Early Neolithic agriculture (2700–2000 <Emphasis Type="SmallCaps">bc</Emphasis>) and Kushan period developments (<Emphasis Type="SmallCaps">ad</Emphasis> 100–300): macrobotanical evidence from Kanispur in Kashmir,India

Here we report the results of an archaeobotanical study carried out on Ceramic Neolithic (2700–2000 bc) and Kushan period (ad 100–300) deposits at Kanispur, Kashmir, northern India. Botanical evidence from the Ceramic Neolithic phase reflects a nascent agriculture based on cold-tolerant crops (barley, wheats, lentil, field pea and grass pea) related to farming patterns of adjacent cultures and possibly evidence for the earliest cultivation in the valley. The Kushan period is characterized by a double-cropping pattern, suggesting a change in agricultural practices associated with a population recovery following a post-Neolithic decline. Finds of Juglans regia, and Prunus cf. amygdalus shells in ceramic Neolithic levels, and Vitis cf. vinifera, Emblica officinalis and Ziziphus cf. nummularia in addition to J. regia, and P. cf. amygdalus during Kushan times suggest that horticulture and foraging played an important role in the diet of the occupants. The present dataset provides new absolute dates for the subsistence economy of the Ceramic Neolithic population in the Kashmir Valley. We also present the oldest directly dated wheat and barley in Kashmir.     

Trends in sightings and population structure of white sharks, <Emphasis Type="Italic">Carcharodon carcharias,</Emphasis> at Seal Island,False Bay,South Africa,and the emigration of subadult female sharks approaching maturity

A long-term sightings and photographic identification (photo-ID) database documented the inter-annual and monthly trends in white shark (Carcharodon carcharias) sightings, sex ratios and life-history stages at Seal Island, False Bay, South Africa, over the period 2004–2012. A total of 1105 sightings were recorded during 171 scientific surveys incorporating 577 h of observation (annual mean 64.10 h, range 23.71–178.69 h). The mean annual sighting rate was 1.87 (range 0.90–3.19) sharks per hour and sighting rates declined over the nine-year study period. It is unknown whether the decline resulted from an actual population decline, or was due to changes in shark distribution or environmental conditions, but it highlights the need for ongoing monitoring at this site. The overall sex ratio was 1.0: 1.0: 2.3 for male: female: unsexed sharks, respectively. Of the 1105 sightings, 39% (n = 433) were photo-ID’d, representing 303 individual sharks (112: 111: 80, male: female: unsexed) and 130 resightings. Of the 303 photo-ID’d sharks, 71% were sighted in a single year only, indicative of transient behaviour. Of the 29% of sharks that were resighted in more than one year, 65% were resighted in the following year, indicating site fidelity to Seal Island, whereas 35% skipped one or more years between encounters, indicative of a temporary absence. The majority (60%) of the photo-ID’d sharks were immature, 32% were subadult and only 8% were mature. No young-of-the-year sharks and few adults were recorded, indicating that Seal Island is not an adult aggregation site, nor a pupping or nursery area, but rather is best described as a seasonal feeding ground. Large females were rarely resighted again after they approached length-at-maturity (≥450 cm TL), whereas some adult males were recorded consistently across years. The emigration of subadult female sharks approaching maturity from Seal Island, combined with the small number of mature sharks of both sexes reported from any South African location, indicate that adult aggregation sites, and thus areas of reproductive importance, still remain unknown.     

