BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis

Amyloids and prion proteins are clinically and biologically important beta-structures, whose supersecondary structures are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Recent work has indicated the utility of pairwise probabilistic statistics in beta-structure prediction. We develop here a new strategy for beta-structure prediction, emphasizing the determination of beta-strands and pairs of beta-strands as fundamental units of beta-structure. Our program, BETASCAN, calculates likelihood scores for potential beta-strands and strand-pairs based on correlations observed in parallel beta-sheets. The program then determines the strands and pairs with the greatest local likelihood for all of the sequence's potential beta-structures. BETASCAN suggests multiple alternate folding patterns and assigns relative a priori probabilities based solely on amino acid sequence, probability tables, and pre-chosen parameters. The algorithm compares favorably with the results of previous algorithms (BETAPRO, PASTA, SALSA, TANGO, and Zyggregator) in beta-structure prediction and amyloid propensity prediction. Accurate prediction is demonstrated for experimentally determined amyloid beta-structures, for a set of known beta-aggregates, and for the parallel beta-strands of beta-helices, amyloid-like globular proteins. BETASCAN is able both to detect beta-strands with higher sensitivity and to detect the edges of beta-strands in a richly beta-like sequence. For two proteins (Abeta and Het-s), there exist multiple sets of experimental data implying contradictory structures; BETASCAN is able to detect each competing structure as a potential structure variant. The ability to correlate multiple alternate beta-structures to experiment opens the possibility of computational investigation of prion strains and structural heterogeneity of amyloid. BETASCAN is publicly accessible on the Web at http://betascan.csail.mit.edu.

1200 years of decadal-scale variability of Mediterranean vegetation and climate at Pantelleria Island, Italy

A new sedimentary sequence from Lago di Venere on Pantelleria Island, located in the Strait of Sicily between Tunisia and Sicily was recovered. The lake is located in the coastal infra-Mediterranean vegetation belt at 2 m a.s.l. Pollen, charcoal and sedimentological analyses are used to explore linkages among vegetation, fire and climate at a decadal scale over the past 1200 years. A dry period from ad 800 to 1000 that corresponds to the ‘Medieval Warm Period’ (WMP) is inferred from sedimentological analysis. The high content of carbonate recorded in this period suggests a dry phase, when the ratio of evaporation/precipitation was high. During this period the island was dominated by thermophilous and drought-tolerant taxa, such as Quercus ilex, Olea, Pistacia and Juniperus. A marked shift in the sediment properties is recorded at ad 1000, when carbonate content became very low suggesting wetter conditions until ad 1850–1900. Broadly, this period coincides with the ‘Little Ice Age’ (LIA), which was characterized by wetter and colder conditions in Europe. During this time rather mesic conifers (i.e. Pinus pinaster), shrubs and herbs (e.g. Erica arborea and Selaginella denticulata) expanded, whereas more drought-adapted species (e.g. Q. ilex) declined. Charcoal data suggest enhanced fire activity during the LIA probably as a consequence of anthropogenic burning and/or more flammable fuel (e.g. resinous Pinus biomass). The last century was characterized by a shift to high carbonate content, indicating a change towards drier conditions, and re-expansion of Q. ilex and Olea. The post-LIA warming is in agreement with historical documents and meteorological time series. Vegetation dynamics were co-determined by agricultural activities on the island. Anthropogenic indicators (e.g. Cerealia-type, Sporormiella) reveal the importance of crops and grazing on the island. Our pollen data suggest that extensive logging caused the local extinction of deciduous Quercus pubescens around ad1750.

Reviving extinct Mediterranean forest communities may improve ecosystem potential in a warmer future

The Mediterranean Basin is the region of Europe most vulnerable to negative climate-change impacts, including forest decline, increased wildfire, and biodiversity loss. Because humans have affected Mediterranean ecosystems for millennia, it is unclear whether the region's native ecosystems were more resilient to climate change than current ecosystems, and whether they would provide sustainable management options if restored. We simulated vegetation with the LandClim model, using present-day climate as well as future climate-change scenarios, in three representative areas that encompass a broad range of Mediterranean conditions and vegetation types. Sedimentary pollen records that document now-extinct forests help to validate the simulations. Forests modeled under present climate closely resemble the extinct forests when human disturbance is limited; under future scenarios, characterized by increased temperatures and decreased precipitation, extinct forests are projected to re-emerge. When combined with modeling, paleoecological evidence reveals the potential of native vegetation to re-establish under current and future climate conditions, and provides a template for novel management strategies to maintain forest productivity and biodiversity in a warmer and drier future.

