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- Aphid host (2)
- Aphidius ervi (2)
- Chemosensory genes (2)
- DNA methylation loss (2)
- GC content (2)
- Lysiphlebus fabarum (2)
- Parasitoid wasp (2)
- Toll and Imd pathways (2)
- Venom proteins (2)
- acute kidney injury (2)
Institute
Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Replication effects were half the magnitude of original effects, representing a substantial decline. Ninety-seven percent of original studies had statistically significant results. Thirty-six percent of replications had statistically significant results; 47% of original effect sizes were in the 95% confidence interval of the replication effect size; 39% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.
Background
Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts.
Results
We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes.
Conclusions
These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.
Background
Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts.
Results
We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes.
Conclusions
These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.
Schlemaite, with the simplified formula (Cu,rectangle)(6)(Pb,Bi)Se-4, is a new mineral species from the Niederschlema-Alberoda vein-type uranium deposit at Hartenstein, Erzgebirge, Germany. It occurs as anhedral to subhedral grains with no obvious forms or twinning, in aggregates of up to several hundred mum across, with berzelianite, eucairite and clausthalite in a dolomite-ankerite matrix. Schlemaite is black with a black streak and opaque with a metallic luster. It is brittle with an uneven fracture and no observable cleavage. It has a mean VHN (25 g load) of 106 kg/mm(2), which roughly equates to a Mobs hardness of 3. In plane-polarized reflected light, schlemaite is grey, non- pleochroic with a very weak bireflectance. It has very weak anisotropy, with rotation tints in shades of very pale metallic orange and blue, and shows no internal reflections. Electron-microprobe analyses yielded a mean composition Cu 38.86, Ag 2.57, An 0.07, Hg 0.09, Pb 13.75, Bi 9.12, Se 35.11, total 99.57 wt.%. The empirical formula (based on 4 Se apfu) is (Cu5.50Ag0.21)(Sigma5.71)(Pb0.60Bi0.39)(Sigma0.99)Se-4. The calculated density is 7.54 g/cm(3) (based on the empirical formula and unit-cell parameters refined from single-crystal data). Schlemaite is monoclinic, P2(1)/m, a 9.5341(8), b 4.1004(3), c 10.2546(8) Angstrom, beta 100.066(2)degrees, V 394.72(9) Angstrom(3), a:b:c 2.3252:1:2.5009, Z = 2. The crystal structure of schlemaite was solved by direct methods and refined to an R index of 4.8% using 1303 unique reflections collected on a four-circle diffractometer equipped with a CCD detector. The structure consists of intercalated ordered and disordered layers. The ordered layer consists of ladders of Ph2+ + Bi3+ coordinated by Se, the former showing strong lone-pair-stereoactive effects, and a network of Cu+ coordinated by Se anions. The disordered layer consists of an array of sites partly occupied by Cu+ and Ag+ in a variety of coordinations, and is characterized by strong short-range order. The strongest seven lines of the X-ray powder-diffraction pattern [d in Angstrom(I)(hkl)] are: 3.189(100)(012), 3.132(100)(112), 2.601(70)(113), 2.505(50)(311), 2.151(60)(014), 2.058(80)(020) and 1.909(50)(314). Although schlemaite is chemically similar to furutobeite, (Cu,Ag)(6)PbS4, it is not isostructural with it. The mineral is named after the Schlema-Alberoda uranium ore field near Schneeberg in the ancient mining region of Saxony, Germany
Rapid decline of glomerular filtration rate estimated from creatinine (eGFRcrea) is associated with severe clinical endpoints. In contrast to cross-sectionally assessed eGFRcrea, the genetic basis for rapid eGFRcrea decline is largely unknown. To help define this, we meta-analyzed 42 genome-wide association studies from the Chronic Kidney Diseases Genetics Consortium and United Kingdom Biobank to identify genetic loci for rapid eGFRcrea decline. Two definitions of eGFRcrea decline were used: 3 mL/min/1.73m(2)/year or more ("Rapid3"; encompassing 34,874 cases, 107,090 controls) and eGFRcrea decline 25% or more and eGFRcrea under 60 mL/min/1.73m(2) at follow-up among those with eGFRcrea 60 mL/min/1.73m(2) or more at baseline ("CKDi25"; encompassing 19,901 cases, 175,244 controls). Seven independent variants were identified across six loci for Rapid3 and/or CKDi25: consisting of five variants at four loci with genome-wide