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1.	Tuskan, G A, et al. (författare) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). 2006 Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 313:5793, s. 1596-604 Tidskriftsartikel (refereegranskat)abstract We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.
2.	Kasliwal, M. M., et al. (författare) Illuminating gravitational waves : A concordant picture of photons from a neutron star merger 2017 Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 358:6370, s. 1559- Tidskriftsartikel (refereegranskat)abstract Merging neutron stars offer an excellent laboratory for simultaneously studying strong-field gravity and matter in extreme environments. We establish the physical association of an electromagnetic counterpart (EM170817) with gravitational waves (GW170817) detected from merging neutron stars. By synthesizing a panchromatic data set, we demonstrate that merging neutron stars are a long-sought production site forging heavy elements by r-process nucleosynthesis. The weak gamma rays seen in EM170817 are dissimilar to classical short gamma-ray bursts with ultrarelativistic jets. Instead, we suggest that breakout of a wide-angle, mildly relativistic cocoon engulfing the jet explains the low-luminosity gamma rays, the high-luminosity ultraviolet-optical-infrared, and the delayed radio and x-ray emission. We posit that all neutron star mergers may lead to a wide-angle cocoon breakout, sometimes accompanied by a successful jet and sometimes by a choked jet.
3.	Ahumada, T., et al. (författare) Discovery and confirmation of the shortest gamma-ray burst from a collapsar 2021 Ingår i: Nature Astronomy. - : Springer Nature. - 2397-3366. ; 5:9, s. 917-927 Tidskriftsartikel (refereegranskat)abstract Gamma-ray bursts (GRBs) are among the brightest and most energetic events in the Universe. The duration and hardness distribution of GRBs has two clusters1, now understood to reflect (at least) two different progenitors2. Short-hard GRBs (SGRBs; T90 < 2 s) arise from compact binary mergers, and long-soft GRBs (LGRBs; T90 > 2 s) have been attributed to the collapse of peculiar massive stars (collapsars)3. The discovery of SN 1998bw/GRB 980425 (ref. 4) marked the first association of an LGRB with a collapsar, and AT 2017gfo (ref. 5)/GRB 170817A/GW170817 (ref. 6) marked the first association of an SGRB with a binary neutron star merger, which also produced a gravitational wave. Here, we present the discovery of ZTF20abwysqy (AT2020scz), a fast-fading optical transient in the Fermi satellite and the Interplanetary Network localization regions of GRB 200826A; X-ray and radio emission further confirm that this is the afterglow. Follow-up imaging (at rest-frame 16.5 days) reveals excess emission above the afterglow that cannot be explained as an underlying kilonova, but which is consistent with being the supernova. Although the GRB duration is short (rest-frame T90 of 0.65 s), our panchromatic follow-up data confirm a collapsar origin. GRB 200826A is the shortest LGRB found with an associated collapsar; it appears to sit on the brink between a successful and a failed collapsar. Our discovery is consistent with the hypothesis that most collapsars fail to produce ultra-relativistic jets.
4.	Kasliwal, M. M., et al. (författare) iPTF SEARCH FOR AN OPTICAL COUNTERPART TO GRAVITATIONAL- WAVE TRANSIENT GW150914 2016 Ingår i: Astrophysical Journal Letters. - 2041-8205 .- 2041-8213. ; 824:2 Tidskriftsartikel (refereegranskat)abstract The intermediate Palomar Transient Factory (iPTF) autonomously responded to and promptly tiled the error region of the first gravitational-wave event GW150914 to search for an optical counterpart. Only a small fraction of the total localized region was immediately visible in the northern night sky, due both to Sun-angle and elevation constraints. Here, we report on the transient candidates identified and rapid follow-up undertaken to determine the nature of each candidate. Even in the small area imaged of 126 deg(2), after extensive filtering, eight candidates were deemed worthy of additional follow-up. Within two hours, all eight were spectroscopically classified by the Keck II telescope. Curiously, even though such events are rare, one of our candidates was a superluminous supernova. We obtained radio data with the Jansky Very Large Array and X-ray follow-up with the Swift satellite for this transient. None of our candidates appear to be associated with the gravitational-wave trigger, which is unsurprising given that GW150914 came from the merger of two stellar-mass black holes. This end-to-end discovery and follow-up campaign bodes well for future searches in this post-detection era of gravitational waves.
5.	Hilson, P., et al. (författare) Versatile gene-specific sequence tags for Arabidopsis functional genomics : Trancript profiling and reverse genetics applications 2004 Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 14:10B, s. 2176-2189 Tidskriftsartikel (refereegranskat)abstract Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics.
6.	Kasliwal, Mansi M., et al. (författare) Kilonova Luminosity Function Constraints Based on Zwicky Transient Facility Searches for 13 Neutron Star Merger Triggers during O3 2020 Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 905:2 Tidskriftsartikel (refereegranskat)abstract We present a systematic search for optical counterparts to 13 gravitational wave (GW) triggers involving at least one neutron star during LIGO/Virgo's third observing run (O3). We searched binary neutron star (BNS) and neutron star black hole (NSBH) merger localizations with the Zwicky Transient Facility (ZTF) and undertook follow-up with the Global Relay of Observatories Watching Transients Happen (GROWTH) collaboration. The GW triggers had a median localization area of 4480 deg(2), a median distance of 267 Mpc, and false-alarm rates ranging from 1.5 to 10(-25) yr(-1). The ZTF coverage in the g and r bands had a median enclosed probability of 39%, median depth of 20.8 mag, and median time lag between merger and the start of observations of 1.5 hr. The O3 follow-up by the GROWTH team comprised 340 UltraViolet/Optical/InfraRed (UVOIR) photometric points, 64 OIR spectra, and three radio images using 17 different telescopes. We find no promising kilonovae (radioactivity-powered counterparts), and we show how to convert the upper limits to constrain the underlying kilonova luminosity function. Initially, we assume that all GW triggers are bona fide astrophysical events regardless of false-alarm rate and that kilonovae accompanying BNS and NSBH mergers are drawn from a common population; later, we relax these assumptions. Assuming that all kilonovae are at least as luminous as the discovery magnitude of GW170817 (-16.1 mag), we calculate that our joint probability of detecting zero kilonovae is only 4.2%. If we assume that all kilonovae are brighter than -16.6 mag (the extrapolated peak magnitude of GW170817) and fade at a rate of 1 mag day(-1) (similar to GW170817), the joint probability of zero detections is 7%. If we separate the NSBH and BNS populations based on the online classifications, the joint probability of zero detections, assuming all kilonovae are brighter than -16.6 mag, is 9.7% for NSBH and 7.9% for BNS mergers. Moreover, no more than <57% (<89%) of putative kilonovae could be brighter than -16.6 mag assuming flat evolution (fading by 1 mag day(-1)) at the 90% confidence level. If we further take into account the online terrestrial probability for each GW trigger, we find that no more than <68% of putative kilonovae could be brighter than -16.6 mag. Comparing to model grids, we find that some kilonovae must have M-ej M, X-lan > 10(-4), or > 30 degrees to be consistent with our limits. We look forward to searches in the fourth GW observing run; even 17 neutron star mergers with only 50% coverage to a depth of -16 mag would constrain the maximum fraction of bright kilonovae to <25%.
