Genome of Tenualosa ilisha from the river Padma, Bangladesh

Objective

Hilsa shad (Tenualosa ilisha), is a popular fish of Bangladesh belonging to the Clupeidae family. An anadromous species, like the salmon and many other migratory fish, it is a unique species that lives in the sea and travels to freshwater rivers for spawning. During its entire life, Tenualosa ilisha migrates both from sea to freshwater and vice versa.

Data description

The genome of Tenualosa ilisha collected from the river Padma of Rajshahi, Bangladesh has been sequenced and its de novo hybrid assembly and structural annotations are being reported here. Illumina and PacBio sequencing platforms were used for high depth sequencing and the draft genome assembly was found to be 816 MB with N50 size of 188 kb. MAKER gene annotation tool predicted 31,254 gene models. Benchmarking Universal Single-Copy Orthologs refer 95% completeness of the assembled genome.

Search for Subsolar-Mass Ultracompact Binaries in Advanced LIGO's First Observing Run

We present the first Advanced LIGO and Advanced Virgo search for ultracompact binary systems with component masses between 0.2  M_{⊙}-1.0  M_{⊙} using data taken between September 12, 2015 and January 19, 2016. We find no viable gravitational wave candidates. Our null result constrains the coalescence rate of monochromatic (delta function) distributions of nonspinning (0.2  M_{⊙}, 0.2  M_{⊙}) ultracompact binaries to be less than 1.0×10^{6}  Gpc^{-3}  yr^{-1} and the coalescence rate of a similar distribution of (1.0  M_{⊙}, 1.0  M_{⊙}) ultracompact binaries to be less than 1.9×10^{4}  Gpc^{-3}  yr^{-1} (at 90% confidence). Neither black holes nor neutron stars are expected to form below ∼1  M_{⊙} through conventional stellar evolution, though it has been proposed that similarly low mass black holes could be formed primordially through density fluctuations in the early Universe and contribute to the dark matter density. The interpretation of our constraints in the primordial black hole dark matter paradigm is highly model dependent; however, under a particular primordial black hole binary formation scenario we constrain monochromatic primordial black hole populations of 0.2  M_{⊙} to be less than 33% of the total dark matter density and monochromatic populations of 1.0  M_{⊙} to be less than 5% of the dark matter density. The latter strengthens the presently placed bounds from microlensing surveys of massive compact halo objects (MACHOs) provided by the MACHO and EROS Collaborations.

Imaging quantum fluctuations near criticality

A quantum phase transition (QPT) occurs between two competing phases of matter at zero temperature, driven by quantum fluctuations. Though the presence of these fluctuations is well established, they have not been locally imaged in space and their local dynamics has not been studied so far. We use a scanning superconducting quantum interference device to image quantum fluctuations in the vicinity of the QPT from a superconductor to an insulator. We find fluctuations of the diamagnetic response in both space and time that survive well below the transition temperature, demonstrating their quantum nature. The fluctuations appear as telegraph-like noise with a range of characteristic times and a non-monotonic temperature dependence, revealing unexpected quantum granularity. The lateral dimension of these fluctuations grows towards criticality, offering a new measurable length scale. Our results provide physical insight about the reorganization of phases across a QPT, with implications for any theoretical description. This paves a new route for future quantum information applications.

GW170817: Measurements of Neutron Star Radii and Equation of State

On 17 August 2017, the LIGO and Virgo observatories made the first direct detection of gravitational waves from the coalescence of a neutron star binary system. The detection of this gravitational-wave signal, GW170817, offers a novel opportunity to directly probe the properties of matter at the extreme conditions found in the interior of these stars. The initial, minimal-assumption analysis of the LIGO and Virgo data placed constraints on the tidal effects of the coalescing bodies, which were then translated to constraints on neutron star radii. Here, we expand upon previous analyses by working under the hypothesis that both bodies were neutron stars that are described by the same equation of state and have spins within the range observed in Galactic binary neutron stars. Our analysis employs two methods: the use of equation-of-state-insensitive relations between various macroscopic properties of the neutron stars and the use of an efficient parametrization of the defining function p(ρ) of the equation of state itself. From the LIGO and Virgo data alone and the first method, we measure the two neutron star radii as R_{1}=10.8_{-1.7}^{+2.0}  km for the heavier star and R_{2}=10.7_{-1.5}^{+2.1}  km for the lighter star at the 90% credible level. If we additionally require that the equation of state supports neutron stars with masses larger than 1.97  M_{⊙} as required from electromagnetic observations and employ the equation-of-state parametrization, we further constrain R_{1}=11.9_{-1.4}^{+1.4}  km and R_{2}=11.9_{-1.4}^{+1.4}  km at the 90% credible level. Finally, we obtain constraints on p(ρ) at supranuclear densities, with pressure at twice nuclear saturation density measured at 3.5_{-1.7}^{+2.7}×10^{34}  dyn cm^{-2} at the 90% level.

