Natural Variation

Nicotinic acetylcholine receptors (nAChRs) are combinations of subunits arranged as pentamers encircling a central cation channel. At least nine ␣ and four ␤ subunits are expressed in the central and peripheral nervous systems; their presence in autonomic ganglia, the adrenal medulla, and central nervous system, with accompanying responses elicited by nicotinic agonists, point to their involvement in cardiovascular homeostasis. nAChRs formed by ␣3, ␣5, and ␤4 subunits may regulate blood pressure (BP) by mediating release of catestatin, the endogenous nicotinic antagonist fragment of chromogranin A (CHGA) and potent inhibitor of catecholamine secretion. Genes encoding these subunits (CHRNA3, CHRNA5, and CHRNB4) are clustered on human chromosome 15q24. Because variation in this cluster may alter autonomic regulation of BP, we sequenced ϳ15 kilobase pairs in 15q24 containing their coding and 5Ј-and 3Ј-untranslated regions in 80 individuals. We identified 63 variants: 25 in coding regions of CHRNA3, CHRNA5, and CHRNB4 and 48 noncoding single-nucleotide polymorphisms (SNPs). Haplotype frequencies varied across ethnic populations. We assessed the contribution of six SNPs in the putative catestatin binding region of CHRNA3 and CHRNB4 to autonomic traits. In twins, catestatin and BP were heritable. CHRNA3 SNPs and haplotypes containing K95K (G285A) associated with circulating plasma catestatin, epinephrine levels, as well as systolic BP, suggesting altered coupling of the nAChRs to BP. Studies of chromaffin cells in vitro reveal that nicotinic agonist stimulation releases catecholamines and CHGA, a process augmented by overexpression of CHRNA3 and blocked by catestatin. These cellular events suggest a homeostatic mechanism underlying the pleiotropic actions of CHRNA3 genetic variation on autonomic function observed in twins.

Human Immunodeficiency Virus-1 (HIV-1) antiviral resistance is a major cause of antiviral therapy failure and compromises future treatment options. As a consequence, resistance testing is the standard of care. Because of the high degree of HIV-1 natural variation and complex interactions, the role of resistance mutations is in many cases insufficiently understood. We applied a probabilistic model, Bayesian networks, to analyze direct influences between protein residues and exposure to treatment in clinical HIV-1 protease sequences from diverse subtypes. We can determine the specific role of many resistance mutations against the protease inhibitor nelfinavir, and determine relationships between resistance mutations and polymorphisms. We can show for example that in addition to the well-known major mutations 90M and 30N for nelfinavir resistance, 88S should not be treated as 88D but instead considered as a major mutation and explain the subtype-dependent prevalence of the 30N resistan...

This study presents a comprehensive archaeometric investigation of three jade figurines attributed to the Hongshan culture (ca. 4500-3000 BCE). Analytical methods included Raman spectroscopy, X-ray fluorescence (XRF), laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), and scanning electron microscopy with energy-dispersive spectroscopy (SEM-EDS), complemented by dynamic wet-dry observations of the patina. Mineralogical and geochemical signatures confirm Xiuyan (Liaoning) as the raw material source: tremolite-actinolite mineralogy, Raman detection of graphite inclusions, trace-element ratios (Ni/Cr, V/Cr), and extremely low, flat REE profiles. Carving traces match Hongshan technological traditions. Patina consists of Mg-O-C porous white zones and Fe-O-C reddish crusts. The reversible disappearance of reddish stains upon wetting and their reappearance upon drying is diagnostic of genuine Fe-hydroxide patina. The overall evidence confirms Neolithic authenticity (~5-6 ka) and introduces a novel validation criterion based on hydration-dependent optical response.

We studied the reproductive biology of a box-nesting population of Tree Swallows Tachycineta bicolor in southeastern Wisconsin, USA. We were interested particularly in the relationship between laying order and hatching order and the extent to which each was a predictor of nestling body mass. We found that laying order was a significant predictor of hatching order. Laying and hatching order were related to nestling mass at 4 days of age and to a lesser extent at 12 days of age. In addition, we investigated the effects of natural variation in hatching asynchrony. Hatching asynchrony was positively related to the range of nestling body masses within a brood at days 4 and 12. The probability that brood reduction occurred was also positively related to the degree of hatching asynchrony, though this effect was significant only at day 4. Our results suggest that laying order and hatching order have their greatest effects on nestling Tree Swallows early in the nestling period.

We examined cellular immunity of adult tree swallows feeding nestlings under variable weather conditions. Birds received an injection of phytohaemagglutinin (PHA), which causes a local swelling, reflecting the strength of T-cell-mediated immunocompetence. There was a negative relationship between the immune response and the number of nestlings in the brood (range 3-6 young) which suggests that parental effort suppresses the immune function. However, there was also a strong effect of ambient temperature and food abundance (aerial insects) on immune response. Parents that received the PHA injection during cold weather and at low food abundance showed a suppressed immune response compared to birds treated during more favourable conditions. They also lost more body mass during the 24 h inoculation period, and their offspring showed reduced growth. When controlling for ambient temperature and food abundance in a multivariate analysis, there was no longer any significant effect of brood size on the parents' immune response. Three of 39 pairs deserted their broods after PHA injection. All three desertions took place when the mean ambient temperature fell below 13°C. The PHA response is known to have both heritable and environmental components; our study emphasizes its condition-dependency. Previous studies of other passerine birds have shown that high levels of parental effort may have an immunosuppressive effect. Our study indicates that weather conditions may override the effects of natural variation in parental effort, and that the PHA response is particularly influenced by short-term fluctuations in energy balance.

Forest Science ProgramThe use of trade, firm, or corporation names in this publication is for the information and convenience of the reader. Such use does not constitute an official endorsement or approval by the Government of British Columbia of any product or service to the exclusion of any others that may also be suitable. Contents of this report are presented for discussion purposes only. Funding assistance does not imply endorsement of any statements or information contained herein by the Government of British Columbia. Uniform Resource Locators (urls), addresses, and contact information contained in this document are current at the time of printing unless otherwise noted.