7.	Purdum, Josiah N., et al. (författare) Time-series and Phase-curve Photometry of the Episodically Active Asteroid (6478) Gault in a Quiescent State Using APO, GROWTH, P200, and ZTF 2021 Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8205 .- 2041-8213. ; 911:2 Tidskriftsartikel (refereegranskat)abstract We observed the episodically active asteroid (6478) Gault in 2020 with multiple telescopes in Asia and North America and found that it is no longer active after its recent outbursts at the end of 2018 and the start of 2019. The inactivity during this apparition allowed us to measure the absolute magnitude of Gault of H ( r ) = 14.63 +/- 0.02, G ( r ) = 0.21 +/- 0.02 from our secular phase-curve observations. In addition, we were able to constrain Gault's rotation period using time-series photometric lightcurves taken over 17 hr on multiple days in 2020 August, September, and October. The photometric lightcurves have a repeating less than or similar to 0.05 mag feature suggesting that (6478) Gault has a rotation period of similar to 2.5 hr and may have a semispherical or top-like shape, much like the near-Earth asteroids Ryugu and Bennu. The rotation period of similar to 2.5 hr is near the expected critical rotation period for an asteroid with the physical properties of (6478) Gault, suggesting that its activity observed over multiple epochs is due to surface mass shedding from its fast rotation spin-up by the Yarkovsky-O'Keefe-Radzievskii-Paddack effect.
8.	Schrader, J., et al. (författare) Cambial meristem dormancy in trees involves extensive remodelling of the transcriptome 2004 Ingår i: The Plant Journal. - Malden : Wiley-Blackwell. - 0960-7412 .- 1365-313X. ; 40:2, s. 173-187 Tidskriftsartikel (refereegranskat)abstract The establishment of the dormant state in meristems involves considerable physiological and metabolic alterations necessary for surviving unfavourable growth conditions. However, a global molecular analysis of dormancy in meristems has been hampered by the difficulty in isolating meristem cells. We used cryosectioning to isolate purified cambial meristem cells from the woody plant Populus tremula during active growth and dormancy. These samples were used to generate meristem-specific cDNA libraries and for cDNA microarray experiments to define the global transcriptional changes underlying cambial dormancy. The results indicate a significant reduction in the complexity of the cambial transcriptome in the dormant state. Although cell division is terminated in the dormant cambium, the cell cycle machinery appears to be maintained in a skeletal state as suggested by the continued presence of transcripts for several cell cycle regulators. The downregulation of PttPIN1 and PttPIN2 transcripts explains the reduced basipetal polar auxin transport during dormancy. The induction of a member of the SINA family of ubiquitin ligases implicated in auxin signalling indicates a potential mechanism for modulation of auxin sensitivity during cambial dormancy. The metabolic alterations during dormancy are mirrored in the induction of genes involved in starch breakdown and the glyoxysomal cycle. Interestingly, the induction of RGA1 like gene suggests modification of gibberellin signalling in cambial dormancy. The induction of genes such as poplar orthologues of FIE and HAP2 indicates a potential role for these global regulators of transcription in orchestrating extensive changes in gene expression during dormancy.
9.	Andreoni, Igor, et al. (författare) Fast-transient Searches in Real Time with ZTFReST : Identification of Three Optically Discovered Gamma-Ray Burst Afterglows and New Constraints on the Kilonova Rate 2021 Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 918:2 Tidskriftsartikel (refereegranskat)abstract The most common way to discover extragalactic fast transients, which fade within a few nights in the optical, is via follow-up of gamma-ray burst and gravitational-wave triggers. However, wide-field surveys have the potential to identify rapidly fading transients independently of such external triggers. The volumetric survey speed of the Zwicky Transient Facility (ZTF) makes it sensitive to objects as faint and fast fading as kilonovae, the optical counterparts to binary neutron star mergers, out to almost 200 Mpc. We introduce an open-source software infrastructure, the ZTF REaltime Search and Triggering, ZTFReST, designed to identify kilonovae and fast transients in ZTF data. Using the ZTF alert stream combined with forced point-spread-function photometry, we have implemented automated candidate ranking based on their photometric evolution and fitting to kilonova models. Automated triggering, with a human in the loop for monitoring, of follow-up systems has also been implemented. In 13 months of science validation, we found several extragalactic fast transients independently of any external trigger, including two supernovae with post-shock cooling emission, two known afterglows with an associated gamma-ray burst (ZTF20abbiixp, ZTF20abwysqy), two known afterglows without any known gamma-ray counterpart (ZTF20aajnksq, ZTF21aaeyldq), and three new fast-declining sources (ZTF20abtxwfx, ZTF20acozryr, ZTF21aagwbjr) that are likely associated with GRB200817A, GRB201103B, and GRB210204A. However, we have not found any objects that appear to be kilonovae. We constrain the rate of GW170817-like kilonovae to R < 900 Gpc(-3) yr(-1) (95% confidence). A framework such as ZTFReST could become a prime tool for kilonova and fast-transient discovery with the Vera Rubin Observatory.
