The pore size distribution and architecture in gas shales were studied using a combination of small-angle neutron scattering (SANS), mercury injection capillary pressure (MICP), and helium ion ...microscopy (HIM). SANS analysis shows that the pore size population is not a power-law distribution across many length scales, typical of sedimentary rocks, but contains an anomalous population of pores on-the-order ∼2 nm, housed primarily in the organic matter. A model is presented showing how a “foamy porosity” with such a characteristic size is a direct result of diagenetic evolution of kerogen. Cross-linking of the kerogen combined with phase separation of gas/oil, leads to arrested coarsening with a length scale set by the cross-length density. These pore populations determined by the scattering model are directly supported by HIM images. Pore connectivity determined through pore-size-to-pore-throat analysis, suggests that interpore connections are also distinct from typical sedimentary rocks. The pore/throat ratio, unlike the simple ratios predicted from sphere packing and found for clastic rocks, is nearly constant over all pore sizes. Kerogen diagenesis is a recognized source of excess internal pressure. When this pressure causes failure of the material surrounding the kerogen to create escape pathways for the phase-separated fluid, it is likely that escape pathways will connect intergranular porosity via microfractures, producing the relatively narrow aperture size distribution.
Monkey B virus (Macacine alphaherpesvirus 1; BV) occurs naturally in macaques of the genus Macaca, which includes rhesus and long-tailed (cynomolgus) monkeys that are widely used in biomedical ...research. BV is closely related to the human herpes simplex viruses (HSV), and BV infections in its natural macaque host are quite similar to HSV infections in humans. Zoonotic BV is extremely rare, having been diagnosed in only a handful of North American facilities with the last documented case occurring in 1998. However, BV is notorious for its neurovirulence since zoonotic infections are serious, usually involving the central nervous system, and are frequently fatal. Little is known about factors underlying the extreme neurovirulence of BV in humans. Here we review what is actually known about the molecular biology of BV and viral factors affecting its neurovirulence. Based on what is known about related herpesviruses, areas for future research that may elucidate mechanisms underlying the neurovirulence of this intriguing virus are also reviewed.
•Complete genomes of six 1978/79 fetal and respiratory BoHV-1 isolates were sequenced.•Vaccine-derived strains, WTs, and one vaccine/WT recombinant virus were recovered.•Fetal recombinant had a WT ...genome with two blocks of vaccine-derived sequences.•Evidence that recombination can occur naturally between BoHV-1 vaccine and WT viruses.•Underscores importance of gene-deleted marker vaccines recombining and losing markers.
Bovine herpesvirus type 1 (BoHV-1) causes various disease syndromes in cattle including respiratory disease and abortions. During an investigation into the potential role of BoHV-1 modified-live vaccines (MLV) causing diseases in cattle, we performed whole genome sequencing on six BoHV-1 field strains isolated at Cornell Animal Health Diagnostic Center in the late 1970s. Three isolates (two respiratory and a fetal) were identified as vaccine-derived isolates, having SNP patterns identical to that of a previously sequenced MLV virus that exhibited a deleted US2 and truncated US1.67 genes. Two other isolates (a respiratory and a fetal) were categorized as wild-type (WT) viruses based on their unique SNP pattern that is distinct from MLV viruses. The sixth isolate from an aborted fetus was a recombinant virus with 62% of its genome exhibiting SNPs identical to one of the above-mentioned WT viruses also recovered from an aborted fetus. The remaining 38% consisted of two blocks of sequences derived from the MLV virus. The first block replaced the UL9-UL19 region, and the second vaccine-derived sequence block encompassed all the genes within the unique short region and the internal/terminal repeats containing the regulatory genes BICP4 and BICP22. This is confirmatory evidence that recombination between BoHV-1 MLV and WT viruses can occur under natural conditions and cause disease. It is important in that it underscores the potential for the glycoprotein E negative (gE−) marker vaccine used to eradicate BoHV-1 in some countries, to recombine with virulent field strains allowing them to capture the gE− marker, thereby endangering the control and eradication programs.
