Evolutionary Computation

This book presents several recent advances on Evolutionary Computation, specially evolution-based optimization methods and hybrid algorithms for several applications, from optimization and learning to pattern recognition and bioinformatics. This book also presents new algorithms based on several analogies and metafores, where one of them is based on philosophy, specifically on the philosophy of praxis and dialectics. In this book it is also presented interesting applications on bioinformatics, specially the use of particle swarms to discover gene expression patterns in DNA microarrays. Therefore, this book features representative work on the field of evolutionary computation and applied sciences. The intended audience is graduate, undergraduate, researchers, and anyone who wishes to become familiar with the latest research work on this field

Elucidating regulators of red blood cell development in health and disease

Red blood cells are are plentiful, flexible and essential. They are the most abundant cell in our body and their mainobject is to carry oxygen, which is essential for cellular respiration. The formation of red blood cells is callederythropoiesis. Erythropoiesis is intimately coupled to cell division and mitochondrial function. Aberrations in thesetwo processes are often associated with red blood cell disorders, which result in anemia. Anemia is characterizedby the lack of red blood cells and/or reduced hemoglobin concentrations resulting in reduced oxygen transport tothe tissue and inevitable to reduced quality of life and increased mortality. My aim in this thesis has been todeepen our understanding of how erythropoiesis is regulated in health and diseaseIn the first paper we demonstrated that anemia caused by pRb deficiency was due to disrupted differentiation withunderlying impairment to mitochondrial function at the orthochromatic erythroblast stage. The MDS-like phenotypeof pRb deficient mice could be rescued by enhanced PPAR pathway signaling, an important signaling axis inmitochondrial biogenesis, in vivo either genetically or therapeutically.In the second paper we translated our findings in the mouse to a human setting by inhibiting PPAR signaling. Wedemonstrated that perturbed PPAR signaling in human hematopoietic stem/progenitor cells from both bonemarrow and cord blood results in impaired formation of early erythroid progenitors and delayed terminal erythroiddifferentiation in vitro. We showed that PPAR signaling is important for iron, heme and globin homeostasis.Furthermore we demonstrated that PPAR signaling affects cell cycle exit indicating that there is a mutualregulation between cell cycle progression and mitochondrial function during terminal erythropoiesis.In the third paper we demonstrated that Ypel4, which is highly expressed in orthochromatic erythroblasts, isimportant for the integrity of red blood cell membrane. Ypel4 null erythroblast had reduced deformability and werecleared at an increased rate. The phenotype resembled defects normally observed in human hereditarymembrane disorders.Overall the papers included in this thesis highlight mechanisms and genes important for terminal erythropoiesisspecifically in the orthochromatic erythroblast. We further described disease associated with the differentperturbations to erythropoiesis. The work presente

Transcription factor regulation of amyloid-beta pathway genes by SP1-Modulating compounds : a novel approach in Alzheimer's Disease

Indiana University-Purdue University Indianapolis (IUPUI)Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the presence of neuritic plaques consisting of extracellular amyloid-beta (Aβ) and neurofibrillary tangles comprised of hyperphosphorylated microtubule associated tau. Aβ is produced following the cleavage of amyloid precursor protein (APP) by the enzyme BACE1. Transcription factors (TFs) are proteins involved in the regulation of gene transcription. Expression levels of some TFs are perturbed in AD. SP1 binding sites on both the APP and BACE1 promoters implicate its potential role in AD. Aβ peptide itself mediates activation of cyclindependent kinase 5 (CDK5), an enzyme which phosphorylates the FOXO (Forkhead Box) TFs. In order to study mechanisms of TF regulation of Aβ production in human models, neuronally differentiated cells as well as a primary human neurosphere culture were used to test the effects of TF-modulating compounds. Our hypothesis is that by targeting relevant TFs via pharmacological inhibitors in human cells, BACE1 activity or APP expression will decrease and Aβ production will be reduced as a result. To test the involvement of TFs in the regulation of APP, we treated several mammalian cells lines and post-mitotic human neuronal cells with roscovitine, mithramycin A (MTM), MTM analogs (MTM-SDK, MTM-SK), and tolfenamic acid (TA). MTM and TA treatment of neurons differentially activated several TFs implicated in AD. Treatment of differentiated neurospheres with MTM led to a significant decrease in APP and SP1 expression along with Aβ40 levels. Epigenetic mechanisms involve alteration of the binding affinity between DNA and transcription factors. We predict that modulation of these TFs may be influenced by epigenetic modifications. To test the effects of drugs on epigenetic markers, histone deacetylase (HDAC) and DNA methyltransferase (DNMT) activity was measured. MTM-SDK significantly decreased DNMT activity in differentiated neuroblastoma cells, this may enhance or decrease the ability of SP1 to bind to target DNA and affect transcription of BACE1 or APP. Targeting TF activity is a novel means to manipulate the amyloid pathway. Compounds modifying TF binding to sites on the BACE1 or APP promoters may provide a means to limit the production of amyloid-beta and slow the symptoms of AD

