Accuracy of quantum chemistry structures of chiral tag complexes and the assignment of absolute configuration.

The absolute configuration of a molecule can be established by analysis of molecular rotational spectra of the analyte complexed with a small chiral molecule of known configuration. This approach of converting the analyte enantiomers, with identical rotational spectra, into diastereomers that can be distinguished spectroscopically is analogous to chiral derivatization in nuclear magnetic resonance (NMR) spectroscopy. For the rotational chiral tag method, the derivatization uses noncovalent interactions to install the new chiral center and avoids complications due to possible racemization of the analyte when covalent chemistry is used. The practical success of this method rests on the ability to attribute assigned rotational spectra to specific geometries of the diastereomeric homochiral and heterochiral tag complexes formed in the pulsed jet expansion that is used to introduce samples into the microwave spectrometer. The assignment of a molecular structure to an experimental rotational spectrum uses quantum chemistry equilibrium geometries to provide theoretical estimates of the spectrum parameters that characterize the rotational spectrum. This work reports the results of a high-sensitivity rotational spectroscopy study of the complexes formed between (3)-butyn-2-ol and verbenone. The rotational spectra of four homochiral and four heterochiral complexes are assigned. In addition, the 14 distinct, singly-substituted 13C isotopomer spectra of five of these species are assigned in natural abundance. Analysis of these spectra provides direct structural characterization of the complexes through determination of the carbon atom position coordinates. This data set is used to benchmark quantum chemistry calculations of candidate equilibrium geometries of the chiral tag complexes. The quantum chemistry calculations are limited to methods commonly used in the field of rotational spectroscopy. It is shown that the accuracy of the structures from quantum chemistry provides a high-confidence assignment of cluster geometries to the observed spectra. As a result, a high-confidence determination of the analyte (verbenone) absolute configuration is achieved.

The molecular structure and curious motions in 1,1-difluorosilacyclopent-3-ene and silacyclopent-3-ene as determined by microwave spectroscopy and quantum chemical calculations.

The molecules 1,1-difluorosilacyclopent-3-ene (3SiCPF2) and silacyclopent-3-ene (3SiCP) have been synthesized and studied using chirped pulse, Fourier transform microwave (CP-FTMW) spectroscopy. For 3SiCP this is the first ever microwave study of the molecule and, for 3SiCPF2, the spectra reported in this work have been combined with that of previous work in a global fit. The spectra of each contain splitting which has been fit using a Hamiltonian consisting of semirigid and Coriolis coupling parameters. A refit of the original 3SiCPF2 work was also carried out. All fits and approaches are reported. Analyses of the spectra provide evidence that the molecule is planar which is in agreement with the high-level calculations, but the source of the splitting in the spectra has not been determined.

Theoretical Calculations, Microwave Spectroscopy, and Ring-Puckering Vibrations of 1,1-Dihalosilacyclopent-2-enes.

High-level theoretical CCSD/cc-pVTZ computations have been carried out to calculate the structures and ring-puckering potential energy functions (PEFs) for 1,1-difluorosilacyclopent-2-ene (2SiCPF2) and 1,1-dichlorosilacyclopent-2-ene (2SiCPCl2). The structure and PEF for 1,1-dibromosilacyclopent-2-ene (2SiCPBr2) were obtained by ab initio MP2/cc-pVTZ computations. The parent silacyclopent-2-ene (2SiCP) is puckered with a 49 cm-1 barrier to planarity, 2SiCPF2 has a planar ring system, 2SiCPCl2 has a calculated tiny 4 cm-1 barrier but is essentially planar, and the dibromide has a calculated barrier of 36 cm-1. Microwave spectra of seven isotopic species of 2SiCPF2 were recorded on a chirped pulse, Fourier transform microwave (CP-FTMW) spectrometer in the 6-18 GHz region. The a-type and b-type transitions were observed. The rotational constants and three quartic centrifugal distortion constants were determined for the parent, 29Si, 30Si, and all singly substituted 13C isotopologues in natural abundance. This allowed for the determination of the heavy-atom structure of the ring and showed the ring to be planar. The experimentally determined rotational constants and geometrical parameters agree very well with the theoretical values and confirm the planarity of the five-membered ring. A comparison of the PEFs for the silane and the three dihalides shows the silane to have the stiffest puckering motion and the dibromide to be the least rigid.

The Conformational Landscape, Internal Rotation, and Structure of 1,3,5-Trisilapentane using Broadband Rotational Spectroscopy and Quantum Chemical Calculations.

