Search

The genetic code is a set of regulatory principles that control the translation of information encoded in messenger RNA (mRNA) into a sequence of amino acids. This study proposes a model starting from the relationships between its physicochemical properties of nucleobase in the codons. We employed a binary metric and the Kronecker product to represent the physicochemical properties of nucleobases in a vector space. This state space has a hierarchical order, with self-similarity and symmetry properties in the hydrogen bonds of triplets. The state space can be mapped under linear transformations to a toroidal geometry with allometric properties. Furthermore, this geometric representation highlights a charge symmetry that exists in amino acids and in the distribution of essential and non-essential amino acids. These results describe a state space between codon-anticodon interactions that can be interpreted as Bell states. This suggests that there is a quantum phenomenon involved in the mechanisms of information storage in DNA. In addition, toroidal geometry can be used to represent the sequences of codons of the mRNA that encode the sequence of amino acids of the proteins to find similarities or homologies between evolutionary related species. [ABSTRACT FROM AUTHOR]

The present study is devoted to describing the "logic" implicit in the standard genetic code. Bases are considered as physicochemical entities possessing two essential properties: molecular type and number of Hydrogen bonds involved (bases pairing) in the codon-anticodon specific interactions. It is proposed that the codon structure possesses a dual informative function: on the one hand, it determines its discriminating or non-discriminating character, and on the other hand, it determines a specific amino acid. These two aspects constitute the codon global information. Two different sets of rules are introduced to describe these different phenomena. It is established that, depending on the type of base occupying the second position, only two or three of the six codon properties located at defined positions determine the discriminating or non-discriminating behavior. With regard to the amino acid determining function of the codons for different sets of synonymous (singlets, doublets, triplets, quadruplets, or sextets), the number of informative properties integrating the codon and their typical positions characteristically change. Based on the rules presented here, it can be postulated that a codon can be defined as an asymmetric informative entity, whose global informative capacity results from the spatially organized combination of the six properties assigned by the three bases. [ABSTRACT FROM AUTHOR]

Abstract Background Sonic hedgehog (Shh)/Gli pathway plays an important regulatory role on the neuroepithelial cells (NEc) proliferation in the dorsal regions of the developing vertebrate Central Nervous System. The aim of this paper was to analyze the effect of the Shh/Gli signaling pathway activation on the proliferation dynamics and/or the spatial organization of the NEc proliferation activity during early stages of the developing chick optic tectum (OT). In ovo pharmacological gain and loss of hedgehog function approaches were complemented with in vivo electroporation experiments in order to create ectopic sources of either Shh or Gli activator (GliA) proteins in the OT. NEc proliferating activity was analyzed at ED 4/4.5 by recording the spatial co-ordinates of the entire population of mitotic NEc (mNEc) located along OT dorsal-ventral sections. Several space signals (numerical sequences) were derived from the mNEc spatial co-ordinate records and analyzed by different standardized non-linear methods of signal analysis. Results In ovo pharmacologic treatment with cyclopamine resulted in dramatic failure in the OT expansion while the agonist purmorphamine produced the opposite result, a huge expansion of the OT vesicle. Besides, GliA and Shh misexpressions interfere with the formation of the intertectal fissure located along the dorsal midline. This morphogenetic alteration is accompanied by an increase in the mNEc density. There is a gradient in the response of NEcs to Shh and GliA: the increase in mNEc density is maximal near the dorsal regions and decrease towards the OT-tegmental boundary. Biomathematical analyses of the signals derived from the mNEc records show that both Shh and GliA electroporations change the proliferation dynamics and the spatial organization of the mNEc as revealed by the changes in the scaling index estimated by these methods. Conclusions The present results show that the Shh/Gli signaling pathway plays a critical role in the OT expansion and modelling. This effect is probably mediated by a differential mitogenic effect that increases the NEc proliferation and modulates the spatial organization of the NEc proliferation activity.

