Effects of periodic bottlenecks on the dynamics of adaptive evolution in microbial populations

Population bottlenecks are common in nature, and they can impact the rate of adaptation in evolving populations. On the one hand, each bottleneck reduces the genetic variation that fuels adaptation. On the other hand, fewer founders can undergo more generations and leave more descendants in a resource-limited environment, which allows surviving beneficial mutations to spread more quickly. Here we investigate the impact of repeated bottlenecks on the dynamics of adaptation in experimental populations of Escherichia coli. We propagated 48 populations under four dilution regimes (2-, 8-, 100-, and 1000-fold), all reaching the same final size each day, for 150 days. A simple model in which adaptation is limited by the supply rate of beneficial mutations predicts that fitness gains should be maximized with ~8-fold dilutions. The model also assumes that selection acts only on the overall growth rate and is otherwise identical across dilution regimes. However, we found that selection in the 2-fold regime was qualitatively different from the other treatments. Moreover, we observed earlier and greater fitness gains in the populations subjected to 100- and 1000-fold dilutions than in those that evolved in the 8 fold regime. We also ran simulations using parameters estimated independently from a long-term experiment using the same ancestral strain and environment. The simulations produced dynamics similar to our empirical results under these regimes, and they indicate that the simple model fails owing to the assumption that the supply of beneficial mutations limits adaptation.

Long-term monitoring of deficit irrigation regimes on citrus orchards in Sicily

The study aims to identify the responses of citrus orchards (C. sinensis (L.) Osbeck), grown under typical Mediterranean climatic conditions, to deficit irrigation (DI) regimes applied over more than a decade (2010-2020). In particular, the DI regimes were declined at the study site in terms of sustained deficit irrigation, regulated deficit irrigation, partial drying of the root-zone, with increasing severity of the water deficit, from 25% to 50% of the crop evapotranspiration, using surface and sub-surface micro-irrigation techniques. Long-term monitoring was set up for identifying the main processes acting at the soil-plant-atmosphere continuum (SPAC) level through direct in situ measurements of mass and energy fluxes (i.e., via micrometeorological technique) and the estimation of ETc and transpiration fluxes (i.e., via sap flow method), and the soil-plant-water processes (via geoelectrical techniques). In addition, the main physiological, qualitative, and quantitative parameters were evaluated since the beginning of the experiment. The results of the long-term experiment demonstrated the great adaptability of the crop species to sustain even the highest water reductions without substantial alterations of the main marketable productive and qualitative characteristics, evidencing the importance of controlling the SPAC dynamics for correctly applying the water restriction regimes.

Variability in Elemental Composition of Conifer Tree Rings

Distribution of chemical elements in tree rings bears important information on various biogeochemical processes. In order to achieve a reliable interpretation of the information, it is necessary to know the degree of variation in the content of chemical elements both at the level of the entire species and at the level of individual trees. The research aims to determine which chemical elements have a stable distribution in the trunks of a number of conifers: Siberian spruce (Picea obovata Ledeb.), Scots pine (Pinus sylvestris L.), Siberian larch (Larix sibirica Ledeb.), and Siberian pine (Pinus sibirica Du Tour). The data for the analysis were obtained on the basis of the long-term experiment in forest growing. The experimental site was laid out in 1971–1972 in the vicinity of Krasnoyarsk by the staff of the Sukachev Institute of Forest of the Siberian Branch of the Russian Academy of Sciences. Before planting the seedlings, the soil ground was mechanically levelled, and thus, sufficiently equal growth conditions were created for all plantings. Cores with a diameter of 12 mm were sampled from three normally developing trees of each species and analyzed using modern X-ray fluorescence methods. Content relative values of elements (counts) were obtained with the Itrax Multiscanner (COX Analytical Systems). The content of elements in the tree rings was characterized by the concentration and reserve of elements. Concentration was calculated as the number of counts per 1 mm2 of the ring area; reserve was calculated as the number of counts over the entire ring area. Each of these variables was defined by the parameters of linear slope in the calendar year series and the standard deviation. The cluster analysis was performed in the 4-dimensional space of the obtained parameters. This allowed determining whether the series of element distributions from different trees and species are grouped. Three elements (Ca, Co, and P) show high stability of distribution parameters in tree rings with no regard to tree species. A number of other elements (Mn, Pb, Cl, Cr, Ni, Sr, and W) are stably grouped depending on the species. The results of the research enable to focus on the study of the elements stably distributed in the conifer trunks. For citation: Gavrikov V.L., Fertikov A.I., Sharafutdinov R.A., Vaganov E.A. Variability in Elemental Composition of Conifer Tree Rings. Lesnoy Zhurnal [Russian Forestry Journal], 2021, no. 6, pp. 24–37. DOI: 10.37482/0536-1036-2021-6-24-37

