Representasi Superhero Dalam Film X-Men: the Days of the Future Past

Penelitian ini untuk mengetahui bagaimana representasi figur superhero dan villain dalam Film X-Men: Days of The Future Past dan mengetahui mengapa karakteristik superhero dan villain dalam X-Men: Days of The Future Past divisualkan menggunakan citraan yang tidak mengikuti ‘tradisi\u27 superhero Amerika. Hal ini dilatarbelakangi karena munculnya banyak film-film superhero yang sangat menonjolkan kekuatan dan superioritas Amerika terhadap musuh-musuh ‘historisnya\u27. Film X-Men The Days of The Future Past tidak lagi menunjukkan figur superhero ikonik khas Amerika dengan bintang dan warna putih biru mengacu bendera Amerika, atau memvisualkan villain sebagaimana musuh dalamhistoris Amerika (Nazi, komunis Rusia-Cina, dan teroris timur tengah). Metode penelitian yang digunakan adalah deskriptif kualitatif dengan memahami bahwa film adalah bentuk hiperealitas yang didalamnya menjadi suatu representasi. Semiologi Roland Barthes dipakai sebagai cara yang memudahkan dalam menganalisis, dimana didalamnya terdapat denotatif, konotatif, dan mitos. Teknik menganalisis dilakukan dengan cara mengumpulkan data tentang film X-Men The Days of The Future Past kemudian dianalisis menggunakan Teori Praktik Pierre Bourdieu yakni habitus: nilai–nilai yang terinternalisasi dalam individu atau kelompok; Kapital: potensi yang dimiliki oleh individu atau kelompok untuk mendapatkan kesempatan di arena; Arena: sebuah tempat dimana didalamnya terdapat berbagai habitus dan kapital yangbersaing; Distinction: sebuah pembeda yang dilakukan untuk menunjukan kelas yang berbeda; Dominasi simbolik: kapital simbolik yang digunakan untuk menindas orang lain; Doxa: pandangan penguasa yang dianggap sebagai kebenaran. Dari deskripsi yang dianalisis menggunakan teori akan memunculkan pemaknaan mengenai film X -Men The Days of The Future Past

Adaptively Biased Sequential Importance Sampling for Rare Events in Reaction Networks with Comparison to Exact Solutions from Finite Buffer dCME Method

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlogl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape

Structural Signatures of Enzyme Binding Pockets from Order-Independent Surface Alignment: A Study of Metalloendopeptidase and NAD Binding Proteins

Detecting similarities between local binding surfaces can facilitate identification of enzyme binding sites and prediction of enzyme functions, and aid in our understanding of enzyme mechanisms. Constructing a template of local surface characteristics for a specific enzyme function or binding activity is a challenging task, as the size and shape of the binding surfaces of a biochemical function often vary. Here we introduce the concept of signature binding pockets, which captures information on preserved and varied atomic positions at multiresolution levels. For proteins with complex enzyme binding and activity, multiple signatures arise naturally in our model, forming a signature basis set that characterizes this class of proteins. Both signatures and signature basis sets can be automatically constructed by a method called SOLAR (Signature Of Local Active Regions). This method is based on a sequence-order-independent alignment of computed binding surface pockets. SOLAR also provides a structure-based multiple sequence fragment alignment to facilitate the interpretation of computed signatures. By studying a family of evolutionarily related proteins, we show that for metzincin metalloendopeptidase, which has a broad spectrum of substrate binding, signature and basis set pockets can be used to discriminate metzincins from other enzymes, to predict the subclass of metzincins functions, and to identify specific binding surfaces. Studying unrelated proteins that have evolved to bind to the same NAD cofactor, we constructed signatures of NAD binding pockets and used them to predict NAD binding proteins and to locate NAD binding pockets. By measuring preservation ratio and location variation, our method can identify residues and atoms that are important for binding affinity and specificity. In both cases, we show that signatures and signature basis set reveal significant biological insight

Lipid-Binding Surfaces of Membrane Proteins: Evidence From Evolutionary and Structural Analysis

