Quasi-cellular Systems: Stochastic Simulation Analysis at Nanoscale Range

I complessi sistemi di reazioni biochimiche all’interno della cellula sono altamente compartimentalizzati, conseguenza di un importante fenomeno di macromolecolar crowding (sovraffollamento molecolare). E’ dunque importante determinare il comportamento e le proprietà di un sistema di reazioni in piccoli volumi. Sono stati riprodotti con successo diversi sistemi di semplici reazioni all’interno di vescicole lipidiche (liposomi) nell’ordine del micro/nanometro di diametro, osservando in molti casi una risposta cinetica diversa dalle reazioni in esame rispetto al comportamento in sistemi di grandi volumi. Questo fenomeno di divergenza tra piccoli e grandi volumi è in gran parte dipendente da fenomeni non completamente chiariti, quali l’incapsulamento delle specie e il crowding molecolare, aspetti sempre più importanti man mano che l’attenzione si sposta verso i piccoli volumi. Recenti dati sperimentali dimostrano che il fenomeno dell'intrappolamento sembra non seguire un andamento casuale squisitamente probabilistico, ma un comportamento di tipo power-law (a legge di potenza), in cui solo pochissime vescicole intrappolano tante specie, mentre la maggior parte resta completamente vuota. A tal proposito è stato intrapreso uno studio sui meccanismi generativi delle distribuzioni a legge di potenza calate nel contesto dell’incapsulamento (entrapment) delle specie all'interno di vescicole lipidiche. Utilizzando un sistema cell-free di trascrizione/traduzione (PURESYSTEM™), volto alla produzione di EGFP all’interno di liposomi di POPC, è possibile monitorare la produzione di proteina fluorescente in liposomi di differente grandezza. Tuttavia, è molto difficile osservare la produzione di molecole fluorescenti in singole vescicole di 100 nm di diametro; diventa così importante poter studiare in silico la di produzione di proteina in singole vescicole virtuali, utilizzando un modello formalmente valido del complesso sistema di reazioni del PURESYSTEM™. QDC (Quick Direct-Method Controlled), è un software di simulazione stocastico precedentemente sviluppato in laboratorio, basato sull’algoritmo di simulazione SSA Direct-Method di Gillespie, tra i più usati in biologia computazionale/systems biology. L’argomento della tesi riguarda l’uso di questo software nello studio delle oltre 100 reazioni biochimiche del PURESYSTEM™, comparando i risultati ottenuti in diverse condizioni (volume totale di reazione, concentrazioni delle specie, costanti cinetiche delle singole reazioni). Dopo aver affinato il modello in silico di Trascrizione/traduzione coupled (accoppiato), sono state effettuate delle simulazioni variando alcune variabili macroscopiche (concentrazioni delle specie e costanti cinetiche), mostrando un'importante dipendenza della traduzione dalla trascrizione, soprattutto considerando il grande limite energetico di un sistema che non produce al suo interno nucleotidi trifosfato

Fictionalism of Anticipation

A promising recent approach for understanding complex phenomena is recognition of anticipatory behavior of living organisms and social organizations. The anticipatory, predictive action permits learning, novelty seeking, rich experiential existence. I argue that the established frameworks of anticipation, adaptation or learning imply overly passive roles of anticipatory agents, and that a fictionalist standpoint reflects the core of anticipatory behavior better than representational or future references. Cognizing beings enact not just their models of the world, but own make-believe existential agendas as well. Anticipators embody plausible scripts of living, and effectively assume neo-Kantian or pragmatist perspectives of cognition and action. It is instructive to see that anticipatory behavior is not without mundane or loathsome deficiencies. Appreciation of ferally fictionalist anticipation suggests an equivalence of semiosis and anticipation

TROM: A Testing-based Method for Finding Transcriptomic Similarity of Biological Samples