The Candamo Cave contains an important group of paleolithic paintings which have been seriously deteriorated due to mass tourism. In this work, an analysis was carried out of different climatic parameters (CO 2 , temperature, humidity, 222 Rn) during annual cycles with the cave closed to the public and during an experimental period of controlled visits. The effect of visits on the geochemical characteristics of karstic water was also analyzed together with the cave ventilation. The natural variations in the cave air CO 2 were above 3000 ppm, the increase produced through visits was only 100-110 ppm and since the humidity is almost permanently at saturation point, the critical parameter which limits the visitor capacity becomes air temperature. The temperature changes during the annual cycle are of the order of 1 7C in the external part and less than 0.5 7C in the internal part of the cave and a maximum increase of 0.13 7C was observed during the period of the visits. The 222 Rn and CO 2 concentration minimums in the summer period (July-October) show that this is the most propitious time for visits, since the greatest ventilation is produced in the cave at this time and, therefore, the greatest capacity for recovery. The geochemistry of the water, on the other hand, indicated that this is the period of the year in which processes of wall corrosion can be most easily introduced, although this would be of limited magnitude. The visitor capacity calculated was 29 visitors/day.

Competition drives habitat segregation between adults and juveniles in many types of organisms, but little is known about this process in anemonefish that compete for host sea anemones which differ in habitat quality. We performed field and laboratory experiments to determine causes of habitat segregation in 2-band anemonefish Amphi prion bicinc tus on coral reefs in the northern Red Sea, where juvenile fish mainly occupy leathery sea ane mones Heteractis crispa, and breeding adults almost exclusively inhabit bulb-tentacle sea anemones Entac maea quadricolor. E. quadricolor were usually larger than H. crispa, and expanded more in response to fish presence. Adult fish visually concealed a larger proportion of their body surface area among the relatively thick tentacles of E. quadricolor than among the thinner tentacles of H. crispa, while juveniles were concealed equally well in both hosts. During field experiments, vacated E. quadricolor were colonized rapidly by fish, whereas H. crispa were not. In laboratory choice experiments, fish at all post-settlement life stages preferred E. quadricolor, and large individuals monopolized this host and relegated subordinates to H. crispa. We conclude that competitive exclusion drives habitat segregation among life stages of this anemonefish and that host anemone traits underlie this process. The non-preferred host H. crispa may func tion as a refuge for juvenile fish while they wait for space to become available in the preferred host E. quadricolor, where they are able to attain sexual maturity.

We aimed to identify genetic variants associated with cortical bone thickness (CBT) and bone mineral density (BMD) by performing two separate genome-wide association study (GWAS) meta-analyses for CBT in 3 cohorts comprising 5,878 European subjects and for BMD in 5 cohorts comprising 5,672 individuals. We then assessed selected single-nucleotide polymorphisms (SNPs) for osteoporotic fracture in 2,023 cases and 3,740 controls. Association with CBT and forearm BMD was tested for ,2.5 million SNPs in each cohort separately, and results were meta-analyzed using fixed effect meta-analysis. We identified a missense SNP (Thr.Ile; rs2707466) located in the WNT16 gene (7q31), associated with CBT (effect size of 20.11 standard deviations [SD] per C allele, P = 6.2610 29 ). This SNP, as well as another nonsynonymous SNP rs2908004 (Gly.Arg), also had genome-wide significant association with forearm BMD (20.14 SD per C allele, P = 2.3610 212 , and 20.16 SD per G allele, P = 1.2610 215 , respectively). Four genome-wide significant SNPs arising from BMD meta-analysis were tested for association with forearm fracture. SNP rs7776725 in FAM3C, a gene adjacent to WNT16, was associated with a genome-wide significant increased risk of forearm fracture (OR = 1.33, P = 7.3610 29 ), with genome-wide suggestive signals from the two missense variants in WNT16 (rs2908004: OR = 1.22, P = 4.9610 26 and rs2707466: OR = 1.22, P = 7.2610 26 ). We next generated a homozygous mouse with targeted disruption of Wnt16. Female Wnt16 2/2 mice had 27% (P,0.001) thinner cortical bones at the femur midshaft, and bone strength measures were reduced between 43%-61% (6.5610 213 ,P,5.9610 24 ) at both femur and tibia, compared with their wild-type littermates. Natural variation in humans and targeted disruption in mice demonstrate that WNT16 is an important determinant of CBT, BMD, bone strength, and risk of fracture.

Michigan has significant forest resources, and there is much debate about the use and protection of the forests. Managers, analysts, and the public have multiple sources for data regarding Michigan's forests, but these sources vary in how accurately they characterize forests. A close examination of three data sources shows considerable differences in accuracies of public land data sets. Forest Inventory and Analysis (FIA) plots were treated as the reference classification system, given their consistent application procedures on the ground. National forest and state forest tactical data sets and the Michigan Department of Natural Resources' remotely sensed data sets were compared with 753 FIA plots. The accuracies of the on-the-ground tactical data sets exceeded 82%, but remotely sensed data were accurate only 65% of the time. The latter may serve as a proxy for private lands that do not have tactical inventory data sets. Aggregating remotely sensed data and combining tactical and remotely sensed data would improve overall accuracy across landscapes with both public and private lands.