Membrane proteins function in the diverse environment of the lipid bilayer. Experimental evidence suggests that some lipid molecules bind tightly to specific sites on the membrane protein surface. These lipid molecules often act as co-factors and play important functional roles. In this study, we have assessed the evolutionary selection pressure experienced at lipid-binding sites in a set of alpha-helical and beta-barrel membrane proteins using posterior probability analysis of the ratio of synonymous vs. nonsynonymous substitutions (omega-ratio). We have also carried out a geometric analysis of the membrane protein structures to identify residues in close contact with co-crystallized lipids. We found that residues forming cholesterol-binding sites in both beta(2)-adrenergic receptor and Na+-K+-ATPase exhibit strong conservation, which can be characterized by an expanded cholesterol consensus motif for GPCRs. Our results suggest the functional importance of aromatic stacking interactions and interhelical hydrogen bonds in facilitating protein-cholesterol interactions, which is now reflected in the expanded motif. We also find that residues forming the cardiolipin-binding site in formate dehydrogenase-N gamma-subunit and the phosphatidylglycerol binding site in KcsA are under strong purifying selection pressure. Although the lipopolysaccharide (LPS)-binding site in ferric hydroxamate uptake receptor (FhuA) is only weakly conserved, we show using a statistical mechanical model that LPS binds to the least stable FhuA beta-strand and protects it from the bulk lipid. Our results suggest that specific lipid binding may be a general mechanism employed by beta-barrel membrane proteins to stabilize weakly stable regions. Overall, we find that the residues forming specific lipid binding sites on the surfaces of membrane proteins often experience strong purifying selection pressure

Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model

<div><p>Nuclear landmarks and biochemical factors play important roles in the organization of the yeast genome. The interaction pattern of budding yeast as measured from genome-wide 3C studies are largely recapitulated by model polymer genomes subject to landmark constraints. However, the origin of inter-chromosomal interactions, specific roles of individual landmarks, and the roles of biochemical factors in yeast genome organization remain unclear. Here we describe a multi-chromosome constrained self-avoiding chromatin model (mC-SAC) to gain understanding of the budding yeast genome organization. With significantly improved sampling of genome structures, both intra- and inter-chromosomal interaction patterns from genome-wide 3C studies are accurately captured in our model at higher resolution than previous studies. We show that nuclear confinement is a key determinant of the intra-chromosomal interactions, and centromere tethering is responsible for the inter-chromosomal interactions. In addition, important genomic elements such as fragile sites and tRNA genes are found to be clustered spatially, largely due to centromere tethering. We uncovered previously unknown interactions that were not captured by genome-wide 3C studies, which are found to be enriched with tRNA genes, RNAPIII and TFIIS binding. Moreover, we identified specific high-frequency genome-wide 3C interactions that are unaccounted for by polymer effects under landmark constraints. These interactions are enriched with important genes and likely play biological roles.</p></div

Comparison of of the loop conformations sampled by Loop Builder and DiSGro using Test Set 4 taken from the Loop Builder study [42].

<p> denote the average RMSD of the lowest energy conformations of the loop ensemble. Results of LoopBuilder were obtained from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003539#pcbi-1003539-t005" target="_blank">Table 5</a> of Ref. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003539#pcbi.1003539-Soto1" target="_blank">[42]</a>.</p

Comparison of , and of the loop conformations sampled by PLOP and DiSGro using Test Set .

<p> and denote the average minimum backbone RMSD and the average RMSD of the lowest energy conformations of the loop ensemble.</p

Comparison of accuracy of modeled loops using the original Fiser data set of loops with – residues.

<p>The accuracy achieved by LOOPER and DiSGro at different loop length using the original Fiser data set of loops with 10–12 residues is listed. , and denote the mean and median of backbone RMSD, while , and denote the mean and median of all-heavy atoms RMSD of the lowest energy conformations with the same loop length.</p

Effects of confinement on the overall folding behavior of budding yeast genome.

<p><b>(A)</b> Overall correlation coefficient of the frequencies between genome-wide 3C measurements and modeled ensemble. As the nuclear size increases, correlation generally decreases. <b>(B)</b> Effects of nuclear size and chromosomal arm length on the median distances between telomeres. Relationships between arm length and median telomere distances at different nuclear sizes for the fully-constrained ensemble, with different telomeres as references are shown. Two linear regimens become one linear regime as <i>D</i> increases from 2 <i>μ</i>m to 4 and to 16 <i>μ</i>m.</p

Comparison of of the loop conformations sampled by DiSGro and six other methods using Test Set 2 used by Ref. [42].

<p> denote the average minimum backbone RMSD of the loop ensemble. Random Tweak, CCD, Wriggling, PLOP-build, Direct Tweak and results were obtained from Table 2 of Ref. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003539#pcbi.1003539-Soto1" target="_blank">[42]</a>.</p