Effect of Dehydrated Trehalose Matrix on the Kinetics of Forward Electron Transfer Reactions in Photosystem I

The effect of dehydration on the kinetics of forward electron transfer (ET) has been studied in cyanobacterial photosystem I (PS I) complexes in a trehalose glassy matrix by time-resolved optical and EPR spectroscopies in the 100 fs to 1 ms time domain. The kinetics of the flash-induced absorption changes in the subnanosecond time domain due to primary and secondary charge separation steps were monitored by pump–probe laser spectroscopy with 20-fs low-energy pump pulses centered at 720 nm. The back-reaction kinetics of P700 were measured by high-field time-resolved EPR spectroscopy and the forward kinetics of A∙−1A/A∙−1B→FX by time-resolved optical spectroscopy at 480 nm. The kinetics of the primary ET reactions to form the primary P∙+700A∙−0 and the secondary P∙+700A∙−1 ion radical pairs were not affected by dehydration in the trehalose matrix, while the yield of the P∙+700A∙−1 was decreased by ~20%. Forward ET from the phylloquinone molecules in the A∙−1A and A∙−1B sites to the iron–sulfur cluster FX slowed from ~220 ns and ~20 ns in solution to ~13 μs and ~80 ns, respectively. However, as shown by EPR spectroscopy, the ~15 μs kinetic phase also contains a small contribution from the recombination between A∙−1B and P∙+700. These data reveal that the initial ET reactions from P700 to secondary phylloquinone acceptors in the A- and B-branches of cofactors (A1A and A1B) remain unaffected whereas ET beyond A1A and A1B is slowed or prevented by constrained protein dynamics due to the dry trehalose glass matrix

Pottery making tradition in Logroño: an archaeometric approach to the Late Medieval workshops

This paper deals with the findings of Hospital Viejo site of Logroño (La Rioja, Spain), which yielded the largest evidence of local pottery production, comprising three kilns and a potters’ dump (13th–15th centuries). The study of pottery production in inland Iberia provides valuable information on the material conditions in which the Iberian medieval and post-medieval society occurred. Yet, the territory of La Rioja has been largely eclipsed by studies at coastal and southern areas of Iberia, due to their role in maritime exchange.With the aim of understanding the specific incidence and evolution of medieval pottery at regional scale, 77 sherds (MNI 637) including glazed and unglazed ware and kiln utensils were archaeometrically examined by combining the use of ICP-MS, XRD and SEM-EDS. Likewise, NAA was applied for provenance analysis, including the collation with a large majolica NAA database. The results provided the first chemical fingerprint of the production from Logroño consisting on three compositional groups within the same workshop (LOG-A, LOG-B and LOG-C). Moreover, pottery trading from Teruel and Valencia was detected, sustaining the historical records of these trade-networks. The imports showed tin lead glazes obtained by known recipes, contrasting with simpler manufactures (mostly unglazed or only lead glazed) of contemporary Logroño.DOKBERRI DOCREC19/39 (University of the Basque Country UPV/EHU), Ministerio de Economía y Competitividad CERANOR-2 (HAR2017-84219-P), Ministerio de Economía y Competitividad Ramon y Cajal (RYC-2014-16835), National Science Foundation grant #191277

Short-Term Vehicle Traffic Prediction for Terahertz Line-of-Sight Estimation and Optimization in Small Cells

Significant efforts have been made and are still being made on short-term traffic prediction methods, specially for highway traffic based on punctual measurements. Literature on predicting the spatial distribution of the traffic in urban intersections is, however, very limited. This work presents a novel data-driven prediction algorithm based on Random Forests regression over spatio-temporal aggregated data of vehicle counts inside a grid. The proposed approach aims to estimate future distribution of V2X traffic demand, providing a valuable input for a dynamic management of radio resources in small cells. Radio Access Networks (RAN) working in the terahertz band and deployed in small cells are expected to meet the high-demanding data rate requirements of connected vehicles. However, terahertz frequency propagation has important limitations in outdoor scenarios, including distance propagation, high absorption coefficients values and low reflection properties. More concretely, in settings such as complex road intersections, dynamic signal blockage and shadowing effects may cause significant power losses and compromise the quality of service for some vehicles. The forthcoming network demand, estimated from the regression algorithm is used to compute the losses expected due to other vehicles potentially located between the transmitter and the receiver. We conclude that our approach, which is designed from a grid-like perspective, outperforms other traffic prediction methods and the combined result of these predictions with a dynamic reflector orientation algorithm, as a use case application, allows reducing the ratio of vehicles that do not receive a minimum signal power

Recently photoassimilated carbon and fungus-delivered nitrogen are spatially correlated in the ectomycorrhizal tissue of Fagus sylvatica

