Alchemical and structural distribution based representation for improved QML

We introduce a representation of any atom in any chemical environment for the generation of efficient quantum machine learning (QML) models of common electronic ground-state properties. The representation is based on scaled distribution functions explicitly accounting for elemental and structural degrees of freedom. Resulting QML models afford very favorable learning curves for properties of out-of-sample systems including organic molecules, non-covalently bonded protein side-chains, (H$_2$O)$_{40}$-clusters, as well as diverse crystals. The elemental components help to lower the learning curves, and, through interpolation across the periodic table, even enable "alchemical extrapolation" to covalent bonding between elements not part of training, as evinced for single, double, and triple bonds among main-group elements

Image_1_Genome-Wide Characterization of Endogenous Retroviruses in Bombyx mori Reveals the Relatives and Activity of env Genes.TIF

<p>Endogenous retroviruses (ERVs) are retroviral sequences that remain fixed in the host genome, where they could play an important role. Some ERVs have been identified in insects and proven to have infectious properties. However, no information is available regarding Bombyx mori ERVs (BmERVs) to date. Here, we systematically identified 256 potential BmERVs in the silkworm genome via a whole-genome approach. BmERVs were relatively evenly distributed across each of the chromosomes and accounted for about 25% of the silkworm genome. All BmERVs were classified as young ERVs, with insertion times estimated to be less than 10 million years. Seven BmERVs possessing the env genes were identified. With the exception of the Orf133 Helicoverpa armigera nuclear polyhedrosis virus, the env sequences of BmERVs were distantly related to genes encoding F (Fa and Fb) and GP64 proteins from Group I and Group II NPVs. In addition, only the amino acid sequence of the BmERV-21 envelope protein shared a similar putative furin-like cleavage site and fusion peptide with Group II baculoviruses. All of the env genes in the seven BmERVs were verified to exist in the genome and be expressed in the midgut and fat bodies, which suggest that BmERVs might play an important role in the host biology.</p

Data_Sheet_3_Genome-Wide Characterization of Endogenous Retroviruses in Bombyx mori Reveals the Relatives and Activity of env Genes.XLSX

<p>Endogenous retroviruses (ERVs) are retroviral sequences that remain fixed in the host genome, where they could play an important role. Some ERVs have been identified in insects and proven to have infectious properties. However, no information is available regarding Bombyx mori ERVs (BmERVs) to date. Here, we systematically identified 256 potential BmERVs in the silkworm genome via a whole-genome approach. BmERVs were relatively evenly distributed across each of the chromosomes and accounted for about 25% of the silkworm genome. All BmERVs were classified as young ERVs, with insertion times estimated to be less than 10 million years. Seven BmERVs possessing the env genes were identified. With the exception of the Orf133 Helicoverpa armigera nuclear polyhedrosis virus, the env sequences of BmERVs were distantly related to genes encoding F (Fa and Fb) and GP64 proteins from Group I and Group II NPVs. In addition, only the amino acid sequence of the BmERV-21 envelope protein shared a similar putative furin-like cleavage site and fusion peptide with Group II baculoviruses. All of the env genes in the seven BmERVs were verified to exist in the genome and be expressed in the midgut and fat bodies, which suggest that BmERVs might play an important role in the host biology.</p

Image_2_Genome-Wide Characterization of Endogenous Retroviruses in Bombyx mori Reveals the Relatives and Activity of env Genes.TIF

<p>Endogenous retroviruses (ERVs) are retroviral sequences that remain fixed in the host genome, where they could play an important role. Some ERVs have been identified in insects and proven to have infectious properties. However, no information is available regarding Bombyx mori ERVs (BmERVs) to date. Here, we systematically identified 256 potential BmERVs in the silkworm genome via a whole-genome approach. BmERVs were relatively evenly distributed across each of the chromosomes and accounted for about 25% of the silkworm genome. All BmERVs were classified as young ERVs, with insertion times estimated to be less than 10 million years. Seven BmERVs possessing the env genes were identified. With the exception of the Orf133 Helicoverpa armigera nuclear polyhedrosis virus, the env sequences of BmERVs were distantly related to genes encoding F (Fa and Fb) and GP64 proteins from Group I and Group II NPVs. In addition, only the amino acid sequence of the BmERV-21 envelope protein shared a similar putative furin-like cleavage site and fusion peptide with Group II baculoviruses. All of the env genes in the seven BmERVs were verified to exist in the genome and be expressed in the midgut and fat bodies, which suggest that BmERVs might play an important role in the host biology.</p

The flowchart of producing infective BmNPV expressing ten heterologous genes in silkworm larvae or pupae.

<p>The target genes are cloned into the three donor vector (pCTdual, pRADM and pUCDMIG) using usual method. The first two genes carried by pCTdual are inserted into BmBacmid through <i>I-Sce</i> I linearization and <i>red-gam</i> homologous recombination. Four genes in pRADM and the other four genes in pUCDMIG are then introduced into BmBacmid via Tn7 transposition and cre-loxp recombination, respectively. As a result, ten foreign expression cassettes and three antibiotic screening markers, as well as a GFP illumination marker are introduced into BmBacmid. The invasive and DAP auxotrophic <i>E. coli</i> carrying recombinant BmBacmid are injected into silkworm larvae at an appropriate dose. Consequently, recombinant BmNPV will be produced and multiple foreign genes will be expressed in green <i>B. mori</i> larvae or pupae.</p

Multiple genes expression and rotavirus-VLPs production in silkworm.

<p>(a) The larvae of six days post injection were observed using the fluorescence detection device. 1: the mock injected larvae; 2&3: the larvae injected with invasive and DAP auxotrophic <i>E. coli</i> carrying BmBacmid with six genes including <i>egfp</i>, <i>dsRed</i>, <i>eyfp</i>, <i>vp2</i>, <i>vp6</i> and <i>vp7</i> at a dose of 8.0×10⁸ cells per larva. (b) The hemolymph from a red larva was observed using laser confocal microscope. The images of hemocytes were taken at the bright (trans) channel (I), GFP (515 nm) detection channel (II), DsRed (590 nm) channel (III) and YFP (530 nm) channel (IV). (c) Western blot analysis of the hemolymph from the red larvae using anti-VP2, anti-VP6 and anti-VP7 rabbit antiserums. (d) The EM image of hemocytes collected from red larvae. R: the round Rotavirus-VLPs; B: the rod shape baculovirus particle, bar = 100 nm.</p

Additional file 1: Table S1. of Analysis of codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus (NPV) and its relation to evolution

All the indices of total genes. (XLS 27 kb

SDS-PAGE analysis of purified VLPs of rotavirus from silkworm.

<p>5 µg VLPs was loaded on 12% SDS-PAGE gel. Lane Marker: standard protein marker. lane VLPs: purified VLPs from silkworm hemolymph. The three bands VP2, VP6 and VP7 were labelled.</p