A momentum-space representation of Feynman propagator in Riemann-Cartan spacetime

We first construct generalized Riemann-normal coordinates by using autoparallels, instead of geodesics, in an arbitrary Riemann-Cartan spacetime. With the aid of generalized Riemann-normal coordinates and their associated orthonormal frames, we obtain a momentum-space representation of the Feynman propagator for scalar fields, which is a direct generalization of Bunch and Parker's works to curved spacetime with torsion. We further derive the proper-time representation in $n$ dimensional Riemann-Cartan spacetime from the momentum-space representation. It leads us to obtain the renormalization of one-loop effective Lagrangians of free scalar fields by using dimensional regularization. When torsion tensor vanishes, our resulting momentum-space representation returns to the standard Riemannian results.Comment: 12 page

Comparative Proteomics of Root Apex and Root Elongation Zones Provides Insights into Molecular Mechanisms for Drought Stress and Recovery Adjustment in Switchgrass

Switchgrass plants were grown in a Sandwich tube system to induce gradual drought stress by withholding watering. After 29 days, the leaf photosynthetic rate decreased significantly, compared to the control plants which were watered regularly. The drought-treated plants recovered to the same leaf water content after three days of re-watering. The root tip (1cm basal fragment, designated as RT1 hereafter) and the elongation/maturation zone (the next upper 1 cm tissue, designated as RT2 hereafter) tissues were collected at the 29th day of drought stress treatment, (named SDT for severe drought treated), after one (D1W) and three days (D3W) of re-watering. The tandem mass tags mass spectrometry-based quantitative proteomics analysis was performed to identify the proteomes, and drought-induced differentially accumulated proteins (DAPs). From RT1 tissues, 6156, 7687, and 7699 proteins were quantified, and 296, 535, and 384 DAPs were identified in the SDT, D1W, and D3W samples, respectively. From RT2 tissues, 7382, 7255, and 6883 proteins were quantified, and 393, 587, and 321 proteins DAPs were identified in the SDT, D1W, and D3W samples. Between RT1 and RT2 tissues, very few DAPs overlapped at SDT, but the number of such proteins increased during the recovery phase. A large number of hydrophilic proteins and stress-responsive proteins were induced during SDT and remained at a higher level during the recovery stages. A large number of DAPs in RT1 tissues maintained the same expression pattern throughout drought treatment and the recovery phases. The DAPs in RT1 tissues were classified in cell proliferation, mitotic cell division, and chromatin modification, and those in RT2 were placed in cell wall remodeling and cell expansion processes. This study provided information pertaining to root zone-specific proteome changes during drought and recover phases, which will allow us to select proteins (genes) as better defined targets for developing drought tolerant plants. The mass spectrometry proteomics data are available via ProteomeXchange with identifier PXD017441

Drought-Induced Leaf Proteome Changes in Switchgrass Seedlings

Switchgrass (Panicum virgatum) is a perennial crop producing deep roots and thus highly tolerant to soil water deficit conditions. However, seedling establishment in the field is very susceptible to prolonged and periodic drought stress. In this study, a “sandwich” system simulating a gradual water deletion process was developed. Switchgrass seedlings were subjected to a 20-day gradual drought treatment process when soil water tension was increased to 0.05 MPa (moderate drought stress) and leaf physiological properties had expressed significant alteration. Drought-induced changes in leaf proteomes were identified using the isobaric tags for relative and absolute quantitation (iTRAQ) labeling method followed by nano-scale liquid chromatography mass spectrometry (nano-LC-MS/MS) analysis. Additionally, total leaf proteins were processed using a combinatorial library of peptide ligands to enrich for lower abundance proteins. Both total proteins and those enriched samples were analyzed to increase the coverage of the quantitative proteomics analysis. A total of 7006 leaf proteins were identified, and 257 (4% of the leaf proteome) expressed a significant difference (p \u3c 0.05, fold change \u3c0.6 or \u3e1.7) from the non-treated control to drought-treated conditions. These proteins are involved in the regulation of transcription and translation, cell division, cell wall modification, phyto-hormone metabolism and signaling transduction pathways, and metabolic pathways of carbohydrates, amino acids, and fatty acids. A scheme of abscisic acid (ABA)-biosynthesis and ABA responsive signal transduction pathway was reconstructed using these drought-induced significant proteins, showing systemic regulation at protein level to deploy the respective mechanism. Results from this study, in addition to revealing molecular responses to drought stress, provide a large number of proteins (candidate genes) that can be employed to improve switchgrass seedling growth and establishment under soil drought conditions (Data are available via ProteomeXchange with identifier PXD004675)