Abstract Background A current paradigm in the treatment of cervical cancer with radiation therapy is that intracavitary brachytherapy is an essential component of radical treatment. This is a matched retrospective comparison of the results of treatment in patients treated with external beam chemoradiation (EBRT-CT) and radical hysterectomy versus those treated with identical chemoradiation followed by brachytherapy. Methods In this non-randomized comparison EBRT-CT protocol was the same in both groups of 40 patients. In the standard treated patients, EBRT-CT was followed by one or two intracavitary Cesium (low-dose rate) applications within 2 weeks of finishing external radiation to reach a point A dose of at least 85 Gy. In the surgically treated patients, radical hysterectomy with bilateral pelvic lymph node dissection and para-aortic lymph node sampling were performed within 7 weeks after EBRT-CT. Response, toxicity and survival were evaluated. Results A total of 80 patients were analyzed. The patients receiving EBRT-CT and surgery were matched with the standard treated cases. There were no differences in the clinicopathological characteristics between groups or in the delivery of EBRT-CT. The pattern of acute and late toxicity differed. Standard treated patients had more chronic proctitis while the surgically treated had acute complications of surgery and hydronephrosis. At a maximum follow-up of 60 months, median follow-up 26 (2–31) and 22 (3–27) months for the surgery and standard therapy respectively, eight patients per group have recurred and died. The progression free and overall survival are the same in both groups. Conclusion The results of this study suggest that radical hysterectomy can be used after EBRT-CT without compromising survival in FIGO stage IB2-IIB cervical cancer patients in settings were brachytherapy is not available. A randomized study is needed to uncover the value of surgery after EBRT-CT.

The central nervous system areas displaying the highest structural and functional complexity correspond to the so called cortices, i.e., concentric alternating neuronal and fibrous layers. Corticogenesis, i.e., the development of the cortical organization, depends on the temporal-spatial organization of several developmental events: (a) the duration of the proliferative phase of the neuroepithelium, (b) the relative duration of symmetric (expansive) versus asymmetric (neuronogenic) sub phases, (c) the spatial organization of each kind of cell division, (e) the time of determination and cell cycle exit and (f) the time of onset of the post-mitotic neuronal migration and (g) the time of onset of the neuronal structural and functional differentiation. The first five events depend on molecular mechanisms that perform a fine tuning of the proliferative activity. Changes in any of them significantly influence the cortical size or volume (tangential expansion and radial thickness), morphology, architecture and also impact on neuritogenesis and synaptogenesis affecting the cortical wiring. This paper integrates information, obtained in several species, on the developmental roles of cell proliferation in the development of the optic tectum (OT) cortex, a multilayered associative area of the dorsal (alar) midbrain. The present review (1) compiles relevant information on the temporal and spatial organization of cell proliferation in different species (fish, amphibians, birds, and mammals), (2) revises the main molecular events involved in the isthmic organizer (IsO) determination and localization, (3) describes how the patterning installed by IsO is translated into spatially organized neural stem cell proliferation (i.e., by means of growth factors, receptors, transcription factors, signaling pathways, etc.) and (4) describes the morpho- and histogenetic effect of a spatially organized cell proliferation in the above mentioned species. A brief section on the OT evolution is also included. This section considers how the differential operation of cell proliferation could explain differences among species. [ABSTRACT FROM AUTHOR]

The developing chick optic tectum is a widely used model of corticogenesis and angiogenesis. Cell behaviors involved in corticogenesis and angiogenesis share several regulatory mechanisms. In this way the 3D organizations of both systems adapt to each other. The consensus about the temporally and spatially organized progression of the optic tectum corticogenesis contrasts with the discrepancies about the spatial organization of its vascular bed as a function of the time. In order to find out spatial and temporal correlations between corticogenesis and angiogenesis, several methodological approaches were applied to analyze the dynamic of angiogenesis in the developing chick optic tectum. The present paper shows that a typical sequence of developmental events characterizes the optic tectum angiogenesis. The first phase, formation of the primitive vascular bed, takes place during the early stages of the tectal corticogenesis along which the large efferent neurons appear and begin their early differentiation. The second phase, remodeling and elaboration of the definitive vascular bed, occurs during the increase in complexity associated to the elaboration of the local circuit networks. The present results show that, apart from the well-known influence of the dorsal-ventral and radial axes as reference systems for the spatial organization of optic tectum angiogenesis, the cephalic-caudal axis also exerts a significant asymmetric influence. The term cortico-angiogenesis to describe the entire process is justified by the fact that tight correlations are found between specific corticogenic and angiogenic events and they take place simultaneously at the same position along the cephalic-caudal and radial axes. [ABSTRACT FROM AUTHOR]