Population diversity of bacterial endophytes from jute (Corchorus olitorius) and evaluation of their potential role as bioinoculants

Endophytes are bacterial or fungal organisms associated with plants in an obligate or facultative manner. In order to maintain a stable symbiosis, many of the endophytes produce compounds that promote plant growth and help them adapt better to the environment. This study was conducted to explore the potential of jute bacterial endophytes for their growth promotion ability in direct and indirect ways. A total of 27 different bacterial species were identified from different varieties of a jute plant (Corchorus olitorius) and different parts of the plant (leaf, root, seed, and seedling) based on 16S rRNA gene sequence. Two of the isolates showed ACC deaminase activity with Staphylococcus pasteuri strain MBL_B3 and Ralstonia solanacearum strain MBL_B6 producing 18.1 and 8.08 μM mg^-1 h^-1 α-ketobutyrate respectively while eighteen had the ACC deaminase gene (acdS). Fourteen were positive for siderophore activity while Kocuria sp. strain MBL_B19 (133.36 μg/ml) and Bacillus sp. strain MBL_B17 (124.72 μg/ml) showed high IAA production ability. Seven bacterial strains were able to fix nitrogen with only one testing positive for nifH gene. Five isolates exhibited phosphorus utilization ability with Bacillus sp. strain MBL_B17 producing 218.47 μg P/ml. Three bacteria were able to inhibit the growth of a phytopathogen, Macrophomina phaseolina and among them Bacillus subtilis strain MBL_B4 was found to be the most effective, having 82% and 53% of relative inhibition ratio (RIR) and percent growth inhibition (PGI) values respectively. Nine bacteria were tested for their in vivo growth promotion ability and most of these isolates increased seed germination potential and vigour index significantly. Bacillus subtilis strain MBL_B13 showed 26.8% more vigour index than the control in which no bacterial inoculum was used. All inoculants were found to increase the dry weight of jute seedlings in comparison to the control plants and the most increase in fresh weight was found for Staphylococcus saprophyticus strain MBL_B9. Staphylococcus pasteuri strain MBL_B3 exhibited diverse in vitro growth promotion activity and significant growth promoting effect in in vivo pot experiments. These bacterial strains with plant growth enhancing abilities have the potential to be used as bioinoculants.

Water treatment: Mn-TiO2 synthesized by ultrasound with increased aromatics adsorption

Pharma-products are mostly single or multiple cyclic compounds. They pollute surface water and are persistent in the aquatic ecosystem. When irradiated by UV light, TiO₂ catalysts cleave or degrade organic contaminants in water. Removal of organics by photocatalysis results from a synergistic effect of adsorption and photocatalysis. Synthesis of catalysts by ultrasound (US) produces high surface area and porous solids. Here, we synthesized Mn-doped TiO₂ with a US-assisted sol-gel method. Compared to the classical synthesis, US increased the BET surface area from 83 m² g^-1 to 90 m² g^-1 in the Mn-TiO₂ sample and from 9.0 m² g^-1 to 53 m² g^-1 in the control TiO₂. Accordingly, acetaminophen and amoxicillin adsorption increased from 44% to 52%, and from 34% to 94% for the Mn-TiO₂ obtained in absence and presence of US, respectively. When in a mixture, the two drugs strongly compete for adsorption on TiO₂.

High-performance solution-based CdS-conjugated hybrid polymer solar cells

In this study, hybrid BHJ – bulk heterojunction polymer solar cells were fabricated by incorporating CdS quantum dots (QDs) in a blend of P3HT (donor) and PCBM (acceptor) using dichlorobenzene and chlorobenzene as solvents. CdS QDs at various ratios were mixed in a fixed amount of the P3HT and PCBM blend. The prepared samples have been characterized by a variety of techniques such as I–V and EQE measurements, atomic force microscopy (AFM), scanning electron microscopy (SEM) and ultraviolet-visible (UV-vis) spectroscopy. The mixing of QDs in the polymer blends improved the PCE – power conversion efficiency of the solar cells under standard light conditions. The improved PCE from 2.95 to 4.41% is mostly due to the increase in the fill factor (FF) and short-circuit current (J_sc) of the devices with an optimum amount of CdS in the P3HT:PCBM blend. The increase in J_sc possibly originated from the formation of a percolation network of CdS. The conjugation of QDs has increased the absorption of the active layers in the visible region. These results well matched as reported, conjugation of CdS in the perovskite active layer increased the absorption and PCE of the devices relative to those of the perovskite films. This increment in parameters is attributed to the decrease in charge recombinations that improved the performance of the doped device.

In this study, hybrid BHJ – bulk heterojunction polymer solar cells were fabricated by incorporating CdS quantum dots (QDs) in a blend of P3HT (donor) and PCBM (acceptor) using dichlorobenzene and chlorobenzene as solvents.

An endophytic Basidiomycete, Grammothele lineata, isolated from Corchorus olitorius, produces paclitaxel that shows cytotoxicity

Grammothele lineata, an endophyte isolated in our laboratory from jute (Corchorus olitorius acc. 2015) was found to be a substantial paclitaxel producer. Taxol and its related compounds, produced by this endophyte were extracted by growing the fungus in simple nutrient media (potato dextrose broth, PDB). Taxol was identified and characterized by different analytical techniques (TLC, HPLC, FTIR, LC-ESI-MS/MS) following its extraction by ethyl acetate. In PDB media, this fungus was found to produce 382.2 μgL-1 of taxol which is about 7.6 x103 fold higher than the first reported endophytic fungi, Taxomyces andreanae. The extracted taxol exhibited cytotoxic activity in an in vitro culture of HeLa cancer cell line. The fungal extract also exhibited antifungal and antibacterial activities against different pathogenic strains. This is the first report of a jute endophytic fungus harboring the capacity to produce taxol and also the first reported taxol producing species that belongs to the Basidiomycota phylum, so far unknown to be a taxol producer. These findings suggest that the fungal endophyte, Grammothele lineata can be an excellent source of taxol and can also serve as a potential species for chemical and genetic engineering to enhance further the production of taxol.