Molecular Characterization of Viruses Causing the Cassava Brown Streak Disease Epidemic in Eastern Africa

Cassava brown streak disease (CBSD) was described for the first time in Tanganyika (now Tanzania) about seven decades ago. Tanganyika (now Tanzania) about seven decades ago. It was endemic in the lowland areas of East Africa and inland parts of Malawi and caused by Cassava brown streak virus (CBSV; genus Ipomovirus; Potyviridae). However, in 1990s CBSD was observed at high altitude areas in Uganda. The causes for spread to new locations were not known.The present work was thus initiated to generate information on genetic variability, clarify the taxonomy of the virus or viruses associated with CBSD in Eastern Africa as well as to understand the evolutionary forces acting on their genes. It also sought to develop a molecular based diagnostic tool for detection of CBSD-associated virus isolates. Comparison of the CP-encoding sequences of CBSD-associated virus isolates collected from Uganda and north-western Tanzania in 2007 and the partial sequences available in Genbank revealed occurrence of two genetically distinct groups of isolates. Two isolates were selected to represent the two groups. The complete genomes of isolates MLB3 (TZ:Mlb3:07) and Kor6 (TZ:Kor6:08) obtained from North-Western (Kagera) and North-Eastern (Tanga) Tanzania, respectively, were sequenced. The genomes were 9069 and 8995 nucleotides (nt), respectively. They translated into polyproteins that were predicted to yield ten mature proteins after cleavage. Nine proteins were typical in the family Potyviridae, namely P1, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP, but the viruses did not contain HC-Pro. Interestingly, genomes of both isolates contained a Maf/HAM1-like sequence (HAM1h; 678 nucleotides, 25 kDa) recombined between the NIb and CP domains in the 3’-proximal part of the genomes. HAM1h was also identified in Euphorbia ringspot virus (EuRSV) whose sequence was in GenBank. The HAM1 gene is widely spread in both prokaryotes and eukaryotes. In yeast (Saccharomyces cerevisiae) it is known to be a nucleoside triphosphate (NTP) pyrophosphatase. Novel information was obtained on the structural variation at the N-termini of polyproteins of viruses in the genus Ipomovirus. Cucumber vein yellowing virus (CVYV) and Squash vein yellowing virus (SqVYV) contain a duplicated P1 (P1a and P1b) but lack the HC-Pro. On the other hand, Sweet potato mild mottle virus (SPMMV), has a single but large P1 and has HC-Pro. Both virus isolates (TZ:Mlb3:07 & TZ:Kor6:08) characterized in this study contained a single P1 and lacked the HC-Pro which indicates unique evolution in the family Potyviridae. Comparison of 12 complete genomes of CBSD-associated viruses which included two genomes characterized in this study, revealed genetic identity of 69.0–70.3% (nt) and amino acid (aa) identities of 73.6–74.4% at polyprotein level. Comparison was also made among 68 complete CP sequences, which indicated 69.0-70.3 and 73.6-74.4 % identity at nt and aa levels, respectively. The genetic variation was large enough for dermacation of CBSD-associated virus isolates into two distinct species. The name CBSV was retained for isolates that were related to CBSV isolates available in database whereas the new virus described for the first time in this study was named Ugandan cassava brown streak virus (UCBSV) by the International Committee on Virus Taxonomy (ICTV). The isolates TZ:Mlb3:07 and TZ:Kor6:08 belong to UCBSV and CBSV, respectively. The isolates of CBSV and UCBSV were 79.3-95.5% and 86.3-99.3 % identitical at nt level, respectively, suggesting more variation amongst CBSV isolates. The main sources of variation in plant viruses are mutations and recombination. Signals for recombination events were detected in 50% of isolates of each virus. Recombination events were detected in coding and non-coding (3’-UTR) sequences except in the 5’UTR and P3. There was no evidence for recombination between isolates of CBSV and UCBSV. The non-synonomous (dN) to synonomous (dS) nucleotide substitution ratio (ω) for the HAM1h and CP domains of both viruses were ≤ 0.184 suggesting that most sites of these proteins were evolving under strong purifying selection. However, there were individual amino acid sites that were submitted to adaptive evolution. For instance, adaptive evolution was detected in the HAM1h of UCBSV (n=15) where 12 aa sites were under positive selection (P< 0.05) but not in CBSV (n=12). The CP of CBSV (n=23) contained 12 aa sites (p<0.01) while only 5 aa sites in the CP gene of UCBSV were predicted to be submitted to positive selection pressure (p<0.01). The advantages offered by the aa sites under positive selection could not be established but occurrence of such sites in the terminal ends of UCBSV-HAMIh, for example, was interpreted as a requirement for proteolysis during polyprotein processing. Two different primer pairs that simultaneously detect UCBSV and CBSV isolates were developed in this study. They were used successfully to study distribution of CBSV, UCBSV and their mixed infections in Tanzania and Uganda. It was established that the two viruses co-infect cassava and that incidences of co-infection could be as high as 50% around Lake Victoria on the Tanzanian side. Furthermore, it was revealed for the first time that both UCBSV and CBSV were widely distributed in Eastern Africa. The primer pair was also used to confirm infection in a close relative of cassava, Manihot glaziovii (Müller Arg.) with CBSV. DNA barcoding of M. glaziovii was done by sequencing the matK gene. Two out of seven M. glaziovii from the coastal areas of Korogwe and Kibaha in north eastern Tanzania were shown to be infected by CBSV but not UCBSV isolates. Detection in M. glaziovii has an implication in control and management of CBSD as it is likely to serve as virus reservoir. This study has contributed to the understanding of evolution of CBSV and UCBSV, which cause CBSD epidemic in Eastern Africa. The detection tools developed in this work will be useful in plant breeding, verification of the phytosanitary status of materials in regional and international movement of germplasm, and in all diagnostic activities related to management of CBSD. Whereas there are still many issues to be resolved such as the function and biological significance of HAM1h and its origin, this work has laid a foundation upon which the studies on these aspects can be based.

