Alpha/beta and gamma interferons are induced by infection with noncytopathic bovine viral diarrhea virus in vivo

In contrast to the results of previous in vitro studies, experimental infection of calves with noncytopathic bovine viral diarrhea virus (ncpBVDV) was found to induce strong alpha/beta and gamma interferon responses in gnotobiotic animals. These responses were associated with depressed levels of transforming growth factor β (TGF-β) in serum. The results of this study indicate that the immunosuppression caused by ncpBVDV is not associated with low interferon responses or elevated levels of TGF-β

Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Modified Vaccinia Virus Ankara-Based Vaccine Vectors Induce Apoptosis in Dendritic Cells Draining from the Skin via both the Extrinsic and Intrinsic Caspase Pathways, Preventing Efficient Antigen Presentation

Dendritic cells (DC) are potent antigen-presenting cells and central to the induction of immune responses following infection or vaccination. The collection of DC migrating from peripheral tissues by cannulation of the afferent lymphatic vessels provides DC which can be used directly ex vivo without extensive in vitro manipulations. We have previously used bovine migrating DC to show that recombinant human adenovirus 5 vectors efficiently transduce afferent lymph migrating DEC-205(+) CD11c(+) CD8(-) DC (ALDC). We have also shown that recombinant modified vaccinia virus Ankara (MVA) infects ALDC in vitro, causing downregulation of costimulatory molecules, apoptosis, and cell death. We now show that in the bovine system, modified vaccinia virus Ankara-induced apoptosis in DC draining from the skin occurs soon after virus binding via the caspase 8 pathway and is not associated with viral gene expression. We also show that after virus entry, the caspase 9 pathway cascade is initiated. The magnitude of T cell responses to mycobacterial antigen 85A (Ag85A) expressed by recombinant MVA-infected ALDC is increased by blocking caspase-induced apoptosis. Apoptotic bodies generated by recombinant MVA (rMVA)-Ag85A-infected ALDC and containing Ag85A were phagocytosed by noninfected migrating ALDC expressing SIRPalpha via actin-dependent phagocytosis, and these ALDC in turn presented antigen. However, the addition of fresh ALDC to MVA-infected cultures did not improve on the magnitude of the T cell responses; in contrast, these noninfected DC showed downregulation of major histocompatibility complex class II (MHC-II), CD40, CD80, and CD86. We also observed that MVA-infected ALDC promoted migration of DEC-205(+) SIRPalpha(+) CD21(+) DC as well as CD4(+) and CD8(+) T cells independently of caspase activation. These in vitro studies show that induction of apoptosis in DC by MVA vectors is detrimental to the subsequent induction of T cell responses

Ang Imeldific: Representasyon at Kapangyarihan sa Sto. Niño Shrine sa Lungsod ng Tacloban

The paper is a reflection on the meaning of the Sto. Niño Shrine (Romualdez Museum) in Tacloban City, Leyte, the mansion Imelda Marcos ordered built in the early 1980s. Using Kapanahong Kasaysayan (the writing of Phiippine contemporaneous history as different from contemporary history and investigative journalism as defined by the West), the reflections will be corroborated with data from documents, biographies and statements of people close to the first lady, including the author’s interview with Madam Marcos herself, and will be contextualized to Philippine history and culture. According to Carmen Pedrosa, Imelda Marcos never lived in the mansion; it was “meant only to be viewed.” The house cum museum reflects the official representation of her past and her role as mother of the country. The design of the house and the many objects collected the world over, not only shows the great wealth and power that she gained, but also her claim of foreign and aristocratic origins. The objects also convey a representation of the first lady that she wanted to make her people and the world believe: That she was born and destined to lead. It will be observed that she wanted to show an image of herself just like the ancient Filipino Babaylan—narrator of the people’s story, healer of physical and social ills, spiritual leader of the people—the bearer of “ginhawa.” In the end, whatever representation a personality or an institution desires to ingrain in the national memory through text or concretely, it is the experience and socialization of the individual which will determine his or her image of that historical figure. The individual has the prerogative not to believe such a fabricated image, especially if it does not square with one’s experience of history. __________ * Lecturer at the Department of History at De La Salle University Manila. Email: [email protected]

Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies

The unpalatable and warning-patterned butterflies _Heliconius erato_ and _Heliconius melpomene_ provide the best studied example of mutualistic Müllerian mimicry, thought – but rarely demonstrated – to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and this was initially hailed as the most striking known case of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of _H. erato_ and _H. melpomene_, supporting repeated codivergence of mimetic populations. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of _H. erato_ and _H. melpomene_ occurred over the same time period, and are compatible with a series of temporally congruent codivergence events. This evidence supports a history of reciprocal coevolution between Müllerian co-mimics characterised by phylogenetic codivergence and parallel phenotypic change

Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss

Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular evolution. While duplication–loss (DL) reconciliation leads to a unique maximum-parsimony solution, duplication-transfer-loss (DTL) reconciliation yields a multitude of optimal solutions, making it difficult to infer the true evolutionary history of the gene family. This problem is further exacerbated by the fact that different event cost assignments yield different sets of optimal reconciliations. Here, we present an effective, efficient, and scalable method for dealing with these fundamental problems in DTL reconciliation. Our approach works by sampling the space of optimal reconciliations uniformly at random and aggregating the results. We show that even gene trees with only a few dozen genes often have millions of optimal reconciliations and present an algorithm to efficiently sample the space of optimal reconciliations uniformly at random in O(mn[superscript 2]) time per sample, where m and n denote the number of genes and species, respectively. We use these samples to understand how different optimal reconciliations vary in their node mappings and event assignments and to investigate the impact of varying event costs. We apply our method to a biological dataset of approximately 4700 gene trees from 100 taxa and observe that 93% of event assignments and 73% of mappings remain consistent across different multiple optima. Our analysis represents the first systematic investigation of the space of optimal DTL reconciliations and has many important implications for the study of gene family evolution.National Science Foundation (U.S.) (CAREER Award 0644282)National Institutes of Health (U.S.) (Grant RC2 HG005639)National Science Foundation (U.S.). Assembling the Tree of Life (Program) (Grant 0936234

Ang Paghiraya sa Bansa ni Don Belong: Pagsusuri ng mga Akda ni Isabelo de los Reyes sa Kanyang Yugto ng Transisyon (1897–1912)

Hangarin ng proyekto ang pagbasa at pagsuri ng mga akda ni Isabelo de los Reyes sa yugto ng transisyon mula sa panahon ng Espanyol tungo sa panahon ng Amerikano (1897–1912). Bukod dito, babalikan ang mga sosyo-historikal na konteskto at pangyayari sa panahong ito upang mabatid ang paghiraya ni de los Reyes sa bansa at lipunang Pilipino. Makabuluhan ang layunin ng proyekto upang maaninag ang isa pang panig ng Ilokanong polimata na nakipagbuno sa loob ng Pilipinas sa ilalim ng panahon ng mga Amerikano. Nahahati sa mga substantibong seksiyon ang papel: 1) nosyon ng nasyon ng Kanluran at kulturang bayan ng lupang sinilangan, 2) mga akda ni de los Reyes na nakapaloob sa yugto ng transisyon, 3) matitingkad na tema at diskurso mula sa mga akda ni de los Reyes, at ang 4) kongklusyon. Higit kailanman, sumulat si de los Reyes sa panahong ito upang makabuo ng matatalas na kaisipan at magmarka sa kasaysayan. Sa gitna ng mga kinaharap na hamon, bumuo ng mga oportunidad ang Ilokanong polimata upang mapagtagumpayan ang mga bagay na pinangarap niya para sa Pilipinas.&nbsp