Vegetation and fire history of coastal north-eastern Sardinia (Italy) under changing Holocene climates and land use

Little is known about the vegetation and fire history of Sardinia, and especially the long-term history of the thermo-Mediterranean belt that encompasses its entire coastal lowlands. A new sedimentary record from a coastal lake based on pollen, spores, macrofossils and microscopic charcoal analysis is used to reconstruct the vegetation and fire history in north-eastern Sardinia. During the mid-Holocene (c. 8,100–5,300 cal bp), the vegetation around Stagno di Sa Curcurica was characterised by dense Erica scoparia and E. arborea stands, which were favoured by high fire activity. Fire incidence declined and evergreen broadleaved forests of Quercus ilex expanded at the beginning of the late Holocene. We relate the observed vegetation and fire dynamics to climatic change, specifically moister and cooler summers and drier and milder winters after 5,300 cal bp. Agricultural activities occurred since the Neolithic and intensified after c. 7,000 cal bp. Around 2,750 cal bp, a further decline of fire incidence and Erica communities occurred, while Quercus ilex expanded and open-land communities became more abundant. This vegetation shift coincided with the historically documented beginning of Phoenician period, which was followed by Punic and Roman civilizations in Sardinia. The vegetational change at around 2,750 cal bp was possibly advantaged by a further shift to moister and cooler summers and drier and milder winters. Triggers for climate changes at 5,300 and 2,750 cal bp may have been gradual, orbitally-induced changes in summer and winter insolation, as well as centennial-scale atmospheric reorganizations. Open evergreen broadleaved forests persisted until the twentieth century, when they were partly substituted by widespread artificial pine plantations. Our results imply that highly flammable Erica vegetation, as reconstructed for the mid-Holocene, could re-emerge as a dominant vegetation type due to increasing drought and fire, as anticipated under global change conditions.

Alternative nighttime nutrition regimens in glycogen storage disease type I: a controlled crossover study

BACKGROUND Traditional approaches for nighttime glycemic control in glycogen storage disease type I (GSDI) include continuous tube feeding, or ingestion of uncooked corn starch (CS) at bedtime. A modified corn starch (MCS) has been shown to prolong euglycemia in some patients. The aim of this study was to evaluate whether stable nighttime glucose control can be achieved with other types of slowly digested carbohydrates in adult GSDI patients. METHODS In this cross-over study, nocturnal glucose control and fasting times were assessed with three different nocturnal nutrition regimens in five patients, using continuous glucose monitoring (CGMS) in an outpatient everyday life setting. For each patient, continuous glucose profiles were measured after ingestion of (1) CS, (2) MCS or (3) a pasta meal at bedtime, during 5 to 6 consecutive nights for each regimen. RESULTS Stable nocturnal glucose control was achieved for all patients with a pasta meal, with a mean duration of glycemia >3.5 mmol/l of 7.6 h (range 5.7-10.8), and >4 mmol/l of 7 h (5.2-9.2), similar to CS and MCS. Fasting glucose before breakfast on workdays (after 7.1 ± 0.8 h) was not significantly different between the three interventions (CS 4.1 ± 0.5 mmol/l, MCS 4.6 ± 0.7 mmol/l, pasta 4.3 ± 0.9 mmol/l). During prolonged fasting on weekends, longer duration of normoglycemia was achieved with CS or MCS than with pasta. CONCLUSION Consumption of cooked pasta is a suitable and more palatable alternative to uncooked corn starch to achieve nighttime glucose control in adult patients with GSDI.

Holocene vegetation and fire history of the mountains of Northern Sicily (Italy)

Knowledge about vegetation and fire history of the mountains of Northern Sicily is scanty. We analysed five sites to fill this gap and used terrestrial plant macrofossils to establish robust radiocarbon chronologies. Palynological records from Gorgo Tondo, Gorgo Lungo, Marcato Cixé, Urgo Pietra Giordano and Gorgo Pollicino show that under natural or near natural conditions, deciduous forests (Quercus pubescens, Q. cerris, Fraxinus ornus, Ulmus), that included a substantial portion of evergreen broadleaved species (Q. suber, Q. ilex, Hedera helix), prevailed in the upper meso-mediterranean belt. Mesophilous deciduous and evergreen broadleaved trees (Fagus sylvatica, Ilex aquifolium) dominated in the natural or quasi-natural forests of the oro-mediterranean belt. Forests were repeatedly opened for agricultural purposes. Fire activity was closely associated with farming, providing evidence that burning was a primary land use tool since Neolithic times. Land use and fire activity intensified during the Early Neolithic at 5000 bc, at the onset of the Bronze Age at 2500 bc and at the onset of the Iron Age at 800 bc. Our data and previous studies suggest that the large majority of open land communities in Sicily, from the coastal lowlands to the mountain areas below the thorny-cushion Astragalus belt (ca. 1,800 m a.s.l.), would rapidly develop into forests if land use ceased. Mesophilous Fagus-Ilex forests developed under warm mid Holocene conditions and were resilient to the combined impacts of humans and climate. The past ecology suggests a resilience of these summer-drought adapted communities to climate warming of about 2 °C. Hence, they may be particularly suited to provide heat and drought-adapted Fagus sylvatica ecotypes for maintaining drought-sensitive Central European beech forests under global warming conditions.