Here, we report the genome sequence of a spider monkey alphaherpesvirus (ateline alphaherpesvirus 1, HVA1) and compare it with that of other primate alphaherpesviruses. The HVA1 genome is 147,346 bp ...long and contains 67 predicted ORFs. The genetic layout of the HVA1 genome is similar to that of the squirrel monkey alphaherpesvirus (saimirine alphaherpesvirus 1, HVS1) in that it lacks inverted repeat regions flanking the unique long region and homologues of the UL43, UL49.5, US8.5 and US10-12 genes. Unlike HVS1, HVA1 also lacks a homologue of the RL1 (γ34.5) gene and a replication origin near the end of the genome. Consistent with previous phylogenetic analyses, all predicted proteins of HVA1 are most closely related to those of HVS1.
Shear-induced structural transitions of a micellar cubic phase during large amplitude oscillatory shear flow is studied with time-resolved oscillatory rheological small angle neutron scattering. This ...technique allows us to resolve the structural changes within a cycle of oscillation. By applying a strain rate near the critical melting shear rate, melting and recrystallization occurs in a cyclic mode. The maximum degree of order is observed when the shear stress reaches a plateau value during the large amplitude oscillatory shear cycle, whereas melting is maximized at the strain rate wave peaks. This structural evolution confirms the cyclic mechanism of sticking and sliding of 2D hexagonal close-packed layers I. W. Hamley et al., Phys. Rev. E 58, 7620 (1998).
Abstract Complete genome sequences of 19 strains of monkey B virus ( Macacine alphaherpesvirus 1; BV) isolated from several macaque species were determined. A low level of sequence variation was ...present among BV isolates from rhesus macaques. Most variation among BV strains isolated from rhesus macaques was located in regions of repetitive or quasi-repetitive sequence. Variation in coding sequences (polypeptides and miRNAs) was minor compared to regions of non-coding sequences. Non-coding sequences in the long and short repeat regions of the genome did however exhibit islands of conserved sequence. Oral and genital isolates from a single monkey were identical in sequence and varied only in the number of iterations of repeat units in several areas of repeats. Sequence variation between BV isolates from different macaque species (different BV genotypes) was much greater and was spread across the entire genome, confirming the existence of different genotypes of BV in different macaque species.
The only genome sequence for monkey B virus (BV; species Macacine herpesvirus 1) is that of an attenuated vaccine strain originally isolated from a rhesus monkey (BVrh). Here we report the genome ...sequence of a virulent BV strain isolated from a cynomolgus macaque (BVcy). The overall genome organization is the same, although sequence differences exist. The greatest sequence divergence is located in non-coding areas of the long and short repeat regions. Like BVrh, BVcy has duplicated Ori elements and lacks an ORF corresponding to the γ34.5 gene of herpes simplex virus. Nine of ten miRNAs and the majority of ORFs are conserved between BVrh and BVcy. The most divergent genes are several membrane-associated proteins and those encoding immediate early proteins.
We review the current literature pertaining to the characterization of soft matter subject to flow utilizing small-angle neutron scattering, flow-SANS, with an emphasis on the simultaneous ...measurement of the rheology, Rheo-SANS. Experimental results are discussed in terms of the flow induced structure and direct connection to the bulk rheology in which we highlight the use of the contrast match method as a unique advantage to neutron scattering techniques. Finally, we discuss specific areas in each field that could benefit from focused flow-SANS experiments, and the projected evolution of specialized flow-SANS sample environments.
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► The application of SANS to the characterization of soft matter under deformation. ► The direct measurement of flow induced structural reorganization. ► The simultaneous measure of both structure and rheology. ► The current development of state-of-the-art dynamic SANS sample environments. ► The current approaches to the data analysis of anisotropic scattering patterns.
