Chromatin Preparation and Chromatin Immuno-precipitation from Drosophila Embryos

This protocol provides specific details on how to perform Chromatin immunoprecipitation (ChIP) from Drosophila embryos. ChIP allows the matching of proteins or histone modifications to specific genomic regions. Formaldehyde-cross-linked chromatin is isolated and antibodies against the target of interest are used to determine whether the target is associated with a specific DNA sequence. This can be performed in spatial and temporal manner and it can provide information about the genome-wide localization of a given protein or histone modification if coupled with deep sequencing technology (ChIP-Seq)

Southern Sky Redshift Survey: Clustering of Local Galaxies

We use the two-point correlation function to calculate the clustering properties of the recently completed SSRS2 survey. The redshift space correlation function for the magnitude-limited SSRS2 is given by xi(s)=(s/5.85 h-1 Mpc)^{-1.60} for separations between 2 < s < 11 h-1 Mpc, while our best estimate for the real space correlation function is xi(r) = (r/5.36 h-1 Mpc)^{-1.86}. Both are comparable to previous measurements using surveys of optical galaxies over much larger and independent volumes. By comparing the correlation function calculated in redshift and real space we find that the redshift distortion on intermediate scales is small. This result implies that the observed redshift-space distribution of galaxies is close to that in real space, and that beta = Omega^{0.6}/b < 1, where Omega is the cosmological density parameter and b is the linear biasing factor for optical galaxies. We also use the SSRS2 to study the dependence of xi on the internal properties of galaxies. We confirm earlier results that luminous galaxies (L>L*) are more clustered than sub-L* galaxies and that the luminosity segregation is scale-independent. We find that early types are more clustered than late types, but that in the absence of rich clusters, the relative bias between early and late types in real space, is not as strong as previously estimated. Furthermore, both morphologies present a luminosity-dependent bias, with the early types showing a slightly stronger dependence on luminosity. We also find that red galaxies are significantly more clustered than blue ones, with a mean relative bias stronger than that seen for morphology. Finally, we find that the relative bias between optical and iras galaxies in real space is b_o/b_I $\sim$ 1.4.Comment: 43 pages, uses AASTeX 4.0 macros. Includes 8 tables and 16 Postscript figures, updated reference

Impact of Orbital Parameters and Greenhouse Gas on the Climate of MIS 7 and MIS 5 Glacial Inceptions

This work explores the impact of orbital parameters and greenhouse gas concentrations on the climate of marine isotope stage (MIS) 7 glacial inception and compares it to that of MIS 5. The authors use a coupled atmosphere-ocean general circulation model to simulate the mean climate state of six time slices at 115, 122, 125, 229, 236, and 239 kyr, representative of a climate evolution from interglacial to glacial inception conditions. The simulations are designed to separate the effects of orbital parameters from those of greenhouse gas (GHG). Their results show that, in all the time slices considered, MIS 7 boreal lands mean annual climate is colder than the MIS 5 one. This difference is explained at 70% by the impact of the MIS 7 GHG. While the impact of GHG over Northern Hemisphere is homogeneous, the difference in temperature between MIS 7 and MIS 5 due to orbital parameters differs regionally and is linked with the Arctic Oscillation. The perennial snow cover is larger in all the MIS 7 experiments compared to MIS 5, as a result of MIS 7 orbital parameters, strengthened by GHG. At regional scale, Eurasia exhibits the strongest response to MIS 7 cold climate with a perennial snow area 3 times larger than in MIS 5 experiments. This suggests that MIS 7 glacial inception is more favorable over this area than over North America. Furthermore, at 239 kyr, the perennial snow covers an area equivalent to that of MIS 5 glacial inception (115 kyr). The authors suggest that MIS 7 glacial inception is more extensive than MIS 5 glacial inception over the high latitudes

Diclofenac sorption from synthetic water: Kinetic and thermodynamic analysis

This work investigated diclofenac sorption on 0.5g L-1 activated carbon in a range of temperature (288-318K) and of initial sorbate concentration (24-218mgL-1). Thermodynamic modelling was carried out with the Langmuir isotherm. For kinetic modelling we compared the so-called Diffusion-Controlled Langmuir Kinetics (DCLK) and the pseudo-second order (PSO) model. The maximum sorption capacity of the sorbent, equal to 180mgg-1, was independent of temperature. Experimental data fitted well with both kinetic models, yet the DCLK model was found to be more informative about the mechanism of the process. Kinetic parameters (α, β) increased with the temperature, with α value rising from 5×10-5 to 20×10-5 L mg-1min-0.5, and β value rising from 3×10-6 to 20×10-6 L mg-1min-1 in the temperature range investigated

