Biochemical Anatomy Research Articles

Abiotic stress tolerance in mangroves with a special reference to salinity

Since mangroves are found near extremely transitional ecosystems, they face a lot of physico-chemical perturbations. As mangroves possess a unique ecotone, they experience many abiotic stressors viz. salinity, metal, oil, humidity temperature, nutrient and a wide range of biotic interactions. Amongst all, salinity is the most important factor affecting mangrove physiology and biochemistry, and thereby regulating the organic matter contribution to the consumers underneath. Exploitation by human, being a dominant biotic interference, is above the rate at which natural replacement of mangrove vegetation occur. Mal-nutrition is a limiting factor in growth and reproduction of many mangroves whereas nutrient replenishment reduces the phytotoxicity of heavy metals. Different environmental pollutants including heavy metals, recalcitrant, cosmetics, petroleum oil and endocrine disrupters have reported impact on various mangroves and associated biota. Stress tolerance in mangroves involves various mechanism including morphological and anatomical features, osmoregulation, water use efficiency, salt secretion, salt exclusion and salt accumulation and molecular regulations. Various aspects of salt tolerance strategies of mangroves related to their growth, biochemical anatomy and physiology were reported by many researchers.

Intercellular Communication in the Central Nervous System as Deduced by Chemical Neuroanatomy and Quantitative Analysis of Images: Impact on Neuropharmacology.

In the last decades, new evidence on brain structure and function has been acquired by morphological investigations based on synergic interactions between biochemical anatomy approaches, new techniques in microscopy and brain imaging, and quantitative analysis of the obtained images. This effort produced an expanded view on brain architecture, illustrating the central nervous system as a huge network of cells and regions in which intercellular communication processes, involving not only neurons but also other cell populations, virtually determine all aspects of the integrative function performed by the system. The main features of these processes are described. They include the two basic modes of intercellular communication identified (i.e., wiring and volume transmission) and mechanisms modulating the intercellular signaling, such as cotransmission and allosteric receptor–receptor interactions. These features may also open new possibilities for the development of novel pharmacological approaches to address central nervous system diseases. This aspect, with a potential major impact on molecular medicine, will be also briefly discussed.

Molecular Interactions between Kv4.3 and DPP6 - The Biochemical Anatomy of Idiopathic Ventricular Fibrillation

The molecular basis of idiopathic ventricular fibrillation (IVF) is poorly understood. Previously, we identified crucial role of DPP6, a Kv4.3-associating β-subunit, in Purkinje fiber Ito and gene variants causing DPP6 gain-of-function in IVF. This study investigated the molecular basis of Kv4.3-DPP6 interaction, about which little is known. A computational model of the Kv4.3-DPP6 interaction (using AutoDock Vina) predicted that the N-terminus and some charged regions of DPP6 might interact with the N-terminus and 3 positively charged residues of Kv4.3. The predictions were verified in a patch-clamp study of wildtype and engineered mutant proteins expressed in HEK cells. Wildtype Kv4.3 showed substantial current enhancement upon co-expression with DPP6 after 48 hrs, as previously reported. Deletion of 5 amino acids in the Kv4.3 N-terminus decreased the peak-current density compared to wildtype Kv4.3 but did not prevent current-enhancement by wildtype DPP6, suggesting that this region of Kv4.3 N-terminus is not essential for interaction with DPP6. Neutralization of the 3 positively charged amino acids in the Kv4.3 N-terminus by alanine mutation enhanced the DPP6-induced current-increase. On the other side, deletion of the N-terminal region of DPP6 prevented its current-enhancing effect on Kv4.3. Neutralization of either positively or negatively charged regions in DPP6 significantly attenuated its ability to increase current density when co-expressed with wildtype Kv4.3. We conclude that Kv4.3 interacts with DPP6 via docking involving the DPP6 N-terminus, and that crucial charged amino acids on both Kv4.3 and DPP6 strongly affect the interaction. However, the opposite effects of charge neutralization in the Kv4.3 and DPP6 N-termini argue against a simple electrostatic interaction. These results provide insights into the biochemical anatomy of IVF and may help to develop effective molecularly-targeted blockers for patients with IVF-inducing DPP6 gain-of-function.

Tyrosinase enzyme: 1. An overview on a pharmacological target.