Combining gene-editing with brain imaging: from genes to molecules to networks

"Receptors, transporters and ion channels are important targets for therapy development in neurological diseases, [...] but their mechanistic role in pathogenesis is often poorly understood. Gene-editing and in vivo imaging approaches will help to identify the molecular and functional role of these targets and the consequence of their regional dysfunction on whole-brain level. Here, we combine CRISPR/Cas9 gene-editing with in vivo PET and fMRI to investigate the direct link between genes, molecules, and the brain connectome. The extensive knowledge of the Slc18a2 gene encoding the VMAT2, involved in the storage and release of DA, makes it an excellent target for studying the gene networks relationships while structurally preserving neuronal integrity and function. We edited the Slc18a2 in the SNc of adult rats and used in vivo molecular imaging besides behavioral, histological, and biochemical assessments to characterize the CRISPR/Cas9-mediated VMAT2 KD. Simultaneous PET/fMRI was performed to inspect the molecular and functional brain adaptations, beyond the predicted dopaminergic changes. We found a regional increase in postsynaptic DA receptor availability, preceded by a reorganization of brain networks that adapt to reduced DA transmission states by becoming functionally connected and organized. We observed that FC adaptations are stage-specific and follow the selective impairment of presynaptic DA storage and release. Further, the observed hyperconnectivity within and between brain networks spreads from the contralateral thalamus and prefrontal cortical regions to the striata and hippocampi. Our study reveals that recruiting different brain networks is an early response to the dopaminergic dysfunction preceding neuronal cell loss. Our combinatorial approach is a novel tool to investigate the impact of specific genes on brain molecular and functional dynamics which will help to develop tailored therapies for normalizing brain function. The method can easily be transferred to higher- order species allowing for a direct comparison of the molecular imaging findings" [1]. 86 Future studies could benefit from in vivo reporter gene PET probes to quantitatively assess and monitor the Cas9 and sgRNA brain expression over time [38, 220]. Indeed, in vivo reporter gene imaging is a powerful tool to monitor gene therapy and image exogenous gene expression in the brain of preclinical models of neurological diseases. Despite several reporter genes have been developed in the last years, these show major limitations. Indeed, most available reporter gene systems are based on endogenously expressed genes, resulting in high background binding or low brain uptake. Here, we characterized the pharmacokinetics and metabolism of [11C]TMP, a novel PET reporter probe which binds to EcDHFR-engineered cells and shows potential for imaging ectopic gene expression in xenografted tumor models in vitro and in vivo [47]. We found that [11C]TMP presents several unfavorable characteristics; dependency on PgP efflux transport at the BBB, hindering its brain uptake in the rat species, and in vivo metabolism, hampering the PET data quantification. Our study shows that [11C]TMP is not a suitable PET reporter gene probe to image exogeneous gene expression in the rat brain, presenting low brain uptake and fast metabolism. Future studies should focus on the investigation of different targets and the development of [11C]TMP analogs with more favorable pharmacokinetics and detectability, which are neither PgP substrate nor rapidely metabolized. [1].Marciano et al., PNAS, 202

Hemodynamics

Hemodynamics is study of the mechanical and physiologic properties controlling blood pressure and flow through the body. The factors influencing hemodynamics are complex and extensive. In addition to systemic hemodynamic alterations, microvascular alterations are frequently observed in critically ill patients. The book "Hemodynamics: New Diagnostic and Therapeuric Approaches" is formed to present the up-to-date research under the scope of hemodynamics by scientists from different backgrounds

The new technique for accurate estimation of the spinal cord circuitry:recording reflex responses of large motor unit populations

We propose and validate a non-invasive method that enables accurate detection of the discharge times of a relatively large number of motor units during excitatory and inhibitory reflex stimulations. HDsEMG and intramuscular EMG (iEMG) were recorded from the tibialis anterior muscle during ankle dorsiflexions performed at 5%, 10%, and 20% of the maximum voluntary contraction (MVC) force, in 9 healthy subjects. The tibial nerve (inhibitory reflex) and the peroneal nerve (excitatory reflex) were stimulated with constant current stimuli. In total, 416 motor units were identified from the automatic decomposition of the HDsEMG. The iEMG was decomposed using a state-of-the-art decomposition tool and provided 84 motor units (average of two recording sites). The reflex responses of the detected motor units were analyzed using the peri-stimulus time histogram (PSTH) and the peri-stimulus frequencygram (PSF). The reflex responses of the common motor units identified concurrently from the HDsEMG and the iEMG signals showed an average disagreement (the difference between number of observed spikes in each bin relative to the mean) of 8.2±2.2% (5% MVC), 6.8±1.0% (10% MVC), and 7.5±2.2% (20% MVC), for reflex inhibition, and 6.5±4.1%, 12.0±1.8%, 13.9±2.4%, for reflex excitation. There was no significant difference between the characteristics of the reflex responses, such as latency, amplitude and duration, for the motor units identified by both techniques. Finally, reflex responses could be identified at higher force (four of the nine subjects performed contraction up to 50% MVC) using HDsEMG but not iEMG, because of the difficulty in decomposing the iEMG at high forces. In conclusion, single motor unit reflex responses can be estimated accurately and non-invasively in relatively large populations of motor units using HDsEMG. This non-invasive approach may enable a more thorough investigation of the synaptic input distribution on active motor units at various force levels