On fractional realizations of graph degree sequences

We introduce fractional realizations of a graph degree sequence and a closely associated convex polytope. Simple graph realizations correspond to a subset of the vertices of this polytope. We describe properties of the polytope vertices and characterize degree sequences for which each polytope vertex corresponds to a simple graph realization. These include the degree sequences of pseudo-split graphs, and we characterize their realizations both in terms of forbidden subgraphs and graph structure.Comment: 18 pages, 4 figure

The principal Erdős–Gallai differences of a degree sequence

The Erdős–Gallai criteria for recognizing degree sequences of simple graphs involve a system of inequalities. Given a fixed degree sequence, we consider the list of differences of the two sides of these inequalities. These differences have appeared in varying contexts, including characterizations of the split and threshold graphs, and we survey their uses here. Then, enlarging upon properties of these graph families, we show that both the last term and the maximum term of the principal Erdős–Gallai differences of a degree sequence are preserved under graph complementation and are monotonic under the majorization order and Rao\u27s order on degree sequences

Recognition of split-graphic sequences

Using different definitions of split graphs we propose quick algorithms for the recognition and extremal reconstruction of split sequences among integer, regular, and graphic sequences

Origin and Functional Evolution of the Cdc48/p97/VCP AAA+ Protein Unfolding and Remodeling Machine

The AAA + Cdc48 ATPase (alias p97 or VCP) is a key player in multiple ubiquitin-dependent cell signaling, degradation, and quality control pathways. Central to these broad biological functions is the ability of Cdc48 to interact with a large number of adaptor proteins and to remodel macromolecular proteins and their complexes. Different models have been proposed to explain how Cdc48 might couple ATP hydrolysis to forcible unfolding, dissociation, or remodeling of cellular clients. In this review, we provide an overview of possible mechanisms for substrate unfolding/remodeling by this conserved and essential AAA + protein machine and their adaption and possible biological function throughout evolution. Keywords: AAA + machine; protein remodeling; human diseaseNational Institutes of Health (U.S.) (Grant AI-16892

In-Depth Analysis of Zero-Length Crosslinking for Structural Mass Spectrometry

The completion of the Human Genome Project revealed the sequence identity of essentially every human protein. However, in most cases, amino acid sequences alone convey little implication on the protein static structures, its dynamic conformational changes, and most importantly, its functions. To fully understand the behaviors and properties of macromolecular complexes, solving their 3D structures is necessary and highly critical. Under this rationale, structural genomics collaborations were initiated aiming to determine high-resolution structures of as many proteins and protein folds as possible, relying mostly on X-ray crystallography and NMR spectroscopy. Yet, very large, highly flexible or disordered, and dynamic protein complexes can exceed the capabilities of these high-resolution techniques. Although computational molecular modeling can be utilized, such structures are highly speculative and often inaccurate unless supported by actual experimental data. Structural mass spectrometry recently emerged as an alternative method which can provide medium-resolution spatial information capable of complementing computational approaches, and are applicable to heterogeneous samples with potentially no limit on complex sizes. In particular, chemical crosslinking coupled with mass spectrometry, has recently received considerable interest. Most recent progress focused on developing crosslinkers with special properties such as enrichment tags, isotopic labeling sites, or MS-cleavable bonds along with accompanying data analysis strategies and software packages. These crosslinkers insert their spacer arm between proximal amino acid residues, greatly reducing the stringency of the derived distance constraints. In contrast, zero-length crosslinkers are crosslinks which do not add any extra atoms to the product crosslinked peptides, therefore providing the tightest possible spatial constraints but rendering enrichment and isotopic labeling strategies inapplicable. As a result, zero-length crosslinking received limited attention and no software tools have previously been specifically developed for it. In this thesis project, we developed a multi-tiered mass spectrometry data acquisition and computational data analysis strategy along with a dedicated software tool to enhance identification of zero-length crosslinks in complex samples. Label-free comparison and targeted high-resolution mass spectrometry were utilized to filter out the vast majority of non-crosslinked peptides and increase confidence of crosslink identification, compensating for the lack of enrichment techniques and characteristic MS patterns employed by non-zero-length crosslinking methods. Each step from mass spectrometer acquisition parameters to MS/MS spectra evaluation functions was optimized based on zero-length crosslinking datasets of proteins with known crystal structures. Our pipeline was then applied to probe structures and conformational changes of mini-spectrin, a 90 kDa recombinant protein that closely mimics erythrocyte spectrin\u27s dynamic dimer-tetramer equilibrium. Compared to previous analyses performed in our laboratory, the current strategy more than doubled the number of identified crosslinks and significantly reduced analysis time per experiment from months to just several days. Distance constraints derived from mini-spectrin crosslinks were used as inputs in subsequent homology modeling, allowing development of experimentally-verified medium-resolution structures for wild-type mini-spectrin tetramer and both wild-type and hereditary elliptocytosis (HE) mutant mini-spectrin dimers. The structure models, in combination with independent biophysical experiments, illustrated how such distal HE-related mutations destabilized spectrin dimer-tetramer equilibrium by simultaneously lowering thermal stability of tetramer and giving rise to a more-compact, more-stable closed dimer conformation

