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Background: Post‐translational histone modifications are among the most common epigenetic modifications that orchestrate gene expression, playing a pivotal role during embryonic development and in various pathological conditions. Among histone lysine demethylases, KDM7A, also known as KIAA1718 or JHDM1D, catalyzes the demethylation of H3K9me1/2 and H3K27me1/2, leading to transcriptional regulation. Previous data suggest that KDM7A plays a central role in several biological processes, including cell proliferation, commitment, differentiation, apoptosis, and maintenance. However, information on the expression pattern of KDM7A in whole organisms is limited, and its functional role is still unclear. Results: In Xenopus development, kdm7a is expressed early, undergoing spatiotemporal regulation in various organs and tissues, including the central nervous system and the eye. Focusing on retinal development, we found that kdm7a overexpression does not affect the expression of genes critically involved in early neural development and eye‐field specification, whereas unbalances the distribution of neural cell subtypes in the mature retina by disfavoring the development of ganglion cells while promoting that of horizontal cells. Conclusions: Kdm7a is dynamically expressed during embryonic development, and its overexpression influences late retinal development, suggesting a potential involvement in the molecular machinery regulating the spatiotemporally ordered generation of retinal neuronal subtypes. Key Findings: Histone methylation are among the most common epigenetic modifications that orchestrate gene expression.Although the histone demethylases kdm7a has been involved in various biological processes, data about its expression pattern and functional role during embryogenesis are still limited.Herein, we analyze the spatio‐temporal expression pattern of kdm7a in Xenopus laevis development and found that kdm7a overexpression specifically affects retinogenesis by disfavouring the development of ganglion cells while promoting that of horizontal cells. [ABSTRACT FROM AUTHOR]

In this paper we describe a 25-year (1986-2010) dataset of phytoplankton cell density abundance and biovolume in Lake Candia, a eutrophic, natural, small, and shallow lake located in north-western Italy, with data that are made available through the GBIF repository. The lake belongs to the national (LTER-Italy), European (LTER-Europe) and International (ILTER) long-term ecological research (LTER) networks. Phytoplankton samples were collected approximately monthly at the maximum depth station of the lake (7.7 m) and analysed with the inverted microscope, estimating both the cell density abundance and biovolume of each taxon. The dataset includes 10,120 georeferenced occurrences related to 545 taxa. During this 25-year period, the lake underwent profound modifications mainly related to the lake biomanipulation activities addressed to the management of aquatic macrophyte and to the evolution of the trophic condition. Making this dataset available represents a contribution to the current activities of the LTER networks for defining and reconstructing spatial and temporal dynamics and to identify and compare reliable trends. [ABSTRACT FROM AUTHOR]

We studied hydrochemistry and plankton dynamics in two remote alpine lakes: lake Nivolet superiore (2530 m asl) and lake Trebecchi superiore (2729 m asl) in the Gran Paradiso National Park (Western Italian Alps) in summer 2009. The aim of this study was to enhance the understanding of natural ecological dynamics in the pelagic habitat of alpine lakes by enlarging the number of biotic and abiotic variables usually considered to this end and by increasing the frequency of samplings, generally low in remote lakes. During the eight samplings performed in 2009, chemical and physical variables were measured both in situ and in the laboratory. We also followed the dynamics of all the compartments of the naturally simplified trophic chain of the two lakes from pico-prokaryotes to phytoplankton and zooplankton. Our results confirm the oligotrophic, close-to-pristine state of lake Nivolet and lake Trebecchi as they are not affected by hydromorphological alterations, they are naturally fishless and are not sensitive to acidification risk and acidity pulses. On the other hand, the two lakes have distinct abiotic conditions due to their glacial origin and to the lithological composition of their watersheds. We found some differences in the spatial variation of pico-prokaryotes, phytoplankton and zooplankton due to the different mixing regimes and maximum depth of the two lakes. Conversely, temporal patterns were similar in both lakes, related to ecological interactions and to changes in the abiotic conditions. The rapid succession of events in extreme ecosystems, such as the alpine lakes studied here, confirm the predominant role of external environmental factors (e.g. the duration of the ice-free season) and of ecological interactions among different trophic compartments. This research underlines the importance of seasonal niche partitioning among organisms with different size.