The origin of Pikrolimni water was investigated in this study, using stable isotopes, to confirm Pliny's description that "chalastraion nitron" was produced in the basin of Lake Pikrolimni (Northern Greece). Lake Pikrolimni is located in the basin of Kilkis plain, northern Greece, formed in a shallow depression. Lake Pikrolimni is not fed by any major river, and the hydrography of the area shows that no perennial streams enter the lake directly. In the past, the major source of water to the lake was ground water. Today the dominant inflow to Lake Pikrolimni is meteoric water. The meteoric origin of the water is one of the necessary geochemical conditions that are indispensable and responsible for the formation of carbonatebicarbonate sodium (Natron, Trona) minerals. Pikrolimni brines lie on an evaporation trend given by dD ¼ 4.74& and d 18 O ¼ À13.38&. Both isotopic values (d 18 O and dD) increase with salinity, which in turn varies considerably with flooding and evaporation. In dry seasons, part of the lake is desiccated and the margins are locally covered by salts, including Na-carbonate-bicarbonate minerals, Na-sulfate and Nachloride minerals. These minerals are submitted to repeated wetting and drying cycles under alkaline and strong evaporating conditions. This salt dissolution is reflected in Cl/Br ratios of Pikrolimni water.

The present communication is a study on the impact of bottom trawling on the sediment characteristics along Veraval coast, which is the largest trawler port of India. Experimental bottom trawling was conducted from MFV Sagarkripa at five transects of water depths 15-20 m, 21-25 m, 26-30 m, 31-35 m and 36-40 m in commercial trawling grounds. Trawling was conducted for 12 months in a span of 15 months (September 2005-November 2006) excluding the trawl ban period (June to August). The sediment texture was analysed by pipette analysis and organic matter by wet oxidation method. The variations in organic matter and sediment texture were prominent between the stations selected at different depths. The sedimentary organic matter exhibited variations with different water depths and seasons. The organic matter content decreased with depth. Experimental trawling considerably reduced the

Tidal flooding is widely believed to be an important determinant of marsh plant distributions but has rarely been tested in the field. In New England the marsh elder Ivafrutescens often dominates the terrestrial border of salt marshes and we examined its flood tolerance and distribution patterns. Marsh elders only occur at elevations where their roots are not subject to prolonged water table flooding. Consequently they are found on the terrestrial border of marshes and at lower elevations associated with drainage ditches and locally elevated surfaces. Marsh elders transplanted to elevations lower than they normally occur died within a year with or without neighbors and greenhouse tests revealed that L frutescens is much less tolerant of flooded soil conditions than plants found at lower marsh elevations. We also manipulated the water table level of field plots and found that increasing or decreasing water table drainage led to enhanced and diminished L frutescens performance, respectively. Our results demonstrate the importance of water table dynamics in generating spatial patterns in marsh plant communities and provide further evidence that supports the hypothesis that the seaward distributional limits of marsh plant populations are generally dictated by physical processes.

We tested the adaptive significance of flowering synchrony by means of a quantitative analysis of selection and by flowering induction experiments with the deciduous shrub Erythroxylum havanense. Temporal schedules of flower and fruit production were determined for a local population (in three sites) in a Mexican seasonal forest for 2 years (1987)(1988). The consequences of natural variation in flowering time (flowering initiation day) on maternal reproductive success (fecundity) were evaluated. We observed high levels of inter-and intraindividual flowering synchrony in 1987, but not in 1988 and this contrast was related to differences in rainfall patterns between the two years. A significant proportion (15.4%) of the phenotypic variation in flowering initiation day was accounted for by environmental variance. The expression of phenotypic variance of flowering time and, consequently, the opportunity for selection to act, are controlled by annual variation in rainfall. Despite the between-year difference in flowering synchrony, we detected a relatively intense directional selection on flowering initiation day in both years, but selection coefficients were of opposite sign (standardized directional gradients were -0.326 and 0.333 for 1987 and 1988, respectively). For both years there was a significant relationship between individual relative fitness and the number of neighbouring flowering plants in a given day, suggesting positive frequency-dependent selection.

Water enrichment has become a national problem that needs to be resolved. This study examined the ability of water fleas Daphnia magna to grow and to control phytoplankton populations in the waters from eutrophic ponds Situ Cikaret and Situ Gunung Putri in Bogor Regency, West Java. Water samples from these water bodies were used to grow the daphnid populations in the styrofoam aquariums without artificial feeding with an initial density of 3.3 individuals/L. The experiment was carried out with three replications. Daphnid population was counted every 4–5 days to observe its growth and development. The chlorophyll content that reflects the phytoplankton biomass at the beginning of the study in the water of Situ Cikaret and Situ Gunung Putri were 52 and 22 μg/L, respectively. The water from fertile ponds allowed the development of phytoplankton populations and be utilized by daphnids to support their growth and reproduction. The results indicated that daphnids showed a preference for s...

The resistance gene Pi-ta protects rice crops against the fungal pathogen Magnaporthe grisea expressing the avirulence gene AVR-Pita in a gene-for-gene manner. Pi-ta, originally introgressed into japonica rice from indica origin, was previously isolated by positional cloning. In this study, we report the nucleotide sequence of a 5,113-base pair region containing a japonica susceptibility pi-ta allele, which has overall 99.6% nucleotide identity to the indica Pi-ta allele conferring resistance. The intron region shows the levels of sequence diversity that typically differentiate genes from indica and japonica rices, but the other gene regions show less diversity. Sequences of the Pi-ta allele from resistant cultivars Katy and Drew from the southern United States are identical to the resistance Pi-ta sequence. Sequences from susceptible cultivars El Paso 144 and Cica 9 from Latin America define a third susceptibility haplotype. This brings the total number of Pi-ta haplotypes identifi...

