Waddington’s Widget: Hsp90 and the Inheritance of Acquired Characters

Conrad Waddington published an influential model for evolution in his 1942 paper, Canalization of Development and Inheritance of Acquired Characters. In this classic, albeit controversial, paper, he proposed that an unknown mechanism exists that conceals phenotypic variation until the organism is stressed. Recent studies have proposed that the highly conserved chaperone Hsp90 could function as a “capacitor,” or an “adaptively inducible canalizer,” that masks silent phenotypic variation of either genetic or epigenetic origin. This review will discuss evidence for, and arguments against, the role of Hsp90 as a capacitor for morphological evolution, and as a key component of what we call “Waddington’s widget.

Effect of hydrostatic pressure on the current-voltage characteristics of GaN∕AlGaN∕GaN heterostructure devices

The current-voltage characteristics of n-GaN∕u-AlGaN∕n-GaN heterostructure devices are investigated for potential pressure sensor applications. Model calculations suggest that the current decreases with pressure as a result of the piezoelectric effect, and this effect becomes more significant with thicker AlGaN layers and increasing AlN composition. The change in current with pressure is shown to be highly sensitive to the change in interfacial polarization charge densities. The concept is verified by measuring the current versus voltage characteristics of an n-GaN∕u-Al0.2Ga0.8N∕n-GaN device under hydrostatic pressure over the range of 0–5 kbars. The measured current is found to decrease approximately linearly with applied pressure in agreement with the model results. A gauge factor, which is defined as the relative change in current divided by the in-plane strain, approaching 500 is extracted from the data, demonstrating the considerable potential of these devices for pressure sensing applications

Drosophila melanogaster as a model for lead neurotoxicology and toxicogenomics research

Drosophila melanogaster is an excellent model animal for studying the neurotoxicology of lead. It has been known since ancient Roman times that long-term exposure to low levels of lead results in behavioral abnormalities, such as what is now known as attention deficit hyperactivity disorder (ADHD). Because lead alters mechanisms that underlie developmental neuronal plasticity, chronic exposure of children, even at blood lead levels below the current CDC community action level (10 μg/dl), can result in reduced cognitive ability, increased likelihood of delinquency, behaviors associated with ADHD, changes in activity level, altered sensory function, delayed onset of sexual maturity in girls, and changes in immune function. In order to better understand how lead affects neuronal plasticity, we will describe recent findings from a Drosophila behavioral genetics laboratory, a Drosophila neurophysiology laboratory, and a Drosophila quantitative genetics laboratory who have joined forces to study the effects of lead on the Drosophila nervous system. Studying the effects of lead on Drosophila nervous system development will give us a better understanding of the mechanisms of Pb neurotoxicity in the developing human nervous system

Exchange Instabilities in Semiconductor Double Quantum Well Systems

We consider various exchange-driven electronic instabilities in semiconductor double-layer systems in the absence of any external magnetic field. We establish that there is no exchange-driven bilayer to monolayer charge transfer instability in the double-layer systems. We show that, within the unrestricted Hartree-Fock approximation, the low density stable phase (even in the absence of any interlayer tunneling) is a quantum ``pseudospin rotated'' spontaneous interlayer phase coherent spin-polarized symmetric state rather than the classical Ising-like charge-transfer phase. The U(1) symmetry of the double quantum well system is broken spontaneously at this low density quantum phase transition, and the layer density develops quantum fluctuations even in the absence of any interlayer tunneling. The phase diagram for the double quantum well system is calculated in the carrier density--layer separation space, and the possibility of experimentally observing various quantum phases is discussed. The situation in the presence of an external electric field is investigated in some detail using the spin-polarized-local-density-approximation-based self-consistent technique and good agreement with existing experimental results is obtained.Comment: 24 pages, figures included. Also available at http://www-cmg.physics.umd.edu/~lzheng/preprint/ct.uu/ . Revised final version to appear in PR

Book Review of Serendipity: An Ecologist’s Quest to Understand Nature

A common thought among graduate students is: “how do established scientists get where they are today?” In Serendipity: An Ecologist’s Quest to Understand Nature, James Estes offers a personal reflection on research experiences spanning his 50-year career, beginning as a Ph.D. student in 1970 and concluding with recognition as a member of the National Academy of Sciences in 2014. Estes chronologically outlines the foundational trophic cascade ecology research that he and colleagues conducted in the Aleutian Islands, examining key relationships among kelp forests, sea otters, sea urchins, and killer whales through anecdotal stories of achievement and challenge. Estes’ 3 main goals in writing this book are to: (1) recount what he had learned from 50 years of research; (2) provide a larger story of how predators and prey interact with one another; and (3) explain how science “really happens.