Background: In the development of the central nervous system (CNS), neuronal migration and neuritogenesis are crucial processes for establishing functional neural circuits. This relies on the regulation exerted by several signaling molecules, which play important roles in axonal growth and guidance. The urokinase-type plasminogen activator (uPA)-in association with its receptor-triggers extracellular matrix proteolysis and other cellular processes through the activation of intracellular signaling pathways. Even though the uPA-uPAR complex is well characterized in nonneuronal systems, little is known about its signaling role during CNS development. Results : In response to uPA, neuronal migration and neuritogenesis are promoted in a dose-dependent manner. After stimulation, uPAR interacts with α5- and β1-integrin subunits, which may constitute an αβ-heterodimer that acts as a uPA-uPAR coreceptor favoring the activation of multiple kinases. This interaction may be responsible for the uPA-promoted phosphorylation of focal adhesion kinase (FAK) and its relocation toward growth cones, triggering cytoskeletal reorganization which, in turn, induces morphological changes related to neuronal migration and neuritogenesis. Conclusions : uPA has a key role during CNS development. In association with its receptor, it orchestrates both proteolytic and nonproteolytic events that govern the proper formation of neural networks. Developmental Dynamics 243:676-689, 2014. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Background: Cell proliferation plays an important morphogenetic role. This work analyzes the temporal-spatial organization of cell proliferation as an attempt to understand its contribution to the chick optic tectum (OT) morphogenesis. Results: A morphogenetic model based on space-dependent differences in cell proliferation is presented. Step1: a medial zone of high mitotic density (mZHMD) appears at the caudal zone. Step2: the mZHMD expands cephalically forming the dorsal curvature and then duplicates into two bilateral ZHMDs (bZHMD). Step3: the bZHMDs move toward the central region of each hemitectum. Step4: the planar expansion of both bZHMD and a relative decrement in the dorsal midline growth produces a dorsal medial groove separating the tectal hemispheres. Step5: a relative caudal displacement of the bZHMDs produces the OT caudal curvature. Numerical sequences derived from records of mitotic cells spatial coordinates, analyzed as stochastic point processes, show that they correspond to 1/f(β) processes. The spatial organization subsumes deterministic and stochastic components. Conclusions: The deterministic component describes the presence of a long-range influence that installs an asymmetric distribution of cell proliferation, i.e., an asymmetrically located ZHMD that print space-dependent differences onto the tectal corticogenesis. The stochastic component reveals short-range anti-correlations reflecting spatial clusterization and synchronization between neighboring cells. Developmental Dynamics 241:1043-1061, 2012. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Background: Retinotopic projection onto the tectum/colliculus constitutes the most studied model of topographic mapping and Eph receptors and their ligands, the ephrins, are the best characterized molecular system involved in this process. Ephrin-As, expressed in an increasing rostro-caudal gradient in the tectum/colliculus, repel temporal retinal ganglion cell (RGC) axons from the caudal tectum and inhibit their branching posterior to their termination zones. However, there are conflicting data regarding the nature of the second force that guides nasal axons to invade and branch only in the caudal tectum/colliculus. The predominant model postulates that this second force is produced by a decreasing rostrocaudal gradient of EphA7 which repels nasal optic fibers and prevents their branching in the rostral tectum/colliculus. However, as optic fibers invade the tectum/colliculus growing throughout this gradient, this model cannot explain how the axons grow throughout this repellent molecule. Methodology/Principal Findings: By using chicken retinal cultures we showed that EphA3 ectodomain stimulates nasal RGC axon growth in a concentration dependent way. Moreover, we showed that nasal axons choose growing on EphA3- expressing cells and that EphA3 diminishes the density of interstitial filopodia in nasal RGC axons. Accordingly, in vivo EphA3 ectodomain misexpression directs nasal optic fibers toward the caudal tectum preventing their branching in the rostral tectum. Conclusions: We demonstrated in vitro and in vivo that EphA3 ectodomain (which is expressed in a decreasing rostro-caudal gradient in the tectum) is necessary for topographic mapping by stimulating the nasal axon growth toward the caudal tectum and inhibiting their branching in the rostral tectum. Furthermore, the ability of EphA3 of stimulating axon growth allows understanding how optic fibers invade the tectum growing throughout this molecular gradient. Therefore, opposing tectal gradients of repellent ephrin-As and of axon growth stimulating EphA3 complement each other to map optic fibers along the rostro-caudal tectal axis. [ABSTRACT FROM AUTHOR]