10.	Benedict, Catherine, et al. (författare) The Role of the CBF-dependent Signalling Pathway in Woody Perennials 2006 Ingår i: Cold Hardiness in Plants. - Wallingford : CABI Publishing. - 9780851990590 ; , s. 167-180 Bokkapitel (övrigt vetenskapligt/konstnärligt)
11.	Coughlin, Michael W., et al. (författare) GROWTH on S190425z : Searching Thousands of Square Degrees to Identify an Optical or Infrared Counterpart to a Binary Neutron Star Merger with the Zwicky Transient Facility and Palomar Gattini-IR 2019 Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8205 .- 2041-8213. ; 885:1 Tidskriftsartikel (refereegranskat)abstract The third observing run by LVC has brought the discovery of many compact binary coalescences. Following the detection of the first binary neutron star merger in this run (LIGO/Virgo S190425z), we performed a dedicated follow-up campaign with the Zwicky Transient Facility (ZTF) and Palomar Gattini-IR telescopes. The initial skymap of this single-detector gravitational wave (GW) trigger spanned most of the sky observable from Palomar Observatory. Covering 8000 deg(2) of the initial skymap over the next two nights, corresponding to 46% integrated probability, ZTF system achieved a depth of 21 m(AB) in g- and r-bands. Palomar Gattini-IR covered 2200 square degrees in J-band to a depth of 15.5 mag, including 32% integrated probability based on the initial skymap. The revised skymap issued the following day reduced these numbers to 21% for the ZTF and 19% for Palomar Gattini-IR. We narrowed 338,646 ZTF transient ?alerts? over the first two nights of observations to 15 candidate counterparts. Two candidates, ZTF19aarykkb and ZTF19aarzaod, were particularly compelling given that their location, distance, and age were consistent with the GW event, and their early optical light curves were photometrically consistent with that of kilonovae. These two candidates were spectroscopically classified as young core-collapse supernovae. The remaining candidates were ruled out as supernovae. Palomar Gattini-IR did not identify any viable candidates with multiple detections only after merger time. We demonstrate that even with single-detector GW events localized to thousands of square degrees, systematic kilonova discovery is feasible.
12.	Druart, Nathalie, et al. (författare) Environmental and hormonal regulation of the activity–dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks 2007 Ingår i: The Plant Journal. ; 50, s. 557-73 Tidskriftsartikel (refereegranskat)abstract We have performed transcript and metabolite profiling of isolated cambial meristem cells of the model tree aspen during the course of their activity–dormancy cycle to better understand the environmental and hormonal regulation of this process in perennial plants. Considerable modulation of cambial transcriptome and metabolome occurs throughout the activity–dormancy cycle. However, in addition to transcription, post-transcriptional control is also an important regulatory mechanism as exemplified by the regulation of cell-cycle genes during the reactivation of cambial cell division in the spring. Genes related to cold hardiness display temporally distinct induction patterns in the autumn which could explain the step-wise development of cold hardiness. Factors other than low temperature regulate the induction of early cold hardiness-related genes whereas abscisic acid (ABA) could potentially regulate the induction of late cold hardiness-related genes in the autumn. Starch breakdown in the autumn appears to be regulated by the ‘short day’ signal and plays a key role in providing substrates for the production of energy, fatty acids and cryoprotectants. Catabolism of sucrose and fats provides energy during the early stages of reactivation in the spring, whereas the reducing equivalents are generated through activation of the pentose phosphate shunt. Modulation of gibberellin (GA) signaling and biosynthesis could play a key role in the regulation of cambial activity during the activity–dormancy cycle as suggested by the induction of PttRGA which encodes a negative regulator of growth in the autumn and that of a GA-20 oxidase, a key gibberellin biosynthesis gene during reactivation in spring. In summary, our data reveal the dynamics of transcriptional and metabolic networks and identify potential targets of environmental and hormonal signals in the regulation of the activity–dormancy cycle in cambial meristem.
13.	Gendre, Delphine, et al. (författare) Journey to the cell surface-the central role of the trans-Golgi network in plants 2015 Ingår i: Protoplasma. - : Springer Science and Business Media LLC. - 0033-183X .- 1615-6102. ; 252, s. 385-398 Forskningsöversikt (refereegranskat)abstract The secretion of proteins, lipids, and carbohydrates to the cell surface is essential for plant development and adaptation. Secreted substances synthesized at the endoplasmic reticulum pass through the Golgi apparatus and trans-Golgi network (TGN) en route to the plasma membrane via the conventional secretion pathway. The TGN is morphologically and functionally distinct from the Golgi apparatus. The TGN is located at the crossroads of many trafficking pathways and regulates a range of crucial processes including secretion to the cell surface, transport to the vacuole, and the reception of endocytic cargo. This review outlines the TGN's central role in cargo secretion, showing that its behavior is more complex and controlled than the bulk-flow hypothesis suggests. Its formation, structure, and maintenance are discussed along with the formation and release of secretory vesicles.
14.	Hertzberg, M., et al. (författare) A transcriptional roadmap to wood formation 2001 Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 98:25, s. 14732-14737 Tidskriftsartikel (refereegranskat)abstract The large vascular meristem of poplar trees with its highly organized secondary xylem enables the boundaries between different developmental zones to be easily distinguished. This property of wood-forming tissues allowed us to determine a unique tissue-specific transcript profile for a well defined developmental gradient. RNA was prepared from different developmental stages of xylogenesis for DNA microarray analysis by using a hybrid aspen unigene set consisting of 2,995 expressed sequence tags. The analysis revealed that the genes encoding lignin and cellulose biosynthetic enzymes, as well as a number of transcription factors and other potential regulators of xylogenesis, are under strict developmental stage-specific transcriptional regulation.
15.	Perley, Daniel A., et al. (författare) Real-time discovery of AT2020xnd : a fast, luminous ultraviolet transient with minimal radioactive ejecta 2021 Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 508:4, s. 5138-5147 Tidskriftsartikel (refereegranskat)abstract The many unusual properties of the enigmatic AT2018cow suggested that at least some subset of the empirical class of fast blue optical transients (FBOTs) represents a genuinely new astrophysical phenomenon. Unfortunately, the intrinsic rarity and fleeting nature of these events have made it difficult to identify additional examples early enough to acquire the observations necessary to constrain theoretical models. We present here the Zwicky Transient Facility discovery of AT2020xnd (ZTF20acigmel, the 'Camel') at z = 0.243, the first unambiguous AT2018cow analogue to be found and confirmed in real time. AT2018cow and AT2020xnd share all key observational properties: a fast optical rise, sustained high photospheric temperature, absence of a second peak attributable to ejection of a radioactively heated stellar envelope, extremely luminous radio, millimetre, and X-ray emission, and a dwarf-galaxy host. This supports the argument that AT2018cow-like events represent a distinct phenomenon from slower-evolving radio-quiet supernovae, likely requiring a different progenitor or a different central engine. The sample properties of the four known members of this class to date disfavour tidal disruption models but are consistent with the alternative model of an accretion powered jet following the direct collapse of a massive star to a black hole. Contextual filtering of alert streams combined with rapid photometric verification using multiband imaging provides an efficient way to identify future members of this class, even at high redshift.