Composite MR image reconstruction and unaliasing for general trajectories using neural networks

In rapid parallel magnetic resonance imaging, the problem of image reconstruction is challenging. Here, a novel image reconstruction technique for data acquired along any general trajectory in neural network framework, called ``Composite Reconstruction And Unaliasing using Neural Networks'' (CRAUNN), is proposed. CRAUNN is based on the observation that the nature of aliasing remains unchanged whether the undersampled acquisition contains only low frequencies or includes high frequencies too. Here, the transformation needed to reconstruct the alias-free image from the aliased coil images is learnt, using acquisitions consisting of densely sampled low frequencies. Neural networks are made use of as machine learning tools to learn the transformation, in order to obtain the desired alias-free image for actual acquisitions containing sparsely sampled low as well as high frequencies. CRAUNN operates in the image domain and does not require explicit coil sensitivity estimation. It is also independent of the sampling trajectory used, and could be applied to arbitrary trajectories as well. As a pilot trial, the technique is first applied to Cartesian trajectory-sampled data. Experiments performed using radial and spiral trajectories on real and synthetic data, illustrate the performance of the method. The reconstruction errors depend on the acceleration factor as well as the sampling trajectory. It is found that higher acceleration factors can be obtained when radial trajectories are used. Comparisons against existing techniques are presented. CRAUNN has been found to perform on par with the state-of-the-art techniques. Acceleration factors of up to 4, 6 and 4 are achieved in Cartesian, radial and spiral cases, respectively. (C) 2010 Elsevier Inc. All rights reserved.

Combination antiretroviral therapy -associated lipodystrophy : insights into pathogenesis and treatment

