Search for: All records

Abstract The radiation mechanism underlying the prompt emission remains unresolved and can be resolved using a systematic and uniform time-resolved spectro-polarimetric study. In this paper, we investigated the spectral, temporal, and polarimetric characteristics of five bright gamma-ray bursts (GRBs) using archival data from AstroSat CZTI, Swift Burst Alert Telescope, and Fermi/GBM. These bright GRBs were detected by CZTI in its first year of operation, and their average polarization characteristics have been published in Chattopadhyay et al. In the present work, we examined the time-resolved (in 100–600 keV) and energy-resolved polarization measurements of these GRBs with an improved polarimetric technique such as increasing the effective area and bandwidth (by using data from low-gain pixels), using an improved event selection logic to reduce noise in the double events and extend the spectral bandwidth. In addition, we also separately carried out detailed time-resolved spectral analyses of these GRBs using empirical and physical synchrotron models. By these improved time-resolved and energy-resolved spectral and polarimetric studies (not fully coupled spectro-polarimetric fitting), we could pin down the elusive prompt emission mechanism of these GRBs. Our spectro-polarimetric analysis reveals that GRB 160623A, GRB 160703A, and GRB 160821A have Poynting flux-dominated jets. On the other hand, GRB 160325A and GRB 160802A have baryonic-dominated jets with mild magnetization. Furthermore, we observe a rapid change in polarization angle by ∼90° within the main pulse of very bright GRB 160821A, consistent with our previous results. Our study suggests that the jet composition of GRBs may exhibit a wide range of magnetization, which can be revealed by utilizing spectro-polarimetric investigations of the bright GRBs. 

Dinoflagellates of the Symbiodiniaceae family encompass diverse symbionts that are critical to corals and other species living in coral reefs. It is well known that sexual reproduction enhances adaptive evolution in changing environments. Although genes related to meiotic functions were reported in Symbiodiniaceae, cytological evidence of meiosis and fertilisation are however yet to be observed in these taxa. Using transcriptome and genome data from 21 Symbiodiniaceae isolates, we studied genes that encode proteins associated with distinct stages of meiosis and syngamy. We report the absence of genes that encode main components of the synaptonemal complex (SC), a protein structure that mediates homologous chromosomal pairing and class I crossovers. This result suggests an independent loss of canonical SCs in the alveolates, that also includes the SC-lacking ciliates. We hypothesise that this loss was due in part to permanently condensed chromosomes and repeat-rich sequences in Symbiodiniaceae (and other dinoflagellates) which favoured the SC-independent class II crossover pathway. Our results reveal novel insights into evolution of the meiotic molecular machinery in the ecologically important Symbiodiniaceae and in other eukaryotes. 

Given the catastrophic changes befalling coral reefs, understanding coral gene function is essential to advance reef conservation. This has proved challenging due to the paucity of genomic data and genetic tools available for corals. Recently, CRISPR/Cas9 gene editing was applied to these species; however, a major bottleneck is the identification and prioritization of candidate genes for manipulation. This issue is exacerbated by the many unknown ('dark') coral genes that may play key roles in the stress response. We review the use of gene coexpression networks that incorporate both known and unknown genes to identify targets for reverse genetic analysis. This approach also provides a framework for the annotation of dark genes in established interaction networks to improve our fundamental knowledge of coral gene function. 

