Studies of subcellular localization and complex formation of the Agrobacterium tumefaciens transport ATPase VirB11

The VirB11 ATPase is an essential component of an Agrobacterium tumefaciens type IV bacterial secretion system that transfers oncogenic nucleoprotein complexes to susceptible plant cells. This dissertation investigates the subcellular localization and homo-oligomeric state of the VirB11 ATPase in order to provide insights about the assembly of the protein as a subunit of this membrane-associated transfer system. Subcellular fractionation studies and quantitative immunoblot analysis demonstrated that $\sim$30% of VirB11 partitioned as soluble protein and $\sim$70% was tightly associated with the bacterial cytoplasmic membrane. No differences were detected in VirB11 subcellular localization and membrane association in the presence or absence of other transport system components. Mutations in virB11 affecting protein function were mapped near the amino terminus, just upstream of a region encoding a Walker 'A' nucleotide-binding site, and within the Walker 'A' motif partitioned almost exclusively with the cytoplasmic membrane, suggesting that an activity associated with nucleotide binding could modulate the affinity of VirB11 for the cytoplasmic membrane. Merodiploid analysis of VirB11 mutant and truncation derivatives provided strong evidence that VirB11 functions as a homo- or heteromultimer and that the C-terminal half of VirB11 contains a protein interaction domain. A combination of biochemical and molecular genetic approaches suggested that VirB11 and the green fluorescence protein (GFP) formed a mixed multimer as demonstrated by immunoprecipitation experiments with anti-GFP antibodies. Second, a hybrid protein composed of VirB11 fused to the N-terminal DNA-binding domain of bacteriophage $\lambda$ cI repressor conferred immunity to $\lambda$ superinfection, demonstrating that VirB11 self-association promotes dimerization of the chimeric repressor. A conserved Walker 'A' motif, though required for VirB11 function in T-complex export, was not necessary for VirB11 self-association. Sequences in both the N- and the C-terminal halves of the protein were found to contribute to self-association of the full length protein. Chemical cross-linking experiments with His$\sb6$ tagged VirB11 suggested that VirB11 probably assembles into a higher order homo-oligomeric complex. ^

U7 snRNP-specific Lsm11 protein: dual binding contacts with the 100 kDa zinc finger processing factor (ZFP100) and a ZFP100-independent function in histone RNA 3' end processing

The 3' cleavage generating non-polyadenylated animal histone mRNAs depends on the base pairing between U7 snRNA and a conserved histone pre-mRNA downstream element. This interaction is enhanced by a 100 kDa zinc finger protein (ZFP100) that forms a bridge between an RNA hairpin element upstream of the processing site and the U7 small nuclear ribonucleoprotein (snRNP). The N-terminus of Lsm11, a U7-specific Sm-like protein, was shown to be crucial for histone RNA processing and to bind ZFP100. By further analysing these two functions of Lsm11, we find that Lsm11 and ZFP100 can undergo two interactions, i.e. between the Lsm11 N-terminus and the zinc finger repeats of ZFP100, and between the N-terminus of ZFP100 and the Sm domain of Lsm11, respectively. Both interactions are not specific for the two proteins in vitro, but the second interaction is sufficient for a specific recognition of the U7 snRNP by ZFP100 in cell extracts. Furthermore, clustered point mutations in three phylogenetically conserved regions of the Lsm11 N-terminus impair or abolish histone RNA processing. As these mutations have no effect on the two interactions with ZFP100, these protein regions must play other roles in histone RNA processing, e.g. by contacting the pre-mRNA or additional processing factors.

