פרסומים

Mapping the ecological networks of microbial communities is a necessary step toward understanding their assembly rules and predicting their temporal behavior. However, existing methods require assuming a particular population dynamics model, which is not known a priori. Moreover, those methods require fitting longitudinal abundance data, which are often not informative enough for reliable inference. To overcome these limitations, here we develop a new method based on steady-state abundance data. Our method can infer the network topology and inter-taxa interaction types without assuming any particular population dynamics model. Additionally, when the population dynamics is assumed to follow the classic Generalized Lotka–Volterra model, our method can infer the inter-taxa interaction strengths and intrinsic growth rates. We systematically validate our method using simulated data, and then apply it to four experimental data sets. Our method represents a key step towards reliable modeling of complex, real-world microbial communities, such as the human gut microbiota.

Aerial thermal remote sensing can provide a means for collecting spatial plant water status data. Many studies have shown their potential in irrigation management but the adaptation of this technology is not straight forward. In this paper, knowledge accumulated in recent years on thermal imagery analysis methodology for water status mapping is summarized aiming at indicating alternatives to calculate the Crop Water Stress Index (CWSI) for commercial scale water status mapping. Based on literature overview, four forms of wet-baselines to calculate CWSI were selected, namely: artificial wet reference surface, two theoretical calculations and a statistical bio-indicator. These baselines were used to calculate CWSI based on multi-temporal aerial thermal images of cotton fields. CWSI based on a statistical bio-indicator and one of the theoretical wet-baselines provided the best correlations. It is argued though that the statistical one is preferable since it includes the plant characteristics and it is farmer-friendly. Based on bio-indicators, leaf water potential maps of three commercial fields were produced on several dates through the season. Water status spatial patterns were not static and the effect of static factors like sandy soil patches also changed through the season. The maps show the importance of in-season variability mapping for rational irrigation management. To improve current variable-rate irrigation, the concept of in-season irrigation management zones (IMZ) based on thermal-images should be considered and integrated with the delineation of static irrigation IMZ.

In order to examine the differences in bone properties between fast-growing and slow-growing broiler embryos and to understand the effects of genotype and egg size on these differences, fast- and slow-growing hens and males were reciprocally crossed to create 4 egg groups: FST (laid by fast-growing hens, inseminated by fast-growing males), H-FST (fast-growing hens and slow-growing males), H-SLW (slow-growing hens and fast-growing males), and SLW (slow-growing hens and slow-growing males). Embryos (n = 8) from these 4 groups were sacrificed and weighed, and both tibiae were harvested on embryonic d (E) 17, 19, and 21. Left tibiae were tested for their whole-bone mechanical properties using a micromechanical device. Cortical bone structure and bone mineral density (BMD) were examined by micro-computed tomography of the left tibiae. Bone mineralization was evaluated by measuring BMD and ash content, while the rate and location of mineralization were evaluated by fluorochrome labeling. Osteoclastic activity and osteocyte density were evaluated by histological stains [TRAP (Tartrate resistant acid phosphatase) and H&E (Hematoxylin and Eosin), respectively]. Groups with larger eggs (FST and H-FST) had higher BW and tibia weight than groups with smaller eggs (SLW and H-SLW); however, they had a lower ratio of tibia weight to BW. Between groups with similar egg weight, stiffness, maximal load, and yield load of the bones were higher in the SLW than the H-SLW, while no differences were found between the FST and H-FST. Additionally, the tibiae of the SLW were stiffer and their osteocyte density higher than in the FST on E21 and their periosteal mineralization rate was higher between E19 and E21. No differences were found between the groups in cortical bone structure. This study demonstrates that faster growing hatchlings, especially those that hatch from relatively small eggs, have inferior bone mechanical properties in comparison to slower growing hatchlings, and suggests that fast-growing chicks hatching from small eggs are at a higher risk for developing bone pathologies. Accordingly, selection for increased egg size may lead to improved mechanical performance of the skeleton of fast-growing broilers.