16.	Perley, Daniel A., et al. (författare) The fast, luminous ultraviolet transient AT2018cow : extreme supernova, or disruption of a star by an intermediate-mass black hole? 2019 Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 484:1, s. 1031-1049 Tidskriftsartikel (refereegranskat)abstract Wide-field optical surveys have begun to uncover large samples of fast (t(rise) less than or similar to 5 d), luminous (M-peak < 18), blue transients. While commonly attributed to the breakout of a supernova shock into a dense wind, the great distances to the transients of this class found so far have hampered detailed investigation of their properties. We present photometry and spectroscopy from a comprehensive worldwide campaign to observe AT 2018cow (ATLAS 18qqn), the first fast-luminous optical transient to be found in real time at low redshift. Our first spectra (<2 days after discovery) are entirely featureless. A very broad absorption feature suggestive of near-relativistic velocities develops between 3 and 8 days, then disappears. Broad emission features of H and He develop after >10 days. The spectrum remains extremely hot throughout its evolution, and the photospheric radius contracts with time (receding below R < 10 (14) cm after 1 month). This behaviour does not match that of any known supernova, although a relativistic jet within a fallback supernova could explain some of the observed features. Alternatively, the transient could originate from the disruption of a star by an intermediate-mass black hole, although this would require long-lasting emission of highly super-Eddington thermal radiation. In either case, AT 2018cow suggests that the population of fast luminous transients represents a new class of astrophysical event. Intensive follow-up of this event in its late phases, and of any future events found at comparable distance, will be essential to better constrain their origins.
17.	Singer, L. P., et al. (författare) The Needle in the 100 deg2 Haystack : Uncovering Afterglows of Fermi GRBs with the Palomar Transient Factory 2015 Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 806:1 Tidskriftsartikel (refereegranskat)abstract The Fermi Gamma-Ray Space Telescope has greatly expanded the number and energy window of observations of gamma-ray bursts (GRBs). However, the coarse localizations of tens to a hundred square degrees provided by the Fermi Gamma-ray Burst Monitor (GBM) instrument have posed a formidable obstacle to locating the bursts' host galaxies, measuring their redshifts, and tracking their panchromatic afterglows. We have built a target of opportunity mode for the intermediate Palomar Transient Factory (iPTF) in order to perform targeted searches for Fermi afterglows. Here, we present the results of one year of this program: eight afterglow discoveries, two of which (GRBs 130702A and 140606B) were at low redshift (z=0.145 and 0.384 respectively) and had spectroscopically confirmed broad-line type Ic supernovae. We present our broadband follow-up including spectroscopy as well as X-ray, UV, optical, millimeter, and radio observations. We study possible selection effects in the context of the total Fermi and Swift GRB samples. We identify one new outlier on the Amati relation. We find that two bursts are consistent with a mildly relativistic shock breaking out from the progenitor star, rather than the ultra-relativistic internal shock mechanism that powers standard cosmological bursts. Finally, in the context of the Zwicky Transient Facility (ZTF), we discuss how we will continue to expand this effort to find optical counterparts of binary neutron star mergers that may soon be detected by Advanced LIGO and Virgo.
18.	Singh, Rajesh Kumar, et al. (författare) Photoperiod- and temperature-mediated control of phenology in trees – a molecular perspective 2017 Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 213:2, s. 511-524 Forskningsöversikt (refereegranskat)abstract (Table presented.). Summary: Trees growing in boreal and temperate regions synchronize their growth with seasonal climatic changes in adaptive responses that are essential for their survival. These trees cease growth before the winter and establish a dormant state during which growth cessation is maintained by repression of responses to growth-promotive signals. Reactivation of growth in the spring follows the release from dormancy promoted by prolonged exposure to low temperature during the winter. The timing of the key events and regulation of the molecular programs associated with the key stages of the annual growth cycle are controlled by two main environmental cues: photoperiod and temperature. Recently, key components mediating photoperiodic control of growth cessation and bud set have been identified, and striking similarities have been observed in signaling pathways controlling growth cessation in trees and floral transition in Arabidopsis. Although less well understood, the regulation of bud dormancy and bud burst may involve cell–cell communication and chromatin remodeling. Here, we discuss current knowledge of the molecular-level regulation of the annual growth cycle of woody trees in temperate and boreal regions, and identify key questions that need to be addressed in the future.
19.	Sterky, Fredrik, et al. (författare) A Populus EST resource for plant functional genomics 2004 Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 101:38, s. 13951-13956 Tidskriftsartikel (refereegranskat)abstract Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide >4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (POPULUSDB) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.
20.	Sterky, Fredrik, et al. (författare) Gene discovery in the wood-forming tissues of poplar : Analysis of 5,692 expressed sequence tags 1998 Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 95:22, s. 13330-13335 Tidskriftsartikel (refereegranskat)abstract A rapidly growing area of genome research is the generation of expressed sequence tags (ESTs) in which large numbers of randomly selected cDNA clones are partially sequenced. The collection of ESTs reflects the level and complexity of gene expression in the sampled tissue, To date, the majority of plant ESTs are from nonwoody plants such as Arabidopsis, Brassica, maize, and rice. Here, we present a large-scale production of ESTs from the wood-forming tissues of two poplars, Populus tremula L, x tremuloides Michx, and Populus trichocarpa 'Trichobel.' The 5,692 ESTs analyzed represented a total of 3,719 unique transcripts for the two cDNA libraries, Putative functions could be assigned to 2,245 of these transcripts that corresponded to 820 protein functions. Of specific interest to forest biotechnology are the 4% of ESTs involved in various processes of cell wall formation, such as lignin and cellulose synthesis, 5% similar to developmental regulators and members of known signal transduction pathways, and 2% involved in hormone biosynthesis. An additional 12% of the ESTs show ed no significant similarity to any other DNA or protein sequences in existing databases. The absence of these sequences from public databases may indicate a specific role for these proteins in wood formation. The cDNA libraries and the accompanying database are valuable resources for forest research directed toward understanding the genetic control of wood formation and future endeavors to modify wood and fiber properties for industrial use.
