A continuous cold rubidium atomic beam with enhanced flux and tunable velocity

We present a cold atomic beam source based on a two-dimensional (2D)+ magneto-optical trap (MOT), capable of generating a continuous cold beam of 87Rb atoms with a flux up to 4.3*10^9 atoms/s, a mean velocity of 10.96(2.20) m/s, and a transverse temperature of 16.90(1.56) uK. Investigating the influence of high cooling laser intensity, we observe a significant population loss of atoms to hyperfine-level dark states. To account for this, we employ a multiple hyperfine level model to calculate the cooling efficiency associated with the population in dark states, subsequently modifying the scattering force. Simulations of beam flux at different cooling and repumping laser intensities using the modified scattering force are in agreement with experimental results. Optimizing repumping and cooling intensities enhances the flux by 50%. The influence of phase modulation on both the pushing and cooling lasers is experimentally studied, revealing that the mean velocity of cold atoms can be tuned from 9.5 m/s to 14.6 m/s with a phase-modulated pushing laser. The versatility of this continuous beam source, featuring high flux, controlled velocity, and narrow transverse temperature, renders it valuable for applications in atom interferometers and clocks, ultimately enhancing bandwidth, sensitivity, and signal contrast in these devices

Effects of fermentation on protein profile of coffee by-products and its relationship with internal protein structure measured by vibrational spectroscopy

Objective To our knowledge, there are few studies on the correlation between internal structure of fermented products and nutrient delivery from by-products from coffee processing in the ruminant system. The objective of this project was to use advanced mid-infrared vibrational spectroscopic technique (ATR-FT/IR) to reveal interactive correlation between protein internal structure and ruminant-relevant protein and energy metabolic profiles of by-products from coffee processing affected by added-microorganism fermentation duration. Methods The by-products from coffee processing were fermented using commercial fermentation product, called Saus Burger Pakan, consisting of various microorganisms: cellulolytic, lactic acid, amylolytic, proteolytic, and xylanolytic microbes, for 0, 7, 14, 21, and 28 days. Protein chemical profiles, Cornell Net Carbohydrate and Protein System crude protein and CHO subfractions, and ruminal degradation and intestinal digestion of protein were evaluated. The attenuated total reflectance-Ft/IR (ATR-FTIR) spectroscopy was used to study protein structural features of spectra that were affected by added microorganism fermentation duration. The molecular spectral analyses were carried using OMNIC software. Molecular spectral analysis parameters in fermented and non-fermented by-products from coffee processing included: Amide I area (AIA), Amide II (AIIA) area, Amide I heigh (AIH), Amide II height (AIIH), α-helix height (αH), β-sheet height (βH), AIA to AIIA ratio, AIH to AIIH ratio, and αH to βH ratio. The relationship between protein structure spectral profiles of by-products from coffee processing and protein related metabolic features in ruminant were also investigated. Results Fermentation decreased rumen degradable protein and increased rumen undegradable protein of by-products from coffee processing (p<0.05), indicating more protein entering from rumen to the small intestine for animal use. The fermentation duration significantly impacted (p<0.05) protein structure spectral features. Fermentation tended to increase (p<0.10) AIA and AIH as well as β-sheet height which all are significantly related to the protein level. Conclusion Protein structure spectral profiles of by-product form coffee processing could be utilized as potential evaluators to estimate protein related chemical profile and protein metabolic characteristics in ruminant system

Plastid-nucleus communication involves calcium-modulated MAPK signalling

Chloroplast retrograde signals play important roles in coordinating the plastid and nuclear gene expression and are critical for proper chloroplast biogenesis and for maintaining optimal chloroplast functions in response to environmental changes in plants. Until now, the signals and the mechanisms for retrograde signalling remain poorly understood. Here we identify factors that allow the nucleus to perceive stress conditions in the chloroplast and to respond accordingly by inducing or repressing specific nuclear genes encoding plastid proteins. We show that ABI4, which is known to repress the LHCB genes during retrograde signalling, is activated through phosphorylation by the MAP kinases MPK3/MPK6 and the activity of these kinases is regulated through 14-3-3 omega-mediated Ca2+-dependent scaffolding depending on the chloroplast calcium sensor protein CAS. These findings uncover an additional mechanism in which chloroplast-modulated Ca2+ signalling controls the MAPK pathway for the activation of critical components of the retrograde signalling chain

Plastid-nucleus communication involves calcium-modulated MAPK signalling

Chloroplast retrograde signals play important roles in coordinating the plastid and nuclear gene expression and are critical for proper chloroplast biogenesis and for maintaining optimal chloroplast functions in response to environmental changes in plants. Until now, the signals and the mechanisms for retrograde signalling remain poorly understood. Here we identify factors that allow the nucleus to perceive stress conditions in the chloroplast and to respond accordingly by inducing or repressing specific nuclear genes encoding plastid proteins. We show that ABI4, which is known to repress the LHCB genes during retrograde signalling, is activated through phosphorylation by the MAP kinases MPK3/MPK6 and the activity of these kinases is regulated through 14-3-3 omega-mediated Ca2+-dependent scaffolding depending on the chloroplast calcium sensor protein CAS. These findings uncover an additional mechanism in which chloroplast-modulated Ca2+ signalling controls the MAPK pathway for the activation of critical components of the retrograde signalling chain

Using advanced vibrational molecular spectroscopy to detect moist heating induced protein structure changes in cool-climate adapted barley grain.