A continuous, natural-gradient field injection experiment, involving 18 xenobiotic compounds and bromide as tracers, was performed in the anaerobic region of a leachate plume downgradient from the Grindsted Landfill, Denmark. The injection lasted for 195 days, and within this period a continuous cloud was established. Over a period of 924 days the cloud movement was monitored in approximately 70 discrete sampling points in the central part of the cloud, and the spatial distribution was described by seven cloud snapshots involving 400-700 sampling points. The bromide cloud movement closely followed the varying flow direction predicted by the water table measurements. Moment analysis showed decreasing tracer flow velocities and reduced capture of bromide mass with time, which may be explained by varying flow conditions (direction, hydraulic gradient) and the heterogeneous geological conditions in the sandy aquifer. Naphthalene, having the highest log Kow value, was the most retarded compound, with a retardation of less than 10%. Therefore sorption was not considered to be a significant attenuation process for any of the compounds studied. Transformation under iron-reducing conditions was observed for toluene, o-xylene, TeCM, 1,1,1-TCA, PCE, and TCE, while transformation of benzene and napthalene was not detected in the aquifer within the time frame of this study. First-order transformation rates were in the range of 0.028-0.039 d -• and 0.0014-0.0028 d -• for the aromatic compounds toluene and o-xylene, respectively. The rates for the chlorinated aliphatic compounds, tetrachloromethane, 1,1,1trichloroethane, tetrachloroethylene, and trichloroethylene, were >0.7 d -•, 0.0044-0.0054 d -•, 0.0012-0.0038 d -•, and 0.0003-0.001 d -•, respectively. Long lag periods and slow transformation rates were observed for some of the compounds, suggesting that lack of transformation reported in the literature may be attributable to short experimental periods in those studies.

A continuous, natural‐gradient field injection experiment, involving 18 xenobiotic compounds and bromide as tracers, was performed in the anaerobic region of a leachate plume downgradient from the Grindsted Landfill, Denmark. The injection lasted for 195 days, and within this period a continuous cloud was established. Over a period of 924 days the cloud movement was monitored in approximately 70 discrete sampling points in the central part of the cloud, and the spatial distribution was described by seven cloud snapshots involving 400–700 sampling points. The bromide cloud movement closely followed the varying flow direction predicted by the water table measurements. Moment analysis showed decreasing tracer flow velocities and reduced capture of bromide mass with time, which may be explained by varying flow conditions (direction, hydraulic gradient) and the heterogeneous geological conditions in the sandy aquifer. Naphthalene, having the highest log Kow value, was the most retarded c...

Catchment management agencies (CMAs) have no tested precedent in South Africa and will have to evolve in complex and changing business, social and natural environments as they strive to ensure that equity and social justice are achieved within ecological limits. Traditionally, very different styles of management have been used for resource exploitation and resource protection and this will present a serious dilemma for CMAs. As the human population has grown and natural resources have declined, there has been increased effort to control nature in order to harvest its products and reduce its threats. Initially such "command-and-control" management has been successful as agencies prosper on short-term gains. However, when natural variation is reduced the ecosystem loses its resilience and ability to "bounce back" from disturbances. The first lesson we can learn is that the longer term consequence of command-and-control management is always either a reduction or cessation of resource supply. The second lesson comes from adaptive resource management (ARM). ARM acknowledges that, because nature is in a continual state of flux and our understanding of ecosystem functioning is poor, a fundamental problem for decision makers is that they must deal with uncertainty from an imperfect knowledge base. A learning-by-doing approach becomes a prerequisite for effective management. Unfortunately, there has been a tendency to superimpose adaptive management on bureaucratic institutional structures. Such flouting of the fundamental management axiom "form must follow function", has thwarted many attempts at adaptive management. This provides our third lesson. Recognition that authoritarian, command-and-control, bureaucracies respond too slowly to survive in changing environments has led managers in government, industry and businesses to create "learning institutions" which combine adaptive operations and generative leadership (lesson four). Effective knowledge management is seen as a critical success factor in turning command-andcontrol management into adaptive, learn-by-doing management (lesson five). CMAs which recognise the dangers of excessive command and control, the need to integrate stakeholder values and activities, and the potential of an adaptive and generative management approach, will need to structure their activities carefully. At present there is much focus on the structure of CMAs and much less on how they should function. Form is preceding function in many instances. When function is discussed it centres on how regulatory mechanisms and permit systems will keep resource use under control. The concern is seldom with how the ecosystem will be managed. This sort of thinking could lead to a classic command-and-control management approach if not tempered with a more adaptive process. Strategic adaptive management (SAM) is a local derivative of ARM designed to generate consensus management which is inclusive, strategic, adaptive and creative. SAM is a process in which effective knowledge management is central to building a partnership between science, management and society to achieve a common vision. It has considerable potential for application to CMAs.

