Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase.

Plant endosymbiosis with nitrogen-fixing cyanobacteria has independently evolved in diverse plant lineages, offering a unique window to study the evolution and genetics of plant-microbe interaction. However, very few complete genomes exist for plant cyanobionts, and therefore little is known about their genomic and functional diversity. Here, we present four complete genomes of cyanobacteria isolated from bryophytes. Nanopore long-read sequencing allowed us to obtain circular contigs for all the main chromosomes and most of the plasmids. We found that despite having a low 16S rRNA sequence divergence, the four isolates exhibit considerable genome reorganizations and variation in gene content. Furthermore, three of the four isolates possess genes encoding vanadium (V)-nitrogenase (vnf), which is uncommon among diazotrophs and has not been previously reported in plant cyanobionts. In two cases, the vnf genes were found on plasmids, implying possible plasmid-mediated horizontal gene transfers. Comparative genomic analysis of vnf-containing cyanobacteria further identified a conserved gene cluster. Many genes in this cluster have not been functionally characterized and would be promising candidates for future studies to elucidate V-nitrogenase function and regulation

Approximation of L\"owdin Orthogonalization to a Spectrally Efficient Orthogonal Overlapping PPM Design for UWB Impulse Radio

In this paper we consider the design of spectrally efficient time-limited pulses for ultrawideband (UWB) systems using an overlapping pulse position modulation scheme. For this we investigate an orthogonalization method, which was developed in 1950 by Per-Olov L\"owdin. Our objective is to obtain a set of N orthogonal (L\"owdin) pulses, which remain time-limited and spectrally efficient for UWB systems, from a set of N equidistant translates of a time-limited optimal spectral designed UWB pulse. We derive an approximate L\"owdin orthogonalization (ALO) by using circulant approximations for the Gram matrix to obtain a practical filter implementation. We show that the centered ALO and L\"owdin pulses converge pointwise to the same Nyquist pulse as N tends to infinity. The set of translates of the Nyquist pulse forms an orthonormal basis or the shift-invariant space generated by the initial spectral optimal pulse. The ALO transform provides a closed-form approximation of the L\"owdin transform, which can be implemented in an analog fashion without the need of analog to digital conversions. Furthermore, we investigate the interplay between the optimization and the orthogonalization procedure by using methods from the theory of shift-invariant spaces. Finally we develop a connection between our results and wavelet and frame theory.Comment: 33 pages, 11 figures. Accepted for publication 9 Sep 201

Can ChatGPT Enable ITS? The Case of Mixed Traffic Control via Reinforcement Learning

The surge in Reinforcement Learning (RL) applications in Intelligent Transportation Systems (ITS) has contributed to its growth as well as highlighted key challenges. However, defining objectives of RL agents in traffic control and management tasks, as well as aligning policies with these goals through an effective formulation of Markov Decision Process (MDP), can be challenging and often require domain experts in both RL and ITS. Recent advancements in Large Language Models (LLMs) such as GPT-4 highlight their broad general knowledge, reasoning capabilities, and commonsense priors across various domains. In this work, we conduct a large-scale user study involving 70 participants to investigate whether novices can leverage ChatGPT to solve complex mixed traffic control problems. Three environments are tested, including ring road, bottleneck, and intersection. We find ChatGPT has mixed results. For intersection and bottleneck, ChatGPT increases number of successful policies by 150% and 136% compared to solely beginner capabilities, with some of them even outperforming experts. However, ChatGPT does not provide consistent improvements across all scenarios

The Chlamydomonas CO2-concentrating mechanism and its potential for engineering photosynthesis in plants