Climate warming can restructure lake food webs if trophic levels differ in their thermal responses, but evidence for these changes and their underlying mechanisms remain scarce in nature. Here we document how warming lake temperatures by up to 2°C, rather than changes in trophic state or fishing effort, have restructured the pelagic food web of a large European lake (Lake Maggiore, Italy). Our approach exploited abundance and biomass data collected weekly to yearly across five trophic levels from 1981 to 2008. Temperature generally had stronger effects on taxa than changes in fish predation or trophic state mediated through primary productivity. Consequently, we found that, as the lake warmed, the food web shifted in numerical abundance towards predators occupying middle trophic positions. Of these taxa, the spiny water flea (Bythotrephes longimanus) most prospered. Bythotrephes strongly limited abundances of the keystone grazer Daphnia, strengthening top‐down structuring of the food web. Warmer temperatures partly restructured the food web by advancing peak Bythotrephes densities by approximately 60 days and extending periods of positive population growth by three times. Nonetheless, our results suggested that advances in the timing and size of peak Bythotrephes densities could not outpace changes in the timing and size of peak densities in their Daphnia prey. Our results provide rare evidence from nature as to how long‐term warming can favour higher trophic levels, with the potential to strengthen top‐down control of food webs. [ABSTRACT FROM AUTHOR]

The accurate quantification of cyanobacteria phycobiliproteins is an important aspect in various research topics, such as cyanobacteria ecology and physiology studies, and especially to calibrate algorithms used in remote sensing of cyanobacterial blooms. Here we present a spectroscopic approach, exploiting spectrophotometric equations, aimed at improving the phycocyanin and allophycocyanin quantification when chlorophyll a is present in the phycobiliprotein aqueous extract. [ABSTRACT FROM AUTHOR]

Through cascading effects within lake food webs, commercial and recreational fisheries may indirectly affect the abundances of organisms at lower trophic levels, such as phytoplankton, even if they are not directly consumed. So far, interactive effects of fisheries, changing trophic state and climate upon lake ecosystems have been largely overlooked. Here we analyse case studies from five European lake basins of differing trophic states (Lake Võrtsjärv, two basins of Windermere, Lake Geneva and Lake Maggiore) with long-term limnological and fisheries data. Decreasing phosphorus concentrations (re-oligotrophication) and increasing water temperatures have been reported in all five lake basins, while phytoplankton concentration has decreased only slightly or even increased in some cases. To examine possible ecosystem-scale effects of fisheries, we analysed correlations between fish and fisheries data, and other food web components and environmental factors. Re-oligotrophication over different ranges of the trophic scale induced different fish responses. In the deeper lakes Geneva and Maggiore, we found a stronger link between phytoplankton and planktivorous fish and thus a more important cascading top-down effect than in other lakes. This connection makes careful ecosystem-based fisheries management extremely important for maintaining high water quality in such systems. We also demonstrated that increasing water temperature might favour piscivores at low phosphorus loading, but suppresses them at high phosphorus loading and might thus either enhance or diminish the cascading top-down control over phytoplankton with strong implications for water quality. [ABSTRACT FROM AUTHOR]

Lake Orta (Northern Italy) became one of the world's largest acidic lakes, following industrial pollution, beginning in the late 1920s. Prior to pollution, Lake Orta supported a rich and diversified phytoplankton community dominated by diatoms, cyanobacteria and dinoflagellates. Their taxonomic composition was comparable to that of the nearby Lake Maggiore, which provides a useful reference comparison. After pollution, Lake Orta was so acidic and contaminated with trace metals that only a few tolerant phytoplankton species persisted, supplemented by sudden and short living outbursts of occasional colonists. The lake was limed in 1989-1990. This has permitted the gradual recovery of its chemistry and biology, and many phytoplankton species that inhabit Lake Maggiore are now re-appearing in Lake Orta. I tested the two hypotheses that Lakes Orta and Maggiore would now have a similar phytoplankton taxonomic assemblages, and similar diversity of functional groups given their similar morphometry, physical features and trophic states. The two hypotheses were tested by comparing the phytoplankton assemblages of lakes Maggiore and Orta for the first 10 years after liming, i.e. 1990 to 2001. Phytoplankton was classified according the Reynolds' Morpho Functional Groups and five diversity indices were calculated (S, number of units; H, Shannon-Wiener; E, evenness; D, dominance; J, equitability). SHE analysis (an analysis of diversity changes based on the relationship among species richness (S), H Index (H) and evenness (E)) was also carried out, in order to compare the long term trend of both functional groups and taxa biodiversity. Both taxonomic and the functional composition differed in the two lakes, likely because chemical quality have played a role in taxa selection. Moreover, it was quite clear that, during the first post-liming decade, Lake Orta's phytoplankton was characterized by low diversity and evenness and by marked year-to-year fluctuations. However, SHE analysis showed that the colonization rate was higher in Lake Orta than in Lake Maggiore, and that the environmental modifications caused by the liming were opening new ecological niches, allowing some colonists to thrive in the changing, albeit still unusual chemical environment of the lake. [ABSTRACT FROM AUTHOR]