Introduction: Combination antiretroviral therapy (cART) has decreased morbidity and mortality of individuals infected with human immunodeficiency virus type 1 (HIV-1). Its use, however, is associated with adverse effects which increase the patients risk of conditions such as diabetes and coronary heart disease. Perhaps the most stigmatizing side effect is lipodystrophy, i.e., the loss of subcutaneous adipose tissue (SAT) in the face, limbs and trunk while fat accumulates intra-abdominally and dorsocervically. The pathogenesis of cART-associated lipodystrophy is obscure. Nucleoside reverse transcriptase inhibitors (NRTI) have been implicated to cause lipoatrophy via mitochondrial toxicity. There is no known effective treatment for cART-associated lipodystrophy during unchanged antiretroviral regimen in humans, but in vitro data have shown uridine to abrogate NRTI-induced toxicity in adipocytes. Aims: To investigate whether i) cART or lipodystrophy associated with its use affect arterial stiffness; ii) lipoatrophic SAT is inflamed compared to non-lipoatrophic SAT; iii) abdominal SAT from patients with compared to those without cART-associated lipoatrophy differs with respect to mitochondrial DNA (mtDNA) content, adipose tissue inflammation and gene expression, and if NRTIs stavudine and zidovudine are associated with different degree of changes; iv) lipoatrophic abdominal SAT differs from preserved dorsocervical SAT with respect to mtDNA content, adipose tissue inflammation and gene expression in patients with cART-associated lipodystrophy and v) whether uridine can revert lipoatrophy and the associated metabolic disturbances in patients on stavudine or zidovudine based cART. Subjects and methods: 64 cART-treated patients with (n=45) and without lipodystrophy/-atrophy (n=19) were compared cross-sectionally. A marker of arterial stiffness, heart rate corrected augmentation index (AgIHR), was measured by pulse wave analysis. Body composition was measured by magnetic resonance imaging and dual-energy X-ray absorptiometry, and liver fat content by proton magnetic resonance spectroscopy. Gene expression and mtDNA content in SAT were assessed by real-time polymerase chain reaction and microarray. Adipose tissue composition and inflammation were assessed by histology and immunohistochemistry. Dorsocervical and abdominal SAT were studied. The efficacy and safety of uridine for the treatment of cART-associated lipoatrophy were evaluated in a randomized, double-blind, placebo-controlled 3-month trial in 20 lipoatrophic cART-treated patients. Results: Duration of antiretroviral treatment and cumulative exposure to NRTIs and protease inhibitors, but not the presence of cART-associated lipodystrophy, predicted AgIHR independent of age and blood pressure. Gene expression of inflammatory markers was increased in SAT of lipodystrophic as compared to non-lipodystrophic patients. Expression of genes involved in adipogenesis, triglyceride synthesis and glucose disposal was lower and of those involved in mitochondrial biogenesis, apoptosis and oxidative stress higher in SAT of patients with than without cART-associated lipoatrophy. Most changes were more pronounced in stavudine-treated than in zidovudine-treated individuals. Lipoatrophic SAT had lower mtDNA than SAT of non-lipoatrophic patients. Expression of inflammatory genes was lower in dorsocervical than in abdominal SAT. Neither depot had characteristics of brown adipose tissue. Despite being spared from lipoatrophy, dorsocervical SAT of lipodystrophic patients had lower mtDNA than the phenotypically similar corresponding depot of non-lipodystrophic patients. The greatest difference in gene expression between dorsocervical and abdominal SAT, irrespective of lipodystrophy status, was in expression of homeobox genes that regulate transcription and regionalization of organs during embryonal development. Uridine increased limb fat and its proportion of total fat, but had no effect on liver fat content and markers of insulin resistance. Conclusions: Long-term cART is associated with increased arterial stiffness and, thus, with higher cardiovascular risk. Lipoatrophic abdominal SAT is characterized by inflammation, apoptosis and mtDNA depletion. As mtDNA is depleted even in non-lipoatrophic dorsocervical SAT, lipoatrophy is unlikely to be caused directly by mtDNA depletion. Preserved dorsocervical SAT of patients with cART-associated lipodystrophy is less inflamed than their lipoatrophic abdominal SAT, and does not resemble brown adipose tissue. The greatest difference in gene expression between dorsocervical and abdominal SAT is in expression of transcriptional regulators, homeobox genes, which might explain the differential susceptibility of these adipose tissue depots to cART-induced toxicity. Uridine is able to increase peripheral SAT in lipoatrophic patients during unchanged cART.

Regulation of respiratory activity of brown adipose tissue mitochondria through changes in cytochromes.

Exposure of cold-acclimatized rats to heat (37 degrees C) for a short period decreased brown adipose tissue (BAT) mitochondrial substrate-dependent oxygen uptake and H2O2 generation. Both the concentration and substrate-dependent rate of cytochrome b reduction decreased as early as 3 h of heat exposure. These results identify cytochrome b as the locus of regulation of electron transport in BAT mitochondria under conditions of heat stress.

