The many ways to delimit species: hairs, genes and surface chemistry

Species identification forms the basis for understanding the diversity of the living world, but it is also a prerequisite for understanding many evolutionary patterns and processes. The most promising approach for correctly delimiting and identifying species is to integrate many types of information in the same study. Our aim was to test how cuticular hydro- carbons, traditional morphometrics, genetic polymorphisms in nuclear markers (allozymes and DNA microsatellites) and DNA barcoding (partial mitochondrial COI gene) perform in delimiting species. As an example, we used two closely related Formica ants, F. fusca and F. lemani, sampled from a sympatric population in the northern part of their distribu- tion. Morphological characters vary and overlap in different parts of their distribution areas, but cuticular hydrocarbons include a strong taxonomic signal and our aim is to test the degree to which morphological and genetic data correspond to the chemical data. In the morphological analysis, species were best separated by the combined number of hairs on pro- notum and mesonotum, but individual workers overlapped in hair numbers, as previously noted by several authors. Nests of the two species were separated but not clustered according to species in a Principal Component Analysis made on nuclear genetic data. However, model-based Bayesian clustering resulted in perfect separation of the species and gave no indication of hybridization. Furthermore, F. lemani and F. fusca did not share any mitochondrial haplotypes, and the species were perfectly separated in a phylogenetic tree. We conclude that F. fusca and F. lemani are valid species that can be separated in our study area relatively well with all methods employed. However, the unusually small genetic differen- tiation in nuclear markers (FST = 0.12) shows that they are closely related, and occasional hybridization between F. fusca and F. lemani cannot be ruled out.

Inhibitory effects of wood extracts on the spoilage flora of marinated poultry meat

Polyphenolic compounds occurring naturally in knotwood of plants are known to have antimicrobial effects. The knots (i.e. the branch bases inside tree stems) and outer branches in pine trees contain a remarkably high concentration of phenolic stilbenes, while lignans are the major phenolic constituents of spruce knots. Large amount of these phenolic compounds can be extracted from wood knots at pulp and paper mills where their presence is undesirable. In Finland, marinating of broiler meat is done not only to increase or add value to the meat, but also to enhance the safety and shelf-life. These products are usually packed under a modified atmosphere for further protection against spoilage microorganisms. However, studies have revealed that addition of marinades to poultry products do not have an inhibitory effect on either some psychrotrophic anaerobic bacteria, such as Brochothrix thermosphacta or lactic acid bacteria associated with spoilage. Also, the activity of pathogenic Campylobacter jejuni is not affected by marinating. The objective of this study was to investigate the inhibitory and lethal activities of extracts from spruce (Picea spp.) and pine (Pinus spp.) knotwood and outer branches that are dissolved in ethanol against the spoilage microorganisms in modified atmosphere packaged marinated broiler products. Modified atmosphere packaged broiler products were separately inoculated with ‘normal’ marinades, marinades with 70% ethanol, marinades with a mixture of spruce and pine extracts dissolved in 70% ethanol or mixture of spruce and pine extracts in powder form. The bacterial colony forming units per gram obtained from each of the samples were analysed on de Man Rogosa and Sharpe agar at days 1, 6, 12 and 15. The results showed that there were significant differences in bacterial colony forming units per gram (P <0.05) between packages with ‘normal’ marinades and packages with extracts added to their marinades on the 12th and 15th day. It can be concluded that the addition of extracts from spruce and pine knotwood to marinades significantly retarded growth of spoilage microorganisms during the 15 day test period. However further research is warranted to characterise and establish the safety and suitability of the compound(s) in spruce and pine knotwood extracts that are responsible for inhibitory or lethal activity against the microbes that may be present in marinated poultry meat.