Variation between European eel <Emphasis Type="Italic">Anguilla anguilla</Emphasis> (L.) stocks in five marshes of the Thames Estuary (United Kingdom)

The European eel (Anguilla anguilla, L.) was historically widely distributed throughout the United Kingdom, in coastal waters, lakes, rivers and wetlands. Recruitment has declined in recent decades and the species is now listed as ‘Critically Endangered’ on the International Union for Conservation of Nature and Natural Resources (IUCN) Red List. Management of suitable wetland habitats may contribute to species recovery; however, little is known about the stocks in these areas. In this study, yellow (adult stage?>?300 mm) eels were sampled in ditches in five marshes bordering the Thames Estuary in England, UK. Ecological variables, including ditch characteristics, invertebrate abundance and water quality parameters were measured. Habitat features were also observed and recorded, including access, land use and water management regimes. Eels were found in all marshes, but at varying catch-per-unit-effort (CPUE). There were no significant correlations between CPUE and the ecological variables, except ditch width. However, a significant difference in CPUE was found between two of the marshes, which may be explained by variations in local habitat management. Mean lengths showed a high proportion of females and mean body condition of four of the marshes was also found to be greater than in three rivers in the same region. These findings suggest that the marshes are potentially favourable eel habitats and that factors influencing habitat quality, such as land use and water management, may affect eel abundance, production of females and body condition. Effective management of such wetlands may therefore contribute to the conservation of European eel.     

Infrared absorbance spectroscopy of aqueous proteins: Comparison of transmission and ATR data collection and analysis for secondary structure fitting

Attenuated total reflectance (ATR) infrared absorbance spectroscopy of proteins in aqueous solution is much easier to perform than transmission spectroscopy, where short path‐length cells need to be assembled reproducibly. However, the shape of the resulting ATR infrared spectrum varies with the refractive index of the sample and the instrument configuration. Refractive index in turn depends on the absorbance of the sample. In this work, it is shown that a room temperature triglycine sulfate detector and a ZnSe ATR unit can be used to collect reproducible spectra of proteins. A simple method for transforming the protein ATR spectrum into the shape of the transmission spectrum is also given, which proceeds by approximating a Kramers‐Krönig–determined refractive index of water as a sum of four linear components across the amide I and II regions. The light intensity at the crystal surface (with 45° incidence) and its rate of decay away from the surface is determined as a function of the wave number–dependent refractive index as well as the decay of the evanescent wave from the surface. The result is a single correction factor at each wave number. The spectra were normalized to a maximum of 1 between 1600 cm^?1 and 1700 cm^?1 and a self‐organizing map secondary structure fitting algorithm, SOMSpec, applied using the BioTools reference set. The resulting secondary structure estimates are encouraging for the future of ATR spectroscopy for biopharmaceutical characterization and quality control applications.     

Customised life cycle assessment tool for sugarcane (CaneLCA)—a development in the evaluation of alternative agricultural practices

Purpose

To promote eco-efficient sugarcane products, there is a need for life cycle assessment (LCA) methods that enable rapid assessment of the environmental implications of alternative agricultural practices. In response, a customised LCA method for sugarcane growing was developed and operationalized in the CaneLCA tool. The aim of the paper was to describe the CaneLCA method in detail and to test the effectiveness of the tool’s parameterisation for evaluating the environmental implications of cane growing practice alternatives.

Methods

CaneLCA (Version 1.03) was developed over 6 years (2011–2017) in conjunction with the Australian sugarcane sector. The LCA process was customised for sugarcane growing by focusing on ‘cradle to farm gate’ operations and relevant impact categories, and by parameterising practice variables. To evaluate the effectiveness of the tool, we used it to assess a case study of actual practice changes in the Wet Tropics region of Australia, in terms of the scope of practice variables and environmental implications that can be accounted for.

Results and discussion

The case study results generated by CaneLCA were consistent with those generated by past studies using LCA software. The parameterisation of practice variables allowed for all the practice changes represented in the case study to be assessed. It is suitable for evaluating such known practice alternatives, but less suited to evaluating very innovative practice alternatives, as it is constrained by the underlying algorithms and factors. Most of the environmental implications could be considered, except for effects on soil quality. This will be an area for future tool development to understand the full implications of agricultural practice change, along with the introduction of dynamic models to better estimate emissions.

