Computational tools for quadratic Chabauty

http://math.bu.edu/people/jbala/2020BalakrishnanMuellerNotes.pdfhttp://math.bu.edu/people/jbala/2020BalakrishnanMuellerNotes.pdfFirst author draf

Putting Synthesis into Biology: A Viral View of Genetic Engineering through De Novo Gene and Genome Synthesis

SummaryThe rapid improvements in DNA synthesis technology hold the potential to revolutionize biosciences in the near future. Traditional genetic engineering methods are template dependent and make extensive but laborious use of site-directed mutagenesis to explore the impact of small variations on an existing sequence “theme.” De novo gene and genome synthesis frees the investigator from the restrictions of the pre-existing template and allows for the rational design of any conceivable new sequence theme.Viruses, being among the simplest replicating entities, have been at the forefront of the advancing biosciences since the dawn of molecular biology. Viral genomes, especially those of RNA viruses, are relatively short, often less than 10,000 bases long, making them amenable to whole genome synthesis with the currently available technology. For this reason viruses are once again poised to lead the way in the budding field of synthetic biology—for better or worse

Quadratic Chabauty for modular curves: algorithms and examples

We describe how the quadratic Chabauty method may be applied to determine the set of rational points on modular curves of genus g whose Jacobians have Mordell–Weil rank g. This extends our previous work on the split Cartan curve of level 13 and allows us to consider modular curves that may have few known rational points or nontrivial local height contributions away from our working prime. We illustrate our algorithms with a number of examples where we determine the set of rational points on several modular curves of genus 2 and 3: this includes Atkin–Lehner quotients X^+_0 (N) of prime level N, the curve X_S4 (13), as well as a few other curves relevant to Mazur’s Program B.https://arxiv.org/abs/2101.01862First author draf

Implementing Silicon Nanoribbon Field-Effect Transistors as Arrays for Multiple Ion Detection

Ionic gradients play a crucial role in the physiology of the human body, ranging from metabolism in cells to muscle contractions or brain activities. To monitor these ions, inexpensive, label-free chemical sensing devices are needed. Field-effect transistors (FETs) based on silicon (Si) nanowires or nanoribbons (NRs) have a great potential as future biochemical sensors as they allow for the integration in microscopic devices at low production costs. Integrating NRs in dense arrays on a single chip expands the field of applications to implantable electrodes or multifunctional chemical sensing platforms. Ideally, such a platform is capable of detecting numerous species in a complex analyte. Here, we demonstrate the basis for simultaneous sodium and fluoride ion detection with a single sensor chip consisting of arrays of gold-coated SiNR FETs. A microfluidic system with individual channels allows modifying the NR surfaces with self-assembled monolayers of two types of ion receptors sensitive to sodium and fluoride ions. The functionalization procedure results in a differential setup having active fluoride-and sodium-sensitive NRs together with bare gold control NRs on the same chip. Comparing functionalized NRs with control NRs allows the compensation of non-specific contributions from changes in the background electrolyte concentration and reveals the response to the targeted species

Microscale spatial distribution and soil organic matter persistence in top and subsoil

The spatial distribution of organic substrates and microscale soil heterogeneity significantly influence organic matter (OM) persistence as constraints on OM accessibility to microorganisms. However, it is unclear how changes in OM spatial heterogeneity driven by factors such as soil depth affect the relative importance of substrate spatial distribution on OM persistence. This work evaluated the decomposition and persistence of 13C and 15N labeled water-extractable OM inputs over 50 days as either hotspot (i.e., pelleted in 1 – 2 mm-size pieces) or distributed (i.e., added as OM < 0.07 µm suspended in water) forms in topsoil (0-0.2 m) and subsoil (0.8-0.9 m) samples of an Andisol. We observed greater persistence of added C in the subsoil with distributed OM inputs relative to hotspot OM, indicated by a 17% reduction in cumulative mineralization of the added C and a 10% higher conversion to mineral-associated OM. A lower substrate availability potentially reduced mineralization due to OM dispersion throughout the soil. NanoSIMS (nanoscale secondary ion mass spectrometry) analysis identified organo-mineral associations on cross-sectioned aggregate interiors in the subsoil. On the other hand, in the topsoil, we did not observe significant differences in the persistence of OM, suggesting that the large amounts of particulate OM already present in the soil outweighed the influence of added OM spatial distribution. Here, we demonstrated under laboratory conditions that the spatial distribution of fresh OM input alone significantly affected the decomposition and persistence of OM inputs in the subsoil. On the other hand, spatial distribution seems to play a lower role in topsoils rich in particulate OM. The divergence in the influence of OM spatial distribution between the top and subsoil is likely driven by differences in soil mineralogy and OM composition.Microscale spatial distribution and soil organic matter persistence in top and subsoilpublishedVersio