Different techniques have been applied in feed processing to improve ruminal degradation and nutrient utilization in ruminant. There are limited studies investigating how moist heating process impacts barley protein utilization and internal molecular structures. The objectives of this study were to investigate: 1) how moist heating affects barley protein chemical profiles and Cornell Net Carbohydrate and Protein System (CNCPS) subfractions, in situ rumen degradation parameters, and predicted intestinal protein supply and feed milk value; 2) how moist heating affects protein molecular spectral features; and 3) the relationship between protein molecular structure spectral features and protein chemical profiles and metabolic characteristics. The barley variety CDC cowboy samples collected from the research farm during two consecutive years were used. Half of each sample was kept as raw and the other half underwent moist heating. The advanced molecular spectroscopy (attenuated total reflectance-fourier transform infrared, ATR-FTIR) was used to detect the barley protein molecular structure spectral features. It was found that moist heating decreased the fractions of soluble protein and increased the moderately degradable protein and ingestible protein fractions. This further resulted in the changes of in situ rumen degradation parameters and intestinal protein digestion characteristics. The protein molecular structure spectral features detected by using ATR-FTIR spectroscopy can be used as potential predictors for protein related chemical and metabolic parameters

Metabolites and chloroplast retrograde signaling

Intracellular signaling from chloroplast to nucleus followed by a subsequent response in the chloroplast is called retrograde signaling. It not only coordinates the expression of nuclear and chloroplast genes, which is essential for chloroplast biogenesis, but also maintains chloroplast function at optimal levels in response to fluxes in metabolites and changes in environmental conditions. In recent years several putative retrograde signals have been identified and signaling pathways have been proposed. Here we review retrograde signals derived from tetrapyrroles, carotenoids, nucleotides and isoprene precursors in response to abiotic stresses, including oxidative stress. We discuss the responses that these signals elicit and show that they not only modify chloroplast function but also influence other aspects of plant development and adaptation

Metabolites and chloroplast retrograde signaling

Intracellular signaling from chloroplast to nucleus followed by a subsequent response in the chloroplast is called retrograde signaling. It not only coordinates the expression of nuclear and chloroplast genes, which is essential for chloroplast biogenesis, but also maintains chloroplast function at optimal levels in response to fluxes in metabolites and changes in environmental conditions. In recent years several putative retrograde signals have been identified and signaling pathways have been proposed. Here we review retrograde signals derived from tetrapyrroles, carotenoids, nucleotides and isoprene precursors in response to abiotic stresses, including oxidative stress. We discuss the responses that these signals elicit and show that they not only modify chloroplast function but also influence other aspects of plant development and adaptation

Effects of feeding blend-pelleted co-products on nutrients intake, digestibility, and production performance of high producing dairy cows

The objectives of this study were to examine the effects of feeding newly-developed blend-pelleted carinata meal (BPPCR) and blend-pelleted canola meal (BPPCN) on nutrients intake, digestibility, and production performance of high producing dairy cows. In this study, nine mid-lactating Holstein cows (BW 679 124 kg; DIM 96 22) were used in a triplicated 33 Latin Square study. Within each square, each cow was randomly assigned to one of the three treatments: Control (typical barley-based diet in western Canada); BPPCR (soybean and canola meal in the control diet replaced by blend-pelleted carinata meal), BPPCN (soybean and canola meal in the control diet replaced by blend-pelleted canola meal). Each period lasted for 21 days, with the first 14 days as an adaptation period. The total collection of feces and urine were conducted on six cows from two Latin squares. The results showed that there were no treatment effects on milk yield, milk composition, milk yield, and nutrients intake and digestibility (P > 0.10). The nitrogen balance among the three treatment groups was not different either. In conclusion, replacing soybean meal and canola meal with blend-pelleted co-products did not affect the nutrient intake, digestibility, and production performance in high producing dairy cows.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Identification of essential proteins based on edge features and the fusion of multiple-source biological information

Abstract Background A major current focus in the analysis of protein–protein interaction (PPI) data is how to identify essential proteins. As massive PPI data are available, this warrants the design of efficient computing methods for identifying essential proteins. Previous studies have achieved considerable performance. However, as a consequence of the features of high noise and structural complexity in PPIs, it is still a challenge to further upgrade the performance of the identification methods. Methods This paper proposes an identification method, named CTF, which identifies essential proteins based on edge features including h-quasi-cliques and uv-triangle graphs and the fusion of multiple-source information. We first design an edge-weight function, named EWCT, for computing the topological scores of proteins based on quasi-cliques and triangle graphs. Then, we generate an edge-weighted PPI network using EWCT and dynamic PPI data. Finally, we compute the essentiality of proteins by the fusion of topological scores and three scores of biological information. Results We evaluated the performance of the CTF method by comparison with 16 other methods, such as MON, PeC, TEGS, and LBCC, the experiment results on three datasets of Saccharomyces cerevisiae show that CTF outperforms the state-of-the-art methods. Moreover, our method indicates that the fusion of other biological information is beneficial to improve the accuracy of identification