Studying standard and rheological quality parameters of winter wheat by Python visualisation

This study was carried out to present an innovative solution for interpreting large data sets in agri-statistics with the invocation of programmed visualisation. Moreover, the following polyfactorial long-term experiment embodies a comprehensive study of 18 wheat quality parameters. The effect of increasing dosages of fertiliser (control, N₉₀PK, N₁₅₀PK) was examined on 3 winter wheat cultivars (KG Kunhalom, GK Csillag, Hybiza) in two consecutive growing seasons (2018–2019). The ecological conditions of 2018 gave a significantly higher yield, meanwhile 2019 significantly augmented gluten spread, alveographic tenacity, alveographic deformation work, valorigraphic stability and quality group and loaf volume. N₉₀PK dosage was enough to realise yield and quality potential as well. Fertilising significantly improved 13 indices, namely yield, crude protein, Zeleny index, wet gluten content, alveographic extensibility, alveographic deformation work, valorigraphic water absorption, quality number and group, dough development time, stability, softening and loaf volume. Considering yield, cv. Hybiza performed better, while cvs. KG Kunhalom and GK Csillag possessed significantly better protein-linked postharvest attributes. One of the most important findings is that waffle chart, joint plot, correlation matrix and complexradar of Python provide a very powerful tool in agri-statistics. Also, the results can potentially improve the knowledge about cultivar-specific agronomy practice, wheat quality and the connections between these parameters.

Different Effects of Soy and Whey on Linear Bone Growth and Growth Pattern in Young Male Sprague-Dawley Rats

The aim of this investigation was to determine the better protein for supporting optimal linear growth, as the exact composition and benefits of specific dietary proteins in supporting linear growth is unknown. In the current study, we compared the effect of soy and whey proteins, both proteins contain all essential amino acids and are considered the best proteins in their categories. Young male rats were subjected to multiple feeding protocols using iso-energetic diets containing soy or whey as the sole protein source. The rats were allowed to eat ad libitum for 11, 24, or 74 days in the first set of experiments, and the soy group was pair-fed to the whey group in the second set. The differences in weight gain, food consumption, and humeri length of the soy group that were greater at the beginning of the ad libitum experiments lessened over time. Pair-fed experiments revealed that the increased weight and humeri length resulted from the differences in food consumption. However, other parameters were protein specific. Bone quality, which was better in the soy group at 24 days, was matched by the whey group and even surpassed that of the soy group in the long-term experiment, with a significantly greater bone mineral density, cortical thickness, and growth plate. Although in the short term the levels of insulin like growth factor (IGF)-I were similar between the groups, IGF-I increased with age in the whey group, and the levels at the long-term experiment were significantly higher compared to the soy group. Furthermore, using the pair fed setup made it clear that when the difference in food consumption were no longer playing part, whey was more efficient in increasing IGF-I. There were no indications of metabolic sequelae. Although the use of soy is gaining in popularity as a sustainable protein, our findings indicate a better effect of whey on linear growth by leading to slower growth with better-organized epiphyseal growth plates and bone quality.

Using prediction polling to harness collective intelligence for disease forecasting

Background The global spread of COVID-19 has shown that reliable forecasting of public health related outcomes is important but lacking. Methods We report the results of the first large-scale, long-term experiment in crowd-forecasting of infectious-disease outbreaks, where a total of 562 volunteer participants competed over 15 months to make forecasts on 61 questions with a total of 217 possible answers regarding 19 diseases. Results Consistent with the “wisdom of crowds” phenomenon, we found that crowd forecasts aggregated using best-practice adaptive algorithms are well-calibrated, accurate, timely, and outperform all individual forecasters. Conclusions Crowd forecasting efforts in public health may be a useful addition to traditional disease surveillance, modeling, and other approaches to evidence-based decision making for infectious disease outbreaks.