Ectomycorrhizal plants trade plant‐assimilated carbon for soil nutrients with their fungal partners. The underlying mechanisms, however, are not fully understood. Here we investigate the exchange of carbon for nitrogen in the ectomycorrhizal symbiosis of Fagus sylvatica across different spatial scales from the root system to the cellular level. We provided (15)N‐labelled nitrogen to mycorrhizal hyphae associated with one half of the root system of young beech trees, while exposing plants to a (13)CO(2) atmosphere. We analysed the short‐term distribution of (13)C and (15)N in the root system with isotope‐ratio mass spectrometry, and at the cellular scale within a mycorrhizal root tip with nanoscale secondary ion mass spectrometry (NanoSIMS). At the root system scale, plants did not allocate more (13)C to root parts that received more (15)N. Nanoscale secondary ion mass spectrometry imaging, however, revealed a highly heterogenous, and spatially significantly correlated distribution of (13)C and (15)N at the cellular scale. Our results indicate that, on a coarse scale, plants do not allocate a larger proportion of photoassimilated C to root parts associated with N‐delivering ectomycorrhizal fungi. Within the ectomycorrhizal tissue, however, recently plant‐assimilated C and fungus‐delivered N were spatially strongly coupled. Here, NanoSIMS visualisation provides an initial insight into the regulation of ectomycorrhizal C and N exchange at the microscale

CogITS: Cognition-enabled network management for 5G V2X Communication

The 5G promise for ubiquitous communications is expected to be a key enabler for transportation efficiency. However, the consequent increase of both data payload and number of users derived from new Intelligent Transport Systems makes network management even more challenging; an ideal network management will need to be capable of self-managing fast moving nodes that sit in the 5G data plane. Platooning applications, for instance, need a highly flexible and high efficient infrastructure for optimal road capacity. Network management solutions have, then, to accommodate more intelligence in its decision-making process due to the network complexity of ITS. This paper proposes this envisioned architecture namely Cognition-enabled network management for 5G V2X Communication (CogITS). It is empowered by machine learning to dynamically allocate resources in the network based on traffic prediction and adaptable physical layer settings. Preliminary proof-of-concept validation results, in a platooning scenario, show that the proposed architecture can improve the overall network latency over time with a minimum increase of control message traffic

Reprogramming human T cell function and specificity with non-viral genome targeting.

Decades of work have aimed to genetically reprogram T cells for therapeutic purposes1,2 using recombinant viral vectors, which do not target transgenes to specific genomic sites3,4. The need for viral vectors has slowed down research and clinical use as their manufacturing and testing is lengthy and expensive. Genome editing brought the promise of specific and efficient insertion of large transgenes into target cells using homology-directed repair5,6. Here we developed a CRISPR-Cas9 genome-targeting system that does not require viral vectors, allowing rapid and efficient insertion of large DNA sequences (greater than one kilobase) at specific sites in the genomes of primary human T cells, while preserving cell viability and function. This permits individual or multiplexed modification of endogenous genes. First, we applied this strategy to correct a pathogenic IL2RA mutation in cells from patients with monogenic autoimmune disease, and demonstrate improved signalling function. Second, we replaced the endogenous T cell receptor (TCR) locus with a new TCR that redirected T cells to a cancer antigen. The resulting TCR-engineered T cells specifically recognized tumour antigens and mounted productive anti-tumour cell responses in vitro and in vivo. Together, these studies provide preclinical evidence that non-viral genome targeting can enable rapid and flexible experimental manipulation and therapeutic engineering of primary human immune cells

ContDist: a tool for the analysis of quantitative gene and promoter properties

<p>Abstract</p> <p>Background</p> <p>The understanding of how promoter regions regulate gene expression is complicated and far from being fully understood. It is known that histones' regulation of DNA compactness, DNA methylation, transcription factor binding sites and CpG islands play a role in the transcriptional regulation of a gene. Many high-throughput techniques exist nowadays which permit the detection of epigenetic marks and regulatory elements in the promoter regions of thousands of genes. However, so far the subsequent analysis of such experiments (e.g. the resulting gene lists) have been hampered by the fact that currently no tool exists for a detailed analysis of the promoter regions.</p> <p>Results</p> <p>We present ContDist, a tool to statistically analyze quantitative gene and promoter properties. The software includes approximately 200 quantitative features of gene and promoter regions for 7 commonly studied species. In contrast to "traditionally" ontological analysis which only works on qualitative data, all the features in the underlying annotation database are quantitative gene and promoter properties.</p> <p>Utilizing the strong focus on the promoter region of this tool, we show its usefulness in two case studies; the first on differentially methylated promoters and the second on the fundamental differences between housekeeping and tissue specific genes. The two case studies allow both the confirmation of recent findings as well as revealing previously unreported biological relations.</p> <p>Conclusion</p> <p>ContDist is a new tool with two important properties: 1) it has a strong focus on the promoter region which is usually disregarded by virtually all ontology tools and 2) it uses quantitative (continuously distributed) features of the genes and its promoter regions which are not available in any other tool. ContDist is available from <url>http://web.bioinformatics.cicbiogune.es/CD/ContDistribution.php</url></p

Rapid Transfer of Plant Photosynthates to Soil Bacteria via Ectomycorrhizal Hyphae and Its Interaction With Nitrogen Availability

