The Structure and Functions of Hantavirus Nucleocapsid Protein

Hantaviruses, members of the genus Hantavirus in the Bunyaviridae family, are enveloped single-stranded RNA viruses with tri-segmented genome of negative polarity. In humans, hantaviruses cause two diseases, hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS), which vary in severity depending on the causative agent. Each hantavirus is carried by a specific rodent host and is transmitted to humans through excreta of infected rodents. The genome of hantaviruses encodes four structural proteins: the nucleocapsid protein (N), the glycoproteins (Gn and Gc), and the polymerase (L) and also the nonstructural protein (NSs). This thesis deals with the functional characterization of hantavirus N protein with regard to its structure. Structural studies of the N protein have progressed slowly and the crystal structure of the whole protein is still not available, therefore biochemical assays coupled with bioinformatical modeling proved essential for studying N protein structure and functions. Presumably, during RNA encapsidation, the N protein first forms intermediate trimers and then oligomers. First, we investigated the role of N-terminal domain in the N protein oligomerization. The results suggested that the N-terminal region of the N protein forms a coiled-coil, in which two antiparallel alpha helices interact via their hydrophobic seams. Hydrophobic residues L4, I11, L18, L25 and V32 in the first helix and L44, V51, L58 and L65 in the second helix were crucial for stabilizing the structure. The results were consistent with the head-to-head, tail-to-tail model for hantavirus N protein trimerization. We demonstrated that an intact coiled-coil structure of the N terminus is crucial for the oligomerization capacity of the N protein. We also added new details to the head-to-head, tail-to-tail model of trimerization by suggesting that the initial step is based on interaction(s) between intact intra-molecular coiled-coils of the monomers. We further analyzed the importance of charged aa residues located within the coiled-coil for the N protein oligomerization. To predict the interacting surfaces of the monomers we used an upgraded in silico model of the coiled-coil domain that was docked into a trimer. Next the predicted target residues were mutated. The results obtained using the mammalian two-hybrid assay suggested that conserved charged aa residues within the coiled-coil make a substantial contribution to the N protein oligomerization. This contribution probably involves the formation of interacting surfaces of the N monomers and also stabilization of the coiled-coil via intramolecular ionic bridging. We proposed that the tips of the coiled-coils are the first to come into direct contact and thus initiate tight packing of the three monomers into a compact structure. This was in agreement with the previous results showing that an increase in ionic strength abolished the interaction between N protein molecules. We also showed that residues having the strongest effect on the N protein oligomerization are not scattered randomly throughout the coiled-coil 3D model structure, but form clusters. Next we found evidence for the hantaviral N protein interaction with the cytoplasmic tail of the glycoprotein Gn. In order to study this interaction we used the GST pull-down assay in combination with mutagenesis technique. The results demonstrated that intact, properly folded zinc fingers of the Gn protein cytoplasmic tail as well as the middle domain of the N protein (that includes aa residues 80 248 and supposedly carries the RNA-binding domain) are essential for the interaction. Since hantaviruses do not have a matrix protein that mediates the packaging of the viral RNA in other negatve stranded viruses (NSRV), hantaviral RNPs should be involved in a direct interaction with the intraviral domains of the envelope-embedded glycoproteins. By showing the N-Gn interaction we provided the evidence for one of the crucial steps in the virus replication at which RNPs are directed to the site of the virus assembly. Finally we started analysis of the N protein RNA-binding region, which is supposedly located in the middle domain of the N protein molecule. We developed a model for the initial step of RNA-binding by the hantaviral N protein. We hypothesized that the hantaviral N protein possesses two secondary structure elements that initiate the RNA encapsidation. The results suggest that amino acid residues (172-176) presumably act as a hook to catch vRNA and that the positively charged interaction surface (aa residues 144-160) enhances the initial N-RNA interacation. In conclusion, we elucidated new functions of hantavirus N protein. Using in silico modeling we predicted the domain structure of the protein and using experimental techniques showed that each domain is responsible for executing certain function(s). We showed that intact N terminal coiled-coil domain is crucial for oligomerization and charged residues located on its surface form a interaction surface for the N monomers. The middle domain is essential for interaction with the cytoplasmic tail of the Gn protein and RNA binding.