The rotational spectrum of 1,3,5-trisilapentane was observed on a chirped-pulse Fourier transform microwave spectrometer and is reported. During assignment, multiple conformations of the molecule were identified in the molecular beam. Prior quantum-chemical calculations performed on the molecule show that the identified spectra correspond to the lowest three calculated energetic structures. These structures are of C2 (Conf.1), C2v (Conf.2), and C1 (Conf.3) symmetry, with relative energy ordering of Conf.1 < Conf.3 < Conf.2, which is in stark contrast to n-pentane and all known silicon-substituted n-pentane derivatives. This is found to most likely arise from the elongation of the Si-C bond and the size of the silicon atoms providing for the C2 and C1 structures relieving steric hindrance in comparison to that of the C2v. In the C2v and C1 conformers, splitting in the spectra due to internal rotation of the -SiH3 end groups of 1,3,5-trisilapentane was observed and determined. The C2v equivalent V3 values are 368.46(33) cm-1, and the C1V3 values are 347.78(21) and 360.18(88) cm-1, respectively. These barriers are compared to similar species in order to help verify their veracity and are determined to be accurate based on similar molecular silyl rotors.

Comparative features of infections of two Massachusetts (Mass) infectious bronchitis virus (IBV) variants isolated from Western Canadian layer flocks.

BACKGROUND: Infectious bronchitis virus (IBV) is one of the leading causes of mortality and morbidity in chickens. There are numerous serotypes and variants, which do not confer cross protection resulting in failure of currently used IBV vaccines. Although variant IBV isolates with major genetic differences have been subjected to comparative studies, it is unknown whether minor genetic differences in IBV variants within a serotype are different in terms of pathogenesis and eliciting host responses. Two Massachusetts (Mass) variant IBV isolates recovered from commercial layer flocks in the Western Canadian provinces of Alberta (AB) and Saskatchewan (SK) were compared genetically and evaluated for their pathogenicity, tissue distribution and ability to recruit and replicate in macrophages. RESULTS: Although whole genome sequencing of these two Mass IBV isolates showed low similarity with the M41 vaccinal strain, they had an identical nucleotide sequence at open reading frames (ORFs) 3a, 3b, envelop (E), matrix (M), 5a and 5b. The rest of the ORFs of these 2 IBV isolates showed 99.9% nucleotide similarity. However, upon experimental infection, we found that the IBV isolate originating from AB was different to the one that originated in SK due to higher tracheal lesion scores and lower lung viral replication and lower genome loads in cecal tonsils. Nevertheless, both IBV isolates elicited host responses characterized by significant macrophage recruitment to the respiratory tract and there was evidence that both IBV isolates replicated within tracheal and lung macrophages. CONCLUSIONS: Overall, this study shows that Mass variant IBV isolates, although possessing minor genetic variations, can lead to significant differences in pathogenicity in young chickens. Further studies are required to investigate the pathogenicity of these two Mass variant IBV isolates in laying hens.

Shell-Less Egg Syndrome (SES) Widespread in Western Canadian Layer Operations Is Linked to a Massachusetts (Mass) Type Infectious Bronchitis Virus (IBV) Isolate.

A disease with a sudden drop in egg production and shell-less eggs called, shell-less egg syndrome (SES) has been observed in Western Canada egg layer flocks since 2010. The etiology of this disease is not known. We hypothesize that SES is caused by an infectious bronchitis virus (IBV) strain since it is known that IBV replicates in the shell gland causing various eggshell abnormalities. In this study, we screened egg layer flocks, in the provinces of Alberta (AB) and Saskatchewan (SK), with and without a history of SES for the presence of IBV infection. During 2015⁻2016, a total of 27 egg layer flocks were screened in AB (n = 7) and SK (n = 20). Eighty-one percent of the screened flocks (n = 22) were positive for IBV infection. Thirty of these isolates were successfully characterized using molecular tools targeting the most variable spike (S) 1 gene. IBV isolates from this study clustered into three genotypes based on partial S1 gene variability. The majority of the IBV isolates (70%) were Massachusetts (Mass) type, and the rest were either Connecticut (Conn) type or an uncharacterized genotype with genetic characteristics of Mass and Conn types. Since the majority of the IBV isolates included within the Mass type, we used a Mass type IBV isolate to reproduce SES in specific pathogen free (SPF) white leghorn chickens in lay. Further studies are warranted to investigate whether other IBV isolates can cause SES, to clarify the pathogenesis of SES and to develop a vaccine in order to prevent SES as observed in Western Canadian layer flocks.

Microwave Spectra and Structure of Ar-1,3-Difluorobenzene.

