Viruses detected from garlic (<i>Allium sativum</i>) and wild garlic (<i>A. vineale</i>) plants.

a<p>Country or area where plant was sourced.</p>b<p>Source: Allium vineale.</p>c<p>AV3, Asparagus virus 3; GCLV, garlic common latent virus; SLV, shallot latent virus; OYDV, onion yellow dwarf virus; LYSV, leek yellow stripe virus; GarVA, garlic virus A; GarVB, garlic virus B; GarVC, garlic virus C; GarVD, garlic virus D; GarVX, garlic virus X. Isolate names, GenBank accession codes, and nucleotide sequence lengths (in parenthesises) are shown. Complete or near-complete genome sequences indicated by an asterisk.</p>d<p>Commercial garlic grower.</p>e<p>Commercial plant nursery.</p>f<p>Kitchen garden.</p

Maximum likelihood phylogenetic tree of amino acid sequences of replicase proteins of isolates of potexviruses.

<p>Shown for each isolate is GenBank accession code, and virus name. The sequence representing the new Asparagus virus 3 (AV3) isolate is indicated by a black dot. The homologous region of an isolate of garlic virus A (<i>Allexivirus</i>) was used as the outgroup.</p

Maximum likelihood phylogenetic tree of amino acid sequences of coat proteins of isolates of the carlaviruses garlic common latent virus (GCLV) (red dots) and shallot latent virus (SLV) (black dots).

<p>Shown for each isolate is GenBank accession code, isolate name and country of origin. Isolates described in this study are indicated by a dot.</p

Maximum likelihood phylogenetic tree of amino acid sequences of coat proteins of isolates of allexiviruses.

<p>Virus sequences analysed were garlic virus A (GarVA) (red dots), garlic virus B (GarVB) (dark green dot), garlic virus C (GarVC) (brown dots), garlic virus D (GarVD) (light green dots), garlic virus E (GarVE) and garlic virus X (GarVX) (black dots). The CP of blackberry virus E (BVE) (Family <i>Alphaflexiviridae</i>) was used as the outgroup. Shown for each isolate is GenBank accession code, isolate name and country of origin. Isolates described in this study are indicated by a dot.</p

Maximum likelihood phylogenetic tree of amino acid sequences of the region of the polyprotein from the beginning of the 6K2 cistron through to the end of the coat protein of isolates of the potyviruses leek yellow stripe virus (LYSV) (black dots) and onion yellow dwarf virus (OYDV) (red dots).

<p>Shown for each isolate is GenBank accession code, isolate name and country of origin. Isolates described in this study are indicated by a dot.</p

Comparison of genomes of three isolates of Asparagus virus 3 (AV3) (<i>syn</i> scallion virus X, ScaVX): AV3-Japan, ScaVX-China and AV3-SW12.

<p>Pairwise identities and sizes of complete genomes, UTRs, and protein coding regions are given.</p>a<p>UTR, untranslated region; Met, methyltransferase; AlkB, alkylated DNA repair protein; Hel, helicase; RdRp, RNA dependent RNA polymerase; TGB, triple gene block; CP, coat protein.</p

Dissociative Electron Attachment to 5‑Iodo-4-thio-2′-deoxyuridine: A Potential Radiosensitizer of Hypoxic Cells

In the search for effective radiosensitizers for tumor cells, halogenated uracils have attracted more attention due to their large cross section for dissociation upon the attachment of low-energy electrons. In this study, we investigated dissociative electron attachment (DEA) to 5-iodo-4-thio-2′-deoxyuridine, a potential radiosensitizer using a crossed electron-molecule beam experiment coupled with quadrupole mass spectrometry. The experimental results were supported by calculations on the threshold energies of formed anions and transition state calculations. We show that low-energy electrons with kinetic energies near 0 eV may effectively decompose the molecule upon DEA. The by far most abundant anion observed corresponds to the iodine anion (I–). Due to the associated bond cleavage, a radical site is formed at the C5 position, which may initiate strand break formation if the molecule is incorporated into a DNA strand. Our results reflect the conclusion from previous radiolysis studies with the title compound, suggesting its potential as a radiosensitizer

Dissociative Electron Attachment to 5‑Iodo-4-thio-2′-deoxyuridine: A Potential Radiosensitizer of Hypoxic Cells