21.	Tylewicz, Szymon, et al. (författare) Photoperiodic control of seasonal growth is mediated by ABA acting on cell-cell communication 2018 Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 360:6385, s. 212-214 Tidskriftsartikel (refereegranskat)abstract In temperate and boreal ecosystems, seasonal cycles of growth and dormancy allow perennial plants to adapt to winter conditions. We show, in hybrid aspen trees, that photoperiodic regulation of dormancy is mechanistically distinct from autumnal growth cessation. Dormancy sets in when symplastic intercellular communication through plasmodesmata is blocked by a process dependent on the phytohormone abscisic acid. The communication blockage prevents growth-promoting signals from accessing the meristem. Thus, precocious growth is disallowed during dormancy. The dormant period, which supports robust survival of the aspen tree in winter, is due to loss of access to growth-promoting signals.
22.	Zhang, B, et al. (författare) PIRIN2 controls chromatin modification of lignin biosynthetic genes and modulates the non-cell autonomous xylem lignification in Arabidopsis thaliana Annan publikation (övrigt vetenskapligt/konstnärligt)
23.	Ahumada, Tomas, et al. (författare) In Search of Short Gamma-Ray Burst Optical Counterparts with the Zwicky Transient Facility 2022 Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 932:1 Tidskriftsartikel (refereegranskat)abstract The Fermi Gamma-ray Burst Monitor (GBM) triggers on-board in response to ∼40 short gamma-ray bursts (SGRBs) per year; however, their large localization regions have made the search for optical counterparts a challenging endeavour. We have developed and executed an extensive program with the wide field of view of the Zwicky Transient Facility (ZTF) camera, mounted on the Palomar 48 inch Oschin telescope (P48), to perform target-of-opportunity (ToO) observations on 10 Fermi-GBM SGRBs during 2018 and 2020–2021. Bridging the large sky areas with small field-of-view optical telescopes in order to track the evolution of potential candidates, we look for the elusive SGRB afterglows and kilonovae (KNe) associated with these high-energy events. No counterpart has yet been found, even though more than 10 ground-based telescopes, part of the Global Relay of Observatories Watching Transients Happen (GROWTH) network, have taken part in these efforts. The candidate selection procedure and the follow-up strategy have shown that ZTF is an efficient instrument for searching for poorly localized SGRBs, retrieving a reasonable number of candidates to follow up and showing promising capabilities as the community approaches the multi-messenger era. Based on the median limiting magnitude of ZTF, our searches would have been able to retrieve a GW170817-like event up to ∼200 Mpc and SGRB afterglows to z = 0.16 or 0.4, depending on the assumed underlying energy model. Future ToOs will expand the horizon to z = 0.2 and 0.7, respectively.
24.	Azeez, Abdul, et al. (författare) A Tree Ortholog of APETALA1 Mediates Photoperiodic Control of Seasonal Growth 2014 Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 24, s. 717-724 Tidskriftsartikel (refereegranskat)abstract Background: Photoperiodic control of development plays a key role in adaptation of plants to seasonal changes. A signaling module consisting of CONSTANS (CO) and FLOWERING LOCUS T (FT) mediates in photoperiodic control of a variety of developmental transitions (e. g., flowering, tuberization, and seasonal growth cessation in trees). How this conserved CO/FT module can mediate in the photoperiodic control of diverse unrelated developmental programs is poorly understood.Results: We show that Like-AP1 (LAP1), a tree ortholog of Arabidopsis floral meristem identity gene APETALA1 (AP1), mediates in photoperiodic control of seasonal growth cessation downstream of the CO/FT module in hybrid aspen. Using LAP1 overexpressors and RNAi-suppressed transgenic trees, we demonstrate that short day (SD)-mediated downregulation of LAP1 expression is required for growth cessation. In contrast with AP1 targets in flowering, LAP1 acts on AINTEGUMENTA-like 1 transcription factor, which is implicated in SD-mediated growth cessation. Intriguingly, unlike AP1 in Arabidopsis, ectopic expression of LAP1 fails to induce early flowering in hybrid aspen trees.Conclusions: These results indicate that AP1 ortholog in trees has acquired a novel function in photoperiodic regulation of seasonal growth. Thus, photoperiodic signaling pathway may have diverged downstream of AP1/LAP1 rather than the CO/FT module during evolution. Moreover, control of flowering by the CO/FT module can be uncoupled from its role in photoperiodic control of seasonal growth in trees. Thus, our findings can explain mechanistically how a conserved signaling module can mediate in the control of a highly diverse set of developmental transitions by a similar input signal, namely photoperiod.
25.	Barlier, I, et al. (författare) The SUR2 gene of Arabidopsis thaliana encodes the cytochrome P450 CYP83B1, a modulator of auxin homeostasis. 2000 Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 97:26 Tidskriftsartikel (refereegranskat)abstract Genetic screens have been performed to identify mutants with altered auxin homeostasis in Arabidopsis. A tagged allele of the auxin-overproducing mutant sur2 was identified within a transposon mutagenized population. The SUR2 gene was cloned and shown to encode the CYP83B1 protein, which belongs to the large family of the P450-dependent monooxygenases. SUR2 expression is up-regulated in sur1 mutants and induced by exogenous auxin in the wild type. Analysis of indole-3-acetic acid (IAA) synthesis and metabolism in sur2 plants indicates that the mutation causes a conditional increase in the pool size of IAA through up-regulation of IAA synthesis.