significance (near UMOD-PDILT (2), PRKAG2, WDR72, OR2S2) and two variants among 265 known eGFRcrea variants (near GATM, LARP4B). All these loci were novel for Rapid3 and/or CKDi25 and our bioinformatic follow-up prioritized variants and genes underneath these loci. The OR2S2 locus is novel for any eGFRcrea trait including interesting candidates. For the five genome-wide significant lead variants, we found supporting effects for annual change in blood urea nitrogen or cystatin-based eGFR, but not for GATM or (LARP4B). Individuals at high compared to those at low genetic risk (8-14 vs. 0-5 adverse alleles) had a 1.20-fold increased risk of acute kidney injury (95% confidence interval 1.08-1.33). Thus, our identified loci for rapid kidney function decline may help prioritize therapeutic targets and identify mechanisms and individuals at risk for sustained deterioration of kidney function.
Rapid decline of glomerular filtration rate estimated from creatinine (eGFRcrea) is associated with severe clinical endpoints. In contrast to cross-sectionally assessed eGFRcrea, the genetic basis for rapid eGFRcrea decline is largely unknown. To help define this, we meta-analyzed 42 genome-wide association studies from the Chronic Kidney Diseases Genetics Consortium and United Kingdom Biobank to identify genetic loci for rapid eGFRcrea decline. Two definitions of eGFRcrea decline were used: 3 mL/min/1.73m(2)/year or more ("Rapid3"; encompassing 34,874 cases, 107,090 controls) and eGFRcrea decline 25% or more and eGFRcrea under 60 mL/min/1.73m(2) at follow-up among those with eGFRcrea 60 mL/min/1.73m(2) or more at baseline ("CKDi25"; encompassing 19,901 cases, 175,244 controls). Seven independent variants were identified across six loci for Rapid3 and/or CKDi25: consisting of five variants at four loci with genome-wide significance (near UMOD-PDILT (2), PRKAG2, WDR72, OR2S2) and two variants among 265 known eGFRcrea variants (near GATM, LARP4B). All these loci were novel for Rapid3 and/or CKDi25 and our bioinformatic follow-up prioritized variants and genes underneath these loci. The OR2S2 locus is novel for any eGFRcrea trait including interesting candidates. For the five genome-wide significant lead variants, we found supporting effects for annual change in blood urea nitrogen or cystatin-based eGFR, but not for GATM or (LARP4B). Individuals at high compared to those at low genetic risk (8-14 vs. 0-5 adverse alleles) had a 1.20-fold increased risk of acute kidney injury (95% confidence interval 1.08-1.33). Thus, our identified loci for rapid kidney function decline may help prioritize therapeutic targets and identify mechanisms and individuals at risk for sustained deterioration of kidney function.
The Siwalik sedimentary rocks of the Himalayan foreland basin preserve a record of Himalayan orogenesis, paleo-drainage evolution, and erosion. This study focuses on the still poorly studied easternmost Himalaya Siwalik record located directly downstream of the Namche Barwa syntaxis. We use luminescence, palaeomagnetism, magnetostratigraphy, and apatite fission-track dating to constrain the depositional ages of three Siwalik sequences: the Sibo outcrop (Upper Siwalik sediments at ca. 200-800 ka), the Remi section (Middle and Upper Siwalik rocks at >0.8-<8.8 +/- 2.4 Ma), and the Siang section (Middle Siwalik rocks at <9.3 +/- 1.5 to <13.5 +/- 1.5 Ma). Cretaceous-Paleogene detrital zircon and apatite U-Pb ages, characteristic of the Transhimalayan Gangdese Batholiths that crop out northwest of the syntaxis, are present throughout the Sibo, Remi, and Siang successions, confirming the existence of a Yarlung-Brahmaputra connection since at least the Late Miocene. A ca. 500 Ma zircon population increases up section, most strikingly sometime between 3.6 to 6.6 Ma, at the expense of Transhimalayan grains. We consider the ca. 500 Ma population to be derived from the Tethyan or Greater Himalaya, and we interpret the up-section increase to reflect progressive exhumation of the Namche Barwa syntaxis. Early Cretaceous zircon and apatite U-Pb ages are rare in the Sibo, Remi, and Siang successions, but abundant in modern Siang River sediments. Zircons of this age range are characteristic of the Transhimalayan Bomi-Chayu batholiths, which crop out east of the syntaxis and are eroded by the Parlung River, a modern tributary of the Siang River. We interpret the difference in relative abundance of Early Cretaceous zircons between the modern and ancient sediments to reflect capture of the Parlung by the Siang after 800 ka.