Background: A current paradigm in the treatment of cervical cancer with radiation therapy is that intracavitary brachytherapy is an essential component of radical treatment. This is a matched retrospective comparison of the results of treatment in patients treated with external beam chemoradiation (EBRT-CT) and radical hysterectomy versus those treated with identical chemoradiation followed by brachytherapy. Methods: In this non-randomized comparison EBRT-CT protocol was the same in both groups of 40 patients. In the standard treated patients, EBRT-CT was followed by one or two intracavitary Cesium (low-dose rate) applications within 2 weeks of finishing external radiation to reach a point A dose of at least 85 Gy. In the surgically treated patients, radical hysterectomy with bilateral pelvic lymph node dissection and para-aortic lymph node sampling were performed within 7 weeks after EBRT-CT. Response, toxicity and survival were evaluated. Results: A total of 80 patients were analyzed. The patients receiving EBRT-CT and surgery were matched with the standard treated cases. There were no differences in the clinicopathological characteristics between groups or in the delivery of EBRT-CT. The pattern of acute and late toxicity differed. Standard treated patients had more chronic proctitis while the surgically treated had acute complications of surgery and hydronephrosis. At a maximum follow-up of 60 months, median follow-up 26 (2-31) and 22 (3-27) months for the surgery and standard therapy respectively, eight patients per group have recurred and died. The progression free and overall survival are the same in both groups. Conclusion: The results of this study suggest that radical hysterectomy can be used after EBRT-CT without compromising survival in FIGO stage IB2-IIB cervical cancer patients in settings were brachytherapy is not available. A randomized study is needed to uncover the value of surgery after EBRT-CT. [ABSTRACT FROM AUTHOR]

The present report describes a systematic study comparing and combining methods currently used for the removal of endogenous factors known to affect the interaction of GABA with its receptor. The effects of these methods were analyzed by performing [H]GABA binding studies, and by measuring the amount of residual GABA left in the different membrane preparations. The effectiveness of these methods were also applied to different developmental stages. The results show that: 1) an exhaustive buffer washing procedure is necessary to accurately measure the maximal binding capacity (Bmax) of the low-affinity GABA binding site, and 2) the use of more drastic methods, including freeze-thawing and Triton treatment allows a clear demonstration of receptor heterogeneity and a precise measurement of the B of the high-affinity GABA binding site as well as increases the affinity of the low-affinity site. The analysis of the B values obtained with these different procedure in relation to the values of GABA removal, strongly indicates that the exhaustive washing procedure removes some unknown endogenous substances required for Triton treatment to exhibit its maximal effectiveness. Finally, a detailed analysis of K and B values obtained with these three methods in the developing nervous tissue shows the existence of significant differences with regard to their effectiveness in removing endogenous substances when applied in different developmental stages. [ABSTRACT FROM AUTHOR]