The function and regulation of the U11-48K protein in U12-dependent splicing

The removal of noncoding sequences, or introns, from the eukaryotic messenger RNA precursors is catalyzed by a ribonucleoprotein complex known as the spliceosome. In most eukaryotes, two distinct classes of introns exist, each removed by a specific type of spliceosome. The major, U2-type introns account for over 99 % of all introns, and are almost ubiquitous. The minor, U12-type introns are found in most but not all eukaryotes, and reside in conserved locations in a specific set of genes. Due to their slow excision rates, the U12-type introns are expected to be involved in the regulation of the genes containing them by inhibiting the maturation of the messenger RNAs. However, little information is currently available on how the activity of the U12-dependent spliceosome itself is regulated. The levels of many known splicing factors are regulated through unproductive alternative splicing events, which lead to inclusion of premature STOP codons, targeting the transcripts for destruction by the nonsense-mediated decay pathway. These alternative splice sites are typically found in highly conserved sequence elements, which also contain binding sites for factors regulating the activation of the splice sites. Often, the activation is achieved by binding of products of the gene in question, resulting in negative feedback loops. In this study, I show that U11-48K, a protein factor specific to the minor spliceosome, specifically recognizes the U12-type 5' splice site sequence, and is essential for proper function of the minor spliceosome. Furthermore, the expression of U11-48K is regulated through a feedback mechanism, which functions through conserved sequence elements that activate alternative splicing and nonsense-mediated decay. This mechanism is conserved from plants to animals, highlighting both the importance and early origin of this mechanism in regulating splicing factors. I also show that the feedback regulation of U11-48K is counteracted by a component of the major spliceosome, the U1 small nuclear ribonucleoprotein particle, as well as members of the hnRNP F/H protein family. These results thus suggest that the feedback mechanism is finely tuned by multiple factors to achieve precise control of the activity of the U12-dependent spliceosome.

Role of GDNF and its Cross-Talk with Other Growth Factors in the Dopaminergic System

Parkinson´s Disease (PD) is a neurodegenerative movement disorder resulting from loss of dopaminergic (DA) neurons in substantia nigra (SN). Possible causative treatment strategies for PD include neurotrophic factors, which protect and in some cases restore the function of dopaminergic neurons. Glial cell line-derived neurotrophic factor (GDNF) family of neurotrophic factors have been to date the most promising candidates for treatment of PD, demonstrating both neuroprotective and neurorestorative properties. We have investigated the role of GDNF in the rodent dopaminergic system and its possible crosstalk with other growth factors. We characterized the GDNF-induced gene expression changes by DNA microarray analysis in different neuronal systems, including in vitro cultured Neuro2A cells treated with GDNF, as well as midbrains from GDNF heterozygous (Hz) knockout mice. These microarray experiments, resulted in the identification of GDNF-induced genes, which were also confirmed by other methods. Further analysis of the dopaminergic system of GDNF Hz mice demonstrated about 40% reduction in GDNF levels, revealed increased intracellular dopamine concentrations and FosB/DeltaFosB expression in striatal areas. These animals did not show any significant changes in behavioural analysis of acute and repeated cocaine administration on locomotor activity, nor did they exhibit any changes in dopamine output following treatment with acute cocaine. We further analysed the significance of GDNF receptor RET signalling in dopaminergic system of MEN2B knock-in animals with constitutively active Ret. The MEN2B animals showed a robust increase in extracellular dopamine and its metabolite levels in striatum, increased tyrosine hydroxylase (TH) and dopamine transporter (DAT) protein levels by immunohistochemical staining and Western blotting, as well as increased Th mRNA levels in SN. MEN2B mice had increased number of DA neurons in SN by about 25% and they also exhibited increased sensitivity to the stimulatory effects of cocaine. We also developed a semi-throughput in vitro micro-island assay for the quantification of neuronal survival and TH levels by computer-assisted methodology from limited amounts of tissue. This assay can be applied for the initial screening for dopaminotrophic molecules, as well as chemical drug library screening. It is applicable to any neuronal system for the screening of neurotrophic molecules. Since our microarray experiments revealed possible GDNF-VEGF-C crosstalk we further concentrated on studying the neurotrophic effects of VEGF-C. We showed that VEGF-C acts as a neurotrophic molecule for the DA neurons both in vitro and in vivo, however without additive effect when used together with GDNF. The neuroprotective effect for VEGF-C in vivo in rat 6-OHDA model of PD was demonstrated. The possible signalling mechanisms of VEGF-C in the nervous system were investigated - infusion of VEGF-C to rat brain induced ERK activation, however no direct activation of RET signalling in vitro was found. VEGF-C treatment of rat striatum lead to up-regulation of VEGFR-1-3, indicating that VEGF-C can regulate the expression level of its own receptor. VEGF-C dopaminotrophic activity in vivo was further supported by increased vascular tissue in the neuroprotection experiments.