Frenelopsis is a frequently found genus of the Cretaceous floras adapted to dry, saline and in general to environmental conditions marked by severe water stress . Stable isotope analysis of fossil organic materials can be used to infer palaeoenvironmental variables helpful to reconstruct plant paleohabitats . In this study stable isotope analysis of organic fossil remains (FR) and humic fractions (FA, HA and humin) of Frenelopsis oligiostomata are studied in bulk (C, H, O, N IRMS) and in specific compounds released by pyrolysis (C, H, Py-CSIA). Well preserved F. oligiostomata fossils were handpicked from a limestone included in compacted marls from Upper Cretaceous (Senonian c. 72 Mya) in Guadalix de la Sierra (Madrid, Spain) . The fossils were decarbonated with 6M HCl. Humic substances were extracted from finely ground fossil remains (FR) by successive treatments with 0.1M Na4P2O7 + NaOH . The extract was acidified resulting into insoluble HA and soluble FA fractions. The HA and FA were purified as in [5] and [6] respectively. Bulk stable isotopic analysis (δ13C, δD, δ18O, δ15N IRMS) was done in an elemental micro-analyser coupled to a continuous flow Delta V Advantage isotope ratio mass spectrometer (IRMS). Pyrolysis compound specific isotopic analysis Py-CSIA (δ13C, δD): was done by coupling a double-shot pyrolyzer to a chromatograph connected to an IRMS. Structural features of specific peaks were inferred by comparing/matching mass spectra from conventional Py-GC/MS (data not shown) with Py-GC/IRMS chromatograms obtained using the same chromatographic conditions. Bulk C isotopic signature found for FR (-20.5±0.02 was in accordance with previous studies [2, 7-9]. This heavy isotopic δ13C signature indicates a depleted stomatal conductance and paleoenvironmental growth conditions of water and salt stress. This is in line with the morphological and depositional characteristics confirming that F. oligostomata was adapted to highly xeric and saline habitats being a component of salt-marsh vegetation. The values obtained for δD (-101.9±2.2 , δ15N (10.7±0.2 and δ18O (20.9±0.39 lay within those previously reported for fossil floras [10] growing in warm environment and probably with very high evaporation rates. δ13C Py-CSIA was recorded for biogenic compound; polysaccharides, lipid series, lignin and degraded lignin compounds (alkyl benzenes and alkyl phenols) and for a S containing compounds probably with a diagenetic origin. In general δ13C Py-CSIA values were more depleted that the bulk ones and can be considered a better approach to the real plant δ13C value (c. -22 . Considering that plant-air C fractionation in degraded lignin compounds for a C4 photosystem plant is c. ∆13C≈ 20.0 [11] and a an extra fractionation (∆13C≈ -3.0 due to the plant depleted stomatal conductance growing in extreme warm, saline and dry conditions, we estimate atmospheric δ13C value in the area during the Upper Cretaceous in c. δ13C = -5.3±0.2 Ṫhis indicates that our F.oligostomata probably grew on a 13C enriched atmosphere, more enriched than preindustrial one (δ13C ≈ -6.5 [12]).T hiscouldbecausedbyacombinationof reasonsi.e. emissionsof heavy13Cisotopetotheatmospherebyanincreaseino V aluesf orδD CSIA of lipid compounds such as n-alkanes with C chain lengths, C23-C31 are believed to derive exclusively from leaf waxes of higher plants. Plant δD carries isotope information of environmental water that is particularly preserved during the geological record in n-alkyl structures, whereas other structures i.e. isoprenoids, are most prone to hydrogen exchange . We were able to measure δD for long chain alkane/alkene series in the range C24-C29 (δD = -1 24.44±5.2 . This was taken as a proxy to infer the original H isotopic signal of water in the area in the Upper Cretaceous. proposed that δDpalaeowarter= δDC24-C29 n-alkanes + 100 giving a value for plaeowater δD = -24.44±5.2 Ṫhis indicates that 75 Mya our plant probably uptake deuterium enriched rain water that again points to warm growing environmental conditions.

We observe in 6 key sectors of East and West Antarctica continental margin a change in the geometry of the sedimentary deposits which is characterized by: margin-wide erosion and subsequent progradation on the continental shelf; downlap on the continental slope; major mass wasting deposits on the continental rise. The change occurs in the late Neogene in all sectors, though some natural variation exists, and the stratigraphic position is not obvious for every margin. The change is apparently synchronous and dated about 3 Ma in Antarctic Peninsula and Prydz Bay margins and broadly concomitant in the others sectors. This suggests a common driving force, which we suggest to be the transition of the Antarctic ice sheet regime from polythermal to present polar cold, dry-based conditions.

We observe in 6 key sectors of East and West Antarctica continental margin a change in the geometry of the sedimentary deposits which is characterized by: margin-wide erosion and subsequent progradation on the continental shelf; downlap on the continental slope; major mass wasting deposits on the continental rise. The change occurs in the late Neogene in all sectors, though some natural variation exists, and the stratigraphic position is not obvious for every margin. The change is apparently synchronous and dated about 3 Ma in Antarctic Peninsula and Prydz Bay margins and broadly concomitant in the others sectors. This suggests a common driving force, which we suggest to be the transition of the Antarctic ice sheet regime from polythermal to present polar cold, dry-based conditions.

The problem of the world greatest lake, the Caspian Sea, level changes attracts the increased attention due to its environmental consequences and unique natural characteristics. Despite the huge number of studies aimed to explain the reasons of the sea level variations the underlying mechanism has not yet been clarified. The important question is to what extent the CSL variability is linked to changes in the global climate system and to what extent it can be explained by internal natural variations in the Caspian regional hydrological system. In this study an evidence of a link between the El Niño/Southern Oscillation phenomenon and changes of the Caspian Sea level is presented. This link was also found to be dominating in numerical experiments with the ECHAM4 atmospheric general circulation model on the 20th century climate.

Elucidating genetic and environmental contributions to dispersal is important to advance our understanding of how such factors influence the distribution of species and communities. I advanced this understanding by examining whether foraging-related search behaviour might provide a basis for differences in dispersal. First, I investigated strains of Drosophila melanogaster that are naturally polymorphic in larval foraging behaviour due to allelic variation at the foraging (for) locus (rovers; for R and sitters; for s ). Laboratory and field experiments demonstrated that rovers and sitters differ in adult dispersal with rovers dispersing more frequently and longer distances than sitters. My experiments further demonstrated that for was the causal agent underlying these differences. Second, I investigated how rovers (more dispersive) and sitters (less dispersive) interacted with habitat structure. I found that both interpatch distance and the distribution of food patches play key roles in habitat connectivity. Critical distances were determined where dispersal in the landscape was reduced to zero. Further, when food was constant rovers and sitters adopted similar dispersal strategies in patchy landscapes, but when food increased with the number of patches rovers and sitters adopted different strategies. This suggests that changes in habitat connectivity may differentially influence populations with multiple dispersal strategies. Lastly, I examined how dispersal responded to changes in climate. In a mark-recapture experiment I used dynamic models to estimate dispersal for rovers, sitters and an outbred population of flies. I found that while temperature elicited a similar response in rovers and sitters, the response differed from the outbred strain. There was a strong general response to wind direction and dispersal increased with wind velocity. This suggests that response to temperature and wind might minimize known differences in dispersal propensity and iii that temperature and wind may play key roles in the distribution of fly populations. My findings are relevant to the study of the spread of invasive species, particularly in taxa where for might contribute to dispersal. More broadly, my findings have implications for understanding how genes and the environment interact to produce dispersal at the population-level and ultimately the distribution of species and communities. iv Statement of Co-authorship I am the primary author of this thesis; however, several researchers were involved in the production of this thesis, and their contributions to the relevant chapters, are outlined below.