Optimal management of conflicting species: Grey seal (Halichoerus grypus) and Atlantic salmon (Salmo salar) in the Baltic Sea

The objective of this thesis is to examine the economic effects in the conflict between grey seal population and the salmon fishery in the Baltic Sea. We will formulate a bioeconomic model which provides new insights on the optimal management of Atlantic salmon with respect to the effects brought about by the grey seal population. As the catch losses caused by seals have an effect on salmon fishery in Baltic, we will study how seal population affects the present value of the salmon fishery. The study considers the Finnish coastal trap net fishery. The bioeconomic model considers a scenario of sole salmon fishery and a scenario of salmon fishery affected by the grey seal population. On the basis of these scenarios, a seal compensation scheme is introduced. We can observe a significant economic seal-induced effect on the salmon fishery. The results suggest that the present seal compensation scheme emploid by the Finnish government is suboptimal. This thesis is part of the TARMO –project, in which the conflict between grey seal population and salmon fishery is studied using the methods of environmental economics.

On the use of weather radar for mesoscale applications in northern conditions

Mesoscale weather phenomena, such as the sea breeze circulation or lake effect snow bands, are typically too large to be observed at one point, yet too small to be caught in a traditional network of weather stations. Hence, the weather radar is one of the best tools for observing, analyzing and understanding their behavior and development. A weather radar network is a complex system, which has many structural and technical features to be tuned, from the location of each radar to the number of pulses averaged in the signal processing. These design parameters have no universal optimal values, but their selection depends on the nature of the weather phenomena to be monitored as well as on the applications for which the data will be used. The priorities and critical values are different for forest fire forecasting, aviation weather service or the planning of snow ploughing, to name a few radar-based applications. The main objective of the work performed within this thesis has been to combine knowledge of technical properties of the radar systems and our understanding of weather conditions in order to produce better applications able to efficiently support decision making in service duties for modern society related to weather and safety in northern conditions. When a new application is developed, it must be tested against ground truth . Two new verification approaches for radar-based hail estimates are introduced in this thesis. For mesoscale applications, finding the representative reference can be challenging since these phenomena are by definition difficult to catch with surface observations. Hence, almost any valuable information, which can be distilled from unconventional data sources such as newspapers and holiday shots is welcome. However, as important as getting data is to obtain estimates of data quality, and to judge to what extent the two disparate information sources can be compared. The presented new applications do not rely on radar data alone, but ingest information from auxiliary sources such as temperature fields. The author concludes that in the future the radar will continue to be a key source of data and information especially when used together in an effective way with other meteorological data.

Peritoneal dialysis and neurological outcome in infants and small children

Although improved outcomes for children on peritoneal dialysis (PD) have been seen in recent years, the youngest patients continue to demonstrate inferior growth, more frequent infections, more neurological sequelae, and higher mortality compared to older children. Also, maintain-ing normal intravascular volume status, especially in anuric patients, has proven difficult. This study was designed to treat and monitor these youngest PD patients, which are relatively many due to the high prevalence of congenital nephrotic syndrome of the Finnish type (CNF, NPHS1) in Finland, with a strict protocol, to evaluate the results and to improve metabolic balance, growth, and development. A retrospective analysis of 23 children under two years of age at onset of PD, treated between 1995 and 2000, was performed to obtain a control population for our prospective PD study. Respectively, 21 patients less than two years of age at the beginning of PD were enrolled in prospective studies between 2001 and 2005. Medication for uremia and nutrition were care-fully adjusted during PD. Laboratory parameters and intravascular volume status were regu-larly analyzed. Growth was analyzed and compared with midparental height. In a prospective neurological study, the risk factors for development and the neurological development was determined. Brain images were surveyed. Hearing was tested. In a retrospective neurological study, the data of six NPHS1 patients with a congruent neurological syndrome was analyzed. All these patients had a serious dyskinetic cerebral palsy-like syndrome with muscular dysto-nia and athetosis (MDA). They also had a hearing defect. Metabolic control was mainly good in both PD patient groups. Hospitalization time shortened clearly. The peritonitis rate diminished. Hypertension was a common problem. Left ventricular hypertrophy decreased during the prospective study period. None of the patients in either PD group had pulmonary edema or dialysis-related seizures. Growth was good and catch-up growth was documented in most patients in both patient groups during PD. Mortality was low (5% in prospective and 9% in retrospective PD patients). In the prospective PD patient group 11 patients (52%) had some risk factor for their neuro-development originating from the predialysis period. The neurological problems, detected be-fore PD, did not worsen during PD and none of the patients developed new neurological com-plications during PD. Brain infarcts were detected in four (19%) and other ischemic lesions in three patients (14%). At the end of this study, 29% of the prospectively followed patients had a major impairment of their neurodevelopment and 43% only minor impairment. In the NPHS1+MDA patients, no clear explanation for the neurological syndrome was found. The brain MRI showed increased signal intensity in the globus pallidus area. Kernic-terus was contemplated to be causative in the hypoproteinemic newborns but it could not be proven. Mortality was as high as 67%. Our results for young PD patients were promising. Metabolic control was acceptable and growth was good. However, the children were significantly smaller when compared to their midparental height. Although many patients were found to have neurological impairment at the end of our follow-up period, PD was a safe treatment whereby the neurodevelopment did not worsen during PD.

