Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein

We use time-resolved crystallography to observe the structural progression of a bacterial blue light photoreceptor throughout its photocycle. Data were collected from 10 ns to 100 ms after photoactivation of the E46Q mutant of photoactive yellow protein. Refinement of transient chromophore conformations shows that the spectroscopically distinct intermediates are formed via progressive disruption of the hydrogen bond network to the chromophore. Although structural change occurs within a few nanoseconds on and around the chromophore, it takes milliseconds for a distinct pattern of tertiary structural change to fully progress through the entire molecule, thus generating the putative signaling state. Remarkably, the coupling between the chromophore conformation and the tertiary structure of this small protein is not tight: there are leads and lags between changes in the conformation of the chromophore and the protein tertiary structure.     

Chromosome studies in southern species of Mimosa (Fabaceae,Mimosoideae) and their taxonomic and evolutionary inferences

In this work, chromosome numbers and karyotype parameters of 36 taxa of the genus Mimosa were studied, especially from the southern South America center of diversification. Results support that x = 13 is the basic chromosome number in the genus. Polyploidy is very frequent, ca. 56 % of the total of the studied species here are polyploid, confirming that polyploids are more frequent at higher latitudes. The most common ploidy levels found are 2x and 4x, but some species studied exhibit 6x and 8x. In different groups, several ploidy levels were found. Parameters of chromosome size show statistically significant differences between close species, and asymmetry index A ₂ exhibited low variation between them. It is possible to infer variations of chromosome size between diploids and tetraploids and between basal and derived taxa. The present studies confirm or reveal polyploidy in several groups of South America which are highly diversified in the southernmost area of distribution of the genus, such as sect. Batocaulon ser. Stipellares and sect. Calothamnos. Our data are discussed in a taxonomic context, making inferences about the origin of some polyploid taxa. Polyploidy could be an important phenomenon that increases the morphologic diversity and specific richness in southern South America. On basis of our data, it is possible to hypothesize hybridization between same-ploidy level or different ploidy level taxa. As already shown in the literature, our results confirm the importance of the polyploidy in the speciation of the genus.     

Changes in metabolite profiles in Norway spruce shoot tips during short-day induced winter bud development and long-day induced bud flush

The seasonal change in photoperiod is a primary environmental signal influencing tree growth. Long days (LD) sustain growth, whereas short days (SD) induce winter bud formation. In this respect, metabolomic responses have been studied to a limited extent only in conifers. Here we identified changes in metabolite profile in the conifer Norway spruce after transition to SD and following re-transfer to LDs inducing bud flush. After 1 week in SD initial changes in metabolite profile was visible but for the majority of compounds magnitudes of changes were small. However, the ascorbate content was strongly reduced and there were often temporary increases in several energy metabolism-related compounds, secondary metabolites, nucleosides, amino acids and lipids. After 8 weeks in SD substantial changes were observed; proper winter buds had high pools of ABA, antioxidants, flavonoids, terpenoids, phenylpropanoids, sugars, amino acids and lipids related to stress tolerance and hardening, and low levels of nucleosides and metabolites in energy metabolism. One week after re-transfer to LD the metabolome was generally relatively similar to under long-term SD, except e.g. increased urate and strongly decreased ABA and oxidized glutathione. Two weeks later, bud flush had occurred, and the metabolite profile resembled the situation before transfer to SD. This study thus revealed comprehensive modulation of the metabolome in Norway spruce in response to a day length shift, indicating substantially increased stress resistance under SD-induced bud set, and reversal upon bud flush in LD.     

Bladder Cancer Biomarker Discovery Using Global Metabolomic Profiling of Urine

Bladder cancer (BCa) is a common malignancy worldwide and has a high probability of recurrence after initial diagnosis and treatment. As a result, recurrent surveillance, primarily involving repeated cystoscopies, is a critical component of post diagnosis patient management. Since cystoscopy is invasive, expensive and a possible deterrent to patient compliance with regular follow-up screening, new non-invasive technologies to aid in the detection of recurrent and/or primary bladder cancer are strongly needed. In this study, mass spectrometry based metabolomics was employed to identify biochemical signatures in human urine that differentiate bladder cancer from non-cancer controls. Over 1000 distinct compounds were measured including 587 named compounds of known chemical identity. Initial biomarker identification was conducted using a 332 subject sample set of retrospective urine samples (cohort 1), which included 66 BCa positive samples. A set of 25 candidate biomarkers was selected based on statistical significance, fold difference and metabolic pathway coverage. The 25 candidate biomarkers were tested against an independent urine sample set (cohort 2) using random forest analysis, with palmitoyl sphingomyelin, lactate, adenosine and succinate providing the strongest predictive power for differentiating cohort 2 cancer from non-cancer urines. Cohort 2 metabolite profiling revealed additional metabolites, including arachidonate, that were higher in cohort 2 cancer vs. non-cancer controls, but were below quantitation limits in the cohort 1 profiling. Metabolites related to lipid metabolism may be especially interesting biomarkers. The results suggest that urine metabolites may provide a much needed non-invasive adjunct diagnostic to cystoscopy for detection of bladder cancer and recurrent disease management.     