26.	Bhalerao, Rupali, et al. (författare) Gene expression in autumn leaves 2003 Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 131:2, s. 430-442 Tidskriftsartikel (refereegranskat)abstract Two cDNA libraries were prepared, one from leaves of a field-grown aspen (Populus tremula) tree, harvested just before any visible sign of leaf senescence in the autumn, and one from young but fully expanded leaves of greenhouse-grown aspen (Populus tremula X tremuloides). Expressed sequence tags (ESTs; 5,128 and 4,841, respectively) were obtained from the two libraries. A semiautomatic method of annotation and functional classification of the ESTs, according to a modified Munich Institute of Protein Sequences classification scheme, was developed, utilizing information from three different databases. The patterns of gene expression in the two libraries were strikingly different. In the autumn leaf library, ESTs encoding metallothionein, early light-inducible proteins, and cysteine proteases were most abundant. Clones encoding other proteases and proteins involved in respiration and breakdown of lipids and pigments, as well as stress-related genes, were also well represented. We identified homologs to many known senescence-associated genes, as well as seven different genes encoding cysteine proteases, two encoding aspartic proteases, five encoding metallothioneins, and 35 additional genes that were up-regulated in autumn leaves. We also indirectly estimated the rate of plastid protein synthesis in the autumn leaves to be less that 10% of that in young leaves.
27.	Bhalerao, Rupali R., et al. (författare) Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins 2015 Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 11 Tidskriftsartikel (refereegranskat)abstract The ability of plants to provide a plastic response to environmental cues relies on the connectivity between signaling pathways. DELLA proteins act as hubs that relay environmental information to the multiple transcriptional circuits that control growth and development through physical interaction with transcription factors from different families. We have analyzed the presence of one DELLA protein at the Arabidopsis genome by chromatin immunoprecipitation coupled to large-scale sequencing and we find that it binds at the promoters of multiple genes. Enrichment analysis shows a strong preference for cis elements recognized by specific transcription factor families. In particular, we demonstrate that DELLA proteins are recruited by type-B ARABIDOPSIS RESPONSE REGULATORS (ARR) to the promoters of cytokinin-regulated genes, where they act as transcriptional co-activators. The biological relevance of this mechanism is underpinned by the necessity of simultaneous presence of DELLAs and ARRs to restrict root meristem growth and to promote photomorphogenesis.
28.	Bolin, Bryce T., et al. (författare) Characterization of the Nucleus, Morphology, and Activity of Interstellar Comet 2I/Borisov by Optical and Near-infrared GROWTH, Apache Point, IRTF, ZTF, and Keck Observations 2020 Ingår i: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 160:1 Tidskriftsartikel (refereegranskat)abstract We present visible and near-infrared (NIR) photometric and spectroscopic observations of interstellar object (ISO) 2I/Borisov taken from 2019 September 10 to 2019 December 20 using the GROWTH, the Apache Point Observatory Astrophysical Research Consortium 3.5 m, and the NASA Infrared Telescope Facility 3.0 m combined with pre- and postdiscovery observations of 2I obtained by the Zwicky Transient Facility from 2019 March 17 to 2019 May 5. Comparison with imaging of distant solar system comets shows an object very similar to mildly active solar system comets with an outgassing rate of similar to 10(27)mol s(-1). The photometry, taken in filters spanning the visible and NIR range, shows a gradual brightening trend of similar to 0.03 mag day(-1)since 2019 September 10 UTC for a reddish object becoming neutral in the NIR. The light curve from recent and prediscovery data reveals a brightness trend suggesting the recent onset of significant H2O sublimation with the comet being active with super volatiles such as CO at heliocentric distances >6 au consistent with its extended morphology. Using the advanced capability to significantly reduce the scattered light from the coma enabled by high-resolution NIR images from Keck adaptive optics taken on 2019 October 4, we estimate a diameter for 2I's nucleus of less than or similar to 1.4 km. We use the size estimates of 1I/'Oumuamua and 2I/Borisov to roughly estimate the slope of the ISO size distribution, resulting in a slope of similar to 3.4 1.2, similar to solar system comets and bodies produced from collisional equilibrium.
29.	Chand, Vikas, et al. (författare) Violation of Synchrotron Line of Death by the Highly Polarized GRB 160802A 2018 Ingår i: Astrophysical Journal. - : Institute of Physics Publishing (IOPP). - 0004-637X .- 1538-4357. ; 862:2 Tidskriftsartikel (refereegranskat)abstract GRB 160802A is one of the brightest gamma-ray bursts (GRBs) observed by the Fermi Gamma-ray Burst Monitor (GBM) in the energy range of 10-1000 keV, while at the same time it is surprisingly faint at energies greater than or similar to 2 MeV. An observation with the AstroSat/CZT Imager also provides the polarization that helps in constraining different prompt emission models using the novel joint spectra-polarimetric data. We analyze the Fermi/GBM data, and find two main bursting episodes that are clearly separated in time, one of which is particularly faint in higher energies and having certain differences in their spectra. The spectrum in general shows a hard-to-soft evolution in both the episodes. Only the later part of the first episode shows intensity tracking behavior corresponding to multiple pulses. The photon index of the spectrum is hard, and in over 90% cases, crosses even the slow cooling limit (alpha = -2/3) of an optically thin synchrotron shock model. Though such hard values are generally associated with a sub-dominant thermal emission, such a component is not statistically required in our analysis. In addition, the measured polarization in 100-300 keV is too high, pi = 85 +/- 29%, to be accommodated in such a scenario. Jitter radiation, which allows a much harder index up to alpha = + 0.5, in principle can produce high polarization, but only beyond the spectral peak, which in our case lies close to 200-300 keV during the time when most of the polarization signal is obtained. The spectro-polarimetric data seems to be consistent with a subphotospheric dissipation process occurring within a narrow jet with a sharp drop in emissivity beyond the jet edge, and viewed along its boundary.