La regionalización de la precipitación es una herramienta fundamental para comprender los fenómenos hidrológicos, particularmente en el contexto de las fases del fenómeno El Niño-Oscilación del Sur (ENOS) (El Niño, La Niña y neutral), y su climatología en Guatemala. Este estudio introduce un marco novedoso que define límites regionales previamente difusos, revelando la naturaleza dinámica de los patrones de precipitación en el país. Los resultados demuestran cómo los límites regionales se desplazan en respuesta a las fases de ENOS, así como en condiciones de climatología y neutral. Estos hallazgos destacan la importancia de considerar la regionalización dinámica para analizar con precisión los impactos climáticos y la variabilidad de la precipitación, proporcionando una base para estrategias más efectivas de adaptación climática.

The success of antihypertensive drugs may be improved by better prediction of their efficacy in individual patients. The objective of our study was to determine whether genetic variation predicts the individual systolic blood pressure (SBP) response to antihypertensive drugs and to assess to what extent the individual treatment response could be explained by the combined effects of known demographic, environmental, and genetic factors. A population-based, crossover, open-label randomized treatment study stratified for ethnicity in 102 mildly hypertensive patients aged 35-60 years in an outpatient hypertension clinic (the ROTATE study). Patients underwent five successive 6-week treatment episodes of single-drug treatment in a randomized order with representatives of the major antihypertensive drug classes. The primary outcome measure was the DeltaSBP after 6-week drug therapy. Participants (n = 97) completed 407 treatment episodes. The estimated unpredictable natural variation of SBP...

Aim: Fowl adenovirus (FAdV) is responsible for causing several diseases such as Inclusion Body Hepatitis, Hydropericardium syndrome, Quail bronchitis in fowl ubiquitously. Adenoviruses are medium-sized (90-100 nm), non-enveloped isohedral ds DNA viruses. This study was performed in the purpose of identifying and then analyzing the putative promoter motifs through in silico approaches in the genome of five FAdV species. Method: Genome sequence of the FAdV species were collected from NCBI and comparisons were done among these genomes. Then putative promoter sites of all species were detected by using Proscan program. Result: The identified different types of promoter motifs from in silico investigation were confirmed and verified with the known experimental data. About 83, 37, 68, 64 and 52 types of promoter sequences were found in FAdV A, FAdV C, FAdV D, FAdV E and FAdV 5, respectively. From the investigation, about 13 types of promoters were found common in all serotypes of Fowl ade...

Telomere length-variation in deletion strains of Saccharomyces cerevisiae was used to identify genes and pathways that regulate telomere length. We found 72 genes that when deleted confer short telomeres, and 80 genes that confer long telomeres relative to those of wild-type yeast. Among identified genes, 88 have not been previously implicated in telomere length control. Genes that regulate telomere length span a variety of functions that can be broadly separated into telomerase-dependent and telomerase-independent pathways. We also found 39 genes that have an important role in telomere maintenance or cell proliferation in the absence of telomerase, including genes that participate in deoxyribonucleotide biosynthesis, sister chromatid cohesion, and vacuolar protein sorting. Given the large number of loci identified, we investigated telomere lengths in 13 wild yeast strains and found substantial natural variation in telomere length among the isolates. Furthermore, we crossed a wild isolate to a laboratory strain and analyzed telomere length in 122 progeny. Genome-wide linkage analysis among these segregants revealed two loci that account for 30%-35% of telomere length-variation between the strains. These findings support a general model of telomere lengthvariation in outbred populations that results from polymorphisms at a large number of loci. Furthermore, our results laid the foundation for studying genetic determinants of telomere length-variation and their roles in human disease.

Urban areas in tropical regions are expanding rapidly, with significant potential to affect local ecosystem dynamics. In particular, nitrogen (N) availability may increase in urban-proximate forests because of atmospheric N deposition. Unlike temperate forests, many tropical forests on highly weathered soils have high background N availability, so plant growth is unlikely to respond to increased N inputs. However, microbial activity and decomposition of carbon-rich plant tissue can respond positively to added N in these forests, as has been observed in a growing number of fertilization studies. The relevance of these controlled studies to landscape-scale dynamics in urban-proximate moist tropical forests requires further investigation. I used ten forest stands in three watersheds along an urban-remote gradient in Puerto Rico to test the hypotheses that urban activity has a positive effect on soil N availability, and that decomposition enzyme activities vary with soil N. I found that mineral N, total dissolved N (TDN), and ammonium:nitrate (NH 4 þ :NO 3 À ) ratios varied by nearly one order of magnitude across the urban-remote gradient, and variability among urban sites was high. On average, urban forests had higher soil NO 3 À , lower NH 4 þ , and lower C:N values than remote forests, suggesting high nitrification rates and/or external inputs of NO 3 À to the urban forests, and enrichment in N relative to C. Total mineral N and total dissolved N were positively correlated with the activities of enzymes that acquire carbon (C) and phosphorus (P) from organic matter. Across this gradient soil N levels were stronger predictors of enzyme activities than soil C or pH, which drive enzyme activities globally. The ratio of NH 4 þ :NO 3 À was the strongest predictor of oxidative enzyme activities. Compared to global averages, ratios of C:N:P enzyme activities across these tropical forests indicated lower relative N-acquisition and higher relative P-acquisition, with N-acquisition lowest in the urban watershed, and P-acquisition highest in the upper-elevation remote watershed. These results suggest a strong urban effect on forest soil N levels, and show a link between changes in N availability and microbial processing of soil organic matter.