Galilee Blooming: First Palynological and Archaeological Data from an Early Byzantine Cistern at Horvat Kur

Preliminary archaeological and palynological results are presented from an early Byzantine cistern of the village Horvat Kur in eastern Lower Galilee/Israel. The rural site was settled from the Hellenistic until the Early Arab period, its synagogue was constructed shortly after 425 AD and renovated sometimes during the 2nd half of the 6th century AD. It was abandoned probably as a consequence of the earthquake of 749 AD. The intact and properly sealed cistern contained complete or fully restorable pottery. Two cooking pots from the early 5th century AD comprised sediments which was sampled for palynological purposes. Both samples, as well as a sample from the soil beneath one of the pots and a modern surface sample from the site, revealed well preserved palynomorphs in comparably high concentration showing a great potential of the cistern as a pollen archive. The pollen content points to an open, grassy semiarid landscape with an apparent scarcity of cultivars and trees in the vicinity of the site and an abundance of herbs, especially Asteraceae, which are still commonly found in modern regional vegetation.

Oxygen Isotopic and Soluble Ionic Composition of a Shallow Firn Core, Inilchek Glacier, Central Tien Shan

Oxygen isotopic and soluble ionic measurements made on snow-pit (2 in depth) and firn-core (12.4 m depth samples recovered from the accumulation zone 5100 m) of Inilchek glacier 43degrees N, 79degrees E) provide information on recent (1992-98) climatic and environmental conditions in the central Tien Shan region of central Asia. The combined 14.4 m snow-pit/firn-core profile lies within the firn zone, arid contains only one observed melt feature (10 m temperature = - 12 degreesC), Although some post-depositional attenuation of the sub-seasonal delta(18)O record is possible, annual cycles are apparent throughout the isotope profile. We therefore use the preserved delta(18)O record to establish a depth/age scale for the core. Mean delta(18)O values for the entire core and for summer periods are consistent with delta(18)O/temperature observations, and suggest the delta(18)O record provides a means to reconstruct past changes in summer surface temperature at the site. Major-ion (Na(+), K(+), Mg(2+), Ca(2+), NH(4)(+), Cl(-), NO(3)(-), SO(4)(2-)) data from the core demonstrate the dominant influence of dust deposition on the soluble chemistry at the site, arid indicate significant interannual variability in atmospheric-dust loading during the 1900s. Anthropogenic impacts oil NH(4)(+) concentrations are observed at the site, and suggest a summer increase in atmospheric NH(4)(+) that may be related to regional agricultural (nitrogen-rich fertilizer use activities.

Organotypic slice cultures from rat brain tissue: a new approach for Naegleria fowleri CNS infection in vitro

The free-living amoeba Naegleria fowleri is the aetiological agent of primary amoebic meningoencephalitis (PAM), a disease leading to death in the vast majority of cases. In patients suffering from PAM, and in corresponding animal models, the brain undergoes a massive inflammatory response, followed by haemorrhage and severe tissue necrosis. Both, in vivo and in vitro models are currently being used to study PAM infection. However, animal models may pose ethical issues, are dependent upon availability of specific infrastructural facilities, and are time-consuming and costly. Conversely, cell cultures lack the complex organ-specific morphology found in vivo, and thus, findings obtained in vitro do not necessarily reflect the situation in vivo. The present study reports infection of organotypic slice cultures from rat brain with N. fowleri and compares the findings in this culture system with in vivo infection in a rat model of PAM, that proved complementary to that of mice. We found that brain morphology, as present in vivo, is well retained in organotypic slice cultures, and that infection time-course including tissue damage parallels the observations in vivo in the rat. Therefore, organotypic slice cultures from rat brain offer a new in vitro approach to study N. fowleri infection in the context of PAM.

Chevkinite-Group Minerals from Granulite-Facies Metamorphic Rocks and Associated Pegmatites of East Antarctica and South India