In order to develop successful strategies for coral reef preservation, it is critical that the biology of both host corals and symbiotic algae are investigated. In the Ryukyu Archipelago, which encompasses many islands spread over ∼500 km of the Pacific Ocean, four major populations of the coral Acropora digitifera have been studied using whole-genome shotgun (WGS) sequence analysis (Shinzato C, Mungpakdee S, Arakaki N, Satoh N. 2015. Genome-wide single-nucleotide polymorphism (SNP) analysis explains coral diversity and recovery in the Ryukyu Archipelago. Sci Rep. 5:18211.). In contrast, the diversity of the symbiotic dinoflagellates associated with these A. digitifera populations is unknown. It is therefore unclear if these two core components of the coral holobiont share a common evolutionary history. This issue can be addressed for the symbiotic algal populations by studying the organelle genomes of their mitochondria and plastids. Here, we analyzed WGS data from ∼150 adult A. digitifera, and by mapping reads to the available reference genome sequences, we extracted 2,250 sequences representing 15 organelle genes of Symbiodiniaceae. Molecular phylogenetic analyses of these mitochondrial and plastid gene sets revealed that A. digitifera from the southern Yaeyama islands harbor a different Symbiodiniaceae population than the islands of Okinawa and Kerama in the north, indicating that the distribution of symbiont populations partially matches that of the four host populations. Interestingly, we found that numerous SNPs correspond to known RNA-edited sites in 14 of the Symbiodiniaceae organelle genes, with mitochondrial genes showing a stronger correspondence than plastid genes. These results suggest a possible correlation between RNA editing and SNPs in the two organelle genomes of symbiotic dinoflagellates. 

Background: Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms that underpin the adaptation of these organisms to diverse ecological niches is limited by the scarce availability of genomic data, partly due to their large genome sizes estimated up to 250 Gbp. Currently available dinoflagellate genome data are restricted to Symbiodiniaceae (particularly symbionts of reef-building corals) and parasitic lineages, from taxa that have smaller genome size ranges, while genomic information from more diverse free living species is still lacking. Results: Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. We found that about 68% of the genomes are composed of repetitive sequence, with long terminal repeats likely contributing to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). For each genome, guided using full-length transcriptome data, we predicted > 50,000 high-quality protein-coding genes, of which ~40% are in unidirectional gene clusters and ~25% comprise single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial origin of ice-binding domains in cold-adapted dinoflagellates. Conclusions: Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Because most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light polar environments. These genomes provide a foundational reference for future research on dinoflagellate evolution. 

Coral reefs are sustained by symbioses between corals and symbiodiniacean dinoflagellates. These symbioses vary in the extent of their permanence in and specificity to the host. Although dinoflagellates are primarily free-living, Symbiodiniaceae diversified mainly as symbiotic lineages. Their genomes reveal conserved symbiosis-related gene functions and high sequence divergence. However, the evolutionary mechanisms that underpin the transition from the free-living lifestyle to symbiosis remain poorly understood. Here, we discuss the genome evolution of Symbiodiniaceae in diverse ecological niches across the broad spectrum of symbiotic associations, from free-living to putative obligate symbionts. We pose key questions regarding genome evolution vis-à-vis the transition of dinoflagellates from free-living to symbiotic and propose strategies for future research to better understand coral-dinoflagellate and other eukaryote-eukaryote symbioses. 

Abstract Multi-pulsed GRB 190530A, detected by the GBM and LAT onboard Fermi, is the sixth most fluent GBM burst detected so far. This paper presents the timing, spectral, and polarimetric analysis of the prompt emission observed using AstroSat and Fermi to provide insight into the prompt emission radiation mechanisms. The time-integrated spectrum shows conclusive proof of two breaks due to peak energy and a second lower energy break. Time-integrated (55.43 ± 21.30 %) as well as time-resolved polarization measurements, made by the Cadmium Zinc Telluride Imager (CZTI) onboard AstroSat, show a hint of high degree of polarization. The presence of a hint of high degree of polarization and the values of low energy spectral index (αpt) do not run over the synchrotron limit for the first two pulses, supporting the synchrotron origin in an ordered magnetic field. However, during the third pulse, αpt exceeds the synchrotron line of death in few bins, and a thermal signature along with the synchrotron component in the time-resolved spectra is observed. Furthermore, we also report the earliest optical observations constraining afterglow polarization using the MASTER (P < 1.3 %) and the redshift measurement (z= 0.9386) obtained with the 10.4m GTC telescopes. The broadband afterglow can be described with a forward shock model for an ISM-like medium with a wide jet opening angle. We determine a circumburst density of n0 ∼ 7.41, kinetic energy EK ∼ 7.24 × 1054 erg, and radiated γ-ray energy Eγ, iso ∼ 6.05 × 1054 erg, respectively.