Comparative transcriptomics has gained increasing popularity in genomic research thanks to the development of high-throughput technologies including microarray and next-generation RNA sequencing that have generated numerous transcriptomic data. An important question is to understand the conservation and differentiation of biological processes in different species. We propose a testing-based method TROM (Transcriptome Overlap Measure) for comparing transcriptomes within or between different species, and provide a different perspective to interpret transcriptomic similarity in contrast to traditional correlation analyses. Specifically, the TROM method focuses on identifying associated genes that capture molecular characteristics of biological samples, and subsequently comparing the biological samples by testing the overlap of their associated genes. We use simulation and real data studies to demonstrate that TROM is more powerful in identifying similar transcriptomes and more robust to stochastic gene expression noise than Pearson and Spearman correlations. We apply TROM to compare the developmental stages of six Drosophila species, C. elegans, S. purpuratus, D. rerio and mouse liver, and find interesting correspondence patterns that imply conserved gene expression programs in the development of these species. The TROM method is available as an R package on CRAN (http://cran.r-project.org/) with manuals and source codes available at http://www.stat.ucla.edu/ jingyi.li/software-and-data/trom.html

Towards Parsimonious Generative Modeling of RNA Families

Generative probabilistic models emerge as a new paradigm in data-driven, evolution-informed design of biomolecular sequences. This paper introduces a novel approach, called Edge Activation Direct Coupling Analysis (eaDCA), tailored to the characteristics of RNA sequences, with a strong emphasis on simplicity, efficiency, and interpretability. eaDCA explicitly constructs sparse coevolutionary models for RNA families, achieving performance levels comparable to more complex methods while utilizing a significantly lower number of parameters. Our approach demonstrates efficiency in generating artificial RNA sequences that closely resemble their natural counterparts in both statistical analyses and SHAPE-MaP experiments, and in predicting the effect of mutations. Notably, eaDCA provides a unique feature: estimating the number of potential functional sequences within a given RNA family. For example, in the case of cyclic di-AMP riboswitches (RF00379), our analysis suggests the existence of approximately $\mathbf{10^{39}}$ functional nucleotide sequences. While huge compared to the known $< \mathbf{4,000}$ natural sequences, this number represents only a tiny fraction of the vast pool of nearly $\mathbf{10^{82}}$ possible nucleotide sequences of the same length (136 nucleotides). These results underscore the promise of sparse and interpretable generative models, such as eaDCA, in enhancing our understanding of the expansive RNA sequence space.Comment: 33 pages (including SI

Tendon proper- and peritenon-derived progenitor cells have unique tenogenic properties.

IntroductionMultipotent progenitor populations exist within the tendon proper and peritenon of the Achilles tendon. Progenitor populations derived from the tendon proper and peritenon are enriched with distinct cell types that are distinguished by expression of markers of tendon and vascular or pericyte origins, respectively. The objective of this study was to discern the unique tenogenic properties of tendon proper- and peritenon-derived progenitors within an in vitro model. We hypothesized that progenitors from each region contribute differently to tendon formation; thus, when incorporated into a regenerative model, progenitors from each region will respond uniquely. Moreover, we hypothesized that cell populations like progenitors were capable of stimulating tenogenic differentiation, so we generated conditioned media from these cell types to analyze their stimulatory potentials.MethodsIsolated progenitors were seeded within fibrinogen/thrombin gel-based constructs with or without supplementation with recombinant growth/differentiation factor-5 (GDF5). Early and late in culture, gene expression of differentiation markers and matrix assembly genes was analyzed. Tendon construct ultrastructure was also compared after 45&nbsp;days. Moreover, conditioned media from tendon proper-derived progenitors, peritenon-derived progenitors, or tenocytes was applied to each of the three cell types to determine paracrine stimulatory effects of the factors secreted from each of the respective cell types.ResultsThe cell orientation, extracellular domain and fibril organization of constructs were comparable to embryonic tendon. The tendon proper-derived progenitors produced a more tendon-like construct than the peritenon-derived progenitors. Seeded tendon proper-derived progenitors expressed greater levels of tenogenic markers and matrix assembly genes, relative to peritenon-derived progenitors. However, GDF5 supplementation improved expression of matrix assembly genes in peritenon progenitors and structurally led to increased mean fibril diameters. It also was found that peritenon-derived progenitors secrete factor(s) stimulatory to tenocytes and tendon proper progenitors.ConclusionsData demonstrate that, relative to peritenon-derived progenitors, tendon proper progenitors have greater potential for forming functional tendon-like tissue. Furthermore, factors secreted by peritenon-derived progenitors suggest a trophic role for this cell type as well. Thus, these findings highlight the synergistic potential of including these progenitor populations in restorative tendon engineering strategies