Electron microprobe data are presented for chevkinite-group minerals from granulite-facies rocks and associated pegmatities of the Napier Complex and Mawson Station charnockite in East Antarctica and from the Eastern Ghats, South India. Their compositions conform to the general formula for this group, viz. A(4)BC(2)D(2)Si(4)O(22) where, in the analysed specimens A = (rare-earth elements (REE), Ca, Y, Th), B = Fe(2+) Mg, C = (Al, Mg, Ti, Fe(2+), Fe(3+), Zr) and D = Ti and plot within the perrierite field oftlic total Fe (as FeO) (wt.%) vs. CaO (wt.%) discriminator diagram of Macdonald and Belkin (2002). In contrast to most chevkinite-group minerals, the A site shows unusual enrichment in the MREE and HREE relative to the LREE and Ca. In one sample from the Napier Complex, Y is the dominant cation among the total REE + Y in the A site, the first reported case of Y-dominance in the chevkinite group. The minerals include the most Al-rich yet reported in the chevkinite group (<= 9.15 wt.% Al(2)O(3)), sufficient to fill the C site in two samples. Conversely, the amount of Ti in these samples does not fill the D site. and, thus, some of the Al could be making up the deficiency at D, a situation not previously reported in the chevkinite group. Fe abudances are low, requiring Mg to occupy up to 45% of the B site. The chevkinite-group minerals analysed originated from three distinct parageneses: (1) pegmatites containing hornblende and orthopyroxene or garnet; (2) orthopyroxene-bearing gneiss and granulite; (3) highly aluminous paragneisses in which the associated minerals are relatively magnesian or aluminous. Chevkinite-group minerals from the first two parageneses have relatively high FeO content and low MgO and Al(2)O(3) contents; their compositions plot in the field for mafic and intermediate igneous rocks. In contrast, chevkinite-group minerals from the third paragenesis are notably more aluminous and have greater Mg/Fe ratios.

Assessment of Skill and Portability in Regional Marine Biogeochemical Models: Role of Multiple Planktonic Groups

Application of biogeochemical models to the study of marine ecosystems is pervasive, yet objective quantification of these models' performance is rare. Here, 12 lower trophic level models of varying complexity are objectively assessed in two distinct regions (equatorial Pacific and Arabian Sea). Each model was run within an identical one-dimensional physical framework. A consistent variational adjoint implementation assimilating chlorophyll-a, nitrate, export, and primary productivity was applied and the same metrics were used to assess model skill. Experiments were performed in which data were assimilated from each site individually and from both sites simultaneously. A cross-validation experiment was also conducted whereby data were assimilated from one site and the resulting optimal parameters were used to generate a simulation for the second site. When a single pelagic regime is considered, the simplest models fit the data as well as those with multiple phytoplankton functional groups. However, those with multiple phytoplankton functional groups produced lower misfits when the models are required to simulate both regimes using identical parameter values. The cross-validation experiments revealed that as long as only a few key biogeochemical parameters were optimized, the models with greater phytoplankton complexity were generally more portable. Furthermore, models with multiple zooplankton compartments did not necessarily outperform models with single zooplankton compartments, even when zooplankton biomass data are assimilated. Finally, even when different models produced similar least squares model-data misfits, they often did so via very different element flow pathways, highlighting the need for more comprehensive data sets that uniquely constrain these pathways.

Impacts of drought stress on water relations and carbon assimilation in grassland species at different altitudes

Grassland is an important ecosystem type which is not only used agriculturally, but also covers sites which cannot be used for other purposes, e.g. in very steep locations or above timberlines. Prolonged summer droughts in the mid-term future, as are predicted for Central Europe, are expected to have a major impact on such ecosystems. To address this topic, rainfall exclusion via shelters was performed on three grassland sites at different altitudes (393, 982 and 1978 m above sea level) in Switzerland. Diurnal drought treatment effects were studied at each study site on a completely sunny day towards the end of an 8–10 week shelter period. Ecophysiological parameters including gas exchange (An, gs and intrinsic WUE) and chlorophyll a fluorescence (Fv/Fm, ΦPSII and NPQ) were considered for several species. The lowland and the Alpine field site were more strongly affected by soil drought than the pre-Alpine site. At all sites, grasses showed different patterns of reductions in stomatal conductance under soil drought compared to legumes and forbs. In addition, grasses were significantly more affected by reductions in assimilation rates at all sites. Time courses of reductions in assimilation rates relative to controls differed between species at the Alpine site, as some species showed reduced assimilation rates at this site in the early morning. Thus, similar rainfall exclusion treatments can trigger different reactions in various species at different sites, which might not become obvious during mere midday measurements. Overall, results suggest strong impacts of prolonged summer drought on grassland net photosynthesis especially at the Alpine site and, within sites, for grasses