Microsomal redox systems in brown adipose tissue: high lipid peroxidation, low cholesterol biosynthesis and no detectable cytochrome P-450

The presence of redox systems in microsomes of brown adipose tissue (BAT) in cold exposed rats was investigated and compared with liver. BAT microsomes showed high activity of lipid peroxidation measured both by the formation of malondialdehyde (MDA) and by oxygen uptake. NADH and NADPH dependent cytochrome c reductase activity were present in both BAT and liver microsomes. Aminopyrine demethylase and aniline hydroxylase activities, the characteristic detoxification enzymes in liver microsomes could not be detected in BAT microsomes. BAT minces showed very poor incorporation of [1-14C]acetate and [2-14C]-mevalonate in unsaponifiable lipid fraction compared to liver. Biosynthesis of cholesterol and ubiquinone, but not fatty acids, and the activity of 3-hydroxy-3-methyl glutaryl CoA reductase appear to be very low in BAT. Examination of difference spectra showed the presence of only cytochrome b 5 in BAT microsomes. In addition to the inability to detect the enzyme activities dependent on cytochrome P-450, a protein with the characteristic spectrum, molecular size in SDS-PAGE and interaction with antibodies in double diffusion test, also could not be detected in BAT microsomes. The high activity of lipid peroxidation in microsomes, being associated with large oxygen uptake and oxidation of NADPH, will also contribute to the energy dissipation as heat in BAT, considered important in thermogenesis.

