Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast

Background The genomic sequences of centromeres, as well as the set of proteins that recognize and interact with centromeres, are known to quickly diverge between lineages potentially contributing to post-zygotic reproductive isolation. However, the actual sequence of events and processes involved in the divergence of the kinetochore machinery is not known. The patterns of gene loss that occur during evolution concomitant with phenotypic changes have been used to understand the timing and order of molecular changes. Methods I screened the high-quality genomes of twenty budding yeast species for the presence of well-studied kinetochore genes. Based on the conserved gene order and complete genome assemblies, I identified gene loss events. Subsequently, I searched the intergenic regions to identify any un-annotated genes or gene remnants to obtain additional evidence of gene loss. Results My analysis identified the loss of four genes (NKP1, NKP2, CENPL/IML3 and CENPN/CHL4) of the inner kinetochore constitutive centromere-associated network (CCAN/also known as CTF19 complex in yeast) in both the Naumovozyma species for which genome assemblies are available. Surprisingly, this collective loss of four genes of the CCAN/CTF19 complex coincides with the emergence of unconventional centromeres in N. castellii and N. dairenensis. My study suggests a tentative link between the emergence of unconventional point centromeres and the turnover of kinetochore genes in budding yeast.

A Bayesian Framework for Inferring the Influence of Sequence Context on Point Mutations

The probability of point mutations is expected to be highly influenced by the flanking nucleotides that surround them, known as the sequence context. This phenomenon may be mainly attributed to the enzyme that modifies or mutates the genetic material, because most enzymes tend to have specific sequence contexts that dictate their activity. Here, we develop a statistical model that allows for the detection and evaluation of the effects of different sequence contexts on mutation rates from deep population sequencing data. This task is computationally challenging, as the complexity of the model increases exponentially as the context size increases. We established our novel Bayesian method based on sparse model selection methods, with the leading assumption that the number of actual sequence contexts that directly influence mutation rates is minuscule compared with the number of possible sequence contexts. We show that our method is highly accurate on simulated data using pentanucleotide contexts, even when accounting for noisy data. We next analyze empirical population sequencing data from polioviruses and HIV-1 and detect a significant enrichment in sequence contexts associated with deamination by the cellular deaminases ADAR 1/2 and APOBEC3G, respectively. In the current era, where next-generation sequencing data are highly abundant, our approach can be used on any population sequencing data to reveal context-dependent base alterations and may assist in the discovery of novel mutable sites or editing sites.

IMMU-24. A COMPREHENSIVE IN SILICO APPROACH TO DISCOVERING TUMOR REJECTION ANTIGENS IN MALIGNANT BRAIN TUMORS

BACKGROUND Proteins that can serve as effective tumor rejection antigens within brain tumors are poorly characterized. Current prediction algorithms relying on identification of mutated epitopes as neoantigens are limited in low mutational burden tumors. We have developed a multi-faceted computer algorighm for identifying tumor rejection antigens called the Open Reading Frame Antigen Network (ORAN). This pipeline provides a comprehensive solution for predicting brain tumor immunogenic targetable epitopes/transcripts. METHODS Human and murine RNASeq and WES data were QCed. Patients individual HLA-I and HLA-II haplotypes were predicted by highly customized Optitype and Phlat Algorithms. SNPs and Indels were called from tumors WES and read through matched RNASeq data. 19,131 transcripts expression were counted per TOIL algorithm. Tumor associate antigens(TAA) of individual patient or murine tumors were selected by setting a cutoff of Transcripts Per Million (TPM) > 1 on individual patient’s tumor, while RNA Seq data from 7000 normal tissues was used to identify tumor unique transcripts. Actual sequence of HLA and SNPed Consenses TAA(CTAA) were called. Only expressed mutations and personalized TAAs were used for antigenic epitope predictions. All neoepitopes were screened against a human reference proteomic library to guarantee that epitopes were not shared by other expressed isoforms or genes. In silico validation were preformed to cross validate predictions made by ORAN. RESULTS In medullobastoma (N=121 samples), ORAN gives an average of 15.6 MHC class I restricted neoepitopes,11.9 epitopes encoded by Indels and with 33.2 MHC class II restricted neoepitopes and 16.2 Indel antigens per patient. The TAAs of each patient reaches average 256 antigenic epitopes per patient. ORAN also predicts the exact HLA and neo-antigens from a validated neoantigens vaccine dataset (Gros A Nat Med 2016). CONCLUSION ORAN accurately identifies validated neoantigens and provides a comprehensive list of potential tumor rejection antigens within human and murine brain tumors.

A New Background Value Improvement of Fractional Order Accumulated FAGM(1,1) Model and Its Application

The prediction accuracy of the fractional FAGM(1,1) model mainly depends on the calculation of the background value. To improve the prediction accuracy of the FAGM(1,1) model, a new background value calculation method is proposed. By analyzing the cause of the background value error, considering the regularity of the fractional-order accumulation sequence with non-homogeneous exponential growth, the non-homogeneous exponential curve is used to fit the fractional-order accumulation sequence, combined with the integral theory, to accumulate the actual sequence on the interval. The result of the integration is used as a new background value. The example shows that using the new background value calculation method combined with the Genetic Algorithm to find the optimal order, the fitting and prediction accuracy of the fractional FAGM(1,1) model is obviously improved, and the background value has the characteristics of simple calculation and strong practicability.

