Early peripheral immunological events dictate chronic wasting disease

2013 Spring.Includes bibliographical references.Chronic wasting disease (CWD) is an emerging prion disease of captive and free-ranging cervid populations that, like scrapie, has been shown to involve the immune system, which most likely contributes to their relatively proficient horizontal and environmental transmission. While CWD prions probably interact with the innate immune system immediately following peripheral exposure, little is known about this initial encounter. In the first chapter of this dissertation we examined initial events in lymphotropic and intranodal prion trafficking by tracking highly enriched, fluorescent CWD prions from infection sites to draining lymph nodes. We observed biphasic lymphotropic transport of prions from the initial entry site upon peripheral prion inoculation. CWD prions rapidly reached draining lymph nodes in a cell autonomous manner within two hours of intraperitoneal administration. Monocytes and dendritic cells (DCs) showed a strong dependence on Complement for optimal prion delivery to lymph nodes hours later in a second wave of prion trafficking. B cells comprised the majority of prion-bearing cells in the mediastinal lymph node by six hours. As most B cells are mainly located in the follicles, acquisition of prions by these cells most likely occurred through interaction with resident DCs, subcapsulary sinus macrophages, or directly from the follicular conduit system. These data highlight a novel mechanism of cell autonomous prion transport, and a vital role for B cells in intranodal prion trafficking. Upon entry into the draining lymph nodes, prion accumulation and replication on follicular dendrtic cells (FDCs) is greatly facilitated by the complement system. Complete elimination of CD21/35 significantly delays splenic prion accumulation and terminal prion disease in mice inoculated intraperitoneally with mouse-adapted scrapie prions. In the second chapter of this thesis we show that mice overexpressing the cervid prion protein and susceptible to CWD (Tg(cerPrP)5037 mice) but lack CD21/35 expression completely resist clinical CWD upon peripheral infection. Ablation of complement receptors CD21/35 greatly diminished splenic prion accumulation and replication throughout the course of disease, similar to CD21/35 deficient murine PrP mice infected with mouse scrapie. Mice with deficiencies in CD21/35 showed a reduction in severity of neuropathology and deposition of misfolded, protease-resistant PrP associated with CWD. Prion infection resulted in translocation of CD21/35 to lipid rafts in B cells, and FDC expression of CD21/35 mediated a strong germinal center response that may be conducive to prion amplification. Complement component C3 is a central protein in the complement system whose activation is essential for the elimination of infectious pathogens. C3 is the most abundant complement protein, being found in the blood at physiological concentrations of 1 mg/ml. Among the complement proteins, C3 is perhaps the most adaptable and multifunctional protein identified to date, having evolved structural characteristics that allow it to associate with over 25 different proteins. Previous experiments suggest a vital role of C3 in scrapie prion pathogenesis. In the last chapter of my thesis we showed that lack of C3 expression by 5037 mice either transiently or genetically leads to delays in prion pathogenesis. C3 impacts disease progression in the early stages of disease by slowing the kinetic rate of accumulation and/or replication of PrPRES. This slower kinetic increase in PrPRES correlates with an increase in survival time in mice deficient in C3. This delay in disease is in sharp contrast to the complete rescue we saw in CWD infected Tg 5037;CD21-/- mice. This suggests a role for CD21/35 in peripheral prion pathogenesis independent of their endogenous ligands. Taken together we show that the innate immune system dictates the course of CWD. We have discovered novel immune cells, trafficking pathways, and complement components important in CWD pathogenesis. These data not only highlight the key role of the innate immune system in CWD, but also provide a strong foundation for future immunological studies of prion diseases

EL-Shellability and Noncrossing Partitions Associated with Well-Generated Complex Reflection Groups

In this article we prove that the lattice of noncrossing partitions is EL-shellable when associated with the well-generated complex reflection group of type $G(d,d,n)$, for $d,n\geq 3$, or with the exceptional well-generated complex reflection groups which are no real reflection groups. This result was previously established for the real reflection groups and it can be extended to the well-generated complex reflection group of type $G(d,1,n)$, for $d,n\geq 3$, as well as to three exceptional groups, namely $G_{25},G_{26}$ and $G_{32}$, using a braid group argument. We thus conclude that the lattice of noncrossing partitions of any well-generated complex reflection group is EL-shellable. Using this result and a construction by Armstrong and Thomas, we conclude further that the poset of $m$-divisible noncrossing partitions is EL-shellable for every well-generated complex reflection group. Finally, we derive results on the M\"obius function of these posets previously conjectured by Armstrong, Krattenthaler and Tomie.Comment: 37 pages, 4 figures. Moved the technical details of the proof of the EL-shellability of $NC_{G(d,d,n)}$ to the appendix. More references adde

