Additional file 1: Table S1. of Modelling input-output flows of severe acute respiratory syndrome in mainland China

Description of O-D variables of SARS input-output flows. Table S2. SARS input-output flows matrix. Table S3. SARS input-output flows estimated using gravity model. Table S4. Direct and indirect effects of SARS input-output flows estimated using an ASIM. (DOC 204 kb

Additional file 1: of A spatiotemporal mixed model to assess the influence of environmental and socioeconomic factors on the incidence of hand, foot and mouth disease

Appendix 1. Non-linear modeling. (DOCX 14 kb

Additional file 2: of A spatiotemporal mixed model to assess the influence of environmental and socioeconomic factors on the incidence of hand, foot and mouth disease

Appendix 2. Spatial effect modeling. (DOCX 18 kb

Development of a TaqMan-based real-time PCR assay for rapid and specific detection of fowl aviadenovirus serotype 4

<p>Twelve serotypes of fowl aviadenovirus, namely, FAdV-(1-8a and 8b-11), have been identified, among which FAdV-4 is the aetiologic agent of hepatitis hydropericardium syndrome (HHS) in chickens. Outbreaks of HHS have been documented in many countries, causing significant economic losses. Real-time PCR methods described so far in the literature cross-detect different serotypes of FAdVs. In this study, we aimed to develop a TaqMan-based real-time PCR assay for the specific detection of FAdV-4. A pair of primers targeting the hexon gene and a TaqMan probe were designed. Using different copy numbers of plasmid DNA carrying the hexon gene as template, we showed the detection limit of this assay was 10¹ copies/reaction, which was 10 times higher than conventional PCR. The assay was highly specific for FAdV-4 and did not cross-detect 11 other serotypes of FAdVs, avian influenza virus, Newcastle disease virus, infectious bronchitis virus or subgroup J of the avian leukosis virus. The reproducibility of the assay was assessed by five independent reactions using different copy numbers of plasmid DNA (10³ and 10⁵) as template, and the results showed 0.56–1.15% coefficient of variation for inter-assay variability. Furthermore, the assay was validated with 80 clinical samples. Real-time PCR showed that 76 out of 80 samples were positive for FAdV-4 (95.0% positivity) while 68 out of 80 were tested positive by conventional PCR (85.0% positivity). Our data suggest this real-time PCR assay could be an attractive tool for screening, confirmatory diagnosis and specific differentiation of FAdV-4 infection.</p

Additional file 3: of A spatiotemporal mixed model to assess the influence of environmental and socioeconomic factors on the incidence of hand, foot and mouth disease

Appendix 3. Cross-validation. (DOCX 15 kb

NMR spectra of ¹¹³Cd/¹⁵N-labeled CXC-3 protein.

<p>(A) 1D ¹H-decoupled ¹¹³Cd spectrum. (B) 2D ¹H-¹⁵N HSQC-TOCSY spectrum. The Cys residues at positions 525, 527, 539, 544, 546, 553, 556, 558 and 561 are sequentially numbered from 1 to 9. Cross-peaks originating from Cys Hβ are labeled with the residue number and dash-separated sequential number of Cys, and cross-peaks from Cys Hα are additionally marked with “a”. The spectrum is divided by a vertical line into two parts. The left Hα region is shown with a higher contour level than the right Hβ region for clarity. Some peaks from Cys527 and Cys561 marked by squares are not visible, and their positions were inferred from a 2D ¹H-¹⁵N HSQC-NOESY spectrum. (C) ¹H-¹¹³Cd HMQC-TOCSY spectra with³J_HB-Cd set to 50 Hz and a mixing time of 30 ms. (D-F) ¹H-¹¹³Cd HSQC spectra with ³J_HB-Cd set to 20 Hz (D), 30 Hz (E) and 50 Hz (F). Assigned cross-peaks are marked with sequential number of Cys and those peaks from Hα are additionally labeled with “a”.</p

Structural similarity between CXC and pre-SET domains.

<p>(A) Structure of MSL2 CXC domain. The Cys ligands and the C-terminal invariant Asn residue are shown as sticks, zinc ions as purple spheres and Zn-S coordination bonds and hydrogen bonds as dotted lines. (B) Structure of the SUV39 family Dim5 pre-SET domain (PDB code 1ML9). The long insertion between Cys-5 and Cys-6 is shown schematically as an oval. (C) Structure of the SET2 family NSD1 pre-SET domain (PDB code 3OOI). The three structures of MSL2 CXC, Dim5 pre-SET and NSD1 pre-SET domains are aligned by their Zn-Cys clusters. (D) The primary sequences of MSL2 CXC domain and pre-SET motifs of <i>Neurospora crassa</i> Dim5, human NSD1 and <i>Drosophila melanogaster</i> E(z). The observed or predicted zinc ligands are numbered sequentially from 1 to 9. The invariant C-terminal Asn is marked with asterisk. The coordination patterns of zinc ions observed in these structures are shown. The starting and ending residues of each sequence are labeled with residue numbers. A 48-residue region is omitted in DIM5 pre-SET. The zinc ligands in NSD1 pre-SET are numbered according to those in the CXC domain.</p

The CXC domain of MSL2 binds three zinc ions.

<p>(A) ¹H-¹⁵N HSQC spectrum of the CXC domain. The spectrum was collected on 1 mM ¹⁵N-labeled CXC-3 protein in 50 mM phosphate buffer (pH 6.0) and 10% ²H₂O at 25°C and 600 MHz. The assigned residues are labeled with full-length MSL2 numbering, and the side-chain amide protons are connected by lines. (B) Electrospray ionization mass spectroscopy reveals three bound Zn²⁺ ions. The CXC-3 protein was exchanged into 200 mM ammonia acetate and analyzed with a Q-Star instrument. The inset shows the major isotopic peak series from a +5 charge species. The monoisotopic peak (m/z 1165.8361) corresponds to an exact mass of 5824.1805 Da, consistent with a complex of CXC-3 and three Zn²⁺ ions (monoisotopic MW = 5824.267 Da). The peak series around m/z = 1460 originates from a +4 charge species.</p

NMR structure and dynamics of MSL2 CXC domain.

<p>(A) Structural superposition of the 20 lowest energy NMR structures. The Cα traces of residues 521–566 and three zinc ions (spheres) are shown in cross-eye stereoview. (B) Steady-state ¹H-¹⁵N heteronuclear NOE values are plotted as a function of residue number. The experiment was conducted for CXC-2, which contains residues 517–572 plus three extra N-terminal residues from the vector. No data were obtained for proline residues that lack amide proton. Error bars represent the experimental uncertainties estimated from the spectrum background noise.</p

Amide proton exchange experiments.

<p>(A–C) ¹H-¹⁵N HSQC spectra collected immediately (A), 2 h (B) or 24 h (C) after dissolving the lyophilized CXC-3 protein in ²H₂O. The peaks are labeled and the side chain amide proton Hδ of N563 is labeled as N563D. (C) Intensity of amide proton peak as a function of exchange time. (D) Distribution of slow exchange amide protons in the CXC domain structure. The protected amide protons are shown as spheres on a backbone trace and are colored pink if present in the first recorded spectrum but not after 2 h, orange if present at 2 h but not after 24 h, and red if present after 24 h. The side chain of N563 is also displayed.</p