30.	Chattopadhyay, Tanmoy, et al. (författare) Hard X-Ray Polarization Catalog for a Five-year Sample of Gamma-Ray Bursts Using AstroSat CZT Imager 2022 Ingår i: Astrophysical Journal. - : IOP Publishing Ltd. - 0004-637X .- 1538-4357. ; 936:1 Tidskriftsartikel (refereegranskat)abstract The Cadmium Zinc Telluride Imager (CZTI) on board AstroSat has been regularly detecting gamma-ray bursts (GRBs) since its launch in 2015. Its sensitivity to polarization measurements at energies above 100 keV allows CZTI to attempt spectropolarimetric studies of GRBs. Here, we present the first catalog of GRB polarization measurements made by CZTI during its first five years of operation. This includes the time-integrated polarization measurements of the prompt emission of 20 GRBs in the energy range 100-600 keV. The sample includes the bright GRBs that were detected within an angle range of 0 degrees-60 degrees and 120 degrees-180 degrees where the instrument has useful polarization sensitivity and is less prone to systematics. We implement a few new modifications in the analysis to enhance the polarimetric sensitivity of the instrument. The majority of the GRBs in the sample are found to possess less/null polarization across the total bursts' duration in contrast to a small fraction of five GRBs that exhibit high polarization. The low polarization across the bursts might be due either to the burst being intrinsically weakly polarized or to a varying polarization angle within the burst even when it is highly polarized. In comparison to POLAR measurements, CZTI has detected a larger number of cases with high polarization. This may be a consequence of the higher energy window of CZTI observations, which results in the sampling of a shorter duration of burst emissions than POLAR, thereby probing emissions with less temporal variation in polarization properties.
31.	Chattopadhyay, Tanmoy, et al. (författare) Prompt Emission Polarimetry of Gamma-Ray Bursts with the AstroSat CZT Imager 2019 Ingår i: Astrophysical Journal. - : Institute of Physics (IOP). - 0004-637X .- 1538-4357. ; 884:2 Tidskriftsartikel (refereegranskat)abstract X-ray and gamma-ray polarization measurements of the prompt emission of gamma-ray bursts (GRBs) are believed to be extremely important for testing various models of GRBs. So far, the available measurements of hard X-ray polarization of GRB prompt emission have not significantly constrained the GRB models, particularly because of the difficulty of measuring polarization in these bands. The CZT Imager (CZTI) on board AstroSat is primarily an X-ray spectroscopic instrument that also works as a wide-angle GRB monitor due to the transparency of its support structure above 100 keV. It also has experimentally verified polarization measurement capability in the energy range 100-300 keV and thus provides a unique opportunity to attempt spectropolarimetric studies of GRBs. Here we present the polarization data for the brightest 11 GRBs detected by CZTI during its first year of operation. Among these, five GRBs show polarization signatures with greater than or similar to 3 sigma, and one GRB shows 2 sigma detection significance. We place upper limits for the remaining five GRBs. We provide details of the various tests performed to validate our polarization measurements. While it is difficult yet to discriminate between various emission models with the current sample alone, the large number of polarization measurements that CZTI expects to gather in its minimum lifetime of five years should help to significantly improve our understanding of the prompt emission.
32.	Chattopadhyay, Tanmoy, et al. (författare) Sub-MeV spectroscopy with AstroSat-CZT imager for gamma ray bursts 2021 Ingår i: Journal of astrophysics and astronomy. - : Springer Nature. - 0250-6335 .- 0973-7758. ; 42:2 Tidskriftsartikel (refereegranskat)abstract Cadmium-Zinc-Telluride Imager (CZTI) onboard AstroSat has been a prolific Gamma-Ray Burst (GRB) monitor. While the 2-pixel Compton scattered events (100-300 keV) are used to extract sensitive spectroscopic information, the inclusion of the low-gain pixels (similar to 20% of the detector plane) after careful calibration extends the energy range of Compton energy spectra to 600 keV. The new feature also allows single-pixel spectroscopy of the GRBs to the sub-MeV range which is otherwise limited to 150 keV. We also introduced a new noise rejection algorithm in the analysis ('Compton noise'). These new additions not only enhances the spectroscopic sensitivity of CZTI, but the sub-MeV spectroscopy will also allow proper characterization of the GRBs not detected by Fermi. This article describes the methodology of single, Compton event and veto spectroscopy in 100-900 keV combined for the GRBs detected in the first year of operation. CZTI in last five years has detected similar to 20 bright GRBs. The new methodologies, when applied on the spectral analysis for this large sample of GRBs, has the potential to improve the results significantly and help in better understanding the prompt emission mechanism.
33.	Jonsson, Kristoffer, et al. (författare) Enrichment of hydroxylated C24-and C26-acyl-chain sphingolipids mediates PIN2 apical sorting at trans-Golgi network subdomains 2016 Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7 Tidskriftsartikel (refereegranskat)abstract The post-Golgi compartment trans-Golgi Network (TGN) is a central hub divided into multiple subdomains hosting distinct trafficking pathways, including polar delivery to apical membrane. Lipids such as sphingolipids and sterols have been implicated in polar trafficking from the TGN but the underlying mechanisms linking lipid composition to functional polar sorting at TGN subdomains remain unknown. Here we demonstrate that sphingolipids with alpha-hydroxylated acyl-chains of at least 24 carbon atoms are enriched in secretory vesicle subdomains of the TGN and are critical for de novo polar secretory sorting of the auxin carrier PIN2 to apical membrane of Arabidopsis root epithelial cells. We show that sphingolipid acyl-chain length influences the morphology and interconnections of TGN-associated secretory vesicles. Our results uncover that the sphingolipids acyl-chain length links lipid composition of TGN subdomains with polar secretory trafficking of PIN2 to apical membrane of polarized epithelial cells.
34.	Kalla, R, et al. (författare) Regulation of phycobilisome rod proteins and messenger-RNA at different light intensities in the cyanobacterium synechococcus 6301 1993 Ingår i: Gene. - 0378-1119 .- 1879-0038. ; 126:1, s. 77-83 Tidskriftsartikel (refereegranskat)abstract The regulation of the light-harvesting antennae, the phycobilisome (Pbs), and the cpcB1A1-cpcH-cpcI-cpcD operon encoding the structural proteins of the Pbs rod, was studied in the cyanobacterium, Synechococcus sp. PCC 6301, when grown at different light intensities (li). Pbs were purified and their linker protein (LP) profiles analyzed on SDS-polyacrylamide gels. At increasing li, the amount of the distal 30-kDa LP decreased prior to any change in the amount of the proximal 33-kDa LP, indicating a sequential increase in the Pbs rod length. While the amount of LP in the rod decreased with increasing li, the levels of the LP mRNAs increased. Post-transcriptional regulation of the expression of the polycistronic cpcB1A1-cpcH-cpcI-cpcD mRNA was inferred from these observations. The half-life of the mRNAs studied was typically found to be 7 min with four exceptions: (1 and 2) the half-lives for the 3.4- and 3.7-kb polycistronic LP mRNAs were 16 and 1 min at the low (lli) and high li (hli), respectively; (3) the half-life of the 1.4-kb cpcB1A1 mRNA was 2 min at lli; and (4) the 1.3-kb cpcB1A1 transcript had a half-life of 10 min at lli. At hli, it was found that the 1.3-kb cpcB1A1 transcript did not start to disappear until the amount of the 1.4-kb cpcB1A1 transcript had reached the level equal to that of the 1.3-kb mRNA, implying that the 1.4-kb transcript might be processed to the 1.3-kb form.