Arctic sea ice dynamics forecasting through interpretable machine learning

Machine Learning (ML) has become an increasingly popular tool to model the evolution of sea ice in the Arctic region. ML tools produce highly accurate and computationally efficient forecasts on specific tasks. Yet, they generally lack physical interpretability and do not support the understanding of system dynamics and interdependencies among target variables and driving factors. Here, we present a 2-step framework to model Arctic sea ice dynamics with the aim of balancing high performance and accuracy typical of ML and result interpretability. We first use time series clustering to obtain homogeneous subregions of sea ice spatiotemporal variability. Then, we run an advanced feature selection algorithm, called Wrapper for Quasi Equally Informative Subset Selection (W-QEISS), to process the sea ice time series barycentric of each cluster. W-QEISS identifies neural predictors (i.e., extreme learning machines) of the future evolution of the sea ice based on past values and returns the most relevant set of input variables to describe such evolution. Monthly output from the Pan-Arctic Ice-Ocean Modeling and Assimilation System (PIOMAS) from 1978 to 2020 is used for the entire Arctic region. Sea ice thickness represents the target of our analysis, while sea ice concentration, snow depth, sea surface temperature and salinity are considered as candidate drivers. Results show that autoregressive terms have a key role in the short term (with lag time 1 and 2 months) as well as the long term (i.e., in the previous year); salinity along the Siberian coast is frequently selected as a key driver, especially with a one-year lag; the effect of sea surface temperature is stronger in the clusters with thinner ice; snow depth is relevant only in the short term. The proposed framework is an efficient support tool to better understand the physical process driving the evolution of sea ice in the Arctic region

Carrot productivity and its physiological response to irrigation methods and regimes in arid regions

The aim of this study is to optimize water irrigation management for improving carrot productivity and water-saving in arid regions of southern Tunisia. Field studies were conducted over two seasons (2017-2019) to evaluate the effects of drip irrigation (DI) and surface irrigation (SI) methods coupled with three irrigation regimes on agronomic parameters of carrot crops. Irrigation regimes consisted of water replacements of cumulated crop evapotranspiration (ETc) at levels of 100% (I100), 70% (I70), and 40% (I40) when the readily available water in I100 treatment was depleted. Results showed a reduction in carrot yield by 13-22% and 22-32% with I70 and I40 treatments compared to I100, respectively. Yield is affected by the irrigation method with a reduction of around 6-7% under the surface method for both years. The water productivity (WP) was found to significantly vary among regimes and methods, where the highest values were observed for the I40 regimes and drip method. Drip and I100 irrigation techniques seem to optimize carrot production. Under situations of water shortage, adopting deficit irrigation treatment (DI70) could be an alternative for managing carrot irrigation and improving water productivity

Depopulation of dense α-synuclein aggregates is associated with rescue of dopamine neuron dysfunction and death in a new Parkinson's disease model.

Parkinson's disease (PD) is characterized by the presence of α-synuclein aggregates known as Lewy bodies and Lewy neurites, whose formation is linked to disease development. The causal relation between α-synuclein aggregates and PD is not well understood. We generated a new transgenic mouse line (MI2) expressing human, aggregation-prone truncated 1-120 α-synuclein under the control of the tyrosine hydroxylase promoter. MI2 mice exhibit progressive aggregation of α-synuclein in dopaminergic neurons of the substantia nigra pars compacta and their striatal terminals. This is associated with a progressive reduction of striatal dopamine release, reduced striatal innervation and significant nigral dopaminergic nerve cell death starting from 6 and 12 months of age, respectively. In the MI2 mice, alterations in gait impairment can be detected by the DigiGait test from 9 months of age, while gross motor deficit was detected by rotarod test at 20 months of age when 50% of dopaminergic neurons in the substantia nigra pars compacta are lost. These changes were associated with an increase in the number and density of 20-500 nm α-synuclein species as shown by dSTORM. Treatment with the oligomer modulator anle138b, from 9 to 12 months of age, restored striatal dopamine release, prevented dopaminergic cell death and gait impairment. These effects were associated with a reduction of the inner density of large α-synuclein aggregates and an increase in dispersed small α-synuclein species as revealed by dSTORM. The MI2 mouse model recapitulates the progressive dopaminergic deficit observed in PD, showing that early synaptic dysfunction is associated to fine behavioral motor alterations, precedes dopaminergic axonal loss and neuronal death that become associated with a more consistent motor deficit upon reaching a certain threshold. Our data also provide new mechanistic insight for the effect of anle138b's function in vivo supporting that targeting α-synuclein aggregation is a promising therapeutic approach for PD