Fast-backward replay of sequentially memorized items in humans

Storing temporal sequences of events (i.e., sequence memory) is fundamental to many cognitive functions. However, it is unknown how the sequence order information is maintained and represented in working memory and its behavioral significance, particularly in human subjects. We recorded electroencephalography (EEG) in combination with a temporal response function (TRF) method to dissociate item-specific neuronal reactivations. We demonstrate that serially remembered items are successively reactivated during memory retention. The sequential replay displays two interesting properties compared to the actual sequence. First, the item-by-item reactivation is compressed within a 200 – 400 ms window, suggesting that external events are associated within a plasticity-relevant window to facilitate memory consolidation. Second, the replay is in a temporally reversed order and is strongly related to the recency effect in behavior. This fast-backward replay, previously revealed in rat hippocampus and demonstrated here in human cortical activities, might constitute a general neural mechanism for sequence memory and learning.

The Freedom Required for Moral Responsibility

Some philosophers argue that we do not need freedom to do otherwise or access to alternative possibilities for moral responsibility. These philosophers are actual-sequence theorists of moral responsibility who are motivated by Frankfurt cases, in which there is pre-emptive overdetermination. They contend that in these cases the agent is morally responsible but does not have freedom to do otherwise or access to alternative possibilities. Others have rejected the actual-sequence approach. They contend that the sort of freedom to do otherwise required for moral responsibility is indeed present in the Frankfurt cases. This essay explores the significance of the debate between these two camps. Are the two views importantly different or mere notational variants of each other? I examine these questions with attention to Terry Irwin’s discussion of Aristotle on responsibility.

Fast-backward replay of sequentially memorized items in humans

Storing temporal sequences of events (i.e., sequence memory) is fundamental to many cognitive functions. However, how the sequence order information is maintained and represented in working memory and its behavioral significance, particularly in human subjects, remains unknown. Here, we recorded electroencephalography (EEG) in combination with a temporal response function (TRF) method to dissociate item-specific neuronal reactivations. We demonstrate that serially remembered items are successively reactivated during memory retention. The sequential replay displays two interesting properties compared to the actual sequence. First, the item-by-item reactivation is compressed within a 200-400 ms window, suggesting that external events are associated within a plasticity-relevant window to facilitate memory consolidation. Second, the replay is in a temporally reversed order and is strongly related to the recency effect in behavior. This fast-backward replay, previously revealed in rat hippocampus and demonstrated here in human cortical activities, might constitute a general neural mechanism for sequence memory and learning.

Free Will and Open Alternatives

In her recent book Causation and Free Will, Carolina Sartorio develops a distinctive version of an actual-sequence account of free will, according to which, when agents choose and act freely, their freedom is exclusively grounded in, and supervenes on, the actual causal history of such choices or actions. Against this proposal, I argue for an alternative- possibilities account, according to which agents’ freedom is partly grounded in their ability to choose or act otherwise. Actual-sequence accounts of freedom (and moral responsibility) are motivated by a reflection on so-called Frankfurt cases. Instead, other cases, such as two pairs of examples originally designed by van Inwagen, threaten actual-sequence accounts, including Sartorio’s. On the basis of her (rather complex) view of causation, Sartorio contends, however, that the two members of each pair have different causal histories, so that her view is not undermined by those cases after all. I discuss these test cases further and defend my alternative-possibilities account of freedom.

Does Free Will Require Alternative Possibilities?

In this introductory study I discuss the notion of alternative possibilities and its relation to contemporary debates on free will and moral responsibility. I focus on two issues: whether Frankfurt-style cases refute the principle of alternative possibilities, and whether alternative possibilities are relevant to grounding free will and moral responsibility. With respect to the first issue, I consider three objections to Frankfurt-syle cases: the flicker strategy, the dilemma defense, and the objection from new dispositionalism. With respect to the second issue, I consider the debate between Alternative Possibilities views and Actual Sequence views, as framed by Carolina Sartorio in her Causation and Free Will. I then explain how these two issues are relevant to the papers included in this volume.

Prestimulus Alpha Oscillations and the Temporal Sequencing of Audiovisual Events

Perceiving the temporal order of sensory events typically depends on participants' attentional state, thus likely on the endogenous fluctuations of brain activity. Using magnetoencephalography, we sought to determine whether spontaneous brain oscillations could disambiguate the perceived order of auditory and visual events presented in close temporal proximity, that is, at the individual's perceptual order threshold (Point of Subjective Simultaneity [PSS]). Two neural responses were found to index an individual's temporal order perception when contrasting brain activity as a function of perceived order (i.e., perceiving the sound first vs. perceiving the visual event first) given the same physical audiovisual sequence. First, average differences in prestimulus auditory alpha power indicated perceiving the correct ordering of audiovisual events irrespective of which sensory modality came first: a relatively low alpha power indicated perceiving auditory or visual first as a function of the actual sequence order. Additionally, the relative changes in the amplitude of the auditory (but not visual) evoked responses were correlated with participant's correct performance. Crucially, the sign of the magnitude difference in prestimulus alpha power and evoked responses between perceived audiovisual orders correlated with an individual's PSS. Taken together, our results suggest that spontaneous oscillatory activity cannot disambiguate subjective temporal order without prior knowledge of the individual's bias toward perceiving one or the other sensory modality first. Altogether, our results suggest that, under high perceptual uncertainty, the magnitude of prestimulus alpha (de)synchronization indicates the amount of compensation needed to overcome an individual's prior in the serial ordering and temporal sequencing of information.