In several cases individuals swam up and down the same line, while some of the lines were followed by more than one individual. Using a remote operated vehicle (ROV) we found a highly visible furrow on the seafloor most likely caused by an otter board of a demersal fish trawl, which ran in a straight line exactly matching the trajectory of a recent line identified from penguin tracks. We noted high abundances of benthic scavengers associated with fisheries-related bottom disturbance. While our data demonstrate the acute way-finding capabilities of benthic foraging yellow-eyed penguins, they also highlight how hidden cascading effects of coastal fisheries may alter behaviour and potentially even population dynamics of marine predators, an often overlooked fact in the examination of fisheries' impacts.

Background: Electrocardiographically occult occlusive myocardial infarction (OOMI), defined as coronary artery occlusion requiring revascularization without ST-segment elevation on electrocardiogram (ECG), is associated with delayed diagnosis resulting in higher morbidity. Left ventricular (LV) wall motion abnormalities (WMA) appreciated on echocardiography can expedite OOMI diagnosis. We sought to determine whether point-of-care ultrasound (PoCUS) demonstrating WMA expedites revascularization time when performed on emergency department patients being evaluated for OOMI.Methods: This was a single-site retrospective cohort study over a 38-month period. All admitted adult ED patients ≥35 years of age evaluated by the emergency physician with PoCUS for LV function, an ECG, and a standard troponin I biomarker assay were included. Patients with ST-segment elevation myocardial infarction (STEMI), prior LV dysfunction, fever ≥100.4 °F, or hypotension were excluded. A structured chart abstraction was performed for relevant demographic and clinical characteristics.Results: We screened 1561 ED patients who underwent cardiac PoCUS for eligibility: 874 met exclusion criteria, 453 were discharged, and 234 were included in the analysis. Twenty-three patients had coronary interventions, of which 14 had WMA. PoCUS was performed 36 min (IQR -9-68) before troponin resulted (n = 234) and 39 min (IQR -23-96) before the first troponin elevation (n = 85). Twenty of the 23 patients diagnosed with OOMI had elevated troponins prior to catheterization with time from PoCUS to first troponin elevation of 43 min (IQR 9-263). Of these patients, 11 had WMA identified on PoCUS, and the WMA was appreciated 47 min (IQR 26-255) prior to troponin elevation. The time from ED arrival to revascularization was 673 min (IQR 251-2158); 432 min (IQR 209-1300) among patients with WMA (n = 14) compared with 2158 min (IQR 552-3390) for those without WMA (n = 9).Conclusion: Cardiac PoCUS may identify OOMI earlier than standard evaluation and may expedite definitive management. [ABSTRACT FROM AUTHOR]

The regulation of cell migration is a highly complex process that is often compromised when cancer cells become metastatic. The microtubule cytoskeleton is necessary for cell migration, but how microtubules and microtubule-associated proteins regulate multiple pathways promoting cell migration remains unclear. Microtubule plus-end binding proteins (+TIPs) are emerging as important players in many cellular functions, including cell migration. Here we identify a +TIP, GTSE1, that promotes cell migration. GTSE1 accumulates at growing microtubule plus ends through interaction with the EB1+TIP. The EB1-dependent +TIP activity of GTSE1 is required for cell migration, as well as for microtubule-dependent disassembly of focal adhesions. GTSE1 protein levels determine the migratory capacity of both nontransformed and breast cancer cell lines. In breast cancers, increased GTSE1 expression correlates with invasive potential, tumor stage, and time to distant metastasis, suggesting that misregulation of GTSE1 expression could be associated with increased invasive potential.

Due to its small size and versatility, the biarsenical-tetracysteine system is an attractive way to label viral proteins for live cell imaging. This study describes the genetic labeling of the human immunodeficiency virus type 1 (HIV-1) structural proteins (matrix, capsid and nucleocapsid), enzymes (protease, reverse transcriptase, RNAse H and integrase) and envelope glycoprotein 120 with a tetracysteine tag in the context of a full-length virus. We measure the impact of these modifications on the natural virus infection and, most importantly, present the first infectious HIV-1 construct containing a fluorescently-labeled nucleocapsid protein. Furthermore, due to the high background levels normally associated with the labeling of tetracysteine-tagged proteins we have also optimized a metabolic labeling system that produces infectious virus containing the natural envelope glycoproteins and specifically labeled tetracysteine-tagged proteins that can easily be detected after virus infection of T-lymphocytes. This approach can be adapted to other viral systems for the visualization of the interplay between virus and host cell during infection.