To meet the food demands of a rising global population, innovative strategies are required to increase crop yields. Improvements in plant photosynthesis by genetic engineering show considerable potential towards this goal. One prospective approach is to introduce a CO2-concentrating mechanism into crop plants to increase carbon fixation by supplying the central carbon-fixing enzyme, Rubisco, with a higher concentration of its substrate, CO2. A promising donor organism for the molecular machinery of this mechanism is the eukaryotic alga Chlamydomonas reinhardtii. This review summarizes the recent advances in our understanding of carbon concentration in Chlamydomonas, outlines the most pressing gaps in our knowledge and discusses strategies to transfer a CO2-concentrating mechanism into higher plants to increase photosynthetic performance

Metal-substituted protein MRI contrast agents engineered for enhanced relaxivity and ligand sensitivity

Engineered metalloproteins constitute a flexible new class of analyte-sensitive molecular imaging agents detectable by magnetic resonance imaging (MRI), but their contrast effects are generally weaker than synthetic agents. To augment the proton relaxivity of agents derived from the heme domain of cytochrome P450 BM3 (BM3h), we formed manganese(III)-containing proteins that have higher electron spin than their native ferric iron counterparts. Metal substitution was achieved by coexpressing BM3h variants with the bacterial heme transporter ChuA in Escherichia coli and supplementing the growth medium with Mn3+-protoporphyrin IX. Manganic BM3h variants exhibited up to 2.6-fold higher T1 relaxivities relative to native BM3h at 4.7 T. Application of ChuA-mediated porphyrin substitution to a collection of thermostable chimeric P450 domains resulted in a stable, high-relaxivity BM3h derivative displaying a 63% relaxivity change upon binding of arachidonic acid, a natural ligand for the P450 enzyme and an important component of biological signaling pathways. This work demonstrates that protein-based MRI sensors with robust ligand sensitivity may be created with ease by including metal substitution among the toolkit of methods available to the protein engineer.National Institutes of Health (U.S.) (NIH Grant R01-DA28299 )National Institutes of Health (U.S.) (NIH NRSA Fellowship (Award F32-GM087102))California Institute of Technology (Caltech Jacobs Grant

The impact of green roof ageing on substrate characteristics and hydrological performance

Green roofs contribute to stormwater management through the retention of rainfall and the detention of runoff. However, there is very limited knowledge concerning the evolution of green roof hydrological performance with system age. This study presents a non-invasive technique which allows for repeatable determination of key substrate characteristics over time, and evaluates the impact of observed substrate changes on hydrological performance. The physical properties of 12 green roof substrate cores have been evaluated using non-invasive X-Ray Microtomography (XMT) imaging. The cores comprised three replicates of two contrasting substrate types at two different ages: unused virgin samples; and 5-year-old samples from existing green roof test beds. Whilst significant structural differences (density, pore and particle sizes, tortuosity) between virgin and aged samples of a crushed brick substrate were observed, these differences did not significantly affect hydrological characteristics (maximum water holding capacity and saturated hydraulic conductivity). A contrasting substrate based upon a light expanded clay aggregate experienced increases in the number of fine particles and pores over time, which led to increases in maximum water holding capacity of 7%. In both substrates, the saturated hydraulic conductivity estimated from the XMT images was lower in aged compared with virgin samples. Comparisons between physically-derived and XMT-derived substrate hydrological properties showed that similar values and trends in the data were identified, confirming the suitability of the non-invasive XMT technique for monitoring changes in engineered substrates over time. The observed effects of ageing on hydrological performance were modelled as two distinct hydrological processes, retention and detention. Retention performance was determined via a moisture-flux model using physically-derived values of virgin and aged maximum water holding capacity. Increased water holding capacity with age increases the potential for retention performance. However, seasonal variations in retention performance greatly exceed those associated with the observed age-related increases in water holding capacity (+72% vs +7% respectively). Detention performance was determined via an unsaturated-flow finite element model, using van Genuchten parameters and XMT-derived values of saturated hydraulic conductivity. Reduced saturated hydraulic conductivity increases detention performance. For a 1-hour 30-year design storm, the peak runoff was found to be 33% lower for the aged brick-based substrate compared with its virgin counterpart