Circadian and Ultradian Time Patterns in Human Behaviour: Part 1: Activity Monitoring of Families from Prepartum to Postpartum

Time patterns of activity-rest rhythms during and after pregnancy are increasingly recognised as important factors for the well-being and health of young families. This longitudinal study examined activity-rest patterns of couples during late pregnancy and subsequently the alterations in the periodic structure of parental and neonatal time patterns during the first four months after birth. Part I concentrates on the effects of late pregnancy and birth to the mother's rest-activity patterns and those of the father and, after birth, what time pattern the infant developed. Part II attempts to clarify how activity patterns of the entire family agree or disagree with each other and investigates how the infant synchronises with the environment that includes the process of parent-infant interaction. Activity data of, so far, seven families (father, mother and child) were continuously recorded using non-invasive Actiwatch units. Recordings of parental activity started at the beginning of the 37th week of gestation, and were continued in parallel with the infants' recordings in three series of three weeks each until four months after birth: 1st to 3rd week, 7th to 9th week and 13th to 15th week of life. In a standardised diary, record was kept of household routines, parental activities, type of feeding, initiation of sleep or waking up. Activity data of seven non-pregnant women were collected and used as a control. Irregular nocturnal activity epochs occurred frequently in pregnant women and were absent in non-pregnant women. Period lengthenings and shortenings of the circadian rhythms appeared in both parents from prepartum to postpartum. Activity at night increased from prepartum to postpartum in mothers and fathers. Three infants showed a marked circadian rhythm between day 3 and 14 after birth. All seven infants showed a predominant circadian rhythm between day 8 and 19 after birth. The onset of daytime activity of mothers and their infants corresponded well to each other. Postpartum frequency spectra of parents and child always had some ultradian components in common. Time patterns of activity-rest rhythms of couples and parents are shown to be altered during and after pregnancy and we suggest that the infants' adaptation to the environment begins during the first week that includes the process of mother-infant interaction.     

Responses of Antarctic Iridaea cordata (Rhodophyta) tetraspores exposed to ultraviolet radiation

In Antarctica ozone depletion is highest during spring, coinciding with the reproduction of many seaweed species. Propagules are the life-stage of an alga most susceptible to environmental perturbations. Therefore, fertile thalli of Iridaea cordata (Turner) Bory (Rhodophyta) were collected in the eulittoral of King George Island (Antarctica) to examine spore susceptibility to ultraviolet radiation (UVR). In the laboratory, freshly released tetraspores were exposed to photosynthetically active radiation (PAR) (400–700 nm), PAR+UV-A (320–700 nm) or PAR+UV-A+UV-B (280–700 nm). Photosynthetic efficiency was measured during 1–8 h of exposure and after 48 h of recovery. Additionally, mycosporine-like amino acids (MAAs) and DNA damage were determined. Saturating irradiance of photosynthesis of freshly released tetraspores was 57 µmol photons m⁻² s⁻¹. Exposure to increasing fluence of PAR reduced photosynthetic efficiency. UVR further decreased the photosynthetic efficiencies of the tetraspores but spores were able to recover completely after UVR exposure and 2 days post-cultivation under low PAR. DNA damage was minimal and lesions were effectively repaired under photoreactivating light. Concentrations of the MAAs shinorine and palythine were higher in tetraspores treated with UVR than in spores only exposed to PAR. Generally, the tetraspores show a good UV tolerance. This flexible response of the tetraspores of this species to changing radiation conditions enables the alga to grow along a considerable depth gradient from the sublittoral to the eulittoral where they can be exposed to enhanced UVBR under conditions of stratospheric ozone depletion.     