Under agricultural conditions where soil moisture is adequate, low nitrogen (N) availability is usually the main soil factor limiting the growth and yield of temperate cereals. As the response to additional N is generally substantial, the strategic application of fertilizer N is an important management tool used to increase yields. Nitrogen availability can affect photosynthetic rate per unit leaf area but often the main reason for the large effect of additional N on crop growth is that it increases leaf area per plant and consequently increases leaf area index (leaf area per unit land area): this results in increased crop photosynthesis. This paper reviews recent work on the influence of N on leaf growth of temperate cereals from seed germination through to maturity. New data are presented in order to provide greater understanding of the mechanism of the nitrate effects on 1) mobilization of seed reserves; 2) partitioning of dry matter to leaf, stem and root and 3) expansion of leaves. The effects of additional Non leaf and plant growth are discussed in relation to crop growth in terms of canopy development and grain yield. Areas where further research is required are highlighted.

The Serchio Valley is one of the regions of highest seismic risk in Tuscany, Italy. As a part of a seismic prevention/prediction pilot project funded by Regional Government of Tuscany, the Pieve Fosciana spring, a perennial thermo-mineral spring emerging in correspondence with some of the most important neo-tectonic structures of the Serchio Valley, was monitored for possible geochemical precursors of earthquakes. The investigation protocol considered the coupled use of chemical analyses on water aliquots sampled during discrete surveys, and of continuous signals for selected physical-chemical parameters acquired via an automatic station equipped with a suite of parameter-specific sensors. By combining these data, the geochemical background of the system was defined, and an integrated hydrogeological and geochemical model of the hydrothermal aquifer feeding the spring was elaborated.

Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified unique variants within the heading date QTLs. Analyses of the RNA-Seq result under both short-day (SD) and long-day (LD) conditions revealed that many differentially expressed genes (DEGs) colocalized with the flowering QTLs, and some DEGs such as Hd1, OsMADS56, Hd3a, and RFT1 had unique variants in PSRR-1. Ehd1, Hd1, OsMADS15, and OsMADS5...

There is growing evidence that for a comprehensive insight into the function of plant genes, it is crucial to assess their functionalities under a wide range of conditions. In this study, we examined the role of LESION SIMULATING DISEASE1 (LSD1), ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1), and PHYTOALEXIN DEFICIENT4 (PAD4) in the regulation of photosynthesis, water use efficiency, reactive oxygen species/hormonal homeostasis, and seed yield in Arabidopsis (Arabidopsis thaliana) grown in the laboratory and in the field. We demonstrate that the LSD1 null mutant (lsd1), which is known to exhibit a runaway cell death in nonpermissive conditions, proves to be more tolerant to combined drought and high-light stress than the wild type. Moreover, depending on growing conditions, it shows variations in water use efficiency, salicylic acid and hydrogen peroxide concentrations, photosystem II maximum efficiency, and transcription profiles. However, despite these changes, lsd1 demonstrates similar...

For millennia farmers have continually improved their crop management and production practices through their observations and experience. More recently modern science and research methods based on controlled experiments became the most visible instrument of technological change in agriculture, nevertheless farmers continued to develop and implement new technologies based on their own observations made under commercial conditions. Modern information technology and social organization of producers make it possible to use operational research, which is based on the observation and analysis of operations so as to improve them, to manage crops better. The article describes two cases, coffee and sugarcane, in which observation of the results obtained by farmers, with the natural variation in the environment and the distinct management practices they apply can be used to determine site specific crop management practices. The basis of the methodology is to (a) obtain data from a series of cropping events that characterizes the conditions under which each crop is grown, how it is managed and how it performs under commercial conditions (data capture), (b) to manage and analyze the data in centralized databases (data management and analysis) and (c) make the information derived from the data analysis available to growers so that they can use it to make better informed decisions (interpretation). All aspects of the methodology depend on the social organization of the growers and the supply chain of which they form a part, and hence social organization is an integral part of the methodology. The processes of characterization of the growing conditions, including both environmental and management parameters, the establishment of databases, the data analysis and interpretation, and mechanisms of interacting with producers are described with emphasis on the importance of social organization and farmers' groups. Examples are given of how this approach can be used to better understand the crop response to variation in the environment and management, and how this can be used by farmers to improve productivity and quality in two contrasting crops. The paper demonstrates that operational research can be used to evaluate farmers' experiences and to share that knowledge amongst them so as to improve their production practices in the context of their particular environment. It is suggested that the operation research approach is particularly effective in heterogeneous landscapes with perennial crops that have not been the subject of intense research. Furthermore operational research is effective in determining the crop response to variables that are not readily studied in small plots and in determining optimal combinations of multiple variables. Producers believe in the results obtained as there are none of the problems of scaling up from experimental plots to commercial conditions. It is proposed that the approaches described can readily be applied to other crop species.

Current climate change projections anticipate that global warming trends will lead to changes in the distribution and intensity of precipitation at a global level. However, few studies have corroborated these model-based results using historical precipitation records at a regional level, especially in our study region, California. In our analyses of 14 long-term precipitation records representing multiple climates throughout the state, we find northern and central regions increasing in precipitation while southern regions are drying. Winter precipitation is increasing in all regions, while other seasons show mixed results. Rain intensity has not changed since the 1920s. While Sacramento shows over 3 more days of rain per year, Los Angeles has almost 4 less days per year in the last century. Both the El Niño-Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO) greatly influence the California precipitation record. The climate change signal in the precipitation records remains unclear as annual variability overwhelms the precipitation trends.

The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by the central, lowrecombination domain is highly correlated between species. However, the C. briggsae intra-species comparison reveals striking variation in the distribution of recombination between domains. Hybrid lines made with the more divergent pair of strains also exhibit pervasive marker transmission ratio distortion, evidence of selection acting on hybrid genotypes. The strongest effect, on chromosome III, is explained by a developmental delay phenotype exhibited by some hybrid F2 animals. In addition, on chromosomes IV and V, cross direction-specific biases towards one parental genotype suggest the existence of cytonuclear epistatic interactions. These interactions are discussed in relation to surprising mitochondrial genome polymorphism in C. briggsae, evidence that the two strains diverged in allopatry, the potential for local adaptation, and the evolution of Dobzhansky-Muller incompatibilities. The genetic and genomic resources resulting from this work will support future efforts to understand inter-strain divergence as well as facilitate studies of gene function, natural variation, and the evolution of recombination in Caenorhabditis nematodes.