Conclusions

CaneLCA makes the LCA process more rapid for evaluating alternative sugarcane growing practices, thereby speeding up progress towards devising more eco-efficient sugarcane products. It provides a model that could be adapted for other sugarcane growing regions, and for other perennial cropping systems. The novelty of the method is the detailed parameterisation of practice variables so that a wide range of alternative practices can be evaluated.

     

The interaction between vitamin D receptor polymorphisms and sun exposure around time of diagnosis influences melanoma survival

Evidence on the relationship between the vitamin D pathway and outcomes in melanoma is growing, although it is not always clear. We investigated the impact of measured levels of sun exposure at diagnosis on associations of vitamin D receptor gene (VDR) polymorphisms and melanoma death in 3336 incident primary melanoma cases. Interactions between six SNPs and a common 3′‐end haplotype were significant (p < .05). These SNPs, and a haplotype, had a statistically significant association with survival among subjects exposed to high UVB in multivariable regression models and exerted their effect in the opposite direction among those with low UVB. SNPs rs1544410/BsmI and rs731236/TaqI remained significant after adjustment for multiple testing. These results suggest that the association between VDR and melanoma‐specific survival is modified by sun exposure around diagnosis, and require validation in an independent study. Whether the observed effects are dependent or independent of vitamin D activation remains to be determined.     

Small-Molecule Screen Identifies De Novo Nucleotide Synthesis as a Vulnerability of Cells Lacking SIRT3

1. Download high-res image (114KB)
2. Download full-size image

     

Hydrilla control with split treatments of fluridone in Lake Harris, Florida

After several unsuccessful management efforts, a split treatment of fluridone was applied to the 6700 ha Lake Harris in March and June 1987, at a rate of 3.4 kg ha^–1 (680 and 340 kg fluridone, respectively) to two 3 m deep, hydrilla-infested bays. Fluridone concentrations in the water were sampled following the June treatment. Average fluridone concentrations were 2.1 µg l^–1 prior to this second application, and a maximum concentration of 30.2 µg l^–1 was detected in the treated area on the day following application. Fluridone residues dissipated out of the plot quickly due to dilution but concentrations declined lake-wide more slowly, following a logarithmic model, with an estimated fluridone half-life of 97 days. Control of hydrilla in Lake Harris resulted from the long exposure (over 25 weeks due to the split application) to fluridone concentrations of 2 µg l^–1, well below the maximum labelled rate of 150 µg l^–1.     

Cortical actin filaments fragment and aggregate to form chloroplast-associated and free F-actin rings in mechanically isolatedZinnia mesophyll cells

Summary Changes in F-actin organization following mechanical isolation ofZinnia mesophyll cells were documented by rhodamine-phalloidin staining. Immediately after isolation, most cells contained irregular cortical actin fragments of varying lengths, and less than 5% of cells contained intact cortical filaments. During the first 8 h of culture, filament fragments were replaced by actin rings, stellate actin aggregates, and bundled filament fragments. Some of these aggregates had no association with organelles (free actin aggregates). Other aggregates were associated with chloroplasts, which changed in shape and location at the same time actin aggregates appeared. F-actin was concentrated within or around the nucleus in a small percentage of cells. After 12 h in culture, the percentage of cells with free actin rings and chloroplast-associated actin aggregates began to decline and the percentage of cells having intact cortical actin filaments increased greatly. Intermediate images were recorded that strongly indicate that free actin rings, chloroplast-associated actin rings, and other actin aggregates self-assemble by successive bundling of actin filament fragments. The fragmentation and bundling of F-actin observed in mechanically isolatedZinnia cells resembles changes in F-actin distribution reported after diverse forms of cell disturbance and appears to be an example of a generalized response of the actin cytoskeleton to cell stress.Abbreviations FITC fluorescein isothiocyanate - MBS m-maleimidobenzoic acid N-hydroxysuccinimide ester - RhPh tetramethylrhodamine isothiocyanate-phalloidin