The microwave spectrum of the dimer Ar-1,3-difluorobenzene from 2 to 18 GHz is reported. The spectrum has been observed using a chirped-pulse Fourier transform microwave (CP-FTMW) spectrometer that has recently been expanded to include the 2-6 GHz region of the electromagnetic spectrum. Details of this upgraded spectrometer are reported. Eighty-seven transitions were observed for the parent dimer spectrum, which was adequately fit to a semirigid rotational Hamiltonian consisting of A, B, and C as well as four quartic centrifugal distortion constants. Observations of 13C species in natural abundance were aided by utilizing smaller chirp ranges of 7-9 and 9-11 GHz for 1.9 million and 3.73 million averages, respectively. Assignment of 13C isotopologues allowed for determination of the Kraitchman coordinates of the carbon atoms as well as inertial fits of the complex. The quantum-chemical structure predicts an Ar to monomer center of mass distance of 3.48 Å, compared with 3.564(1) Å determined from experimental structural analysis. This new study indicates that in fluorinated benzene-Ar dimers, when the fluorines are separated by more carbon atoms, the Ar-ring center distance decreases.

Probe-free real-time reverse transcription polymerase chain reaction assays for the detection and typing of porcine reproductive and respiratory syndrome virus in Canada.

Porcine reproductive and respiratory syndrome (PRRS) has tremendous impact on the pork industry in North America. The molecular diagnosis of infection with PRRS virus (PRRSV) is hampered by its considerable strain diversity. In this study, 43 previously published or newly developed primers for probe-free real-time reverse transcription polymerase chain reaction (RT-PCR) were evaluated on their sensitivity, specificity, reproducibility, and repeatability, using a diverse panel of 36 PRRSV strains as well as other arteriviruses and unrelated porcine viruses. Three primer pairs had excellent diagnostic and analytical sensitivity on par with a probe-based reference assay, absolute specificity to virus genotype and species, as well as over 95% reproducibility and repeatability across a wide dynamic range.

Le syndrome dysgénésique et respiratoire du porc (SDRP) a un impact énorme sur l'industrie du porc en l'Amérique du Nord. Le diagnostic moléculaire de l'infection avec le virus du SDRP est entravée par sa diversité considérable. Dans cette étude, 43 amorces publiées antérieurement ou nouvellement développés pour RT-PCR en temps réel sans d'une sonde spécifique ont été évalués sur leur sensibilité, la spécificité, la reproductibilité et la répétabilité. Un groupe varié de 36 souches de virus du SDRP, d'autres virus appartenant au genre des arterivirus et les virus porcins indépendants a été utilisé. Trois paires d'amorces ont une excellente sensibilité de diagnostic and d'analyse qui équivaut à un test de référence basé sur des sondes. Ils avaient une spécificité absolue de génotype et des espèces du virus, et la reproductibilité et la répétabilité a été plus de 95 % sur une large plage dynamique.(Traduit par les auteurs).

Assessment of neutralizing and non-neutralizing antibody responses against Porcine circovirus 2 in vaccinated and non-vaccinated farmed pigs.

Vaccination is the most efficacious procedure to curtail Porcine circovirus 2 (PCV2)-associated diseases (PCVAD). Experimental studies indicate that PCV2 vaccine-induced virus-neutralizing antibodies play a major role in protection from PCVAD. However, the immune response to PCV2 vaccination of pigs on farms is less clear. Analysing groups of age-matched vaccinated and non-vaccinated farmed pigs, we found significantly increased levels of virus-neutralizing antibodies only in vaccinated pigs belonging to the age group with the highest risk for developing PCVAD. Serum levels of PCV2 genomes were not different between corresponding age groups. Levels of antibodies directed against a linear peptide from the PCV2 capsid protein correlated with those of virus-neutralizing antibodies and reached the highest levels in older, non-vaccinated animals, pointing towards an intense interaction between PCV2-infected cells and the immune system. In conclusion, current PCV2 vaccines are in need of improvement to induce stronger and more rapid immunity to prevent PCV2 infection.

Swine outbreak of pandemic influenza A virus on a Canadian research farm supports human-to-swine transmission.