Työhön liittyvä kilpailu 18 - 65-vuotiaiden pyhtääläisten kuvaamana

Tutkimuksen kohteena olivat Pyhtään työikäisten asukkaiden näkemykset ja kokemukset työssä esiintyvästä kilpailusta Tutkimusongelma oli työhön liittyvän kilpailun ilmiön hahmottaminen. Tutkimuksen tarkoitus oli valottaa työhön liittyvän kilpailun moninaisuutta antaen esimerkkejä sen eri muodoista, esittäen ajatuksia uusien tulkintojen tekemiselle ja herättäen ideoita kilpailun eri muotojen soveltamiselle työn ja työilmapiirin tutkimuksissa. Tavoitteena oli tutkia haastatteluissa esiintyviä tapoja käsittää työhön liittyvä kilpailu ja sitä, missä määrin eri ammateissa kuvattiin sosiaalista kilpailua verrattuna välineelliseen kilpailuun. Työyhteisöön samastumista tarkasteltiin kilpailun ja koetun oikeudenmukaisuuden näkökulmista. Työn arvostusta käsiteltiin tarkastellen haastateltujen käsitystä ammattinsa yleisestä arvostuksesta sekä haastateltujen omia arvioita ammatistaan, sekä millä tavalla ammattirooli nousi esiin haastateltujen itsen kuvauksissa. Työpaikan ihmissuhteita ja valtaa tarkasteltiin kohdistamalla huomio työtovereiden kanssa toimeen tulemiseen ja työpaikan ihmissuhteiden aiheuttamaan stressiin sekä haastateltujen työssään kokeman oman vaikutusvallan, tasavertaisuuden, epäreiluuden, arvostuksen ja kilpailun määrään. Selvitettiin myös miten vallankäyttöä ja kiusaamista kuvattiin ja millä tavalla vallankäytön ja kiusaamisen katsottiin edesauttavan tavoitteiden saavuttamisessa. Lopuksi tarkastelun kohteina olivat ongelmien käsittely, työssä viihtyminen ja viihtymiseen vaikuttavat seikat. Aineisto kerättiin Pyhtäällä kesällä 2007. Vastaajia oli yhteensä 245 ja vastausprosentti oli 50. Tutkimuksessa mukana olivat kalkki työilmapiiriä ja työpaikan ihmissuhteita koskeviin kysymyksiin vastanneet haastatellut (N = 167). Suurimmaksi osaksi tutkimus oli kuvailevaa, mutta siinä oli myös kvantitatiivista kysymyksenasettelua. Tutkimuksessa käytettiin sekä kvalitatiivisia että kvantitatiivisia analyysimenetelmiä. Puolistrukturoiduissa yksilöhaastatteluissa hyödynnettiin tulkitsevaa fenomenologista analyysia. Kirjattuja avovastauksia tutkittiin luokittavalla ja tulkitsevalla sisällönanalyysilla. Lisäksi laskettiin tilastollisia merkitsevyyksiä Työpaikalla esiintyvä kilpailu nähtiin haastateltujen selonteoissa hyvin moninaisena, sekä myönteisenä että haitallisena. Siihen ymmärrettiin kuuluvan niin resursseihin, työtehtäviin, tuloksiin ja palkkioihin liittyvää välineellistä kilpailua, kuin ihmisten välistä sosiaalista valtataisteluakin. Suhteessa välineelliseen kilpailuun sosiaalista kilpailua kuvattiin eniten hoiva- ja sosiaalialan ammateissa. Suhteessa sosiaaliseen kilpailuun välineellistä kilpailua kuvasivat eniten yrittäjät Vastausten perusteella suun kilpailun määrä korreloi työpaikan ihmissuhteiden aiheuttamaan stressiin, mutta vain silloin, kun kokemus työpaikan oikeudenmukaisuudesta oli matala. Kilpailun eri muotojen (kilpailu omien tavoitteiden saavuttamisesta vs. kilpailu organisaation tavoitteiden saavuttamisesta) väliset yhteydet työyhteisöön samastumiseen eivät aineistossa olleet tilastollisesti merkitseviä. Haastatellun arvio oman ammattinsa arvostuksesta ei myöskään ennustanut haastatellun todennäköisyyttä esittää itsensä ammattikuntansa edustajana avoimen itsen kuvauksen tilanteessa. Koettu oikeudenmukaisuus kuitenkin korreloi työyhteisöön samastumiseen. Mitä oikeudenmukaisempana haastatellut työpaikkaansa pitivät, sitä tärkeämmäksi samastumiskohteeksi he sen tyypillisesti arvioivat. Myös työssä viihtymisen ja työpaikan koetun oikeudenmukaisuuden välinen korrelaatio oli aineistossa voimakas. Lisäksi silloin, kun kokemus oikeudenmukaisuudesta oli matalalla tasolla, oli myös työpaikan ihmissuhteiden aiheuttama stressi yhteydessä vähäiseen työssä viihtymiseen. Tärkeimmät läheet tutkimuksessa olivat: Turner. John C 1975. Social comparison and social identity. Some prospects for intergroup behaviour. European Journal of Social Psychology, 5(1), 5-34. Haslam, S. Alexander 2004. Psychology in organizalions. The social identity approach Second Edition. London: SAGE Publications. Tyler, Tom - Blader. Steven 2000. Cooperation in Groups: Procedural Justice, Social Identity, and Behavioural Engagement. Essays in Social Psychology. Philadelphia: Psychology Press / Taylor & Francis Group. Kantolahti, T. - Tikander, T. 2010. Puheenvuoroja työn kuormittavuudesta. Sosiaali- ja terveysministeriön selvityksiä 2010:17

Modeling Of Hydrolytic Polymerization In A Semibatch Nylon 6 Reactor

Hydrolytic polymerization of caprolactam to Nylon 6 in a semibatch reactor is carried out by heating a mixture of water and caprolactam. Evaporation of volatiles caused by heating results in a pressure build-up. After the pressure reaches a predetermined value, vapors are vented to keep the pressure constant for some time, and thereafter, to lower the pressure to a value slightly above atmospheric in a preprogrammed manner. The characteristics of the polymer are determined by the chemical reactions and the vaporization of water and caprolactam. The semibatch operation has been simulated and the predictions have been compared with industria data. The observed temperature and pressure histories were predicted with a fair degree of accuracy. It was found that the predictions of the degree of polymerization however are sensitive to the vapor-liquid equilibrium relations. A comparison with an earlier model, which neglected mass transfer resistance, indicates that simulation using the VLE data of Giori and Hayes and accounting for mass transfer resistance is more reliable.