FGF signaling in neurogenesis and patterning of the developing midbrain and anterior hindbrain

Embryonic midbrain and hindbrain are structures which will give rise to brain stem and cerebellum in the adult vertebrates. Brain stem contains several nuclei which are essential for the regulation of movements and behavior. They include serotonin-producing neurons, which develop in the hindbrain, and dopamine-producing neurons in the ventral midbrain. Degeneration and malfunction of these neurons leads to various neurological disorders, including schizophrenia, depression, Alzheimer s, and Parkinson s disease. Thus, understanding their development is of high interest. During embryogenesis, a local signaling center called isthmic organizer regulates the development of midbrain and anterior hindbrain. It secretes peptides belonging to fibroblast growth factor (FGF) and Wingless/Int (Wnt) families. These factors bind to their receptors in the surrounding tissues, and activate various downstream signaling pathways which lead to alterations in gene expression. This in turn affects the various developmental processes in this region, such as proliferation, survival, patterning, and neuronal differentiation. In this study we have analyzed the role of FGFs in the development of midbrain and anterior hindbrain, by using mouse as a model organism. We show that FGF receptors cooperate to receive isthmic signals, and cell-autonomously promote cell survival, proliferation, and maintenance of neuronal progenitors. FGF signaling is required for the maintenance of Sox3 and Hes1 expression in progenitors, and Hes1 in turn suppresses the activity of proneural genes. Loss of Hes1 is correlated with increased cell cycle exit and premature neuronal differentiation. We further demonstrate that FGF8 protein forms an antero-posterior gradient in the basal lamina, and might enter the neuronal progenitors via their basal processes. We also analyze the impact of FGF signaling on the various neuronal nuclei in midbrain and hindbrain. Rostral serotonergic neurons appear to require high levels of FGF signaling in order to develop. In the absence of FGF signaling, these neurons are absent. We also show that embryonic meso-diencephalic dopaminergic domain consists of two populations in the anterior-posterior direction, and that these populations display different molecular profiles. The anterior diencephalic domain appears less dependent on isthmic FGFs, and lack several genes typical of midbrain dopaminergic neurons, such as Pitx3 and DAT. In Fgfr compound mutants, midbrain dopaminergic neurons begin to develop but soon adopt characteristics which highly resemble those of diencephalic dopaminergic precursors. Our results indicate that FGF signaling regulates patterning of these two domains cell-autonomously.