The tyrosinase enzyme (EC 1.14.18.1) is an oxidoreductase inside the general enzyme classification and is involved in the oxidation and reduction process in the epidermis. These chemical reactions that the enzyme catalyzes are of principal importance in the melanogenesis process. This process of melanogenesis is related to the melanin formation, a heteropolymer of indolic nature that provides the different tonalities in the skin and helps to the protection from the ultraviolet radiation. However, a pigment overproduction, come up by the action of the tyrosinase, can cause different disorders in the skin related to the hyperpigmentation. Several studies mainly focused on the characteristics of the enzyme have been reported. In this work, an approximation to general aspects related to this enzyme is made. Besides, it is treated the researches that have been published in the part of the biochemical anatomy dealing with diseases associated with this protein (melanogenesis), its active place and its physiological states, the molecular mechanism, the methods carried out to detect the inhibitory activity, and the used substrates.

The biochemical anatomy of cortical inhibitory synapses.

Classical electron microscopic studies of the mammalian brain revealed two major classes of synapses, distinguished by the presence of a large postsynaptic density (PSD) exclusively at type 1, excitatory synapses. Biochemical studies of the PSD have established the paradigm of the synapse as a complex signal-processing machine that controls synaptic plasticity. We report here the results of a proteomic analysis of type 2, inhibitory synaptic complexes isolated by affinity purification from the cerebral cortex. We show that these synaptic complexes contain a variety of neurotransmitter receptors, neural cell-scaffolding and adhesion molecules, but that they are entirely lacking in cell signaling proteins. This fundamental distinction between the functions of type 1 and type 2 synapses in the nervous system has far reaching implications for models of synaptic plasticity, rapid adaptations in neural circuits, and homeostatic mechanisms controlling the balance of excitation and inhibition in the mature brain.

Use of imaging multivariate analysis to improve biochemical and anatomical discrimination in desorption electrospray ionisation mass spectrometry imaging

Desorption electrospray ionisation (DESI) mass spectrometry images usually contain a large amount of information that can be difficult to interpret in an objective manner. We explore the use of imaging multivariate analysis (MVA) on DESI images of protein spots and rat brain sections to automatically assign peaks and improve discrimination of spatially important features. DESI parameters were optimised on an ion trap mass spectrometer for (a) consistent imaging of dried single and mixture spots of insulin, myoglobin and BSA from a Permanox slide, and (b) to produce a MS image of rat brain coronal section at 100 μm resolution. Multivariate curve resolution (MCR), an imaging MVA technique was applied to these images after appropriate data binning. MCR analysis on DESI images of protein mixture spots allowed the multiply charged peaks of a number of proteins to be distinctly separated. Application of MCR to a DESI image of a rat brain coronal section deconvoluted the image into components that showed biologically important features. Further application of MCR to a subsection of the image produced a component that clearly separated out the substantia nigra region, which allowed us to produce a biochemical anatomy for this area of the brain. We have demonstrated the ability of imaging MVA to automatically and objectively analyse DESI images of standardised and complex biological samples, and have shown its capacity for detailed spatial profiling of biomolecules in specific morphological regions. We propose the routine use of this technique for future DESI imaging experiments.

X-Ray and Biochemical Anatomy of an Archaeal XPF/Rad1/Mus81 Family Nuclease: Similarity between Its Endonuclease Domain and Restriction Enzymes

The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. Here, we report the domain organization of an archaeal homolog (Hef) of this family and the X-ray crystal structure of the middle domain, with the nuclease activity. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases, including the correspondence of the GDX nERKX 3D signature motif in Hef to the PDX n(E/D)XK motif in restriction enzymes. This structural study also suggests that the XPF/Rad1/Mus81/ERCC1 proteins form a dimer through each interface of the nuclease domain and the helix-hairpin-helix domain. Simultaneous disruptions of both interfaces result in their dissociation into separate monomers, with strikingly reduced endonuclease activities.

Catecholaminergic neurons in the ventrolateral medulla and nucleus of the solitary tract in the human.