Interpretation of Human Immunodeficiency Virus 1 (HIV-1) genotypic drug resistance is still a major challenge in the follow-up of antiviral therapy in infected patients. Because of the high degree of HIV-1 natural variation, complex interactions and stochastic behaviour of evolution, the role of resistance mutations is in many cases not well understood. Using Bayesian network learning of HIV-1 sequence data from diverse subtypes (A, B, C, F and G), we could determine the specific role of many resistance mutations against the protease inhibitors (PIs) nelfinavir (NFV), indinavir (IDV), and saquinavir (SQV). Such networks visualize relationships between treatment, selection of resistance mutations and presence of polymorphisms in a graphical way. The analysis identified 30N, 88S, and 90M for nelfinavir, 90M for saquinavir, and 82A/T and 46I/L for indinavir as most probable major resistance mutations. Moreover we found striking similarities for the role of many mutations against all of these drugs. For example, for all three inhibitors, we found that the novel mutation 89I was minor and associated with mutations at positions 90 and 71. Bayesian network learning provides an autonomous method to gain insight in the role of resistance mutations and the influence of HIV-1 natural variation.

Theory suggests that variation in resource supply should propagate up trophic webs influencing plant–herbivore interactions and abundances. Community regulation models have been tested in several ecosystems, but benthic marine ecologists have largely overlooked bottom‐up factors except at the largest spatial scales. We used naturally occurring variation in nutrient supply associated with upwelling intensity (over 10s of kilometre) to test community regulation models. Higher upwelling intensity was strongly associated with increased abundance of late‐successional, corticated algae, which in turn had apparent negative effects on ephemeral algae. Corticated algae were resistant to extant levels of herbivory. As a result, corticated algae were more abundant at sites of high upwelling intensity, while ephemeral algae were more abundant at sites of low upwelling intensity. We speculate that human removal of large grazers that can feed on corticated algae may interact with natural variatio...

The long-term success of restored populations may be jeopardized by the collection locality of transplants if they are ill matched to their new environment. The home-site advantage hypothesis predicts that the relative success of introduced populations will decrease as their genetic and environmental distance to the local native population increases. We evaluated this hypothesis for a geographically variable shrub, Lotus scoparius , in southern Californian coastal sage scrub by planting two common-garden experiments with seedlings from 12 source populations. The common-garden sites differed in environment and were each home to different source populations of the two taxonomic varieties, L. s. var. scoparius or L. s . var. brevialatus . We used allozyme data from each source population to calculate genetic distances between populations, and a combination of climatic data and soil traits to calculate environmental distances. At the more mesic, coastal common garden, cumulative fitness of transplants (survival ϫ flower production) was inversely related to genetic distance between source and resident populations. At the more xeric, inland common garden, cumulative fitness (survival ϫ size) decreased significantly with both genetic and environmental distance after one taxonomic variety was excluded from analyses. Geographic distance was only weakly correlated with genetic distance and had little value in predicting cumulative fitness of transplants. Our data support the home-site advantage hypothesis and the idea that mis-matching source populations of these genetically differentiated seed sources may result in lowered success of restored or constructed populations. The genetic and environmental similarities of source populations should be considered when source materials are chosen for transplantation. Resumen: El éxito a largo plazo de poblaciones restauradas puede ser expuesto a riesgos por la localización de la colecta de transplantes si estos no corresponden adecuadamente a su nuevo ambiente. La hipótesis sobre las ventajas de la ubicación del hogar predice que el éxito relativo de poblaciones introducidas decrecerá al incrementarse su distancia genética y ambiental de la población nativa local. Evaluamos esta hipótesis para un arbusto geográficamente variable, Lotus scoparius , en el matorral de salvia costero del sur de California, sembrado en dos experimentos en jardines comunes con plántulas de 12 poblaciones fuente. Los sitios de jardines comunes difirieron en ambientes y cada uno fue hogar de una de las diferentes poblaciones fuente de las dos variedades taxonómicas, L. s. var. scoparius , o L. s . var. brevialatus . Utilizamos datos de alozimas de cada población fuente para calcular las distancias genéticas entre poblaciones, y una combinación de datos climáticos y datos de características del suelo para calcular las distancias ambientales. En el jardín común costero más mésico, la adaptabilidad acumulativa de transplantes (sobrevivencia ϫ producción de flores) estuvo inversamente relacionada con la distancia genética entre las poblaciones fuente y residente. En el jardín común tierra adentro, más xérico la adaptabilidad acumulativa (sobrevivencia ϫ tamaño) disminuyó significativamente tanto con la distancia, tanto genética como ambiental, después de excluir una variedad taxonómica del análisis. La distancia geográfica estuvo solo débilmente correlacionada con la distancia genética y tuvo muy poco valor en la predicción de la adaptabilidad acumulativa de los transplantes.

Tobacco is one of the most economically important non-food crop in Zimbabwe and other tobacco producing countries globally. Currently, little is known about the genetic diversity of tobacco germplasm in Zimbabwe. Understanding the genetic diversity of tobacco germplasm offers significant help in the selection of suitable material for breeding superior cultivars. In this study, 10 SSR markers were employed to assess the genetic diversity and population structure of 93 tobacco breeding lines and cultivars. A total of 50 alleles on 10 SSR loci were detected and the allele number per loci ranged from 3 to 14. The average gene diversity index and average polymorphism information content (PIC) ranged from 0.53 and 0.48, respectively, showing low levels of genetic diversity among tobacco cultivars. The AMOVA result revealed a low level of differentiation among accessions from different origins. Based on SSR markers, the tobacco germplasm collections consistently showed very low levels of g...