In the search for effective radiosensitizers for tumor cells, halogenated uracils have attracted more attention due to their large cross section for dissociation upon the attachment of low-energy electrons. In this study, we investigated dissociative electron attachment (DEA) to 5-iodo-4-thio-2′-deoxyuridine, a potential radiosensitizer using a crossed electron-molecule beam experiment coupled with quadrupole mass spectrometry. The experimental results were supported by calculations on the threshold energies of formed anions and transition state calculations. We show that low-energy electrons with kinetic energies near 0 eV may effectively decompose the molecule upon DEA. The by far most abundant anion observed corresponds to the iodine anion (I–). Due to the associated bond cleavage, a radical site is formed at the C5 position, which may initiate strand break formation if the molecule is incorporated into a DNA strand. Our results reflect the conclusion from previous radiolysis studies with the title compound, suggesting its potential as a radiosensitizer

Cadmium tolerance and phytoremediation potential of acacia (<i>Acacia nilotica</i> L.) under salinity stress

<p>In this study, we explored the effect of salinity on cadmium (Cd) tolerance and phytoremediation potential of <i>Acacia nilotica</i>. Two-month-old uniform plants of <i>A. nilotica</i> were grown in pots contaminated with various levels of Cd (0, 5, 10, and 15 mg kg⁻¹), NaCl (0%, 0.5%, 1.0% (hereafter referred as salinity), and all possible combinations of Cd + salinity for a period of six months. Results showed that shoot and root growth, biomass, tissue water content and chlorophyll (chl a, chl b, and total chl a+b) contents decreased more in response to salinity and combination of Cd + salinity compared to Cd alone. Shoot and root K concentrations significantly decreased with increasing soil Cd levels, whereas Na and Cl concentrations were not affected significantly. Shoot and root Cd concentrations, bioconcentration factor (BCF) and translocation factor (TF) increased with increasing soil Cd and Cd + salinity levels. At low level of salinity (0.5%), shoot and root Cd uptake enhanced, while it decreased at high level of salinity (1.0%). Due to Cd tolerance, high shoot biomass and shoot Cd uptake, this tree species has some potential for phytoremediation of Cd from the metal contaminated saline and nonsaline soils.</p

Image1_Identification of genetic variants associated with a wide spectrum of phenotypes clinically diagnosed as Sanfilippo and Morquio syndromes using whole genome sequencing.jpeg

Mucopolysaccharidoses (MPSs) are inherited lysosomal storage disorders (LSDs). MPSs are caused by excessive accumulation of mucopolysaccharides due to missing or deficiency of enzymes required for the degradation of specific macromolecules. MPS I-IV, MPS VI, MPS VII, and MPS IX are sub-types of mucopolysaccharidoses. Among these, MPS III (also known as Sanfilippo) and MPS IV (Morquio) syndromes are lethal and prevalent sub-types. This study aimed to identify causal genetic variants in cases of MPS III and MPS IV and characterize genotype-phenotype relations in Pakistan. We performed clinical, biochemical and genetic analysis using Whole Genome Sequencing (WGS) in 14 Pakistani families affected with MPS III or MPS IV. Patients were classified into MPS III by history of aggressive behaviors, dementia, clear cornea and into MPS IV by short trunk, short stature, reversed ratio of upper segment to lower segment with a short upper segment. Data analysis and variant selections were made based on segregation analysis, examination of known MPS III and MPS IV genes, gene function, gene expression, the pathogenicity of variants based on ACMG guidelines and in silico analysis. In total, 58 individuals from 14 families were included in the present study. Six families were clinically diagnosed with MPS III and eight families with MPS IV. WGS revealed variants in MPS-associated genes including NAGLU, SGSH, GALNS, GNPTG as well as the genes VWA3B, BTD, and GNPTG which have not previously associated with MPS. One family had causal variants in both GALNS and BTD. Accurate and early diagnosis of MPS in children represents a helpful step for designing therapeutic strategies to protect different organs from permanent damage. In addition, pre-natal screening and identification of genetic etiology will facilitate genetic counselling of the affected families. Identification of novel causal MPS genes might help identifying new targeted therapies to treat LSDs.</p