Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets.

Cell type-specific gene expression patterns are outputs of transcriptional gene regulatory networks (GRNs) that connect transcription factors and signaling proteins to target genes. Single-cell technologies such as single cell RNA-sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq), can examine cell-type specific gene regulation at unprecedented detail. However, current approaches to infer cell type-specific GRNs are limited in their ability to integrate scRNA-seq and scATAC-seq measurements and to model network dynamics on a cell lineage. To address this challenge, we have developed single-cell Multi-Task Network Inference (scMTNI), a multi-task learning framework to infer the GRN for each cell type on a lineage from scRNA-seq and scATAC-seq data. Using simulated and real datasets, we show that scMTNI is a broadly applicable framework for linear and branching lineages that accurately infers GRN dynamics and identifies key regulators of fate transitions for diverse processes such as cellular reprogramming and differentiation.

Estimation of nitrogen leaching load from agricultural fields in the Puck Commune with an interactive calculator.

BACKGROUND: Nutrient leaching from agricultural fields is one of the main causes of pollution and eutrophication of the Baltic Sea. The quantity of nitrogen (N) leached from a particular field can be very different from the amount of N leached from other fields in a given region or even within a single farm. Therefore, it is necessary to estimate the quantity of N leached for each field separately. METHODS: An opinion poll has been conducted on 31 farms within the Puck Commune, which is approximately 3.6% of all farms located in this commune. Farmers provided data on the manner of fertilizing and cultivating crops on all their farms. For each field individually, on the basis of collected data, an estimated amount of the N leaching from the field has been determined. RESULTS: An interactive calculator to assist farmers in determining the quantity of N leaching from the agricultural field has been developed. The influence of factors shaping the amount of N leaching from a single field has been analyzed, and it has been determined that autumn plowing (specifically its absence) and the type of cultivated soil had the greatest average influence on this value in the studied sample. DISCUSSION: Due to the possible ways of reducing N leaching from agricultural fields, most of the studied fields were fertilized in an appropriate manner. However, in the studied sample there were fields for which the fertilization intensity significantly exceeded the recommended doses. In this context, a tool in the form of an interactive, easy-to-use N leaching calculator should help farmers to select appropriate doses and optimal fertilization practices.

The impact of pesticides used at the agricultural land of the Puck commune on the environment of the Puck Bay.

BACKGROUND: The Puck commune is one of the largest agricultural regions in the Pomeranian Voivodship that due to the pollution of the coastal zone negatively affects the functioning of the Puck Bay, including health of its inhabitants, and causes decrease in tourism as well as in overall economic value of the region. The objective of the undertaken study was to assess the extent of risk to the environment posed by the pesticides used in agricultural production in the coastal area of the Puck commune. METHODS: The study focused on organochlorine insecticides (DDT and its metabolites: α, ß, ϒ, δ-HCH, aldrin, dieldrin, endrin, isodrine), glyphosate and its metabolite AMPA, and 309 active substances used as pesticides. Analyses were carried out using GC-MS, GC-MS/MS and LC-MS/MS techniques. The undertaken novel approach included "tracking" of a large number of substances in multiple environmental matrices (surface water, groundwater, seawater, soil, sediment and fish), along with examination of their transport routes from the pesticides application locality to the Puck Bay. RESULTS: Glyphosate and its metabolite AMPA, anthraquinone, boscalid, chlorpyrifos-ethyl, dimethachlor, diflufenican, difenoconazole, epoxiconazole, fluopicolide and metazachlor were found in soil samples and surface water samples collected from drainage ditches surrounding the studied agricultural plots. In the samples of seawater and fish taken from the Puck Bay no studied pesticides were found.

Beta Cell Dedifferentiation Induced by IRE1α Deletion Prevents Type 1 Diabetes.

