68 research outputs found

    Transcriptome and Genome Analyses Applied to Aquaculture Research

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    Aquaculture is an important economic activity for food production all around the world that has experienced an exponential growth during the last few decades. However, several weaknesses and bottlenecks still need to be addressed in order to improve the aquaculture productive system. The recent fast development of the omics technologies has provided scientists with meaningful tools to elucidate the molecular basis of their research interests. This reprint compiles different works about the use of transcriptomics and genomics technologies in different aspects of the aquaculture research, such as immunity, stress response, development, sexual dimorphism, among others, in a variety of fish and shellfish, and even in turtles. Different transcriptome (mRNAs and non-coding RNAs (ncRNAs)), genome (Single Nucleotide Polymorphisms (SNPs)), and metatranscriptome analyses were conducted to unravel those different aspects of interest

    Green Functions Approach to Graphene Nanostructures

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    Due to their fascinating optoelectronic properties, finite graphene nanostructures are expected to find use in a number of technological applications, ranging from field effect transistors and solar cells to quantum computers and even biomedical treatments. However, despite their small size, these systems can contain several hundred to thousands of electrons, unfortunately, making their theoretical modeling a major challenge. The main drawback of the established theoretical formalism, the nonequilibrium Green functions approach, is its high numerical effort, which scales cubically with the number of required time steps. Therefore, performing time-dependent simulations of the nonequilibrium dynamics of excited finite graphene nanostructures is not feasible, which makes further improvements urgently necessary. Such a feat was achieved by the author and coworkers during the work on this thesis by developing the G1–G2 scheme. It constitutes the first formulation of the nonequilibrium Green functions approach with linearly-scaling numerical effort with respect to the propagation time. Because of the great importance of this discovery, this thesis addresses two main topics. The first is the aforementioned theoretical framework in general and its application to finite graphene nanostructures. The focus is on special topologically protected states that can occur in these systems. Moreover, the G1–G2 scheme is used to study the ultrafast response of various graphene nanostructures to an external laser pulse. The second aspect includes a detailed discussion of the G1–G2 scheme. Many questions that have arisen in previous publications on the subject are answered. The central insight is that the derivation of the G1–G2 scheme holds many more advantages, besides the obvious numerical ones. These findings can contribute decisively to the further development of approximation methods in many-particle theory

    Tools and Algorithms for the Construction and Analysis of Systems

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    This book is Open Access under a CC BY licence. The LNCS 11427 and 11428 proceedings set constitutes the proceedings of the 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2019, which took place in Prague, Czech Republic, in April 2019, held as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2019. The total of 42 full and 8 short tool demo papers presented in these volumes was carefully reviewed and selected from 164 submissions. The papers are organized in topical sections as follows: Part I: SAT and SMT, SAT solving and theorem proving; verification and analysis; model checking; tool demo; and machine learning. Part II: concurrent and distributed systems; monitoring and runtime verification; hybrid and stochastic systems; synthesis; symbolic verification; and safety and fault-tolerant systems

    Cell mechanics and cell-cell interactions of fibroblasts from Dupuytren's Patient : Atomic Force Microscopy Investigation

