Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Origin of two contrasting latest Permian–Triassic volcanic rock suites in the northern North China Craton: implications for early Mesozoic lithosphere thinning

<div><p>New geological, geochronological, and geochemical results on volcanic rocks and cobbles from early Mesozoic sedimentary rocks identify two contrasting latest Permian–Triassic volcanic rock suites in the northern North China Craton (NCC). The early rock suite erupted during the latest Permian–Early Triassic at ca. 255–245 Ma and was probably widely distributed in the northern NCC prior to the Early Jurassic. It comprises rhyolitic welded tuff, rhyolite, and tuffaceous sandstone and is characterized by high contents of SiO₂ and K₂O, moderate initial ⁸⁷Sr/⁸⁶Sr, low negative <i>ε</i>_Nd(<i>t</i>) and <i>ε</i>_Hf(<i>t</i>) values, and old Nd-Hf isotopic model ages. It was likely produced by fractional crystallization of lower crustal-derived magmas due to underplating by lithospheric mantle-derived magmas near the crust–mantle boundary in syncollisional to post-collisional/post-orogenic tectonic settings. The late rock suite, erupted during the Middle–Late Triassic at ca. 238–228 Ma, displays adakitic geochemical signatures and consists of intermediate volcanic rocks such as andesite, trachyandesite, and autoclastic trachyandesite breccia, with minor felsic rocks. This suite is characterized by high Al₂O₃, MgO, Sr, Ba, Cr, V, and Ni concentrations; high Mg# values; low Y and Yb concentrations and high Sr/Y ratios; low initial ⁸⁷Sr/⁸⁶Sr; high negative <i>ε</i>_Nd(<i>t</i>) and <i>ε</i>_Hf(<i>t</i>) values; and young Nd-Hf isotopic model ages. The younger suite was generated by mixing of magmas derived from melting of upwelling asthenosphere, with melts of ancient lower crust induced by underplating of basaltic magmas in an intraplate extensional setting. Strong upwelling of asthenospheric mantle and significant involvement of the asthenospheric mantle materials indicate that the lithospheric mantle beneath the northern NCC was partially delaminated during Middle–Late Triassic time, representing the initial destruction and lithospheric thinning of the northern NCC. Lithospheric thinning and delamination are likely the most important reasons for the Triassic tectonic transition and change of magmatism and deformation patterns in the northern NCC.</p></div

Exploring the use of diverse replicas for big location tracking data

The value of large amount of location tracking data has received wide attention in many applications including human behavior analysis, urban transportation planning, and various location-based services (LBS). Nowadays, both scientific and industrial communities are encouraged to collect as much location tracking data as possible, which brings about two issues: 1) it is challenging to process the queries on big location tracking data efficiently, and 2) it is expensive to store several exact data replicas for fault-tolerance. So far, several dedicated storage systems have been proposed to address these issues. However, they do not work well when the query ranges vary widely. In this paper, we present the design of a storage system using diverse replica scheme which improves the query processing efficiency with reduced cost of storage space. To the best of our knowledge, we are the first to investigate the data storage and processing in the context of big location tracking data. Specifically, we conduct in-depth theoretical and empirical analysis of the trade-offs between different spatio-temporal partitioning schemes as well as data encoding schemes. Then we propose an effective approach to select an appropriate set of diverse replicas, which is optimized for the expected query loads while conforming to the given storage space budget. The experiment results confirm that using diverse replicas can significantly improve the overall query performance. The results also demonstrate that the proposed algorithms for the replica selection problem is both effective and efficient

Moderate Soil Drying-Induced Alternative Splicing Provides a Potential Novel Approach for the Regulation of Grain Filling in Rice Inferior Spikelets