Immune-mediated destruction of insulin-producing ß cells causes type 1 diabetes (T1D). However, how ß cells participate in their own destruction during the disease process is poorly understood. Here, we report that modulating the unfolded protein response (UPR) in ß cells of non-obese diabetic (NOD) mice by deleting the UPR sensor IRE1α prior to insulitis induced a transient dedifferentiation of ß cells, resulting in substantially reduced islet immune cell infiltration and ß cell apoptosis. Single-cell and whole-islet transcriptomics analyses of immature ß cells revealed remarkably diminished expression of ß cell autoantigens and MHC class I components, and upregulation of immune inhibitory markers. IRE1α-deficient mice exhibited significantly fewer cytotoxic CD8+ T cells in their pancreata, and adoptive transfer of their total T cells did not induce diabetes in Rag1-/- mice. Our results indicate that inducing ß cell dedifferentiation, prior to insulitis, allows these cells to escape immune-mediated destruction and may be used as a novel preventive strategy for T1D in high-risk individuals.

Risk of phosphorus losses in surface runoff from agricultural land in the Baltic Commune of Puck in the light of assessment performed on the basis of DPS indicator.

BACKGROUND: In order to counteract the eutrophication of waterways and reservoirs, a basic risk assessment of phosphorus (P) losses in the surface runoff from agricultural land should be included in water management plans. A new method has been developed to assess the risk of P losses by estimating the degree of P saturation (DPS) based on the P concentration of the water extract water-soluble P. METHODS: The risk of P losses in surface runoff from agricultural land in the Puck Commune on the Baltic Sea Coast was assessed with the DPS method. The results were compared to an agronomic interpretation of the soil test P concentration (STP). Research was conducted on mineral and organic soils from 50 and 11 separate agricultural plots with a total area of 133.82 and 37.23 ha, respectively. Phosphorus was extracted from the collected samples using distilled water on all soil samples, acid ammonium lactate on mineral soils, and an extract of 0.5 mol HCl·dm-3 on organic soils. The organic matter content and pH values were also determined. The results of the P content in the water extracted from the soils were converted into DPS values, which were then classified by appropriate limit intervals. RESULTS AND DISCUSSION: There was a high risk of P losses from the soil via surface runoff in 96.7% of the agricultural parcels tested (96% of plots with mineral soils and 100% of plots with organic soils). Simultaneously, a large deficiency of plant-available P was found in soils from 62% of agricultural plots. These data indicate that the assessment of P concentration in soils made on the basis of an environmental soil P test conflicts with the assessment made based on STP and create a cognitive dissonance. The risk level of P losses through surface runoff from the analyzed plots as determined by the DPS indicator is uncertain. This uncertainty is increased as the DPS index is not correlated with other significant factors in P runoff losses, such as the type of crop and area inclination.

Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency.

Elucidating the mechanism of reprogramming is confounded by heterogeneity due to the low efficiency and differential kinetics of obtaining induced pluripotent stem cells (iPSCs) from somatic cells. Therefore, we increased the efficiency with a combination of epigenomic modifiers and signaling molecules and profiled the transcriptomes of individual reprogramming cells. Contrary to the established temporal order, somatic gene inactivation and upregulation of cell cycle, epithelial, and early pluripotency genes can be triggered independently such that any combination of these events can occur in single cells. Sustained co-expression of Epcam, Nanog, and Sox2 with other genes is required to progress toward iPSCs. Ehf, Phlda2, and translation initiation factor Eif4a1 play functional roles in robust iPSC generation. Using regulatory network analysis, we identify a critical role for signaling inhibition by 2i in repressing somatic expression and synergy between the epigenomic modifiers ascorbic acid and a Dot1L inhibitor for pluripotency gene activation.

Impact of agricultural farms on the environment of the Puck Commune: Integrated agriculture calculator-CalcGosPuck.