Molecular diagnosis of developmental disorders

ABSTRACT Idiopathic developmental disorders (DDs) affect ~1% of the population worldwide. This being a considerable amount, efforts are being made to elucidate the disease mechanisms. One or several genetic factors cause 30-40% of DDs, and only 10% are caused by environmental factors. The remaining 50% of DD patients go undiagnosed, mostly due to a lack of diagnostic techniques. The cause in most undiagnosed cases is though to be a genetic factor or a combination of genetic and environmental factors. Despite the surge of new technologies entering the market, their implementation into diagnostic laboratories is hampered by costs, lack of information about the expected diagnostic yield, and the wide range of selection. This study evaluates new microarray methods in diagnosing idiopathic DDs, providing information about their added diagnostic value. Study I analysed 150 patients by array comparative genomic hybridization (array CGH, 44K and 244K), with a subsequent 18% diagnostic yield. These results are supported by other studies, indicating an enourmous added diagnostic value of array CGH, compared with conventional cytogenetic analysis. Nevertheless, 80% of the patients remained undiagnosed in Study I. In an effort to diagnose more patients, in Study IV the resolution was increased from 8.9 Kb of the 244K CGH array to 0.7 Kb, by using a single-nucleotide polymorphism (SNP) array. However, no additional pathogenic changes were detected in the 35 patients assessed, and thus, for diagnostic purposes, an array platform with ca 9 Kb resolution appears adequate. The recent vast increase in reports of detected aberrations and associated phenotypes has enabled characterization of several new syndromes first based on a common aberration and thereafter by delineation of common clinical characteristics. In Study II, a familial deletion at 9q22.2q22.32 with variable penetrance was described. Despite several reports of aberrations in the adjacent area at 9q associated with Gorlin syndrome, the patients in this family had a unique phenotype and did not present with the syndrome. In Study III, a familial duplication of chromosome 6p22.2 was described. The duplication caused increased expression of an important enzyme of the γ-aminobutyric acid (GABA) degradation pathway, causing oxidative stress of the brain, and thus, very likely, the mild mental retardation of these patients. These two case studies attempted to pinpoint candidate genes and to resolve the pathogenic mechanism causing the clinical characteristics of the patients. Presenting rare genetic and clinical findings to the international science and medical community enables interpretation of similar findings in other patients. The added value of molecular karyotyping in patients with idiopathic DD is evident. As a first line of testing, arrays with a median resolution of at least 9 Kb should be considered and further characterization of detected aberrations undertaken when possible. Diagnostic whole-exome sequencing may be the best option for patients who remain undiagnosed after high-resolution array analysis.

Supermacroporous Polymer-Based Cryogel Bioreactor for Monoclonal Antibody Production in Continuous Culture Using Hybridoma Cells

Cryogel matrices composed of different polymeric blends were synthesized, yielding a unique combination of hydrophilicity and hydrophobicity with the presence or absence of charged surface. Four such cryogel matrices composed of polyacrylamide-chitosan (PAAC), poly(N-isopropylacrylamide)-chitosan, polyacrylonitrile (PAN), and poly(N-isopropylacrylamide) were tested for growth of different hybridoma cell lines and production of antibody in static culture. All the matrices were capable for the adherence of hybridoma cell lines 6A4D7, B7B10, and H9E10 to the polymeric surfaces as well as for the efficient monoclonal antibody (mAb) production. PAAC proved to be relatively better in terms of both mAb production and cell growth. Further, PAAC cryogel was designed into three different formats, monolith, disks, and beads, and used as packing material for packed-bed bioreactor. Longterm cultivation of 6A4D7 cell line on PAAC cryogel scaffold in all the three formats could be successfully done for a period of 6 weeks under static conditions. Continuous packed-bed bioreactor was setup using 6A4D7 hybridoma cell line in the three reactor formats. The reactors ran continuously for a period of 60 days during which mAb production and metabolism of cells in the bioreactors were monitored periodically. The monolith bioreactor performed most efficiently over a period of 60 days and produced a total of 57.5 mg of antibody in the first 30 days (in 500 mL) with a highest concentration of 115 mu g mL(-1), which is fourfold higher than t-flask culture. The results demonstrate that appropriate chemistry and geometry of the bioreactor matrix for cell growth and immobilization can enhance the reactor productivity. (C) 2010 American Institute of Chemical Engineers Biotechnol. Prog., 27: 170-180, 2011

Si, Si-Ge and the new heterostructure world

Semiconductor heterostructures based on AlAs/GaAs and other III-V compounds have been the focus of active research for some time now. Ih the last decade, a new heterostructure material, the strained Si/SiGe system, has emerged. This heterojunction technology can potentially be integrated into the current VLSI environment with large-scale impact in the growing microelectronics market. Si/SiGe heterojunction bipolar transistors with cut-off frequencies exceeding 100 GHz and other electronic and optical devices with superior properties compared to all-Si technology have been demonstrated in laboratories worldwide.