Early onset and late acceleration of rapid exhumation in the Namche Barwa syntaxis, eastern Himalaya
(2020)
The Himalayan syntaxes, characterized by extreme rates of rock exhumation co-located with major trans-orogenic rivers, figure prominently in the debate on tectonic versus erosional forcing of exhumation. Both the mechanism and timing of rapid exhumation of the Namche Barwa massif in the eastern syntaxis remain controversial. It has been argued that coupling between crustal rock advection and surface erosion initiated in the late Miocene (8-10 Ma). Recent studies, in contrast, suggest a Quaternary onset of rapid exhumation linked to a purely tectonic mechanism. We report new multisystem detrital thermochronology data from the most proximal Neogene clastic sediments downstream of Namche Barwa and use a thermo-kinematic model constrained by new and published data to explore its exhumation history. Modeling results show that exhumation accelerated to similar to 4 km/m.y. at ca. 8 Ma and to similar to 9 km/m.y. after ca. 2 Ma. This three-stage history reconciles apparently contradictory evidence for early and late onset of rapid exhumation and suggests efficient coupling between tectonics and erosion since the late Miocene. Quaternary acceleration of exhumation is consistent with river-profile evolution and may be linked to a Quaternary river-capture event.
Birth weight within the normal range is associated with a variety of adult-onset diseases, but the mechanisms behind these associations are poorly understood(1). Previous genome-wide association studies of birth weight identified a variant in the ADCY5 gene associated both with birth weight and type 2 diabetes and a second variant, near CCNL1, with no obvious link to adult traits(2). In an expanded genome-wide association metaanalysis and follow-up study of birth weight (of up to 69,308 individuals of European descent from 43 studies), we have now extended the number of loci associated at genome-wide significance to 7, accounting for a similar proportion of variance as maternal smoking. Five of the loci are known to be associated with other phenotypes: ADCY5 and CDKAL1 with type 2 diabetes, ADRB1 with adult blood pressure and HMGA2 and LCORL with adult height. Our findings highlight genetic links between fetal growth and postnatal growth and metabolism.
During aging, intracranial volume remains unchanged and represents maximally attained brain size, while various interacting biological phenomena lead to brain volume loss. Consequently, intracranial volume and brain volume in late life reflect different genetic influences. Our genome-wide association study (GWAS) in 8,175 community-dwelling elderly persons did not reveal any associations at genome-wide significance (P < 5 x 10(-8)) for brain volume. In contrast, intracranial volume was significantly associated with two loci: rs4273712 (P = 3.4 x 10(-11)), a known height-associated locus on chromosome 6q22, and rs9915547 (P = 1.5 x 10(-12)), localized to the inversion on chromosome 17q21. We replicated the associations of these loci with intracranial volume in a separate sample of 1,752 elderly persons (P = 1.1 x 10(-3) for 6q22 and 1.2 x 10(-3) for 17q21). Furthermore, we also found suggestive associations of the 17q21 locus with head circumference in 10,768 children (mean age of 14.5 months). Our data identify two loci associated with head size, with the inversion at 17q21 also likely to be involved in attaining maximal brain size.