Mixed Traffic Control and Coordination from Pixels

Traffic congestion is a persistent problem in our society. Existing methods for traffic control have proven futile in alleviating current congestion levels leading researchers to explore ideas with robot vehicles given the increased emergence of vehicles with different levels of autonomy on our roads. This gives rise to mixed traffic control, where robot vehicles regulate human-driven vehicles through reinforcement learning (RL). However, most existing studies use precise observations that involve global information, such as environment outflow, and local information, i.e., vehicle positions and velocities. Obtaining this information requires updating existing road infrastructure with vast sensor environments and communication to potentially unwilling human drivers. We consider image observations as the alternative for mixed traffic control via RL: 1) images are ubiquitous through satellite imagery, in-car camera systems, and traffic monitoring systems; 2) images do not require a complete re-imagination of the observation space from environment to environment; and 3) images only require communication to equipment. In this work, we show robot vehicles using image observations can achieve similar performance to using precise information on environments, including ring, figure eight, intersection, merge, and bottleneck. In certain scenarios, our approach even outperforms using precision observations, e.g., up to 26% increase in average vehicle velocity in the merge environment and a 6% increase in outflow in the bottleneck environment, despite only using local traffic information as opposed to global traffic information

Multiple viral infections in Agaricus bisporus - characterisation of 18 unique RNA viruses and 8 ORFans identified by deep sequencing

Thirty unique non-host RNAs were sequenced in the cultivated fungus, Agaricus bisporus, comprising 18 viruses each encoding an RdRp domain with an additional 8 ORFans (non-host RNAs with no similarity to known sequences). Two viruses were multipartite with component RNAs showing correlative abundances and common 3′ motifs. The viruses, all positive sense single-stranded, were classified into diverse orders/families. Multiple infections of Agaricus may represent a diverse, dynamic and interactive viral ecosystem with sequence variability ranging over 2 orders of magnitude and evidence of recombination, horizontal gene transfer and variable fragment numbers. Large numbers of viral RNAs were detected in multiple Agaricus samples; up to 24 in samples symptomatic for disease and 8–17 in asymptomatic samples, suggesting adaptive strategies for co-existence. The viral composition of growing cultures was dynamic, with evidence of gains and losses depending on the environment and included new hypothetical viruses when compared with the current transcriptome and EST databases. As the non-cellular transmission of mycoviruses is rare, the founding infections may be ancient, preserved in wild Agaricus populations, which act as reservoirs for subsequent cell-to-cell infection when host populations are expanded massively through fungiculture

Safe Design Suggestions for Vegetated Roofs

Rooftop vegetation is becoming increasingly popular because of its environmental benefits and its ability to earn green-building certification credits. With the exception of one international guideline, there is little mention of worker safety and health in vegetated-roof codes and literature. Observations and field investigations of 19 vegetated roofs in the United States revealed unsafe access for workers and equipment, a lack of fall-protection measures, and other site-specific hazards. Design for safety strategies and the integration of life-cycle safety thinking with green-building credits systems are the preferred methods to reduce risk to workers on vegetated roofs. Design suggestions have been developed to add to the body of knowledge. The findings complement several National Institute for Occupational Safety and Health (NIOSH) construction and prevention through design (PtD) goals and are congruent with NIOSH’s Safe Green Jobs initiative. Organizations that install and maintain vegetated roofs can utilize the findings to understand hazards, take precautions, and incorporate safety into their bids The published version of this article is available here: 10.1061/(ASCE)CO.1943-7862.0000500Support from the the Virginia Tech Occupational Safety and Health Research Center through the Kevin P. Granata Pilot Program funded by the Institute for Critical Technology and Applied Sciences

Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken

Background: EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallusgallus and several inbred experimental lines using whole-genome sequence data. Results: An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5% are common to 90% of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P<2.31−6), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P<0.05). Conclusions: Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts