Population dynamics of rhesus macaques and associated foamy virus in Bangladesh.

Foamy viruses are complex retroviruses that have been shown to be transmitted from nonhuman primates to humans. In Bangladesh, infection with simian foamy virus (SFV) is ubiquitous among rhesus macaques, which come into contact with humans in diverse locations and contexts throughout the country. We analyzed microsatellite DNA from 126 macaques at six sites in Bangladesh in order to characterize geographic patterns of macaque population structure. We also included in this study 38 macaques owned by nomadic people who train them to perform for audiences. PCR was used to analyze a portion of the proviral gag gene from all SFV-positive macaques, and multiple clones were sequenced. Phylogenetic analysis was used to infer long-term patterns of viral transmission. Analyses of SFV gag gene sequences indicated that macaque populations from different areas harbor genetically distinct strains of SFV, suggesting that geographic features such as forest cover play a role in determining the dispersal of macaques and SFV. We also found evidence suggesting that humans traveling the region with performing macaques likely play a role in the translocation of macaques and SFV. Our studies found that individual animals can harbor more than one strain of SFV and that presence of more than one SFV strain is more common among older animals. Some macaques are infected with SFV that appears to be recombinant. These findings paint a more detailed picture of how geographic and sociocultural factors influence the spectrum of simian-borne retroviruses

SpitzerSpitzer Parallax of OGLE-2018-BLG-0596: A Low-mass-ratio Planet around an M-dwarf

We report the discovery of a $Spitzer$ microlensing planet OGLE-2018-BLG-0596Lb, with preferred planet-host mass ratio $q \sim 2\times10^{-4}$. The planetary signal, which is characterized by a short $(\sim 1~{\rm day})$ "bump" on the rising side of the lensing light curve, was densely covered by ground-based surveys. We find that the signal can be explained by a bright source that fully envelops the planetary caustic, i.e., a "Hollywood" geometry. Combined with the source proper motion measured from $Gaia$, the $Spitzer$ satellite parallax measurement makes it possible to precisely constrain the lens physical parameters. The preferred solution, in which the planet perturbs the minor image due to lensing by the host, yields a Uranus-mass planet with a mass of $M_{\rm p} = 13.9\pm1.6~M_{\oplus}$ orbiting a mid M-dwarf with a mass of $M_{\rm h} = 0.23\pm0.03~M_{\odot}$. There is also a second possible solution that is substantially disfavored but cannot be ruled out, for which the planet perturbs the major image. The latter solution yields $M_{\rm p} = 1.2\pm0.2~M_{\oplus}$ and $M_{\rm h} = 0.15\pm0.02~M_{\odot}$. By combining the microlensing and $Gaia$ data together with a Galactic model, we find in either case that the lens lies on the near side of the Galactic bulge at a distance $D_{\rm L} \sim 6\pm1~{\rm kpc}$. Future adaptive optics observations may decisively resolve the major image/minor image degeneracy.Comment: 34 pages, 8 figures, Submitted to AAS journa

Sustainable Sources of Biomass for Bioremediation of Heavy Metals in Waste Water Derived from Coal-Fired Power Generation

Biosorption of heavy metals using dried algal biomass has been extensively described but rarely implemented. We contend this is because available algal biomass is a valuable product with a ready market. Therefore, we considered an alternative and practical approach to algal bioremediation in which algae were cultured directly in the waste water stream. We cultured three species of algae with and without nutrient addition in water that was contaminated with heavy metals from an Ash Dam associated with coal-fired power generation and tested metal uptake and bioremediation potential. All species achieved high concentrations of heavy metals (to 8% dry mass). Two key elements, V and As, reached concentrations in the biomass of 1543 mg.kg−1 DW and 137 mg.kg−1 DW. Growth rates were reduced by more than half in neat Ash Dam water than when nutrients were supplied in excess. Growth rate and bioconcentration were positively correlated for most elements, but some elements (e.g. Cd, Zn) were concentrated more when growth rates were lower, indicating the potential to tailor bioremediation depending on the pollutant. The cosmopolitan nature of the macroalgae studied, and their ability to grow and concentrate a suite of heavy metals from industrial wastes, highlights a clear benefit in the practical application of waste water bioremediation

Relation of DNA Methylation of 5′-CpG Island of ACSL3 to Transplacental Exposure to Airborne Polycyclic Aromatic Hydrocarbons and Childhood Asthma

In a longitudinal cohort of ∼700 children in New York City, the prevalence of asthma (>25%) is among the highest in the US. This high risk may in part be caused by transplacental exposure to traffic-related polycyclic aromatic hydrocarbons (PAHs) but biomarkers informative of PAH-asthma relationships is lacking. We here hypothesized that epigenetic marks associated with transplacental PAH exposure and/or childhood asthma risk could be identified in fetal tissues. Mothers completed personal prenatal air monitoring for PAH exposure determination. Methylation sensitive restriction fingerprinting was used to analyze umbilical cord white blood cell (UCWBC) DNA of 20 cohort children. Over 30 DNA sequences were identified whose methylation status was dependent on the level of maternal PAH exposure. Six sequences were found to be homologous to known genes having one or more 5′-CpG island(s) (5′-CGI). Of these, acyl-CoA synthetase long-chain family member 3 (ACSL3) exhibited the highest concordance between the extent of methylation of its 5′-CGI in UCWBCs and the level of gene expression in matched fetal placental tissues in the initial 20 cohort children. ACSL3 was therefore chosen for further investigation in a larger sample of 56 cohort children. Methylation of the ACSL3 5′-CGI was found to be significantly associated with maternal airborne PAH exposure exceeding 2.41 ng/m3 (OR = 13.8; p<0.001; sensitivity = 75%; specificity = 82%) and with a parental report of asthma symptoms in children prior to age 5 (OR = 3.9; p<0.05). Thus, if validated, methylated ACSL3 5′CGI in UCWBC DNA may be a surrogate endpoint for transplacental PAH exposure and/or a potential biomarker for environmentally-related asthma. This exploratory report provides a new blueprint for the discovery of epigenetic biomarkers relevant to other exposure assessments and/or investigations of exposure-disease relationships in birth cohorts. The results support the emerging theory of early origins of later life disease development

A nuclear role for the respiratory enzyme CLK-1 in regulating mitochondrial stress responses and longevity

The coordinated regulation of mitochondrial and nuclear activities is essential for cellular respiration and its disruption leads to mitochondrial dysfunction, a hallmark of ageing. Mitochondria communicate with nuclei through retrograde signalling pathways that modulate nuclear gene expression to maintain mitochondrial homeostasis. The monooxygenase CLK-1 (human homologue COQ7) was previously reported to be mitochondrial, with a role in respiration and longevity. We have uncovered a distinct nuclear form of CLK-1 that independently regulates lifespan. Nuclear CLK-1 mediates a retrograde signalling pathway that is conserved from Caenorhabditis elegans to humans and is responsive to mitochondrial reactive oxygen species, thus acting as a barometer of oxidative metabolism. We show that, through modulation of gene expression, the pathway regulates both mitochondrial reactive oxygen species metabolism and the mitochondrial unfolded protein response. Our results demonstrate that a respiratory enzyme acts in the nucleus to control mitochondrial stress responses and longevity

Evidence of gene-environment interaction for two genes on chromosome 4 and environmental tobacco smoke in controlling the risk of nonsyndromic cleft palate

Nonsyndromic cleft palate (CP) is one of the most common human birth defects and both genetic and environmental risk factors contribute to its etiology. We conducted a genome-wide association study (GWAS) using 550 CP case-parent trios ascertained in an international consortium. Stratified analysis among trios with different ancestries was performed to test for GxE interactions with common maternal exposures using conditional logistic regression models. While no single nucleotide polymorphism (SNP) achieved genome-wide significance when considered alone, markers in SLC2A9 and the neighboring WDR1 on chromosome 4p16.1 gave suggestive evidence of gene-environment interaction with environmental tobacco smoke (ETS) among 259 Asian trios when the models included a term for GxE interaction. Multiple SNPs in these two genes were associated with increased risk of nonsyndromic CP if the mother was exposed to ETS during the peri-conceptual period (3 months prior to conception through the first trimester). When maternal ETS was considered, fifteen of 135 SNPs mapping to SLC2A9 and 9 of 59 SNPs in WDR1 gave P values approaching genome-wide significance (10-6<P<10-4) in a test for GxETS interaction. SNPs rs3733585 and rs12508991 in SLC2A9 yielded P = 2.26×10-7 in a test for GxETS interaction. SNPs rs6820756 and rs7699512 in WDR1 also yielded P = 1.79×10-7 and P = 1.98×10-7 in a 1 df test for GxE interaction. Although further replication studies are critical to confirming these findings, these results illustrate how genetic associations for nonsyndromic CP can be missed if potential GxE interaction is not taken into account, and this study suggest SLC2A9 and WDR1 should be considered as candidate genes for CP. © 2014 Wu et al