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    Cells as a biological entity of tissue, itself made of biomolecules such as mostly proteins, lipids and carbohydrates, creates its own meshwork of biopolymers named extracellular matrix (ECM) particularly fibroblasts. With the advanced light and force microscopies, inter-cellular, cell-ECM and intracellular signaling pathways are deeply explored either by tagging the biomolecule of interest with fluorophores or by applying certain forces(in the order of pN to nN). In the field of mechanobiology, interplay between cell function and physical forces are studied using biophysical tools thatprobe their diverse mechanisms. Cells exert forces( inside-out signalling)and also respond to physical forces from their micro-environment( outside-in signalling) through participation of chain of varying protein signaling molecules. Actin molecules from cytoskeleton family form filaments in the cytoplasmic side of the cell and myosin walk on these filaments generates contractile tension. These traction forces get transmitted to the extracellular matrixof the cell or to the neighboring cells through protein complexes such as integrin and cadherins, respectively. Fibroblasts,from the mesenchymal family, are the abundant cells found in the connective tissue. Basically, fibroblasts synthesize,degrade and maintain the extracellular matrix components of the tissue. Fibroblasts, by acquiring different phenotypes called protomyofibroblast/myofibroblast, play a huge participation in various connective tissue related diseases. Myofibroblast are large cells possessing large bundles of actin filaments of isomers named alpha smooth muscle actin (I /--SMA). On the other hand, protomyofibroblast share the similar characteristic appearance but shows I /--SMA negative large stress fibres. In Dupuytrena s disease, thesemyofibroblasts persists and deform the surrounding matrix environment thus results in tissue stiffening and further leads to tissue contracture. Existing various biophysical tools maps forces such as tractile force, cell-cell interaction force and cell-ECM interaction force. One among such tool is Atomic Force Microscopy, a multifunctional toolbox in cellular biology to observe various cell types mechanics. Observing cell viscoelastic properties by application of controlled force (nanonewton) to the adherent cell become more common in the biomedical community. This thesis demonstrates the measurement of viscoelastic properties of fibroblast of different phenotypes extracted from a Dupuytrena s diseased patient and ECM derived from various tissues.The bio-mechanical interplay between cell and ECM has been studied with careful design of the AFM experiments. Fibroblasts extracted from the cords and nodular region of the palmar fascia exhibits myofibroblast phenotype and migrate slower than the fibroblast extracted from dermal and scar region. Normal and scar fibroblasts migrate faster in the wound healing assay.On the decellularized matrices, scar fibroblasts exhibitprotomyofibroblast phenotype by expressing large stress fibres. Whereas, normal fibroblasts derived from the dermal region express the healthy phenotypic appearance. From AFM based Single-cell force spectroscopy (SCFS), cell-cell interaction force measurements evaluatethe homophilic and heterophilic cadherinpairs mechanical bond strength expressed in homo-cellular (fibroblast of similar phenotype) and hetero-cellular (fibroblast-epithelial cell) arrangements. SCFS measurements also illustrate the significant role of actomyosin contractile apparatus in cadherin extracellular iidomain binding dynamics. With this evidence, SCFS setup has become an excellent spectroscopic tool to study the intracellular signalingcascades that are linked to the extracellular domain consisting transmembrane proteins such as cadherins. Therefore, an understanding of the unique fibroblasts mechanobiology is necessary to study the healthy and diseased tissue dynamics. The cell-cell and cell-ECM bio-chemical and bio-mechanical cues are strongly interdependent. Finally, the current thesis opens the basic understanding of the fibroblasts biophysical properties using AFM nano-mechanical tool and unravels the fibroblasts biomechanical function in sub-tissue level biology

    Performance Evaluation of Software using Formal Methods

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    Formal Methods (FMs) can be used in varied areas of applications and to solve critical and fundamental problems of Performance Evaluation (PE). Modelling and analysis techniques can be used for both system and software performance evaluation. The functional features and performance properties of modern software used for performance evaluation has become so intertwined. Traditional models and methods for performance evaluation has been studied widely which culminated into the modern models and methods for system and software engineering evaluation such as formal methods. Techniques have transcended from functionality to performance modeling and analysis. Formal models help in identifying faulty reasoning far earlier than in traditional design; and formal specification has proved useful even on already existing software and systems. Formal approach eliminates ambiguity. The basic and final goal of the performance evaluation technique is to come to a conclusion, whether the software and system are working in a good condition or satisfactorily

    Cryo-EM Studies of Vesicle Inducing Protein in Plastids (Vipp1)

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    Differential Effects of Dry Eye Disorders on Metabolomic Profile by 1 H Nuclear Magnetic Resonance Spectroscopy

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    We used 1 H NMR spectroscopy to analyze the metabolomic profile of reflex tears from patients with dry eye disorders (DEDs). 90 subjects were divided into 2 groups: (1) patients with DEDs (DEDG; = 55) and (2) healthy subjects (CG; = 35). Additionally, the DEDG was subdivided into 2 subgroups based on DED severity: mild-to-moderate and moderate ( = 22 and = 33, resp.). Personal interviews and systematized ophthalmologic examinations were carried out. Reflex tears (20-30 L) were collected by gently rubbing in the inferior meniscus of both eyelids with a microglass pipette and stored at −80 ∘ C until analysis. NMR spectra were acquired using a standard one-dimensional pulse sequence with water suppression. Data were processed and transferred to MATLAB for further chemometric analysis. Main differences in tear composition between DEDG and CG were found in cholesterol, N-acetylglucosamine, glutamate, creatine, amino-n-butyrate, choline, acetylcholine, arginine, phosphoethanolamine, glucose, and phenylalanine levels. This metabolic fingerprint helped also to discriminate between the three additional subgroups of DEDG. Our results suggest that tear metabolic differences between DEDG and CG identified by NMR could be useful in understanding ocular surface pathogenesis and improving biotherapy
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