BACKGROUND: Swine outbreaks of pandemic influenza A (pH1N1) suggest human introduction of the virus into herds. This study investigates a pH1N1 outbreak occurring on a swine research farm with 37 humans and 1300 swine in Alberta, Canada, from 12 June through 4 July 2009. METHODS: The staff was surveyed about symptoms, vaccinations, and livestock exposures. Clinical findings were recorded, and viral testing and molecular characterization of isolates from humans and swine were performed. Human serological testing and performance of the human influenza-like illness (ILI) case definition were also studied. RESULTS: Humans were infected before swine. Seven of 37 humans developed ILI, and 2 (including the index case) were positive for pH1N1 by reverse-transcriptase polymerase chain reaction (RT-PCR). Swine were positive for pH1N1 by RT-PCR 6 days after contact with the human index case and developed symptoms within 24 h of their positive viral test results. Molecular characterization of the entire viral genomes from both species showed minor nucleotide heterogeneity, with 1 amino acid change each in the hemagglutinin and nucleoprotein genes. Sixty-seven percent of humans with positive serological test results and 94% of swine with positive swab specimens had few or no symptoms. Compared with serological testing, the human ILI case definition had a specificity of 100% and sensitivity of 33.3%. The only factor associated with seropositivity was working in the swine nursery. CONCLUSIONS: Epidemiologic data support human-to-swine transmission, and molecular characterization confirms that virtually identical viruses infected humans and swine in this outbreak. Both species had mild illness and recovered without sequelae.

Cytotoxicity of ORF3 proteins from a nonpathogenic and a pathogenic porcine circovirus.

Porcine circovirus type 2 (PCV2) infection is associated with significant and serious swine diseases worldwide, while PCV1 appears to be a nonpathogenic virus. Previous studies demonstrated that the ORF3 protein of PCV2 (PCV2ORF3) was involved in PCV2 pathogenesis via its proapoptotic capability (J. Liu, I. Chen, Q. Du, H. Chua, and J. Kwang, J. Virol. 80:5065-5073, 2006). If PCV2ORF3-induced apoptosis is a determinant of virulence, PCV1ORF3 is hypothesized to lack this ability. The properties of PCV1 and PCV2 ORF3, expressed as fusion proteins to an enhanced green fluorescent protein (eGFP), were characterized with regard to their ability to cause cellular morphological changes, detachment, death, and apoptosis. PCV1ORF3 significantly induced more apoptotic cell death and was toxic to more different cell types than PCV2ORF3 was. PCV1ORF3-associated cell death was caspase dependent. PCV1ORF3 also induced poly(ADP-ribose) polymerase 1 (PARP) cleavage; however, whether PARP was involved in cell death requires further studies. Truncation of PCV1 and elongation of PCV2 ORF3 proteins revealed that the first 104 amino acids contain a domain capable of inducing cell death, whereas the C terminus of PCV1ORF3 contains a domain possibly responsible for enhancing cell death. These results suggest that the pathogenicity of PCV2 for pigs is either not determined or not solely determined by the ORF3 protein.

Genomic analysis of porcine circovirus type-2 isolates in Alberta pigs demonstrating clinical porcine circovirus associated disease (PCVAD).

Nineteen pigs with clinical signs of porcine circovirus associated diseases (PCVAD) on 5 Alberta pig farms were examined pathologically, including gross pathology, histopathology, and immunohistochemistry. Polymerase chain reaction (PCR) for porcine circovirus type-2 (PCV-2) and sequence analysis was performed on tissue samples of 12 animals. Results showed that new strains of porcine circovirus type-2 genogroup b were present in most pigs that were positive for PCV-2. Furthermore, a mixed infection with PCV-2a and PCV-2b occurred in the liver and lungs of 1 pig. Comparison of whole genome sequences representing known viruses and the newly discovered Alberta viruses revealed mutations distributed over the entire genome of PCV-2; however, sequences encoding for immunodominant epitopes of PCV-2 appear to be unaffected by these mutations.

Swine influenza (H3N2) infection in a child and possible community transmission, Canada.

An influenza A virus (H3N2) of probable swine origin, designated A/Canada/1158/2006, was isolated from a 7-month-old hospitalized child who lived on a communal farm in Canada. The child recovered uneventfully. A serosurvey that used a hemagglutination-inhibition assay for A/Canada/1158/2006 was conducted on 54 of the 90 members of the farm. Seropositivity was demonstrated in the index patient, 4 of 7 household members, and 4 of 46 nonhousehold members; none had a history of hospital admission for respiratory illness in the preceding year. Serologic evidence for this strain of swine influenza was also found in 1 of 10 pigs (12 weeks-6 months of age) on the farm. Human infection with swine influenza virus is underrecognized in Canada, and because viral strains could adapt or reassort into a form that results in efficient human-to-human transmission, routine surveillance of swine workers should be considered as part of pandemic influenza preparedness.

Getting your game on with business data.

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