Transformation of 16-dehydroprogesterone and 17?-hydroxyprogesterone by Mucor piriformis

Mucor piriformis was used to study the mode of transformation of 16-dehydroprogesterone (I, pregna-4, 16-diene-3, 20-dione) and 17 alpha-hydroxyprogesterone (II, 17 alpha-hydroxypregn-4-ene-3, 20-dione). Biotransformation products formed from I were 14 alpha-hydroxypregna-4, 16-diene-3, 20-dione (Ia), 7 alpha, 14 alpha-dihydroxypregna-4 16-diene-3, 20-dione (Ib), 3 beta, 7 alpha, 14 alpha-trihydroxy-5 alpha-pregn-16-en-20-one (Ic), and 3 alpha, 7 alpha, 14 alpha-trihydroxy-5 alpha-pregn-16-en-20-one (Id). Metabolites Ic and Id appear to be hitherto unknown. Timecourse studies suggested that the transformation is initiated by hydroxylation at the 14 alpha-position (Ia) followed by hydroxylation at the 7 alpha-position (Ib). Microsomes (105,000 g sediment) prepared from 16-dehydroprogesterone-induced cells hydroxylate I to its 14 alpha-hydroxy derivative (Ia) in the presence of NADPH. Incubation of Ia with the organism resulted in the formation of Ib, Ic and Id. Biotransformation products formed from compound II were 17 alpha, 20 alpha-dihydroxypregn-4-en-3-one (IIa), 7 alpha, 17 alpha-dihydroxypregn-4-ene-3, 20-dione (IIb), 6 beta, 17 alpha, 20 alpha-trihydroxypregn-4-en-3-one (IIc) and 11 alpha, 17 alpha, 20 alpha-trihydroxypregn-4-en-3-one (IId). Time-course studies indicated that IIa is the initial product formed, which is further hydroxylated either at the 6 beta or 11 alpha position. Incubation of IIa with the organism resulted in the formation of IIc and IId. Reduction of the 4-en-3-one system and 20-keto group has not been observed before in organisms of the order Mucorales. In addition, M. piriformis has been shown to carry out hydroxylation at the C-6, C-7, C-11 and C-14 positions in the steroid molecules tested.

Transformation of dehydroepiandrosterone and pregnenolone by Mucor piriformis

The mode of transformation of dehydroepiandrosterone (I, 3 beta-hydroxyandrost-5-en-17-one) and pregnenolone (II, 3 beta-hydroxypregn-5-en-20-one) was studied using Mucor piriformis. Biotransformation products formed from I were 3 beta,17 beta-dihydroxyandrost-5-ene (Ia), 3 beta-hydroxyandrost-5-ene-7,17-dione (Ib), 3 beta,17 beta-dihydroxyandrost-5-en-7-one (Ic), 3 beta,7 alpha-dihydroxyandrost-5-en-17-one (Id) and 3 beta,7 alpha,17 beta-trihydroxyandrost-5-ene (Ie). Biotransformation products formed from compound II were 3 beta,7 alpha-dihydroxypregn-5-en-20-one (IIa) and 3 beta,7 alpha,11 alpha-trihydroxypregn-5-en-20-one (IIb). The organism did not carry out isomerization of the 5-en-3 beta-ol to a 4-en-3-one system in the steroid molecules tested. In addition, it failed to carry out 14 alpha-hydroxylation possibly because of the lack of a 4-en-3-one system in I and II, and stereospecific hydroxylation at the C-7 position in I and II.