Galaxy source counts at 7.7 μ\mum, 10 μ\mum and 15 μ\mum with the James Webb Space Telescope

We present mid-infrared galaxy number counts based on the Early Release Observations obtained by the James Webb Space Telescope (JWST) at 7.7-, 10- and 15-$\mu$m (F770W, F1000W and F1500W, respectively) bands of the Mid-Infrared Instrument (MIRI). Due to the superior sensitivity of JWST, the 80 percent completeness limits reach 0.32, 0.79 and 2.0 $\mu$Jy in F770W, F1000W and F1500W filters, respectively, i.e., $\sim$100 times deeper than previous space infrared telescopes such as Spitzer or AKARI. The number counts reach much deeper than the broad bump around $0.05\sim0.5$ mJy due to polycyclic aromatic hydrocarbon (PAH) emissions. An extrapolation towards fainter flux from the evolutionary models in the literature agrees amazingly well with the new data, where the extrapolated faint-end of infrared luminosity functions combined with the cosmic star-formation history to higher redshifts can reproduce the deeper number counts by JWST. Our understanding of the faint infrared sources has been confirmed by the observed data due to the superb sensitivity of JWST.Comment: 6 pages, 8 figures. Accepted for publication in MNRA

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

International audienceJASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release

Polycyclic aromatic hydrocarbon (PAH) luminous galaxies in JWST CEERS data

It has been an unanswered question how many dusty galaxies have been undetected from the state-of-the-art observational surveys. JWST enables us to detect faint IR galaxies that have prominent polycyclic aromatic hydrocarbon (PAH) features in the mid-IR wavelengths. PAH is a valuable tracer of star formation and dust properties in the mid-infrared wavelength. The JWST Cosmic Evolution Early Release Science (CEERS) fields provide us with wavelength coverage from 7.7 to 21 $\mu$m using six photometric bands of the mid-infrared instrument (MIRI). We have identified galaxies dominated by mid-IR emission from PAHs, termed PAH galaxies. From our multi-band photometry catalogue, we selected ten PAH galaxies displaying high flux ratios of $\log(S_{15}/S_{10}) > 0.8$. The SED fitting analysis indicates that these galaxies are star-forming galaxies with total IR luminosities of $10^{10}$ $\sim$ $10^{11.5}$ $L_{\odot}$ at z $\sim 1$. The morphology of PAH galaxies does not show any clear signatures of major merging or interaction within the MIRI resolution. The majority of them are on the star-formation main sequence at $z \sim 1$. Our result demonstrates that JWST can detect PAH emissions from normal star-forming galaxies at $z \sim 1$, in addition to ultra-luminous infrared galaxies (ULIRGs) or luminous infrared galaxies (LIRGs).Comment: 12 pages, 20 figures, 4 tables. Accepted by MNRAS. A summary video is at https://www.youtube.com/watch?v=UtPaVTFM4f8&ab_channel=NTHUCosmolog

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

International audienceJASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release

Postnatal expression profiles of atypical cadherin FAT1 suggest its role in autism

Genetic studies have linked FAT1 (FAT atypical cadherin 1) with autism spectrum disorder (ASD); however, the role that FAT1 plays in ASD remains unknown. In mice, the function of Fat1 has been primarily implicated in embryonic nervous system development with less known about its role in postnatal development. We show for the first time that FAT1 protein is expressed in mouse postnatal brains and is enriched in the cerebellum, where it localizes to granule neurons and Golgi cells in the granule layer, as well as inhibitory neurons in the molecular layer. Furthermore, subcellular characterization revealed FAT1 localization in neurites and soma of granule neurons, as well as being present in the synaptic plasma membrane and postsynaptic densities. Interestingly, FAT1 expression was decreased in induced pluripotent stem cell (iPSC)-derived neural precursor cells (NPCs) from individuals with ASD. These findings suggest a novel role for FAT1 in postnatal development and may be particularly important for cerebellum function. As the cerebellum is one of the vulnerable brain regions in ASD, our study warrants further investigation of FAT1 in the disease etiology