Quantitative trait loci (QTL) are genetic regions that influence phenotypic variation of a complex trait, often through genetic interactions with each other and the environment. These are commonly ...identified through a statistical genetic analysis known as QTL mapping. Here, I present a step-by-step, practical approach to QTL mapping along with a sample data file. I focus on methods commonly used and discoveries that have been made in fishes, and utilize a multiple QTL mapping (MQM) approach in the free software package R/qtl.
Double-stranded RNA (dsRNA) molecules are used as a novel class of biopesticides. To enable assessments of the ecological risk associated with their release to receiving environments, we developed an ...approach to quantify dsRNA in agricultural soils using quantitative reverse transcription-polymerase chain reaction (RT-qPCR). To allow quantification of dsRNA adsorbed to particles, we also developed a protocol to transfer dsRNA from particles to the extraction buffer by changing particle surface charge and adding constituents to compete with dsRNA for adsorption sites. Our approach could quantify dsRNA amounts as low as 0.003 ngdsRNA/gsoil. This approach is the first available field-applicable approach able to quantify dsRNA biopesticides down to environmentally relevant concentrations. We applied this approach to investigate dsRNA dissipation (including dilution, degradation, and adsorption) in two agricultural soils. When we applied a low amount of dsRNA (1 ngdsRNA/gsoil) to the soils, we observed that a greater fraction of dsRNA was adsorbed to and extractable from soil particles in a silty clay loam soil than in a fine sandy loam soil. In both soils, dsRNA dissipated on the timescale of hours. Overall, these results demonstrate that our approach can be applied to assess the environmental fate of dsRNA biopesticides at concentrations relevant to their release to soils.
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High-affinity B cell selection in the germinal center (GC) is governed by signals delivered by follicular helper T (Tfh) cells to B cells. Selected B cells undergo clonal expansion and affinity ...maturation in the GC dark zone in direct proportion to the amount of antigen they capture and present to Tfh cells in the light zone. Here, we examined the mechanisms whereby Tfh cells program the number of GC B cell divisions. Gene expression analysis revealed that Tfh cells induce Myc expression in light-zone B cells in direct proportion to antigen capture. Conditional Myc haplo-insufficiency or overexpression combined with cell division tracking showed that MYC expression produces a metabolic reservoir in selected light-zone B cells that is proportional to the number of cell divisions in the dark zone. Thus, MYC constitutes the GC B cell division timer that when deregulated leads to emergence of B cell lymphoma.
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•MYC expression in light-zone B cells is proportional to the magnitude of T cell help•MYC proportionally regulates the size of light-zone germinal center B cells•MYC amounts dictate division capacity and residence time in the dark zone
B cell clonal expansion is regulated by Tfh cells in the germinal center. Finkin et al. report that Tfh cells induce Myc expression by light-zone B cells in direct proportion to the amount of antigen presented, and that MYC proportionally regulates B cell size and division in the dark zone.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Offspring survival, cohort performance, and ultimately population dynamics are strongly influenced by maternal characteristics (e.g., fecundity), whereas paternal contribution is often considered ...limited to genetic-driven fitness of males through sexual selection. However, male contribution to reproductive success can be particularly influential in species exhibiting paternal offspring care. Polychlorinated biphenyls (PCBs) are widespread, persistent contaminants that can disrupt maternal reproductive processes and negatively affect offspring. In contrast, how PCBs affect paternal reproductive success is largely unknown, but could ultimately affect population dynamics. We examined the effects of lifelong PCB exposure on the reproductive processes of male fathead minnows (Pimephales promelas), a species exhibiting sole paternal offspring care, by examining endocrine-associated gene expression, testes histology, secondary sexual characteristics, courtship ability, offspring care, and offspring survival. PCBs minimized male secondary sexual characteristics, but did not affect gonadal end points or inhibit ability to court females. Fathers exposed to high concentrations of dioxin-like PCBs had changes in gene expression, reduced offspring care behavior, and higher embryo mortality, possibly due to fathers spending less time within nests and less frequently tending to embryos. Through complex interactions among gene expression, physical characteristics, and behavior, PCBs inhibit paternal reproductive success and have the potential to suppress population size.
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We present the drastic transformation of the X-ray properties of the active galactic nucleus (AGN) 1ES 1927+654, following a changing-look event. After the optical/ultraviolet outburst the power-law ...component, produced in the X-ray corona, disappeared, and the spectrum of 1ES 1927+65 instead became dominated by a blackbody component (kT ∼ 80-120 eV). This implies that the X-ray corona, ubiquitously found in AGNs, was destroyed in the event. Our dense ∼450 days long X-ray monitoring shows that the source is extremely variable in the X-ray band. On long timescales the source varies up to ∼4 dex in ∼100 days, while on short timescales up to ∼2 dex in ∼8 hr. The luminosity of the source is found to first show a strong dip down to , and then a constant increase in luminosity to levels exceeding the pre-outburst level 300 days after the optical event detection, rising up asymptotically to . As the X-ray luminosity of the source increases, the X-ray corona is recreated, and a very steep power-law component (Γ 3) reappears, and dominates the emission for 0.3-2 keV luminosities , ∼300 days after the beginning of the event. We discuss possible origins of this event, and speculate that our observations could be explained by the interaction between the accretion flow and debris from a tidally disrupted star. Our results show that changing-look events can be associated with dramatic and rapid transformations of the innermost regions of accreting supermassive black holes.