Limnologists have long recognized that one of the goals of their discipline is to increase its predictive capability. In recent years, the role of prediction in applied ecology escalated, mainly due to man's increased ability to change the biosphere. Such alterations often came with unplanned and noticeably negative side effects mushrooming from lack of proper attention to long-term consequences. Regression analysis of common limnological parameters has been successfully applied to develop predictive models relating the variability of limnological parameters to specific key causes. These approaches, though, are biased by the requirement of a priori causerelation assumption, oftentimes difficult to find in the complex, nonlinear relationships entangling ecological data. A set of quantitative tools that can help addressing current environmental challenges avoiding such restrictions is currently being researched and developed within the framework of ecological informatics. One of these approaches attempting to model the relationship between a set of inputs and known outputs, is based on Genetic Algorithms (GA) and Genetic Programming (GP). This stochastic optimization tool is based on the process of evolution in natural systems and was inspired by a direct analogy to sexual reproduction and Charles Darwin's principle of natural selection. GP is an evolutionary algorithm that uses selection and recombination operators to generate a population of equations. Thanks to a 25-year long time-series of regular limnological data, the deep, large, oligotrophic Lake Maggiore (Northern Italy) is the ideal case study to test the predictive ability of GP. Testing of GP on the multi-year data series of this lake has allowed us to verify the forecasting efficacy of the models emerging from GP application. In addition, this non-deterministic approach leads to the discovery of non-obvious relationships between variables and enabled the formulation of new stochastic models. [ABSTRACT FROM AUTHOR]

Increases in atmospheric temperature and nutrients from land are thought to be promoting the expansion of harmful cyanobacteria in lakes worldwide, yet to date there has been no quantitative synthesis of long-term trends. To test whether cyanobacteria have increased in abundance over the past ~ 200 years and evaluate the relative influence of potential causal mechanisms, we synthesised 108 highly resolved sedimentary time series and 18 decadal-scale monitoring records from north temperate-subarctic lakes. We demonstrate that: (1) cyanobacteria have increased significantly since c. 1800 ce, (2) they have increased disproportionately relative to other phytoplankton, and (3) cyanobacteria increased more rapidly post c. 1945 ce. Variation among lakes in the rates of increase was explained best by nutrient concentration (phosphorus and nitrogen), and temperature was of secondary importance. Although cyanobacterial biomass has declined in some managed lakes with reduced nutrient influx, the larger spatio-temporal scale of sedimentary records show continued increases in cyanobacteria throughout the north temperate-subarctic regions. [ABSTRACT FROM AUTHOR]

A complex network approach is combined with time dynamics in order to conduct a space-time analysis applicable to longitudinal studies aimed to characterize the progression of Alzheimer's disease (AD) in individual patients. The network analysis reveals how patient-specific patterns are associated with disease progression, also capturing the widespread effect of local disruptions. This longitudinal study is carried out on resting electroence phalography (EEGs) of seven AD patients. The test is repeated after a three months' period. The proposed methodology allows to extract some averaged information and regularities on the patients' cohort and to quantify concisely the disease evolution. From the functional viewpoint, the progression of AD is shown to be characterized by a loss of connected areas here measured in terms of network parameters (characteristic path length, clustering coefficient, global efficiency, degree of connectivity and connectivity density). The differences found between baseline and at follow-up are statistically significant. Finally, an original topographic multiscale approach is proposed that yields additional results. [ABSTRACT FROM AUTHOR]