Horrifically ambiguous : a formal analysis of ambiguating cinematography and narrative elements in Absentia (2011), Hereditary (2018), and The Lodge (2019)

Esta dissertação analisa os filmes Absentia (Mike Flanagan, 2011), Hereditary (Ari Aster, 2018) e The Lodge (Severin Fiala e Veronika Franz, 2019) com a intenção de descrever como a cinematografia é usada para estimular leituras ambíguas e hesitação no espectador. O uso de ambiguidade está presente em muitas, se não em todas, as tendências cinematográficas de horror desde o surgimento do cinema; no entanto, o ciclo em que esses filmes estão inseridos— o polêmico post-horror—é descrito por suas características marcantes de uso de apreensão prolongada, ritmo lento e preterição por edição dinâmica e jump scares para criar narrativas contemplativas, portentosas e opressivas que privilegiam afetos negativos. Sem cooptar emoções direcionadas a um objeto ou usar resoluções claras, esse ciclo cinemático possibilita a proliferação da hesitação e estimula uma apreensão generalizada a respeito da natureza dos eventos retratados; assim, potencializa o desconforto de navegar entre o sobrenatural e a plausibilidade do mundo real. Considerando afirmações de que, com seu estilo associado a uma estética artística virtuosa, o post-horror desestabiliza o horror, propõe-se aqui uma discussão para situar o gênero na tradição do horror em um esforço de contextualização informado pelos trabalhos de teóricos como Noël Carroll (1990), Fred Botting (1996), Isabel Pinedo (1996), Tim Woods (2003), Kevin Wetmore (2012) e Carol Clover (2015); além disso, as características formais do post-horror são descritas de acordo com a obra de David Church (2021). Adotando uma abordagem qualitativa baseada principalmente na obra de Bruce Mamer (2009) e Peter Verstraten (2009), realiza-se uma análise dos elementos formais desses filmes para explorar as estratégias narrativas e cinematográficas empregadas para ativar um olhar subjetivo e sugerir falhas na percepção, um princípio estético que é explorado de acordo com a obra de Uri Margolin (2011). Por fim, a discussão proposta por Sternberg e Yacobi (2015) sobre não confiabilidade narrativa é apresentada para revelar as possíveis estratégias interpretativas às quais possivelmente recorrem os espectadores desses filmes para resolver ambiguidade e tensões textuais.This thesis analyzes the films Absentia (Mike Flanagan, 2011), Hereditary (Ari Aster, 2018), and The Lodge (Severin Fiala and Veronika Franz, 2019) with the intent of describing the use of cinematography to elicit ambiguous readings and hesitation in the viewer. The use of ambiguity has been observed in many, if not all, horror cinematic trends since the dawn of cinema; nonetheless, the cycle in which these films are included—the so-called post-horror— is described for its distinct characteristics of employing lingering dread, slow pacing, and for its lack of dynamic editing, and jump scares with the effect of creating haunting and oppressive narratives privileging negative affects. Without co-opting object-directed emotions or using clear resolutions, hesitation festers in this cinematic cycle, and the generalized apprehension over the nature of the events depicted potentializes the uneasiness of treading between supernatural and real-world plausibility. Considering the claims that post-horror unsettles the broader, originating genre for its arthouse aesthetic, a discussion is proposed here to place the genre within the horror tradition in a contextualizing effort informed by the works of theorists such as Noël Carroll (1990), Fred Botting (1996), Isabel Pinedo (1996), Tim Woods (2003), Kevin Wetmore (2012), and Carol Clover (2015); moreover, the formal characteristics of post horror are described according to the work of David Church (2021). Adopting a qualitative approach based mainly on the work of Bruce Mamer (2009) and Peter Verstraten (2009), an analysis of the formal elements in these films is carried out to explore the narrative and cinematographic strategies employed to give rise to subjectivity and imply missteps in perception, an aesthetic endeavor that is considered in accordance with the work of Uri Margolin (2011). Furthermore, the discussion proposed by Sternberg and Yacobi (2015) on narrative unreliability is introduced to shed light onto the possible interpretive strategies to which viewers of such films might resort in order to resolve ambiguity and textual tensions