Three Saturn-mass planets transiting F-type stars revealed with TESS and HARPS

While the sample of confirmed exoplanets continues to increase, the population of transiting exoplanets around early-type stars is still limited. These planets allow us to investigate the planet properties and formation pathways over a wide range of stellar masses and study the impact of high irradiation on hot Jupiters orbiting such stars. We report the discovery of TOI-615b, TOI-622b, and TOI-2641b, three Saturn-mass planets transiting main sequence, F-type stars. The planets were identified by the Transiting Exoplanet Survey Satellite (TESS) and confirmed with complementary ground-based and radial velocity observations. TOI-615b is a highly irradiated ($\sim$1277 $F_{\oplus}$) and bloated Saturn-mass planet (1.69$^{+0.05}_{-0.06}$$R_{Jup}$ and 0.43$^{+0.09}_{-0.08}$$M_{Jup}$) in a 4.66 day orbit transiting a 6850 K star. TOI-622b has a radius of 0.82$^{+0.03}_{-0.03}$$R_{Jup}$ and a mass of 0.30$^{+0.07}_{-0.08}$~$M_{Jup}$ in a 6.40 day orbit. Despite its high insolation flux ($\sim$600 $F_{\oplus}$), TOI-622b does not show any evidence of radius inflation. TOI-2641b is a 0.37$^{+0.05}_{-0.04}$$M_{Jup}$ planet in a 4.88 day orbit with a grazing transit (b = 1.04$^{+0.05}_{-0.06 }$) that results in a poorly constrained radius of 1.61$^{+0.46}_{-0.64}$$R_{Jup}$. Additionally, TOI-615b is considered attractive for atmospheric studies via transmission spectroscopy with ground-based spectrographs and $\textit{JWST}$. Future atmospheric and spin-orbit alignment observations are essential since they can provide information on the atmospheric composition, formation and migration of exoplanets across various stellar types.Comment: 16 pages, 17 figures, submitted to A&

KMT-2021-BLG-1547Lb: Giant microlensing planet detected through a signal deformed by source binarity

We investigate the previous microlensing data collected by the KMTNet survey in search of anomalous events for which no precise interpretations of the anomalies have been suggested. From this investigation, we find that the anomaly in the lensing light curve of the event KMT-2021-BLG-1547 is approximately described by a binary-lens (2L1S) model with a lens possessing a giant planet, but the model leaves unexplained residuals. We investigate the origin of the residuals by testing more sophisticated models that include either an extra lens component (3L1S model) or an extra source star (2L2S model) to the 2L1S configuration of the lens system. From these analyses, we find that the residuals from the 2L1S model originate from the existence of a faint companion to the source. The 2L2S solution substantially reduces the residuals and improves the model fit by $\Delta\chi^2=67.1$ with respect to the 2L1S solution. The 3L1S solution also improves the fit, but its fit is worse than that of the 2L2S solution by $\Delta\chi^2=24.7$. According to the 2L2S solution, the lens of the event is a planetary system with planet and host masses $(M_{\rm p}/M_{\rm J}, M_{\rm h}/M_\odot)=\left( 1.47^{+0.64}_{-0.77}, 0.72^{+0.32}_{-0.38}\right)$ lying at a distance \D_{\rm L} =5.07^{+0.98}_{-1.50}~kpc, and the source is a binary composed of a subgiant primary of a late G or an early K spectral type and a main-sequence companion of a K spectral type. The event demonstrates the need of sophisticated modeling for unexplained anomalies for the construction of a complete microlensing planet sample.Comment: 9 pages, 4 tables, 7 figure

KMT-2022-BLG-0440Lb: A New q<10−4q < 10^{-4} Microlensing Planet with the Central-Resonant Caustic Degeneracy Broken

We present the observations and analysis of a high-magnification microlensing planetary event, KMT-2022-BLG-0440, for which the weak and short-lived planetary signal was covered by both the KMTNet survey and follow-up observations. The binary-lens models with a central caustic provide the best fits, with a planet/host mass ratio, $q = 0.75$--$1.00 \times 10^{-4}$ at $1\sigma$. The binary-lens models with a resonant caustic and a brown-dwarf mass ratio are both excluded by $\Delta\chi^2 > 70$. The binary-source model can fit the anomaly well but is rejected by the ``color argument'' on the second source. From Bayesian analyses, it is estimated that the host star is likely a K or M dwarf located in the Galactic disk, the planet probably has a Neptune-mass, and the projected planet-host separation is $1.9^{+0.6}_{-0.7}$ or $4.6^{+1.4}_{-1.7}$ au, subject to the close/wide degeneracy. This is the third $q < 10^{-4}$ planet from a high-magnification planetary signal ($A \gtrsim 65$). Together with another such planet, KMT-2021-BLG-0171Lb, the ongoing follow-up program for the KMTNet high-magnification events has demonstrated its ability in detecting high-magnification planetary signals for $q < 10^{-4}$ planets, which are challenging for the current microlensing surveys.Comment: MNRAS accepte

Genomic insights into rapid speciation within the world's largest tree genus Syzygium

The relative importance of the mechanisms underlying species radiation remains unclear. Here, the authors combine reference genome assembly and population genetics analyses to show that neutral forces have contributed to the radiation of the most species-rich tree genus Syzygium. Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.Peer reviewe