Busy Beaver Scores and Alphabet Size

We investigate the Busy Beaver Game introduced by Rado (1962) generalized to non-binary alphabets. Harland (2016) conjectured that activity (number of steps) and productivity (number of non-blank symbols) of candidate machines grow as the alphabet size increases. We prove this conjecture for any alphabet size under the condition that the number of states is sufficiently large. For the measure activity we show that increasing the alphabet size from two to three allows an increase. By a classical construction it is even possible to obtain a two-state machine increasing activity and productivity of any machine if we allow an alphabet size depending on the number of states of the original machine. We also show that an increase of the alphabet by a factor of three admits an increase of activity

Forecasting Flashover in a Compartment Fire by Using a Real-time Moving Average from Temperature Recordings

A series of flashover fire tests were carried out using standard wood as fuel with various ventilation, and a comprehensive set of experimental data is presented. Fighting against compartment fires with occurance of flashover could cause fatal consequences on firefighters. This work shows that the potential dangers as flashover can be detected as soon as possible thanks to the comparison between two moving averages in the past calculated from a temperature recording in a very short time. The present study aims to evaluate the possibility of using only commonly available measurements as data to be assimilated into the model. A real-time decision method is developed, allowing to the selection of optimal intervention to minimize firefight occupant exposure to the detected hazard. This approach includes the mathematical analysis which is based on the comparison of two moving averages centered in the past, calculated on the recordings of the smoke temperature. Firefighters would greatly benefit from this predictive method in real time, able to assist their decision making process during operations against a compartment fire. From the safety point of view, the model gives conservative predictions for flashover fire

Embrace the Gap: VAEs Perform Independent Mechanism Analysis

Variational autoencoders (VAEs) are a popular framework for modeling complex data distributions; they can be efficiently trained via variational inference by maximizing the evidence lower bound (ELBO), at the expense of a gap to the exact (log-)marginal likelihood. While VAEs are commonly used for representation learning, it is unclear why ELBO maximization would yield useful representations, since unregularized maximum likelihood estimation cannot invert the data-generating process. Yet, VAEs often succeed at this task. We seek to elucidate this apparent paradox by studying nonlinear VAEs in the limit of near-deterministic decoders. We first prove that, in this regime, the optimal encoder approximately inverts the decoder -- a commonly used but unproven conjecture -- which we refer to as {\em self-consistency}. Leveraging self-consistency, we show that the ELBO converges to a regularized log-likelihood. This allows VAEs to perform what has recently been termed independent mechanism analysis (IMA): it adds an inductive bias towards decoders with column-orthogonal Jacobians, which helps recovering the true latent factors. The gap between ELBO and log-likelihood is therefore welcome, since it bears unanticipated benefits for nonlinear representation learning. In experiments on synthetic and image data, we show that VAEs uncover the true latent factors when the data generating process satisfies the IMA assumption.Comment: 47 pages, accepted at NeurIPS202

Reproductive isolation between two populations of Aglaoctenus lagotis , a funnel-web wolf spider

Aglaoctenus lagotis (Lycosidae: Sosippinae) is a spider that, in contrast to the predominant wandering habit of the family, constructs funnel webs. The species is widely distributed throughout the Neotropics and is credited with high levels of intraspecific variation. Here, we evaluate whether reproductive isolating barriers operate between some populations of A. lagotis. We used heterotypic encounters between individuals from two distant localities: southern Uruguay (SU) and Central Argentina (CA). Additionally, we used spiders from an ntermediate locality, western Uruguay (WU), where both forms of the species overlap (SU.WU was used to describe individuals from WU reminiscent of those from SU; and CA.WU was used to describe individuals from WU reminiscent of those from CA). No copulations occurred between SU and CA individuals, whereas a single and atypical copulation occurred between SU.WU and CA.WU individuals. Attacks (only by females on males) were rare. In tests of choice based on silk cues, SU males did not prefer homotypic cues but almost did not court CA females, whereas CA males preferred homotypic cues but usually courted heterotypic females. These findings, with a previously reported temporal asynchrony between populations, suggest the occurrence of reproductive isolation between both spider forms and a speciation process favoured by the wide distribution and plasticity of the species.Fil: González Pérez, María de la Macarena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Cátedra de Diversidad Animal I; ArgentinaFil: Peretti, Alfredo Vicente. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Cátedra de Diversidad Animal I; ArgentinaFil: Costa, Fernando G.. Instituto de Investigaciones Biológicas "Clemente Estable"; Urugua