Catecholaminergic neurons in the ventrolateral medulla (VLM) and nucleus of the solitary tract (NTS) are important because of their presumed roles in autonomic regulation, including the tonic and reflex control of arterial pressure, neuroendocrine functions, and the chemosensitivity associated with the ventral medullary surface. However, little is known about the connections of these neurons in the human brain. As a first step in analyzing the functional biochemical anatomy of catecholamine neurons in the human, we used antisera against tyrosine hydroxylase (TH) and phenylethanolamine N-methyltransferase (PNMT) to localize medullary catecholamine-containing neurons and processes in the VLM and the NTS. Cells staining for TH were located throughout the VLM. Most cells staining for TH and PNMT, which are therefore adrenergic, occurred in an area of the VLM probably corresponding to the rostroventrolateral reticular nucleus. Axons of TH-immunoreactive neurons in the VLM projected (1) dorsally, in a series of parallel transtegmental trajectories, toward the dorsomedial reticular formation, the NTS, and vagal motor nucleus, (2) longitudinally, through the central tegmental field, as fascicles running parallel to the neuraxis, (3) ventrolaterally toward the ventral surface (VS) of the rostral VLM where they appeared to terminate, and (4) medially into the raphe, where they arborized. Similar systems of fibers were labeled for PNMT; the longitudinal bundles of PNMT-labeled axons were limited to the principal tegmental bundle and concentrated dorsally. Fibers containing PNMT were also identified in the medullary raphe, on the medullary ventral surface, and contacting intraparenchymal blood vessels. In the NTS, neurons exhibited immunoreactivity to both TH and PNMT: Four principal subgroups of TH-immunoreactive neurons were seen: a ventral, an intermediate, a medial, and a dorsal group. Perikarya containing PNMT were restricted to the dorsolateral aspect of the NTS. Processes containing TH and PNMT immunoreactivity were identified in the medial and dorsolateral NTS; others appeared to project between the NTS and the VLM and within the solitary tract. The presence of catecholaminergic fibers of the VLM interconnecting with the NTS, raphe, intraparenchymal microvessels, VS, and possibly the spinal cord suggests that the autonomic and chemoreceptor functions attributed to these neurons also may apply to the human.

Biochemical Anatomy of Human Bone: Comparative Study of Compact and Spongy Bone in Femur, Rib and Iliac Crest

Using EDTA extraction procedure, compact and spongy bone from human femur, rib and iliac crest were compared in terms of their content in collagen, sialoprotein, proteoglycan and carbohydrate. The bone matrix sizes displayed significant variations, the femur having the smallest size and iliac crest the largest one. No significant difference in the matrix size has been found between the spongy and compact bone. The EDTA extractability of the spongy bone was higher than that of the compact bone, with femur showing the lowest extractability. The collagen content of the 3 bones studied was similar although the femur had slightly lower values. The sialic and uronic acids and hexose contents were higher in the femur than in the rib and iliac crest. The collagen/hexose, collagen/sialic acid and collagen/uronic acid ratios in the bone matrix were highest in the iliac crest and lowest in the femur, suggesting that alterations in the amounts of bone matrix can affect the mechanical properties of different parts of the bony skeleton and vice versa.

Membrane populations of bovine choroid plexus: separation by density gradient centrifugation in modified colloidal silica.

Abstract: The choroid plexus is intimately involved in the production and regulation of the cerebrospinal fluid. Populations of surface membranes from this epithelial tissue were separated by density gradient centrifugation by use of modified colloidal silica (Percoll). A fraction of heavy microsomes (P3) containing plasma membranes was prepared by differential centrifugation. Membranes in fraction P3 were mixed with a given concentration of Percoll and density gradients generated during centrifugation. When fraction P3 was mixed with 20% (v/v) Percoll and centrifuged at 20,000 r.p.m. for 1 h in a 50.2 Ti fixed‐angle rotor, membranes containing alkaline phosphatase (AP) were found at a density of 1.037 g/cm3 while those containing NaK ATPase were found at 1.047 g/cm3. With more shallow density gradients using 12% and 14% Percoll, a broad shoulder of AP activity became manifest at densities greater than 1.060 g/cm3 suggesting multiple populations of membranes containing AP. Membranes containing AP could also be separated from membranes containing γ‐glutamyl transpeptidase (γ‐GTP); this separation was most pronounced in 12% Percoll. The activity of γ‐GTP could not be separated from activity of NaK ATPase. Total protein was distributed broadly throughout the gradients. Studies have been undertaken to compare the behavior of choroidal membranes in Percoll gradients with that of renal membranes because the biochemical anatomy of the kidney has been extensively studied. In contrast to choroidal membranes, renal membranes with NaK ATPase activity were found to have densities lower than those membranes with AP. Thus, the distribution of membrane‐bound enzymes from kidney in a Percoll gradient was exactly the opposite of that observed for these same enzymes from choroid plexus. In addition, unlike the γ‐GTP activity of choroid plexus, γ‐GTP from kidney could be separated from the activities of both alkaline phosphatase and NaK ATPase. These marked differences in membrane populations between choroid plexus and kidney as defined by Percoll density gradient centrifugation analyses are presumably reflective of differences in the functions of the two epithelial tissues.