Effects of long-term open-air exposure to fluoride,nitrogen compounds and SO2 on visible symptoms,pollutant accumulation and ultrastructure of Scots pine and Norway spruce seedlings

 Effects of SO₂, aqueous fluoride (NaF) and a solution of nitrogen compounds (NH₄NO₃) on the visible symptoms, pollutant accumulation and ultrastructure of Scots pine (Pinus sylvestris L.) and Norway spruce [Picea abies (L.) Karst.] seedlings were studied in an open-air experiment lasting for 3 consecutive years. Visible injury symptoms were most pronounced in combination exposures and whenever F was applied. Visible symptoms correlated well with needle pollutant concentrations. Exposure to NaF increased needle F contents particularly when F was applied with SO₂ or NH₄NO₃. This suggests that a reduction in N or SO₂ emissions, in F polluted areas, could improve the condition of conifers via decreased accumulation of phytotoxic F in the needles. Norway spruce needles accumulated 2 – 10 times as much S and F as those of Scots pine. Microscopic observations showed various changes in the needle mesophyll cell ultrastructure. In both species, exposure to SO₂ increased significantly the amount of cytoplasmic vacuoles, suggesting detoxification of excess sulphate or low pH. F treatments resulted in a significant enlargement of plastoglobuli in Scots pine and a darkening of plastoglobuli in Norway spruce. All exposures enhanced the accumulation of lipid bodies. An increased portion of translucent plastoglobuli was most pronounced in N treatments. Many of the ultrastructural changes and visible symptoms appeared only as number of years exposed increased, indicating that long-term experiments are needed. Both visible symptoms and ultrastructural changes pointed to the more pronounced sensitivity of Norway spruce compared to Scots pine. Ultrastructural results mostly supported earlier qualitative observations of F, N and SO₂ effects on needle mesophyll cell ultrastructure. However, no reduction of thylakoids in SO₂ containing exposure or curling of thylakoids in F exposure could be detected in the present study. Received: 5 December 1994 / Accepted: 28 April 1995     

Domain swapping and gene shuffling identify sequences required for induction of an Avr-dependent hypersensitive response by the tomato Cf-4 and Cf-9 proteins

The tomato Cf-4 and Cf-9 genes confer resistance to infection by the biotrophic leaf mold pathogen Cladosporium. Their protein products induce a hypersensitive response (HR) upon recognition of the fungus-encoded Avr4 and Avr9 peptides. Cf-4 and Cf-9 share >91% sequence identity and are distinguished by sequences in their N-terminal domains A and B, their N-terminal leucine-rich repeats (LRRs) in domain C1, and their LRR copy number (25 and 27 LRRs, respectively). Analysis of Cf-4/Cf-9 chimeras, using several different bioassays, has identified sequences in Cf-4 and Cf-9 that are required for the Avr-dependent HR in tobacco and tomato. A 10-amino acid deletion within Cf-4 domain B relative to Cf-9 was required for full Avr4-dependent induction of an HR in most chimeras analyzed. Additional sequences required for Cf-4 function are located in LRRs 11 and 12, a region that contains only eight of the 67 amino acids that distinguish it from Cf-9. One chimera, with 25 LRRs that retained LRR 11 of Cf-4, induced an attenuated Avr4-dependent HR. The substitution of Cf-9 N-terminal LRRs 1 to 9 with the corresponding sequences from Cf-4 resulted in attenuation of the Avr9-induced HR, as did substitution of amino acid A433 in LRR 15. The amino acids L457 and K511 in Cf-9 LRRs 16 and 18 are essential for induction of the Avr9-dependent HR. Therefore, important sequence determinants of Cf-9 function are located in LRRs 10 to 18. This region contains 15 of the 67 amino acids that distinguish it from Cf-4, in addition to two extra LRRs. Our results demonstrate that sequence variation within the central LRRs of domain C1 and variation in LRR copy number in Cf-4 and Cf-9 play a major role in determining recognition specificity in these proteins.     

Quantitative Organization of GABAergic Synapses in the Molecular Layer of the Mouse Cerebellar Cortex

In the cerebellar cortex, interneurons of the molecular layer (stellate and basket cells) provide GABAergic input to Purkinje cells, as well as to each other and possibly to other interneurons. GABAergic inhibition in the molecular layer has mainly been investigated at the interneuron to Purkinje cell synapse. In this study, we used complementary subtractive strategies to quantitatively assess the ratio of GABAergic synapses on Purkinje cell dendrites versus those on interneurons. We generated a mouse model in which the GABA_A receptor α1 subunit (GABA_ARα1) was selectively removed from Purkinje cells using the Cre/loxP system. Deletion of the α1 subunit resulted in a complete loss of GABA_AR aggregates from Purkinje cells, allowing us to determine the density of GABA_AR clusters in interneurons. In a complementary approach, we determined the density of GABA synapses impinging on Purkinje cells using α-dystroglycan as a specific marker of inhibitory postsynaptic sites. Combining these inverse approaches, we found that synapses received by interneurons represent approximately 40% of all GABAergic synapses in the molecular layer. Notably, this proportion was stable during postnatal development, indicating synchronized synaptogenesis. Based on the pure quantity of GABAergic synapses onto interneurons, we propose that mutual inhibition must play an important, yet largely neglected, computational role in the cerebellar cortex.     

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