Poor grain filling of inferior spikelets, especially in some large-panicle rice varieties, is becoming a major limitation in breaking the ceiling of rice production. In our previous studies, we proved that post-anthesis moderate soil drying (MD) was an effective way to promote starch synthesis and inferior grain filling. As one of the most important regulatory processes in response to environmental cues and at different developmental stages, the function of alternative splicing (AS) has not yet been revealed in regulating grain filling under MD conditions. In this study, AS events at the most active grain-filling stage were identified in inferior spikelets under well-watered control (CK) and MD treatments. Of 16,089 AS events, 1840 AS events involving 1392 genes occurred differentially between the CK and MD treatments, many of which function on spliceosome, ncRNA metabolic process, starch, and sucrose metabolism, and other functions. Some of the splicing factors and starch synthesis-related genes, such as SR protein, hnRNP protein, OsAGPL2, OsAPS2, OsSSIVa, OsSSIVb, OsGBSSII, and OsISA1 showed differential AS changes under MD treatment. The expression of miR439f and miR444b was reduced due to an AS event which occurred in the intron where miRNAs were located in the MD-treated inferior spikelets. On the contrary, OsAGPL2, an AGPase encoding gene, was alternatively spliced, resulting in different transcripts with or without the miR393b binding site, suggesting a potential mechanism for miRNA-mediated gene regulation on grain filling of inferior spikelets in response to MD treatment. This study provides some new insights into the function of AS on the MD-promoted grain filling of inferior spikelets, and potential application in agriculture to increase rice yields by genetic approaches

Environmental Stimuli: A Major Challenge during Grain Filling in Cereals

Light, temperature, water, and fertilizer are arguably the most important environmental factors regulating crop growth and productivity. Environmental stimuli, including low light, extreme temperatures, and water stresses caused by climate change, affect crop growth and production and pose a growing threat to sustainable agriculture. Furthermore, soil salinity is another major environmental constraint affecting crop growth and threatening global food security. The grain filling stage is the final stage of growth and is also the most important stage in cereals, directly determining the grain weight and final yield. However, the grain filling process is extremely vulnerable to different environmental stimuli, especially for inferior spikelets. Given the importance of grain filling in cereals and the deterioration of environmental problems, understanding environmental stimuli and their effects on grain filling constitutes a major focus of crop research. In recent years, significant advances made in this field have led to a good description of the intricate mechanisms by which different environmental stimuli regulate grain filling, as well as approaches to adapt cereals to changing climate conditions and to give them better grain filling. In this review, the current environmental stimuli, their dose–response effect on grain filling, and the physiological and molecular mechanisms involved are discussed. Furthermore, what we can do to help cereal crops adapt to environmental stimuli is elaborated. Overall, we call for future research to delve deeper into the gene function-related research and the commercialization of gene-edited crops. Meanwhile, smart agriculture is the development trend of the future agriculture under environmental stimuli

T-Watcher: A New Visual Analytic System for Effective Traffic Surveillance

Nowadays, big cities are suffering from severe traffic congestion as a result of the continuing increase in vehicles. Taxis equipped with GPS can be viewed as sensors of the traffic situation in city. However, trajectory data generated by taxi's GPS traces are often high-dimensional and contain large spatial and temporal attributes, which pose challenges for analysts. In this paper, based on taxi trajectory data, we present an interactive visual analytics system, T-Watcher, for monitoring and analyzing complex traffic situations in big cities. Users are able to use a carefully designed interface to monitor and inspect data interactively from three levels (region, road and vehicle views). We develop a visualization method to monitor and analyze traffic patterns for abnormal behaviors detection. In the region view of our system, global temporal changes in spatial evolution will be presented to users and can be interactively explored. The road view shows temporal changes to the traffic situations of significant segments of roads. The vehicle view uses a novel visualization method to track individual vehicles. Furthermore, the three views integrate important statistical and historical information related to traffic, which illustrate temporal changes of the traffic. We find that this design can help users explore historical information while monitoring traffic. We test our system on a real-life vehicle dataset collected from thousands of taxis and obtained some interesting findings. The experimental results confirm the effectiveness and efficiency of the proposed visual detection method. The analysis of the results also shows that our system is capable of effectively monitoring traffic and detecting abnormal traffic patterns