Recoding of the Vesicular Stomatitis Virus L Gene by Computer-Aided Design Provides a Live, Attenuated Vaccine Candidate

ABSTRACT Codon pair bias (CPB), which has been observed in all organisms, is a neglected genomic phenomenon that affects gene expression. CPB results from synonymous codons that are paired more or less frequently in ORFeomes regardless of codon bias. The effect of an individual codon pair change is usually small, but when it is amplified by large-scale genome recoding, strikingly altered biological phenotypes are observed. The utility of codon pair bias in the development of live attenuated vaccines was recently demonstrated by recodings of poliovirus (a positive-strand RNA virus) and influenza virus (a negative-strand segmented RNA virus). Here, the L gene of vesicular stomatitis virus (VSV), a nonsegmented negative-sense RNA virus, was partially recoded based on codon pair bias. Totals of 858 and 623 silent mutations were introduced into a 5′-terminal segment of the viral L gene (designated L1) to create sequences containing either overrepresented or underrepresented codon pairs, designated L1sdmax and L1min, respectively. Analysis revealed that recombinant VSV containing the L1min sequence could not be recovered, whereas the virus with the sdmax sequence showed a modest level of attenuation in cell culture. More strikingly, in mice the L1sdmax virus was almost as immunogenic as the parental strain but highly attenuated. Taken together, these results open a new road to attain a balance between VSV virulence and immunogenicity, which could serve as an example for the attenuation of other negative-strand, nonsegmented RNA viruses

Decomposition of the QCD String into Dipoles and Unintegrated Gluon Distributions

We present the perturbative and non-perturbative QCD structure of the dipole-dipole scattering amplitude in momentum space. The perturbative contribution is described by two-gluon exchange and the non-perturbative contribution by the stochastic vacuum model which leads to confinement of the quark and antiquark in the dipole via a string of color fields. This QCD string gives important non-perturbative contributions to high-energy reactions. A new structure different from the perturbative dipole factors is found in the string-string scattering amplitude. The string can be represented as an integral over stringless dipoles with a given dipole number density. This decomposition of the QCD string into dipoles allows us to calculate the unintegrated gluon distribution of hadrons and photons from the dipole-hadron and dipole-photon cross section via kT-factorization.Comment: 43 pages, 14 figure

NGC6240: Merger-Induced Star Formation & Gas Dynamics

We present spatially resolved integral field spectroscopic K-band data at a resolution of 0.13" (60pc) and interferometric CO(2-1) line observations of the prototypical merging system NGC6240. Despite the clear rotational signature, the stellar kinematics in the two nuclei are dominated by dispersion. We use Jeans modelling to derive the masses and the mass-to-light ratios of the nuclei. Combining the luminosities with the spatially resolved Br-gamma equivalent width shows that only 1/3 of the K-band continuum from the nuclei is associated with the most recent star forming episode; and that less than 30% of the system's bolometric luminosity and only 9% of its stellar mass is due to this starburst. The star formation properties, calculated from typical merger star formation histories, demonstrate the impact of different assumptions about the star formation history. The properties of the nuclei, and the existence of a prominent old stellar population, indicate that the nuclei are remnants of the progenitor galaxies' bulges.Comment: 18 pages, 14 figures. Accepted for publication in A&

Machine-learning based patient classification using Hepatitis B virus full-length genome quasispecies from Asian and European cohorts

Chronic infection with Hepatitis B virus (HBV) is a major risk factor for the development of advanced liver disease including fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). The relative contribution of virological factors to disease progression has not been fully defined and tools aiding the deconvolution of complex patient virus profiles is an unmet clinical need. Vari