Abstract
In recent work with high-resolution reflection grating spectrometers (RGS) aboard XMM–Newton, Pinto et al. have discovered that two bright and archetypal ultraluminous X-ray sources (ULXs) ...have strong relativistic winds in agreement with theoretical predictions of high accretion rates. It has been proposed that such winds can become optically thick enough to block and reprocess the disc X-ray photons almost entirely, making the source appear as a soft thermal emitter or ultraluminous supersoft X-ray source (ULS). To test this hypothesis, we have studied a ULX where the wind is strong enough to cause significant absorption of the hard X-ray continuum: NGC 55 ULX. The RGS spectrum of NGC 55 ULX shows a wealth of emission and absorption lines blueshifted by significant fractions of the light speed (0.01–0.20)c indicating the presence of a powerful wind. The wind has a complex dynamical structure with the ionization state increasing with the outflow velocity, which may indicate launching from different regions of the accretion disc. The comparison with other ULXs such as NGC 1313 X-1 and NGC 5408 X-1 suggests that NGC 55 ULX is being observed at higher inclination. The wind partly absorbs the source flux above 1 keV, generating a spectral drop similar to that observed in ULSs. The softening of the spectrum at lower (∼ Eddington) luminosities and the detection of a soft lag agree with the scenario of wind clumps crossing the line of sight, partly absorbing and reprocessing the hard X-rays from the innermost region.
Abstract
Tidal disruption events (TDEs) are exotic transients that can lead to temporary super-Eddington accretion onto a supermassive black hole. Such an accretion mode is naturally expected to ...result in powerful outflows of ionized matter. However, to date such an outflow has only been directly detected in the X-ray band in a single TDE, ASASSN-14li. This outflow has a low velocity of just a few 100 km s
−1
, although there is also evidence for a second, ultrafast phase. Here we present the detection of a low-velocity outflow in a second TDE, ASASSN-20qc. The high-resolution X-ray spectrum reveals an array of narrow absorption lines, each blueshifted by a few 100 km s
−1
, which cannot be described by a single photoionization phase. For the first time, we confirm the multiphase nature of a TDE outflow, with at least two phases and two distinct velocity components. One highly ionized phase is outflowing at
910
−
80
+
90
km s
−1
, while a lower ionization component is blueshifted by
400
−
120
+
100
km s
−1
. We perform a time-resolved analysis of the X-ray spectrum and detect that, surprisingly, the ionization parameter of the mildly ionized absorber strongly varies over the course of a single 60 ks observation, indicating that its distance from the black hole may be as low as 400 gravitational radii. We discuss these findings in the context of TDEs and compare this newly detected outflow with that of ASASSN-14li.
Abstract
Ark 564 is an archetypal narrow-line Seyfert 1 that has been well observed in soft X-rays from 0.3–10 keV, revealing a steep spectrum, strong soft excess, iron K emission line and dramatic ...variability on the order of hours. Because of its very steep spectrum, observations of the source above 10 keV have been sparse. We report here on the first NuSTAR observation of Ark 564. The source was observed for 200 ks with NuSTAR, 50 ks of which were concurrent with Suzaku observations. NuSTAR and Suzaku observed a dramatic flare, in which the hard emission is clearly delayed with respect to the soft emission, consistent with previous detections of a low-frequency hard lag found in XMM–Newton data. The NuSTAR spectrum is well described by a low-temperature Comptonization continuum (with an electron temperature of 15 ± 2 keV), which irradiates a highly ionized disc. No further relativistic broadening or ionized absorption is required. These spectral results show that Ark 564 has one of the lowest temperature coronae observed by NuSTAR to date. We discuss possible reasons for low-temperature coronae in high-Eddington sources.
Increased production of fetal hemoglobin (HbF) can ameliorate the severity of sickle cell disease and β-thalassemia. BCL11A has been identified as a key regulator of HbF silencing, although its ...precise mechanisms of action remain incompletely understood. Recent studies have identified pathogenic mutations that cause heterozygous loss-of-function of BCL11A and result in a distinct neurodevelopmental disorder that is characterized by persistent HbF expression. While the majority of cases have deletions or null mutations causing haploinsufficiency of BCL11A, several missense variants have also been identified. Here, we perform functional studies on these variants to uncover specific liabilities for BCL11A's function in HbF silencing. We find several mutations in an N-terminal C2HC zinc finger that increase proteasomal degradation of BCL11A. We also identify a distinct C-terminal missense variant in the fifth zinc finger domain that we demonstrate causes loss-of-function through disruption of DNA binding. Our analysis of missense variants causing loss-of-function in vivo illuminates mechanisms by which BCL11A silences HbF and also suggests potential therapeutic avenues for HbF induction to treat sickle cell disease and β-thalassemia.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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