Differences in the climatic adaptation of silver birch (Betula pendula) and downy birch (B. pubescens) in Finland based on male flowering phenology.

Male flowering was studied at the canopy level in 10 silver birch (Betula pendula Roth) stands from 8 localities and in 14 downy birch (B. pubescens Ehrh.) stands from 10 localities in Finland from 1963 to 1973. Distributions of cumulative pollen catches were compared to the normal Gaussian distribution. The basis for the timing of flowering was the 50 per cent point of the anthesis-fitted normal distribution. To eliminate effects of background pollen, only the central, normally distributed part of the cumulative distribution was used. Development up to the median point of the distribution was measured and tested in calendar days, in degree days (> 5 °C) and in period units. The count of each parameter began on and included March 19. Male flowering in silver birch occurred from late April to late June depending on latitude, and flowering in downy birch took place from early May to early July. The heat sums needed for male flowering varied in downy birch stands latitudinally but there was practically no latitudinal variation in heat sums needed for silver birch flowering. The amount of male flowering in stands of both birch species were found to have a large annual variation but without any clear periodicity. The between years pollen catch variation in stands of either birch species did not show any significant latitudinal correlation in contrast to Norway spruce stands. The period unit heat sum gave the most accurate forecast of the timing of flowering for 60 per cent of the silver birch stands and for 78.6 per cent of the for downy birch stands. Calendar days, however, gave the best forecast for silver birch in 25 per cent of the cases, while degree days gave the best forecast for downy birch in 21.4 per cent of the cases. Silver birch seems to have a local inclination for a more fixed flowering date compared to downy birch, which could mean a considerable photoperiodic influence on flowering time of silver birch. Silver birch and downy birch had different geographical correlations. Frequent hybridization of birch species occurs more often in northern Finland in than in more southern latitudes. The different timing in flowering caused increasing scatter in flowering times in the north, especially in the case of downy birch. The chance of simultaneous flowering of silver birch and downy birch so increased northwards due to a more variable climate and also higher altitudinal variations. Compared with conifers, the reproduction cycles of both birch species were found to be well protected from damage by frost.

Modeling and optimization of a natural convection-based agricultural dryer

This study presents development of a computational fluid dynamic (CFD) model to predict unsteady, two-dimensional temperature, moisture and velocity distributions inside a novel, biomass-fired, natural convection-type agricultural dryer. Results show that in initial stages of drying, when material surface is wet and moisture is easily available, moisture removal rate from surface depends upon the condition of drying air. Subsequently, material surface becomes dry and moisture removal rate is driven by diffusion of moisture from inside to the material surface. An optimum 9-tray configuration is found to be more efficient than for the same mass of material and volume of dryer. A new configuration of dryer, mainly to explore its potential to increasing uniformity in drying across all trays, is also analyzed. This configuration involves diverting a portion of hot air before it enters over the first tray and is supplied directly at an intermediate location in the dryer. Uniformity in drying across trays has increased for the kind of material simulated.