Environmental Stimuli: A Major Challenge during Grain Filling in Cereals

Light, temperature, water, and fertilizer are arguably the most important environmental factors regulating crop growth and productivity. Environmental stimuli, including low light, extreme temperatures, and water stresses caused by climate change, affect crop growth and production and pose a growing threat to sustainable agriculture. Furthermore, soil salinity is another major environmental constraint affecting crop growth and threatening global food security. The grain filling stage is the final stage of growth and is also the most important stage in cereals, directly determining the grain weight and final yield. However, the grain filling process is extremely vulnerable to different environmental stimuli, especially for inferior spikelets. Given the importance of grain filling in cereals and the deterioration of environmental problems, understanding environmental stimuli and their effects on grain filling constitutes a major focus of crop research. In recent years, significant advances made in this field have led to a good description of the intricate mechanisms by which different environmental stimuli regulate grain filling, as well as approaches to adapt cereals to changing climate conditions and to give them better grain filling. In this review, the current environmental stimuli, their dose&ndash;response effect on grain filling, and the physiological and molecular mechanisms involved are discussed. Furthermore, what we can do to help cereal crops adapt to environmental stimuli is elaborated. Overall, we call for future research to delve deeper into the gene function-related research and the commercialization of gene-edited crops. Meanwhile, smart agriculture is the development trend of the future agriculture under environmental stimuli

Proposition pour un tiroir de sélection de référence pour les alimentations programmables utilisables à hautes et à basses énergies: cas particulier des alimentations PFW

(a) Effect of varying pH on activities of GLO isozymes. Each buffer (50 mM) was made of respective PBS (pH 6.0-8.0) and Tris-HCl (pH 8.0-9.0). (The highest activity of each GLO isozyme at pH 7.8 was set as 1). (b) Effect of temperature on activities of GLO isozymes. Enzymes in 50 mM PBS buffer (pH 7.8) were pre-incubated at various temperatures (22-60 °C) for 5 min, and then activities were measured at the same temperature (For GLO1 and GLO1 + 4, the highest activity at 45 °C was set as 1; For GLO3, the highest activity at 47 °C was set as 1; For GLO4, the highest activity at 42 °C was set as 1). Values are means ± SD (n = 3). (TIFF 7340 kb

NLP2-NR Module Associated NO Is Involved in Regulating Seed Germination in Rice under Salt Stress

Salt stress has the most severe impact on plant growth and development, including seed germination. However, little is known about the mechanism of NR (nitrate reductase)-associated nitric oxide (NO) regulates salt tolerance during seed germination in rice. Herein, we shown that inhibition of seed germination by salt stress was significantly impaired by sodium nitroferricyanide (SNP), a NO donor. Then a triple mutant, nr1/nr2/nr3, was generated. Results shown that germination of triple mutants were delayed and were much more sensitive to salt stress than WT plant, which can be rescued by application of SNP. qPCR analysis revealed that expressions of abscisic acid (ABA) catabolism gene, OsABA8ox1, was suppressed in triple mutants under salt stress, resulting in an elevated ABA content. Similar to SNP, application of nitrate also rescued seed germination under salt stress, which, however, was blocked in the triple mutants. Further study revealed that a nitrate responsive transcript factor, OsNLP2, was induced by salt stress, which thus up-regulates the expression of OsNRs and NR activity, resulting in promoted salt tolerance during seed germination. In addition, nitrate-mediated salt tolerance was impaired in mutant of aba8ox1, a target gene for NLP2. Transient trans-activation assays further revealed NLP2 can significantly activate the expression of OsABA8ox1 and OsNR1, suggesting that NLP2 activates expression of ABA catabolism gene directly or indirectly via NR-associated NO. Taken together, our results demonstrate that NLP2-NR associated NO was involved in salt response by increasing ABA catabolism during seed germination and highlight the importance of NO for stress tolerance of plants