35.	Karpinska, B., et al. (författare) MYB transcription factors are differentially expressed and regulated during secondary vascular tissue development in hybrid aspen 2004 Ingår i: Plant Molecular Biology. - : Springer Science and Business Media LLC. - 0167-4412 .- 1573-5028. ; 56:2, s. 255-270 Tidskriftsartikel (refereegranskat)abstract More than 120,000 poplar ESTs have been sequenced from 20 different cDNA libraries by the Swedish Centre for Tree Functional Genomics. We screened this EST collection for MYB transcription factors involved in secondary vascular tissue formation, and genes assigned as PttMYB3Ra, PttMYB4a and PttMYB21a were selected for further characterisation. Three MYB genes showed different expression patterns in various organs, tissues and stem sub-sections representing different developmental stages of vascular tissue formation. Furthermore, the analysis showed that PttMYB21a expression was much higher in secondary cell wall formation zone of xylem and phloem fibers than in other developmental zones. Transgenic hybrid aspen plants, expressing the 3'-part of the PttMYB21a gene in antisense orientation were generated to assess the function of PttMYB21a gene in vascular tissue formation and lignification. All transgenic lines showed reduced growth and had fewer internodes compared to the wild-type. The analysis of selected lines showed that acid soluble lignin present in the bark was higher in transgenic lines as compared to wild-type plants. Moreover a higher transcript level of caffeoyl-CoA 3-O-methyltransferase [CCoAOMT];EC2.1.1.104) was found in the phloem of the transgenic plants, suggesting that PttMYB21a might function as a transcriptional repressor.
36.	Mooley, K., et al. (författare) A mildly relativistic wide-angle outflow in the neutron-star merger event GW170817 2018 Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 554:7691, s. 207-210 Tidskriftsartikel (refereegranskat)abstract GW170817 was the first gravitational-wave detection of a binary neutron-star merger. It was accompanied by radiation across the electromagnetic spectrum and localized to the galaxy NGC 4993 at a distance of 40 megaparsecs. It has been proposed that the observed γ-ray, X-ray and radio emission is due to an ultra-relativistic jet being launched during the merger (and successfully breaking out of the surrounding material), directed away from our line of sight (off-axis). The presence of such a jet is predicted from models that posit neutron-star mergers as the drivers of short hard-γ-ray bursts. Here we report that the radio light curve of GW170817 has no direct signature of the afterglow of an off-axis jet. Although we cannot completely rule out the existence of a jet directed away from the line of sight, the observed γ-ray emission could not have originated from such a jet. Instead, the radio data require the existence of a mildly relativistic wide-angle outflow moving towards us. This outflow could be the high-velocity tail of the neutron-rich material that was ejected dynamically during the merger, or a cocoon of material that breaks out when a jet launched during the merger transfers its energy to the dynamical ejecta. Because the cocoon model explains the radio light curve of GW170817, as well as the γ-ray and X-ray emission (and possibly also the ultraviolet and optical emission), it is the model that is most consistent with the observational data. Cocoons may be a ubiquitous phenomenon produced in neutron-star mergers, giving rise to a hitherto unidentified population of radio, ultraviolet, X-ray and γ-ray transients in the local Universe.
37.	Nystedt, Björn, et al. (författare) The Norway spruce genome sequence and conifer genome evolution 2013 Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 497:7451, s. 579-584 Tidskriftsartikel (refereegranskat)abstract Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
38.	Ranjan, Alok, et al. (författare) Molecular basis of differential adventitious rooting competence in poplar genotypes 2022 Ingår i: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 73:12, s. 4046-4064 Tidskriftsartikel (refereegranskat)abstract Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotypes remains unknown. To address this, we generated cambium tissue-specific transcriptomic data from stem cuttings of hybrid aspen, T89 (difficult-to-root) and hybrid poplar OP42 (easy-to-root), and used transgenic approaches to verify the role of several transcription factors in the control of adventitious rooting. Increased peroxidase activity was positively correlated with better rooting. We found differentially expressed genes encoding reactive oxygen species scavenging proteins to be enriched in OP42 compared with T89. A greater number of differentially expressed transcription factors in cambium cells of OP42 compared with T89 was revealed by a more intense transcriptional reprograming in the former. PtMYC2, a potential negative regulator, was less expressed in OP42 compared with T89. Using transgenic approaches, we demonstrated that PttARF17.1 and PttMYC2.1 negatively regulate adventitious rooting. Our results provide insights into the molecular basis of genotypic differences in AR and implicate differential expression of the master regulator MYC2 as a critical player in this process.
39.	Sharma, Vidushi, et al. (författare) Time-varying Polarized Gamma-Rays from GRB 160821A : Evidence for Ordered Magnetic Fields 2019 Ingår i: Astrophysical Journal Letters. - : IOP PUBLISHING LTD. - 2041-8205 .- 2041-8213. ; 882:1 Tidskriftsartikel (refereegranskat)abstract GRB 160821A is the third most energetic gamma-ray burst observed by the Fermi gamma-ray space telescope. Based on the observations made by the Cadmium Zinc Telluride Imager on board AstroSat, here we report the most conclusive evidence to date of (i) high linear polarization (66(27)(+26)%; 5.3 sigma detection), and (ii) variation of polarization angle with time, occurring twice during the rise and decay phase of the burst at 3.5 sigma and 3.1 sigma detections, respectively. All confidence levels are reported for two parameters of interest. These observations strongly suggest synchrotron radiation produced in magnetic field lines that are highly ordered on angular scales of 1/Gamma, where Gamma is the Lorentz factor of the outflow.

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