Simple Estimation of Incident HIV Infection Rates in Notification Cohorts Based on Window Periods of Algorithms for Evaluation of Line-Immunoassay Result Patterns

Background Tests for recent infections (TRIs) are important for HIV surveillance. We have shown that a patient's antibody pattern in a confirmatory line immunoassay (Inno-Lia) also yields information on time since infection. We have published algorithms which, with a certain sensitivity and specificity, distinguish between incident (< = 12 months) and older infection. In order to use these algorithms like other TRIs, i.e., based on their windows, we now determined their window periods. Methods We classified Inno-Lia results of 527 treatment-naïve patients with HIV-1 infection < = 12 months according to incidence by 25 algorithms. The time after which all infections were ruled older, i.e. the algorithm's window, was determined by linear regression of the proportion ruled incident in dependence of time since infection. Window-based incident infection rates (IIR) were determined utilizing the relationship ‘Prevalence = Incidence x Duration’ in four annual cohorts of HIV-1 notifications. Results were compared to performance-based IIR also derived from Inno-Lia results, but utilizing the relationship ‘incident = true incident + false incident’ and also to the IIR derived from the BED incidence assay. Results Window periods varied between 45.8 and 130.1 days and correlated well with the algorithms' diagnostic sensitivity (R2 = 0.962; P<0.0001). Among the 25 algorithms, the mean window-based IIR among the 748 notifications of 2005/06 was 0.457 compared to 0.453 obtained for performance-based IIR with a model not correcting for selection bias. Evaluation of BED results using a window of 153 days yielded an IIR of 0.669. Window-based IIR and performance-based IIR increased by 22.4% and respectively 30.6% in 2008, while 2009 and 2010 showed a return to baseline for both methods. Conclusions IIR estimations by window- and performance-based evaluations of Inno-Lia algorithm results were similar and can be used together to assess IIR changes between annual HIV notification cohorts.

Higher plant diversity promotes higher diversity of fungal pathogens, while it decreases pathogen infection per plant

Fungal plant pathogens are common in natural communities where they affect plant physiology, plant survival, and biomass production. Conversely, pathogen transmission and infection may be regulated by plant community characteristics such as plant species diversity and functional composition that favor pathogen diversity through increases in host diversity while simultaneously reducing pathogen infection via increased variability in host density and spatial heterogeneity. Therefore, a comprehensive understanding of multi-host multi-pathogen interactions is of high significance in the context of biodiversity-ecosystem functioning. We investigated the relationship between plant diversity and aboveground obligate parasitic fungal pathogen (''pathogens'' hereafter) diversity and infection in grasslands of a long-term, large-scale, biodiversity experiment with varying plant species (1-60 species) and plant functional group diversity (1-4 groups). To estimate pathogen infection of the plant communities, we visually assessed pathogen-group presence (i.e., rusts, powdery mildews, downy mildews, smuts, and leaf-spot diseases) and overall infection levels (combining incidence and severity of each pathogen group) in 82 experimental plots on all aboveground organs of all plant species per plot during four surveys in 2006. Pathogen diversity, assessed as the cumulative number of pathogen groups on all plant species per plot, increased log-linearly with plant species diversity. However, pathogen incidence and severity, and hence overall infection, decreased with increasing plant species diversity. In addition, co-infection of plant individuals by two or more pathogen groups was less likely with increasing plant community diversity. We conclude that plant community diversity promotes pathogen-community diversity while at the same time reducing pathogen infection levels of plant individuals.