Sheared Flow As A Stabilizing Mechanism In Astrophysical Jets

It has been hypothesized that the sustained narrowness observed in the asymptotic cylindrical region of bipolar outflows from Young Stellar Objects (YSO) indicates that these jets are magnetically collimated. The j cross B force observed in z-pinch plasmas is a possible explanation for these observations. However, z-pinch plasmas are subject to current driven instabilities (CDI). The interest in using z-pinches for controlled nuclear fusion has lead to an extensive theory of the stability of magnetically confined plasmas. Analytical, numerical, and experimental evidence from this field suggest that sheared flow in magnetized plasmas can reduce the growth rates of the sausage and kink instabilities. Here we propose the hypothesis that sheared helical flow can exert a similar stabilizing influence on CDI in YSO jets.Comment: 13 pages, 2 figure

Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees

Abstract Background Previous whole-genome shotgun bisulfite sequencing experiments showed that DNA cytosine methylation in the honey bee (Apis mellifera) is almost exclusively at CG dinucleotides in exons. However, the most commonly used method, bisulfite sequencing, cannot distinguish 5-methylcytosine from 5-hydroxymethylcytosine, an oxidized form of 5-methylcytosine that is catalyzed by the TET family of dioxygenases. Furthermore, some analysis software programs under-represent non-CG DNA methylation and hydryoxymethylation for a variety of reasons. Therefore, we used an unbiased analysis of bisulfite sequencing data combined with molecular and bioinformatics approaches to distinguish 5-methylcytosine from 5-hydroxymethylcytosine. By doing this, we have performed the first whole genome analyses of DNA modifications at non-CG sites in honey bees and correlated the effects of these DNA modifications on gene expression and alternative mRNA splicing. Results We confirmed, using unbiased analyses of whole-genome shotgun bisulfite sequencing (BS-seq) data, with both new data and published data, the previous finding that CG DNA methylation is enriched in exons in honey bees. However, we also found evidence that cytosine methylation and hydroxymethylation at non-CG sites is enriched in introns. Using antibodies against 5-hydroxmethylcytosine, we confirmed that DNA hydroxymethylation at non-CG sites is enriched in introns. Additionally, using a new technique, Pvu-seq (which employs the enzyme PvuRts1l to digest DNA at 5-hydroxymethylcytosine sites followed by next-generation DNA sequencing), we further confirmed that hydroxymethylation is enriched in introns at non-CG sites. Conclusions Cytosine hydroxymethylation at non-CG sites might have more functional significance than previously appreciated, and in honey bees these modifications might be related to the regulation of alternative mRNA splicing by defining the locations of the introns

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer.

Many animal species are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and could act as reservoirs; however, transmission in free-living animals has not been documented. White-tailed deer, the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 is circulating in deer, 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through January of 2021 were assayed for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 (33.2%) deer samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, following the November 2020 peak of human cases in Iowa, and coinciding with the onset of winter and the peak deer hunting season, SARS-CoV-2 RNA was detected in 80 of 97 (82.5%) RPLN samples collected over a 7-wk period. Whole genome sequencing of all 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%) and B.1.311 (n = 19; 20%) accounting for ∼75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple human-to-deer transmission events followed by subsequent deer-to-deer spread. These discoveries have important implications for the long-term persistence of the SARS-CoV-2 pandemic. Our findings highlight an urgent need for a robust and proactive "One Health" approach to obtain enhanced understanding of the ecology, molecular evolution, and dissemination of SARS-CoV-2

Progressive, Transgenerational Changes in Offspring Phenotype and Epigenotype following Nutritional Transition

Induction of altered phenotypes during development in response to environmental input involves epigenetic changes. Phenotypic traits can be passed between generations by a variety of mechanisms, including direct transmission of epigenetic states or by induction of epigenetic marks de novo in each generation. To distinguish between these possibilities we measured epigenetic marks over four generations in rats exposed to a sustained environmental challenge. Dietary energy was increased by 25% at conception in F0 female rats and maintained at this level to generation F3. F0 dams showed higher pregnancy weight gain, but lower weight gain and food intake during lactation than F1 and F2 dams. On gestational day 8, fasting plasma glucose concentration was higher and β-hydroxybutyrate lower in F0 and F1 dams than F2 dams. This was accompanied by decreased phosphoenolpyruvate carboxykinase (PEPCK) and increased PPARα and carnitine palmitoyl transferase-1 mRNA expression. PEPCK mRNA expression was inversely related to the methylation of specific CpG dinucleotides in its promoter. DNA methyltransferase (Dnmt) 3a2, but not Dnmt1 or Dnmt3b, expression increased and methylation of its promoter decreased from F1 to F3 generations. These data suggest that the regulation of energy metabolism during pregnancy and lactation within a generation is influenced by the maternal phenotype in the preceding generation and the environment during the current pregnancy. The transgenerational effects on phenotype were associated with altered DNA methylation of specific genes in a manner consistent with induction de novo of epigenetic marks in each generation