Structural Health Monitoring (SHM) Using Strain Gauges, PVDF Film and Fiber Bragg Grating (FBG) Sensors: A Comparative Study

The term Structural Health Monitoring has gained wide acceptance in the recent pastas a means to monitor a structure and provide an early warning of an unsafe conditionusing real-time data. Utilization of structurally integrated, distributed sensors tomonitor the health of a structure through accurate interpretation of sensor signals andreal-time data processing can greatly reduce the inspection burden. The rapidimprovement of the Fiber Bragg Grating sensor technology for strain, vibration andacoustic emission measurements in recent times make them a feasible alternatives tothe traditional strain gauges transducers and conventional Piezoelectric sensors usedfor Non Destructive Evaluation (NDE) and Structural Health Monitoring (SHM).Optical fiber-based sensors offers advantages over conventional strain gauges, PVDFfilm and PZT devices in terms of size, ease of embedment, immunity fromelectromagnetic interference(EMI) and potential for multiplexing a number ofsensors. The objective of this paper is to demonstrate the feasibility of Fiber BraggGrating sensor and compare its utility with the conventional strain gauges and PVDFfilm sensors. For this purpose experiments are being carried out in the laboratory on acomposite wing of a mini air vehicle (MAV). In this paper, the results obtained fromthese preliminary experiments are discussed.

Magnetoresistance and electroresistance effects in Fe3O4 nanoparticle system

Nearly monodisperse spherical magnetite (Fe3O4) nanoparticles are prepared by colloidal chemistry route. Magnetic and electronic transport properties of the annealed pellets of these nanoparticles are reported. Effect of external magnetic and electric fields on the magnetic and transport properties of the material are studied as a function of temperature. We find that the highest resistance state of the ferromagnetic system occurs at a magnetic field which is approximately equal to its magnetic coercivity; this establishes the magnetoresistance (MR) in this system to be of the conventional tunnelling type MR as against the spin-valve type MR found more recently in some ferromagnetic oxide systems. The material also shows electroresistance (ER) property with its low-temperature resistance being strongly dependent on the excitation current that is used for the measurement. This ER effect is concluded to be intrinsic to the material and is attributed to the electric field-induced melting of the charge-order state in magnetite.

Analysis of composite single lap joints using numerical and experimental approach

Adhesives are widely used to execute the assembly of aerospace and automotive structures due to their ability to join dissimilar materials, reduced stress concentration, and improved fatigue resistance. The mechanical behavior of adhesive joints can be studied either using analytical models or by conducting mechanical tests. However, the complexity owing to multiple interfaces, layers with different properties, material and geometric nonlinearity and its three-dimensional nature combine to increase the difficulty in obtaining an overall system of governing equations to predict the joint behavior. On the other hand, experiments are often time consuming and expensive due to a number of parameters involved. Finite element analysis (FEA) is profoundly used in recent years to overcome these limitations. The work presented in this paper involves the finite element modeling and analysis of a composite single lap joint where the adhesive-adherend interface region was modeled using connector elements. The computed stresses were compared with the experimental stresses obtained using digital image correlation technique. The results showed an agreement. Further, the failure load predicted using FEA was found to be closer to the actual failure load obtained by mechanical tests.

Evaluación de pollitas Hy-Line variedad Brown, en etapa de inicio a rompimiento de postura, bajo manejo tradicional

Se evaluó el comportamiento productivo de pollitas Hy- Line var. Brown, durante las primeras diecisiete semanas de desarrollo con la guía de manejo comercial para estas aves. Se utilizó un lote de 4,591 aves distribuidas en dos galeras. Se muestreó el 4% de la población de forma aleatoria y sin reemplazo, registrando peso, alimento consumido y mortalidad. Se realizaron los cálculos de consumo, uniformidad de peso, mortalidad de lote y se registraron las prácticas sanitarias de la granja. El consumo total obtenido fue un 15.6% inferior al reportado por la guía de manejo (803 g), viéndose afectado por cambios en el manejo del alimento, el que fue suministrado de acuerdo al peso vivo y no a la edad de las aves. El peso de las aves resultó 9.3% inferior al estipulado por la guía de manejo. La uniformidad del lote fue del 80% con una variación de ±10% igual al esperado para este tipo de aves. La mortalidad de la granja fue inferior al 0.04% expresado por la guía de manejo comercial. La aplicación del plan sanitario sufrió alteración en el tiempo de ejecución, sin embargo no tuvo efecto sobre la mortalidad de la granja. El manejo zootécnico de la granja está dentro de lo esperado en granjas de pequeños productores avícolas en condiciones tropicales.