BACKGROUND: Leaching of nutrients from agricultural areas is the main cause of water pollution and eutrophication of the Baltic Sea. A variety of remedial actions to reduce nitrogen and phosphorus losses from agricultural holdings and cultivated fields have been taken in the past. However, knowledge about the risk of nutrient leaching has not yet reached many farmers operating in the water catchment area of the Baltic Sea. METHODS: The nutrient balance method known as "At the farm gate" involves calculating separate balances for nitrogen (N), phosphorus (P) and potassium (K). After estimating all the components of the nutrient balance, the total balance for NPK is calculated and the data obtained is expressed as the ratio of total change (surplus) to the area of arable land on a farm. In addition, the nutrient usage efficiency on a farm is also calculated. An opinion poll was conducted in 2017 on 3.6% (n = 31) of the farms located in commune of Puck. The total area of the farms including arable and grass land ranged from 5 to 130 ha with an average of 45.82 ha. The arable land was on average 30.79 ha ranging from 4.45 to 130 ha while the grassland averaged 12.77 ha and ranged from 0 to 53 ha. RESULTS: The average consumption of mineral fertilizer in the sample population of farms was 114.9 kg N, 9.3 kg P, and 22.9 kg K·ha-1of agricultural land (AL), respectively. N balance in the sample farms being ranged from -23.3 to 254.5 kg N·ha-1AL while nutrient use efficiency ranged from 0.40% to 231.3%. In comparison, P surplus in the sample farms was 5.0 kg P·ha-1AL with the P use efficiency of 0.4-266.5%. DISCUSSION: Mean N fertilizer consumption in the tested farms was higher than the average usage across Poland and in the Pomeranian Voivodeship. However, mean consumption of potassium fertilizers was lower than mentioned averages. Mean P fertilizer consumption was higher than in the Pomeranian Voivodeship, but lower compared to the entire country. Generally, on the basis of designated research indicators of farm pressures on water quality, concentrations of total nitrogen and total phosphorus were obtained. CalcGosPuck (an integrated agriculture calculator) will help to raise farmers' awareness about NPK flow on farm scale and to improve nutrient management.

Distinguishing sources of N2O in European grasslands by stable isotope analysis.

Nitrifiers and denitrifiers are the main producers of the greenhouse gas nitrous oxide (N(2)O). Knowledge of the respective contributions of each of these microbial groups to N(2)O production is a prerequisite for the development of effective mitigation strategies for N(2)O. Often, the differentiation is made by the use of inhibitors. Measurements of the natural abundance of the stable isotopes of N and O in N(2)O have been suggested as an alternative for the often unreliable inhibition studies. Here, we tested the natural abundance incubation method developed by Tilsner et al.1 with soils from four European grasslands differing in long-term management practices. Emission rates of N(2)O and stable isotope natural abundance of N(2)O and mineral N were measured in four different soil incubations: a control with 60% water-filled pore space (WFPS), a treatment with 60% WFPS and added ammonium (NH(4) (+)) to support nitrifiers, a control with 80% WFPS and a treatment with 80% WFPS and added nitrate (NO(3) (-)) to support denitrifiers. Decreases in NH(4) (+) concentrations, linked with relative (15)N-enrichment of residual NH(4) (+) and production of (15)N-depleted NO(3) (-), showed that nitrification was the main process for mineral N conversions. The N(2)O production, however, was generally dominated by reduction processes, as indicated by the up to 20 times larger N(2)O production under conditions favouring denitrification than under conditions favouring nitrification. Interestingly, the N(2)O concentration in the incubation atmospheres often levelled off or even decreased, accompanied by increases in delta(15)N and delta(18)O values of N(2)O. This points to uptake and further reduction of N(2)O to N(2), even under conditions with small concentrations of N(2)O in the atmosphere. The measurements of the natural abundances of (15)N and (18)O proved to be a valuable integral part of the natural abundance incubation method. Without these measurements, nitrification would not have been identified as essential for mineral N conversions and N(2)O consumption could not have been detected.

Nutrient management in food production: achieving agronomic and environmental targets.

The notion of management has undergone many changes during the past century. Nowadays, management is perceived as "specialized activity to achieve targets." Skill in management is the single most important factor determining the economic and environmental performance of agroecosystems. Nutrient management is "management of nutrients to achieve agronomic and environmental targets;" it requires proper understanding of nutrient cycling, site- and farm-specific guidelines and technology, and often direct coaching. These activities are diverse and complicated, especially in mixed farming systems that involve both crop and animal production. To be effective, economic and environmental targets must be coherent, flexible, and controllable. They also must be defined and implemented quantitatively at strategic, tactical, and operational levels. Data from farms in Poland and The Netherlands are used to show how economic incentives, provided through governmental policies and measures in both countries, can improve nutrient-use efficiency by a factor of 2 on many intensively managed mixed farming systems.