Oxidation of aqueous sulphur dioxide catalysed by poly-4-vinylpyridine-Cu(II) complex .2. Combined homogeneous and heterogeneous phase oxidation

Aqueous phase oxidation of sulphur dioxide at low concentrations catalysed by a PVP-Cu complex in the solid phase and dissolved Cu(II) in the liquid phase is studied in a rotating catalyst basket reactor (RCBR). The equilibrium adsorption of Cu(II) and S(VI) on PVP particles is found to be of the Langmuir-type. The diffusional effects of S(IV) species in PVP-Cu resin are found to be insignificant whereas that of product S(VI) are found to be significant. The intraparticle diffusivity of S(VI) is obtained from independent tracer experiments. In the oxidation reaction HSO3- is the reactive species. Both the S(IV) species in the solution, namely SO2(aq) and HSO3- get adsorbed onto the active PVP-Cu sites of the catalyst, but only HSO3- undergoes oxidation. A kinetic mechanism is proposed based on this feature which shows that SO2(aq) has a deactivating effect on the catalyst. A rate model is developed for the three-phase reaction system incorporating these factors along with the effect of concentration of H2SO4 on the solubility of SO2 in the dilute aqueous solutions of Cu(II). Transient oxidation experiments are conducted at different conditions of concentration of SO2 and O-2 in the gas phase and catalyst concentration, and the rate parameters are estimated from the data. The observed and calculated profiles are in very good agreement. This confirms the deactivating effect of nonreactive SO2(aq) on the heterogeneous catalysis.

Robust controller for an autonomous small refrigeration unit

The authors describe the constructional features of a controller for operating an autonomous refrigeration unit powered by a field of photovoltaic panels and backed up by a generator set. The controller enables three voltage levels of operation of an inverter to meet the start, run and off cycle conditions of the refrigerator compressor. The algorithm considers several input and output parameters and status signals from each subsystem of the unit to deduce a control strategy. Such units find application for storage of vaccines and life-saving medicines requiring uninterrupted refrigeration, in medical shops, rural health centres, veterinary laboratories etc.

Nonlinear dynamics of eucaryotic pyruvate dehydrogenase multienzyme complex: Decarboxylation rate, oscillations, and multiplicity

Pyruvate conversion to acetyl-CoA by the pyruvate dehydrogenase (PDH) multienzyme complex is known as a key node in affecting the metabolic fluxes of animal cell culture. However, its possible role in causing possible nonlinear dynamic behavior such as oscillations and multiplicity of animal cells has received little attention. In this work, the kinetic and dynamic behavior of PDH of eucaryotic cells has been analyzed by using both in vitro and simplified in vivo models. With the in vitro model the overall reaction rate (v(1)) of PDH is shown to be a nonlinear function of pyruvate concentration, leading to oscillations under certain conditions. All enzyme components affect v, and the nonlinearity of PDH significantly, the protein X and the core enzyme dihydrolipoamide acyltransferase (E2) being mostly predominant. By considering the synthesis rates of pyruvate and PDH components the in vitro model is expanded to emulate in vivo conditions. Analysis using the in vivo model reveals another interesting kinetic feature of the PDH system, namely, multiple steady states. Depending on the pyruvate and enzyme levels or the operation mode, either a steady state with high pyruvate decarboxylation rate or a steady state with significantly lower decarboxylation rate can be achieved under otherwise identical conditions. In general, the more efficient steady state is associated with a lower pyruvate concentration. A possible time delay in the substrate supply and enzyme synthesis can also affect the steady state to be achieved and lead's to oscillations under certain conditions. Overall, the predictions of multiplicity for the PDH system agree qualitatively well with recent experimental observations in animal cell cultures. The model analysis gives some hints for improving pyruavte metabolism in animal cell culture.

Novel phase-transition behavior near liquid/liquid critical points of aqueous solutions: Formation of a third phase at the interface

We report a novel phase behavior in aqueous solutions of simple organic solutes near their liquid/liquid critical points, where a solid-like third phase appears at the liquid/liquid interface. The phenomenon has been found in three different laboratories. It appears in many aqueous systems of organic solutes and becomes enhanced upon the addition of salt to these solutions.