Expansion of the Parkinson disease-associated SNCA-Rep1 allele upregulates human alpha-synuclein in transgenic mouse brain.

Alpha-synuclein (SNCA) gene has been implicated in the development of rare forms of familial Parkinson disease (PD). Recently, it was shown that an increase in SNCA copy numbers leads to elevated levels of wild-type SNCA-mRNA and protein and is sufficient to cause early-onset, familial PD. A critical question concerning the molecular pathogenesis of PD is what contributory role, if any, is played by the SNCA gene in sporadic PD. The expansion of SNCA-Rep1, an upstream, polymorphic microsatellite of the SNCA gene, is associated with elevated risk for sporadic PD. However, whether SNCA-Rep1 is the causal variant and the underlying mechanism with which its effect is mediated by remained elusive. We report here the effects of three distinct SNCA-Rep1 variants in the brains of 72 mice transgenic for the entire human SNCA locus. Human SNCA-mRNA and protein levels were increased 1.7- and 1.25-fold, respectively, in homozygotes for the expanded, PD risk-conferring allele compared with homozygotes for the shorter, protective allele. When adjusting for the total SNCA-protein concentration (endogenous mouse and transgenic human) expressed in each brain, the expanded risk allele contributed 2.6-fold more to the SNCA steady-state than the shorter allele. Furthermore, targeted deletion of Rep1 resulted in the lowest human SNCA-mRNA and protein concentrations in murine brain. In contrast, the Rep1 effect was not observed in blood lysates from the same mice. These results demonstrate that Rep1 regulates human SNCA expression by enhancing its transcription in the adult nervous system and suggest that homozygosity for the expanded Rep1 allele may mimic locus multiplication, thereby elevating PD risk

Estudios moleculares revelan la existencia de un proceso de especiación en Ryvardenia cretacea (Polyporales, Basidiomycota)

rDNA sequentiation and phylogenetic analysis of the ITS region of strains of the brown-rot polypore Ryvardenia cretacea from Australia (Tasmania, Victoria) and Argentina (Patagonia) revealed the existence of two well supported clades. Each clade appears restricted to one side of the Pacific indicating a strong biogeographical isolation between strains and populations in the process of speciation. Nevertheless, detailed studies and comparisons did not show the existence of significant morphological differences. This fact, coupled with previously reported dikaryon x monosporic mating tests which showed biological compatibility between specimens from both regions, supports the maintenance of a complex but taxonomically single entity.La secuenciación molecular del segmento ITS del ADNr de cepas del políporo de pudrición castaña Ryvardenia cretacea provenientes de Australia (Tasmania, Victoria) y de Argentina (Patagonia) y su posterior análisis filogenético permitió revelar la existencia de dos clados con buen soporte. Cada una de ellos aparece con una distribución geográfica restringida a cada lado del Pacífico austral, indicando la existencia de un proceso de especiación. No obstante, estudios morfológicos comparativos detallados no revelaron la existencia de diferencias morfológicas entre materiales de herbario de esas procedencias. Ello, junto al hecho que investigaciones previas demostraron la compatibilidad entre cultivos secundarios y primarios entre especímenes de ambas regiones, sostiene el considerar a este taxón como un complejo con una única entidad taxonómica a nivel de especie.Fil: Rajchenberg, Mario. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Provincia del Chubut. Centro de Investigación y Extensión Forestal Andino Patagónico; ArgentinaFil: Pildain, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Provincia del Chubut. Centro de Investigación y Extensión Forestal Andino Patagónico; Argentin