Updated Planetary Mass Constraints of the Young V1298 Tau System Using MAROON-X

The early K-type T-Tauri star, V1298 Tau ($V=10\,{\rm mag}$, ${\rm age}\approx20-30\,{\rm Myr}$) hosts four transiting planets with radii ranging from $4.9-9.6\,R_\oplus$. The three inner planets have orbital periods of $\approx8-24\,{\rm d}$ while the outer planet's period is poorly constrained by single transits observed with \emph{K2} and \emph{TESS}. Planets b, c, and d are proto-sub-Neptunes that may be undergoing significant mass loss. Depending on the stellar activity and planet masses, they are expected to evolve into super-Earths/sub-Neptunes that bound the radius valley. Here we present results of a joint transit and radial velocity (RV) modelling analysis, which includes recently obtained \emph{TESS} photometry and MAROON-X RV measurements. Assuming circular orbits, we obtain a low-significance ($\approx2\sigma$) RV detection of planet c implying a mass of $19.8_{-8.9}^{+9.3}\,M_\oplus$ and a conservative $2\sigma$ upper limit of $<39\,M_\oplus$. For planets b and d, we derive $2\sigma$ upper limits of $M_{\rm b}<159\,M_\oplus$ and $M_{\rm d}<41\,M_\oplus$. For planet e, plausible discrete periods of $P_{\rm e}>55.4\,{\rm d}$ are ruled out at a $3\sigma$ level while seven solutions with $43.3<P_{\rm e}/{\rm d}<55.4$ are consistent with the most probable $46.768131\pm000076\,{\rm d}$ solution within $3\sigma$. Adopting the most probable solution yields a $2.6\sigma$ RV detection with mass a of $0.66\pm0.26\,M_{\rm Jup}$. Comparing the updated mass and radius constraints with planetary evolution and interior structure models shows that planets b, d, and e are consistent with predictions for young gas-rich planets and that planet c is consistent with having a water-rich core with a substantial ($\sim5\%$ by mass) H$_2$ envelope.Comment: 18 pages, 13 figures, accepted for publication in A

A method to sequence and quantify DNA integration for monitoring outcome in gene therapy

Human genetic diseases have been successfully corrected by integration of functional copies of the defective genes into human cells, but in some cases integration of therapeutic vectors has activated proto-oncogenes and contributed to leukemia. For this reason, extensive efforts have focused on analyzing integration site populations from patient samples, but the most commonly used methods for recovering newly integrated DNA suffer from severe recovery biases. Here, we show that a new method based on phage Mu transposition in vitro allows convenient and consistent recovery of integration site sequences in a form that can be analyzed directly using DNA barcoding and pyrosequencing. The method also allows simple estimation of the relative abundance of gene-modified cells from human gene therapy subjects, which has previously been lacking but is crucial for detecting expansion of cell clones that may be a prelude to adverse events

B Cells Regulate Neutrophilia during Mycobacterium tuberculosis Infection and BCG Vaccination by Modulating the Interleukin-17 Response

We have previously demonstrated that B cells can shape the immune response to Mycobacterium tuberculosis, including the level of neutrophil infiltration and granulomatous inflammation at the site of infection. The present study examined the mechanisms by which B cells regulate the host neutrophilic response upon exposure to mycobacteria and how neutrophilia may influence vaccine efficacy. To address these questions, a murine aerosol infection tuberculosis (TB) model and an intradermal (ID) ear BCG immunization mouse model, involving both the μMT strain and B cell-depleted C57BL/6 mice, were used. IL (interleukin)-17 neutralization and neutrophil depletion experiments using these systems provide evidence that B cells can regulate neutrophilia by modulating the IL-17 response during M. tuberculosis infection and BCG immunization. Exuberant neutrophilia at the site of immunization in B cell-deficient mice adversely affects dendritic cell (DC) migration to the draining lymph nodes and attenuates the development of the vaccine-induced Th1 response. The results suggest that B cells are required for the development of optimal protective anti-TB immunity upon BCG vaccination by regulating the IL-17/neutrophilic response. Administration of sera derived from M. tuberculosis-infected C57BL/6 wild-type mice reverses the lung neutrophilia phenotype in tuberculous μMT mice. Together, these observations provide insight into the mechanisms by which B cells and humoral immunity modulate vaccine-induced Th1 response and regulate neutrophila during M. tuberculosis infection and BCG immunization. © 2013 Kozakiewicz et al