Ultrasonic Guided Wave Characterization and Damage Detection in Foam-core Sandwich Panel using PWAS and LDV

Lamb wave type guided wave propagation in foam core sandwich structures and detectability of damages using spectral analysis method are reported in this paper. An experimental study supported by theoretical evaluation of the guided wave characteristics is presented here that shows the applicability of Lamb wave type guided ultrasonic wave for detection of damage in foam core sandwich structures. Sandwich beam specimens were fabricated with 10 mm thick foam core and 0.3 mm thick aluminum face sheets. Thin piezoelectric patch actuators and sensors are used to excite and sense guided wave. Group velocity dispersion curves and frequency response of sensed signal are obtained experimentally. The nature of damping present in the sandwich panel is monitored by measuring the sensor signal amplitude at various different distances measured from the center of the linear phased array. Delaminations of increasing width are created and detected experimentally by pitch-catch interrogation with guided waves and wavelet transform of the sensed signal. Signal amplitudes are analyzed for various different sizes of damages to differentiate the damage size/severity. A sandwich panel is also fabricated with a planer dimension of 600 mm x 400 mm. Release film delamination is introduced during fabrication. Non-contact Laser Doppler Vibrometer (LDV) is used to scan the panel while exciting with a surface bonded piezoelectric actuator. Presence of damage is confirmed by the reflected wave fringe pattern obtained from the LDV scan. With this approach it is possible to locate and monitor the damages by tracking the wave packets scattered from the damages.

Guided wave based detection of damage in honeycomb core sandwich structures

We report on the Lamb wave type guided wave propagation in honeycomb core sandwich structures. An experimental study supported by theoretical evaluation of the guided wave characteristics is presented that proves the potential of Lamb wave type guided wave for detection of damage in sandwich structures. A sandwich panel is fabricated with planar dimension of 600 mm x 600 mm, having a core thickness of 7 mm, cell size of 5 mm and 0.1 mm thick aluminum face sheets. Thin piezoelectric patch actuators and sensors are used to excite and sense a frequency band limited guided wave with a central frequency. A linear phased array of piezoelectric patch actuators is used to achieve higher signal strength and directivity. Group velocity dispersion curves and corresponding frequency response of sensed signal are obtained experimentally. Linearity between the excitation signal amplitude and the corresponding sensed signal amplitude is found for certain range of parameters. The nature of damping present in the sandwich panel is monitored by measuring the sensor signal amplitude at various different distances measured from the center of the linear phased array. Indentation and low velocity impact induced damages of increasing diameter covering several honeycomb cells are created. Crushing of honeycomb core with rupture of face sheet is observed while introducing the damage. The damages are then detected experimentally by pitch-catch interrogation with guided waves and wavelet transform of the sensed signal. Signal amplitudes are analyzed for various different sizes of damages to differentiate the damage size/severity. Monotonic changes in the sensor signal amplitude due to increase in the damage size has been established successfully. With this approach it is possible to locate and monitor the damages with the help of phased array and by tracking the wave packets scattered from the damages. (C) 2012 Elsevier Ltd. All rights reserved.

Crystal-structure analysis of cis-X-pro-containing peptidomimetics: understanding the steric interactions at cis X-pro amide bonds

Catch the twist: The cis Piv-Pro conformer (Piv=pivaloyl) of peptides is no longer inaccessible. Any cis X-Pro tertiary-amide-bond conformer can be stabilized in crystals of peptides by accommodating the unavoidable distortion of the dihedral angle of the peptide bond to the carbonyl group of the Pro residue (see picture), in this case through ni−1→πi* interactions. Steric clashes were not observed in the cis Piv-Pro rotamers studied.

Simulations reveal that the HIV-1 gp120-CD4 complex dissociates via complex pathways and is a potential target of the polyamidoamine (PAMAM) dendrimer

The polyamidoamine (PAMAM) dendrimer prevents HIV-1 entry into target cells in vitro. Its mechanism of action, however, remains unclear and precludes the design of potent dendrimers targeting HIV-1 entry. We employed steered molecular dynamics simulations to examine whether the HIV-1 gp120-CD4 complex is a target of PAMAM. Our simulations mimicked single molecule force spectroscopy studies of the unbinding of the gp120-CD4 complex under the influence of a controlled external force. We found that the complex dissociates via complex pathways and defies the standard classification of adhesion molecules as catch and slip bonds. When the force loading rate was large, the complex behaved as a slip bond, weakening gradually. When the loading rate was small, the complex initially strengthened, akin to a catch bond, but eventually dissociated over shorter separations than with large loading rates. PAMAM docked to gp120 and destabilized the gp120-CD4 complex. The rupture force of the complex was lowered by PAMAM. PAMAM disrupted salt bridges and hydrogen bonds across the gp120-CD4 interface and altered the hydration pattern of the hydrophobic cavity in the interface. In addition, intriguingly, PAMAM suppressed the distinction in the dissociation pathways of the complex between the small and large loading rate regimes. Taken together, our simulations reveal that PAMAM targets the gp120-CD4 complex at two levels: it weakens the complex and also alters its dissociation pathway, potentially inhibiting HIV-1 entry.

PICES-GLOBEC International Program on Climate Change and Carrying Capacity: Report of the 1999 MONITOR and REX Workshops, and the 2000 MODEL Workshop on Lower Trophic Level Modelling

Table of Contents [pdf, 0.11 Mb] Executive Summary [pdf, 0.07 Mb] MODEL Task Team Workshop Report Final Report of the International Workshop to Develop a Prototype Lower Trophic Level Ecosystem Model for Comparison of Different Marine Ecosystems in the North Pacific [pdf, 11.64 Mb] Report of the 1999 MONITOR Task Team Workshop [pdf, 0.32 Mb] Report of the 1999 REX Task Team Workshop Herring and Euphausiid population dynamics Douglas E. Hay and Bruce McCarter Spatial, temporal and life-stage variation in herring diets in British Columbia [pdf, 0.10 Mb] Augustus J. Paul and J. M. Paul Over winter changes in herring from Prince William Sound, Alaska [pdf, 0.08 Mb] N. G. Chupisheva Qualitative texture characteristic of herring (Clupea pallasi pallasi) pre-larvae developed from the natural and artificial spawning-grounds in Severnaya Bay (Peter the Great Bay) [pdf, 0.07 Mb] Gordon A. McFarlane, Richard J. Beamish and Jake SchweigertPacific herring: Common factors have opposite impacts in adjacent ecosystems [pdf, 0.15 Mb] Tokimasa Kobayashi, Keizou Yabuki, Masayoshi Sasaki and Jun-Ichi Kodama Long-term fluctuation of the catch of Pacific herring in Northern Japan [pdf, 0.39 Mb] Jacqueline M. O’Connell Holocene fish remains from Saanich Inlet, British Columbia, Canada [pdf, 0.40 Mb] Elsa R. Ivshina and Irina Y. Bragina On relationship between crustacean zooplankton (Euphausiidae and Copepods) and Sakhalin-Hokkaido herring (Tatar Strait, Sea of Japan) [pdf, 0.14 Mb] Stein Kaartvbeedt Fish predation on krill and krill antipredator behaviour [pdf, 0.08 Mb] Nikolai I. Naumenko Euphausiids and western Bering Sea herring feeding [pdf, 0.07 Mb] David M. Checkley, Jr. Interactions Between Fish and Euphausiids and Potential Relations to Climate and Recruitment [pdf, 0.08 Mb] Vladimir I. Radchenko and Elena P. Dulepova Shall we expect the Korf-Karaginsky herring migrations into the offshore western Bering Sea? [pdf, 0.75 Mb] Young Shil Kang Euphausiids in the Korean waters and its relationship with major fish resources [pdf, 0.29 Mb] William T. Peterson, Leah Feinberg and Julie Keister Ecological Zonation of euphausiids off central Oregon [pdf, 0.11 Mb] Scott M. Rumsey Environmentally forced variability in larval development and stage-structure: Implications for the recruitment of Euphausia pacifica (Hansen) in the Southern California Bight [pdf, 3.26 Mb] Scott M. Rumsey Inverse modelling of developmental parameters in Euphausia pacifica: The relative importance of spawning history and environmental forcing to larval stage-frequency distributions [pdf, 98.79 Mb] Michio J. Kishi, Hitoshi Motono & Kohji Asahi An ecosystem model with zooplankton vertical migration focused on Oyashio region [pdf, 33.32 Mb] PICES-GLOBEC Implementation Panel on Climate Change and Carrying Capacity Program Executive Committee and Task Team List [pdf, 0.05 Mb] (Document pdf contains 142 pages)

Yemaya, No. 28, August 2008

Reflections/ Women in Fisheries Policies - Meeting the challenge. Africa/ South Africa - Righting gender injustices. Asia/ China - Contributing significantly. Europe/ Norway - Taking along the 'crewmembers'. Africa/ Uganda - Bringing in the catch. Reflections/ Women in Fisheries Policies - Recognizing women in fisheries: Policy considerations for developing countries. Asia/ The Philippines - 'Engendering' the fisheries industry development plan. Yemaya Recommends - Women in the Fishing: The Roots of Power between the Sexes. Profile - Meet Sherry Pictou. Q&A - Interview with Dr. Cornelia E. Nauen. Milestones - International legal instruments of relevance to women in fisheries. What's New, Webby? - Statement from Women’s Workshop, South Africa. Yemaya Mama in Bangkok – Cartoon. Poem - Ancient food for future generations.

The Use of Herbicides to Control Hydrilla and the Effects on Young Largemouth Bass Population Characteristics and Aquatic Vegetation in Lake Seminole, Georgia

From 1997 to 2003, we examined the impacts of two aquatic herbicides, fluridone (Sonar; 1-methyl-3-phenyl-5-[3-(trifluromethl) phenyl]-4(1H)-pyridinone), and dipotassium salt of endothall (Aquathol K; 7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid), used to control dense hydrilla (Hydrilla verticillata L. f. Royle), on population characteristics of juvenile largemouth bass (Micropterus salmoides Lacepede) in small coves (<10 ha) in Lake Seminole, Georgia. In addition, we estimated areal coverage and species composition of submersed aquatic vegetation (SAV) communities in each cove. Fish and plants were sampled in both control (hydrilla infested)and herbicide treated coves in November and March- April each year. Electrofishing catch-per-effort for both number and weight of age-0 and age-1 fish for the 1997 to 2002 year classes was either the same or higher (p < 0.05) in herbicide treated than in control coves. Age-0 fish were larger (p <0.05) in treated, than in control coves in November, but at age-1 in the following spring, fish were slightly longer (p <0.05) in the control coves. Higher age-0 catches were associated with greater percent reductions in numeric catch between age-0 and age-1 and reduced lengths of fish in November indicating density-dependent effects. Age-0 fish lengths were also negatively correlated to percent cover of both total and native SAV. Total or native SAV coverages were not associated with catch-per-unit effort for number and weight, but nearly all control and herbicide treated coves had total SAV coverage greater than 40%. Applications of both Sonar and Aquathol K reduced total SAV coverage and hydrilla, permitted the establishment of native SAVs, and had either neutral or positive impacts on young largemouth bass in small coves in Lake Seminole. (PDF contains 7 pages.)

STREAM Journal, Vol. 5, No. 2, pp 1-17. April-June 2006

CONTENTS: First one-stop aqua shop in Pakistan, by Syed Nadeem Sharib and Muhammad Junaid Wattoo. Dad Karim: a fisherman of Gwadar, by Abdul Rahim. Learning to fish in the deep sea of Sindh Province, by Muhammad Alam. Freshwater prawn fishery of Pakistan, by Muhammad Yaqoob. Cephalopod fishery: a local technique to catch cuttlefish in the coastal waters of Pakistan, by Shabir Ali Amir. Grouper culture in Pakistan, by S. Makhdoom Hussain and Zakia Khatoon.

Quota and Licensing Systems in the VIII Division European Anchovy

Paper presented at 12th Annual Conference of EAERE 2003 Bilbao (Spain)