Accuracy of the withdrawal reflex for localization of the site of cervical disk herniation in dogs: 35 cases (2004-2007)

OBJECTIVE To evaluate the accuracy of neurologic examination versus magnetic resonance imaging (MRI) in localization of cervical disk herniation and evaluate the usefulness of withdrawal reflex testing in dogs. DESIGN Retrospective case series. ANIMALS 35 client-owned dogs with a single-level cervical disk herniation as determined via MRI. PROCEDURES 1 of 2 board-certified neurologists performed a complete neurologic examination in each dog. Clinical signs of a cervical lesion included evidence of neck pain and tetraparesis. The withdrawal reflex was used for neuroanatomic localization (C1-C5 or C6-T2). Agreement between results of neurologic and MRI examinations was determined. RESULTS Agreement between neurologic and MRI diagnoses was 65.8%. In 11 dogs in which the lesion was clinically localized to the C6-T2 segment on the basis of a decreased withdrawal reflex in the forelimbs, MRI revealed an isolated C1-C5 disk lesion. In 1 dog, in which the lesion was suspected to be at the C1-C5 level, MRI revealed a C6-T2 lesion. Cranial cervical lesions were significantly associated with an incorrect neurologic diagnosis regarding site of the lesion. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that the withdrawal reflex in dogs with cervical disk herniation is not reliable for determining the affected site and that a decreased withdrawal reflex does not always indicate a lesion from C6 to T2.

Fatal contact shot to the chest caused by the gas jet from a muzzle-loading pistol discharging only black powder and no bullet: case study and experimental simulation of the wounding effect.

In modern medico-legal literature, only a small number of publications deal with fatal injuries from black powder guns. Most of them focus on the morphological features such as intense soot soiling, blast tattooing and burn effects in close-range shots or describe the wound ballistics of spherical lead bullets. Another kind of "unusual" and potentially lethal weapons are handguns destined for firing only blank cartridges such as starter and alarm pistols. The dangerousness of these guns is restricted to very close and contact range shots and results from the gas jet produced by the deflagration of the propellant. The present paper reports on a suicide committed with a muzzle-loading percussion pistol cal. 45. An unusually large stellate entrance wound was located in the precordial region, accompanied by an imprint mark from the ramrod and a faint greenish discoloration (apparently due to the formation of sulfhemoglobin). Autopsy revealed an oversized powder cavity, multiple fractures of the anterior thoracic wall as well as ruptures of the heart, the aorta, the left hepatic lobe and the diaphragm. In total, the zone of mechanical destruction had a diameter of approx. 15 cm. As there was no exit wound and no bullet lodged in the body, the injury was caused exclusively by the inrushing combustion gases of the propellant (black powder) comparable with the gas jet of a blank cartridge gun. In contact shots to ballistic gelatine using the suicide's pistol loaded with black powder but no projectile, the formation of a nearly spherical cavity could be demonstrated by means of a high-speed camera. The extent of the temporary cavity after firing with 5 g of black powder roughly corresponded to the zone of destruction found in the suicide's body.

John Garstang at Sirkeli Höyük, Cilician Plain, in 1936-1937: Old Photographs and New Evidence from the Renewed Excavations

During the winter of 1936-1937, British archaeologist John Garstang (1876-1956) excavated several trenches at the site of Sirkeli Höyük, located in the Plain of Cilicia (18 km west of modern-day Ceyhan). After a single campaign, however, he left the site and his interest shifted to site of Yumuktepe/Mersin, where he then excavated for a number of years. Apart from two very brief preliminary reports of his excavations at Sirkeli Höyük, which were published in the journal 'Annals of Archaeology and Anthropology of the University of Liverpool', not much is known about the trenches and their associated finds. Unpublished photographs kept in the Special Archives of University College London shed new light on the location and orientation of some of Garstang’s trenches at the site. Furthermore, in the 2012 campaign of the renewed Turkish-Swiss excavations at the site, a trench was found in the western part of the northern terrace that most probably was excavated by Garstang, but was not mentioned by him in his reports. This hitherto unknown trench may be related to his discovery of a lion-shaped column base made of basalt that is now kept in the collections of the Archaeological Museum of Adana.