Plant roots release recent photosynthates into the rhizosphere, accelerating decomposition of organic matter by saprotrophic soil microbes (“rhizosphere priming effect”) which consequently increases nutrient availability for plants. However, about 90% of all higher plant species are mycorrhizal, transferring a significant fraction of their photosynthates directly to their fungal partners. Whether mycorrhizal fungi pass on plant-derived carbon (C) to bacteria in root-distant soil areas, i.e., incite a “hyphosphere priming effect,” is not known. Experimental evidence for C transfer from mycorrhizal hyphae to soil bacteria is limited, especially for ectomycorrhizal systems. As ectomycorrhizal fungi possess enzymatic capabilities to degrade organic matter themselves, it remains unclear whether they cooperate with soil bacteria by providing photosynthates, or compete for available nutrients. To investigate a possible C transfer from ectomycorrhizal hyphae to soil bacteria, and its response to changing nutrient availability, we planted young beech trees (Fagus sylvatica) into “split-root” boxes, dividing their root systems into two disconnected soil compartments. Each of these compartments was separated from a litter compartment by a mesh penetrable for fungal hyphae, but not for roots. Plants were exposed to a 13C-CO2-labeled atmosphere, while 15N-labeled ammonium and amino acids were added to one side of the split-root system. We found a rapid transfer of recent photosynthates via ectomycorrhizal hyphae to bacteria in root-distant soil areas. Fungal and bacterial phospholipid fatty acid (PLFA) biomarkers were significantly enriched in hyphae-exclusive compartments 24 h after 13C-CO2-labeling. Isotope imaging with nanometer-scale secondary ion mass spectrometry (NanoSIMS) allowed for the first time in situ visualization of plant-derived C and N taken up by an extraradical fungal hypha, and in microbial cells thriving on hyphal surfaces. When N was added to the litter compartments, bacterial biomass, and the amount of incorporated 13C strongly declined. Interestingly, this effect was also observed in adjacent soil compartments where added N was only available for bacteria through hyphal transport, indicating that ectomycorrhizal fungi were acting on soil bacteria. Together, our results demonstrate that (i) ectomycorrhizal hyphae rapidly transfer plant-derived C to bacterial communities in root-distant areas, and (ii) this transfer promptly responds to changing soil nutrient conditions

The Nlrp3 inflammasome regulates acute graft-versus-host disease

The success of allogeneic hematopoietic cell transplantation is limited by acute graft-versus-host disease (GvHD), a severe complication accompanied by high mortality rates. Yet, the molecular mechanisms initiating this disease remain poorly defined. In this study, we show that, after conditioning therapy, intestinal commensal bacteria and the damage-associated molecular pattern uric acid contribute to Nlrp3 inflammasome-mediated IL-1β production and that gastrointestinal decontamination and uric acid depletion reduced GvHD severity. Early blockade of IL-1β or genetic deficiency of the IL-1 receptor in dendritic cells (DCs) and T cells improved survival. The Nlrp3 inflammasome components Nlrp3 and Asc, which are required for pro-IL-1β cleavage, were critical for the full manifestation of GvHD. In transplanted mice, IL-1β originated from multiple intestinal cell compartments and exerted its effects on DCs and T cells, the latter being preferentially skewed toward Th17. Compatible with these mouse data, increased levels of active caspase-1 and IL-1β were found in circulating leukocytes and intestinal GvHD lesions of patients. Thus, the identification of a crucial role for the Nlrp3 inflammasome sheds new light on the pathogenesis of GvHD and opens a potential new avenue for the targeted therapy of this severe complication

Pubertal maturation and sex effects on the default-mode network connectivity implicated in mood dysregulation

This study examines the effects of puberty and sex on the intrinsic functional connectivity (iFC) of brain networks, with a focus on the default-mode network (DMN). Consistently implicated in depressive disorders, the DMN’s function may interact with puberty and sex in the development of these disorders, whose onsets peak in adolescence, and which show strong sex disproportionality (females > males). The main question concerns how the DMN evolves with puberty as a function of sex. These effects are expected to involve within- and between-network iFC, particularly, the salience and the central-executive networks, consistent with the Triple-Network Model. Resting-state scans of an adolescent community sample (n = 304, male/female: 157/147; mean/std age: 14.6/0.41 years), from the IMAGEN database, were analyzed using the AFNI software suite and a data reduction strategy for the effects of puberty and sex. Three midline regions (medial prefrontal, pregenual anterior cingulate, and posterior cingulate), within the DMN and consistently implicated in mood disorders, were selected as seeds. Within- and between-network clusters of the DMN iFC changed with pubertal maturation differently in boys and girls (puberty-X-sex). Specifically, pubertal maturation predicted weaker iFC in girls and stronger iFC in boys. Finally, iFC was stronger in boys than girls independently of puberty. Brain–behavior associations indicated that lower connectivity of the anterior cingulate seed predicted higher internalizing symptoms at 2-year follow-up. In conclusion, weaker iFC of the anterior DMN may signal disconnections among circuits supporting mood regulation, conferring risk for internalizing disorders