In order to examine the differences in bone properties between fast-growing and slow-growing broiler embryos and to understand the effects of genotype and egg size on these differences, fast- and slow-growing hens and males were reciprocally crossed to create 4 egg groups: FST (laid by fast-growing hens, inseminated by fast-growing males), H-FST (fast-growing hens and slow-growing males), H-SLW (slow-growing hens and fast-growing males), and SLW (slow-growing hens and slow-growing males). Embryos (n = 8) from these 4 groups were sacrificed and weighed, and both tibiae were harvested on embryonic d (E) 17, 19, and 21. Left tibiae were tested for their whole-bone mechanical properties using a micromechanical device. Cortical bone structure and bone mineral density (BMD) were examined by micro-computed tomography of the left tibiae. Bone mineralization was evaluated by measuring BMD and ash content, while the rate and location of mineralization were evaluated by fluorochrome labeling. Osteoclastic activity and osteocyte density were evaluated by histological stains [TRAP (Tartrate resistant acid phosphatase) and H&E (Hematoxylin and Eosin), respectively]. Groups with larger eggs (FST and H-FST) had higher BW and tibia weight than groups with smaller eggs (SLW and H-SLW); however, they had a lower ratio of tibia weight to BW. Between groups with similar egg weight, stiffness, maximal load, and yield load of the bones were higher in the SLW than the H-SLW, while no differences were found between the FST and H-FST. Additionally, the tibiae of the SLW were stiffer and their osteocyte density higher than in the FST on E21 and their periosteal mineralization rate was higher between E19 and E21. No differences were found between the groups in cortical bone structure. This study demonstrates that faster growing hatchlings, especially those that hatch from relatively small eggs, have inferior bone mechanical properties in comparison to slower growing hatchlings, and suggests that fast-growing chicks hatching from small eggs are at a higher risk for developing bone pathologies. Accordingly, selection for increased egg size may lead to improved mechanical performance of the skeleton of fast-growing broilers. © 2017 Poultry Science Association Inc.

Electric-field noise from the surfaces of ion-trap electrodes couples to the ion's charge causing heating of the ion's motional modes. This heating limits the fidelity of quantum gates implemented in quantum information processing experiments. The exact mechanism that gives rise to electric-field noise from surfaces is not well-understood and remains an active area of research. In this work, we detail experiments intended to measure ion motional heating rates with exchangeable surfaces positioned in close proximity to the ion, as a sensor to electric-field noise. We have prepared samples with various surface conditions, characterized in situ with scanned probe microscopy and electron spectroscopy, ranging in degrees of cleanliness and structural order. The heating-rate data, however, show no significant differences between the disparate surfaces that were probed. These results suggest that the driving mechanism for electric-field noise from surfaces is due to more than just thermal excitations alone.

Summary Grasses take up silicic acid from soil and deposit it in their leaves as solid silica. This mineral, comprising 1–10% of the grass dry weight, improves plants' tolerance to various stresses. The mechanisms promoting stress tolerance are mostly unknown, and even the mineralization process is poorly understood. To study leaf mineralization in sorghum (Sorghum bicolor), we followed silica deposition in epidermal silica cells by in situ charring and air-scanning electron microscopy. Our findings were correlated to the viability of silica cells tested by fluorescein diacetate staining. We compared our results to a sorghum mutant defective in root uptake of silicic acid. We showed that the leaf silicification in these plants is intact by detecting normal mineralization in leaves exposed to silicic acid. Silica cells were viable while condensing silicic acid into silica. The controlled mineral deposition was independent of water evapotranspiration. Fluorescence recovery after photobleaching suggested that the forming mineral conformed to the cellulosic cell wall, leaving the cytoplasm well connected to neighboring cells. As the silicified wall thickened, the functional cytoplasm shrunk into a very small space. These results imply that leaf silica deposition is an active, physiologically regulated process as opposed to a simple precipitation.

In ruminants, uterine pulses of prostaglandin (PG) F2α characterize luteolysis, while increased PGE2/PGE1 distinguish early pregnancy. This study evaluated intrauterine (IU) infusions of PGF2α and PGE1 pulses on corpus luteum (CL) function and gene expression. Cows on day 10 of estrous cycle received 4 IU infusions (every 6 h; n = 5/treatment) of saline, PGE1 (2 mg PGE1), PGF2α (0.25 mg PGF2α), or PGE1 + PGF2α. A luteal biopsy was collected at 30 min after third infusion for determination of gene expression by RNA-Seq. As expected, IU pulses of PGF2α decreased (P < 0.01) P4 luteal volume. However, there were no differences in circulating P4 or luteal volume between saline, PGE1, and PGE1 + PGF2α, indicating inhibition of PGF2α-induced luteolysis by IU pulses of PGE1. After third pulse of PGF2α, luteal expression of 955 genes were altered (false discovery rate [FDR] < 0.01), representing both typical and novel luteolytic transcriptomic changes. Surprisingly, after third pulse of PGE1 or PGE1 + PGF2α, there were no significant changes in luteal gene expression (FDR > 0.10) compared to saline cows. Increased circulating concentrations of the metabolite of PGF2α (PGFM; after PGF2α and PGE1 + PGF2α) and the metabolite PGE (PGEM; after PGE1 and PGE1 + PGF2α) demonstrated that PGF2α and PGE1 are entering bloodstream after IU infusions. Thus, IU pulses of PGF2α and PGE1 allow determination of changes in luteal gene expression that could be relevant to understanding luteolysis and pregnancy. Unexpectedly, by third pulse of PGE1, there is complete blockade of either PGF2α transport to the CL or PGF2α action by PGE1 resulting in complete inhibition of transcriptomic changes following IU PGF2α pulses.