Immunization against gonadotropin-releasing hormone in dairy cattle: Antibody titers, ovarian function, hormonal levels, and reversibility

Suppression of cyclic activity in cattle is often desired in alpine farming and for feedlot cattle not intended for breeding. A cattle-specific anti-GnRH vaccination (Bopriva, Zoetis Australia Ltd., West Ryde, Australia) is approved for use in heifers and bulls in New Zealand, Australia, Mexico, Brazil, Argentina, Turkey, and Peru. Eleven healthy, cyclic Swiss Fleckvieh cows were included in the study and vaccinated twice with Bopriva 4wk apart. Injection site, rectal body temperature, and heart and respiratory rates were recorded before and 3d following each vaccination. Blood samples were taken weekly for progesterone and estrogen analysis and to determine GnRH antibody titer. Ovaries were examined weekly, using ultrasound to count the number of follicles and identify the presence of a corpus luteum. Thirty weeks after the first vaccination, the cows were subjected to a controlled internal drug-releasing device-based Select-Synch treatment. The GnRH antibody titers increased after the second vaccination and peaked 2wk later. Estrogen levels were not influenced by vaccination, and progesterone level decreased in 7 of 11 cows up to 3wk after the second vaccination and remained low for 10 to 15wk following the second vaccination. The number of class I follicles (diameter ≤5mm) was not influenced by vaccination, whereas the number of class II follicles (diameter 6-9mm) decreased between 7 and 16wk after the first vaccination. Class III follicles (diameter >9mm) were totally absent during this period in most cows. The median period until recurrence of class III follicles was 78d from the day of the second vaccination (95% confidence interval: 60-92d). After vaccination, all cows showed swelling and pain at the injection site, and these reactions subsided within 2wk. Body temperature and heart and respiratory rates increased after the first and second vaccinations and returned to normal values within 2d of each vaccination. The cows in our study were not observed to display estrus behavior until 30wk after the first vaccination. Therefore, a Select-Synch protocol was initiated at that time. Ten cows became pregnant after the first insemination (the remaining cow was reinseminated once until confirmed pregnancy). Bopriva induced a reliable and reversible suppression of reproductive cyclicity for more than 2mo. The best practical predictor for the length of the anestrus period was the absence of class III follicles.

Glycosylation of TRPM4 and TRPM5 channels: molecular determinants and functional aspects

The transient receptor potential channel, TRPM4, and its closest homolog, TRPM5, are non-selective cation channels that are activated by an increase in intracellular calcium. They are expressed in many cell types, including neurons and myocytes. Although the electrophysiological and pharmacological properties of these two channels have been previously studied, less is known about their regulation, in particular their post-translational modifications. We, and others, have reported that wild-type (WT) TRPM4 channels expressed in HEK293 cells, migrated on SDS-PAGE gel as doublets, similar to other ion channels and membrane proteins. In the present study, we provide evidence that TRPM4 and TRPM5 are each N-linked glycosylated at a unique residue, Asn(992) and Asn(932), respectively. N-linked glycosylated TRPM4 is also found in native cardiac cells. Biochemical experiments using HEK293 cells over-expressing WT TRPM4/5 or N992Q/N932Q mutants demonstrated that the abolishment of N-linked glycosylation did not alter the number of channels at the plasma membrane. In parallel, electrophysiological experiments demonstrated a decrease in the current density of both mutant channels, as compared to their respective controls, either due to the Asn to Gln mutations themselves or abolition of glycosylation. To discriminate between these possibilities, HEK293 cells expressing TRPM4 WT were treated with tunicamycin, an inhibitor of glycosylation. In contrast to N-glycosylation signal abolishment by mutagenesis, tunicamycin treatment led to an increase in the TRPM4-mediated current. Altogether, these results demonstrate that TRPM4 and TRPM5 are both N-linked glycosylated at a unique site and also suggest that TRPM4/5 glycosylation seems not to be involved in channel trafficking, but mainly in their functional regulation.