Although severe coronavirus disease 2019 (COVID-19) and hospitalization associated with COVID-19 are generally preventable among healthy vaccine recipients, patients with immunosuppression have poor ...immunogenic responses to COVID-19 vaccines and remain at high risk of infection with SARS-CoV-2 and hospitalization. In addition, monoclonal antibody therapy is limited by the emergence of novel SARS-CoV-2 variants that have serially escaped neutralization. In this context, there is interest in understanding the clinical benefit associated with COVID-19 convalescent plasma collected from persons who have been both naturally infected with SARS-CoV-2 and vaccinated against SARS-CoV-2 ("vax-plasma"). Thus, we report the clinical outcome of 386 immunocompromised outpatients who were diagnosed with COVID-19 and who received contemporary COVID-19-specific therapeutics (standard-of-care group) and a subgroup who also received concomitant treatment with very high titer COVID-19 convalescent plasma (vax-plasma group) with a specific focus on hospitalization rates. The overall hospitalization rate was 2.2% (5 of 225 patients) in the vax-plasma group and 6.2% (10 of 161 patients) in the standard-of-care group, which corresponded to a relative risk reduction of 65% (
= 0.046). Evidence of efficacy in nonvaccinated patients cannot be inferred from these data because 94% (361 of 386 patients) of patients were vaccinated. In vaccinated patients with immunosuppression and COVID-19, the addition of vax-plasma or very high titer COVID-19 convalescent plasma to COVID-19-specific therapies reduced the risk of disease progression leading to hospitalization.IMPORTANCEAs SARS-CoV-2 evolves, new variants of concern (VOCs) have emerged that evade available anti-spike monoclonal antibodies, particularly among immunosuppressed patients. However, high-titer COVID-19 convalescent plasma continues to be effective against VOCs because of its broad-spectrum immunomodulatory properties. Thus, we report clinical outcomes of 386 immunocompromised outpatients who were treated with COVID-19-specific therapeutics and a subgroup also treated with vaccine-boosted convalescent plasma. We found that the administration of vaccine-boosted convalescent plasma was associated with a significantly decreased incidence of hospitalization among immunocompromised COVID-19 outpatients. Our data add to the contemporary data providing evidence to support the clinical utility of high-titer convalescent plasma as antibody replacement therapy in immunocompromised patients.
•Selected BoHV1.1 isolates from fetuses and neonates correspond to MLV vaccine strains.•Selected respiratory isolates were related, but not identical to MLV vaccines, and designated ...unclassified.•BoHV1.1 was isolated from genital tract instead of BoHV1.2b.•Potential MLV vaccine latency as vaccine strain from a fetus in a herd with no viral vaccines for at least 2 years.•Isolates from BRD cases designated “wild type” had no definite evidence of relationship to vaccine strains.
Bovine herpesvirus-1 (BoHV-1) causes disease in cattle with varied clinical forms. In the U.S. there are two BoHV1 subtypes, BoHV-1.1 and BoHV-1.2b. Control programs in North America incorporate modified live (MLV) or killed (KV) viral vaccines. However, BoHV-1 strains continue to be isolated from diseased animals or fetuses after vaccination. It is possible to differentiate BoHV-1 wild-type from MLV vaccine strains by determining their single nucleotide polymorphism (SNP) patterns through either whole-genome sequencing or PCR sequencing of genomic regions containing vaccine-defining SNPs. To determine the BoHV-1 subtype in clinical isolates and their relationship to MLV strains, 8 isolates from varied clinical disease at three different laboratories in the U.S. were sequenced and phylogenetically analyzed. Five samples were isolated within the past 5 years from New York and 3 were archived samples recovered 35 years prior from Oklahoma and Louisiana. Based on phylogenetic analysis, four of the cases appeared to be due to an MLV vaccine: 3 cases of aborted fetuses and one neonate with systemic BoHV-1 disease. One aborted fetus was from a herd with no reported history of MLV vaccination in two years. The remaining four isolates did not group with any MLV vaccines: two were associated with bovine respiratory disease, one with vulvovaginitis, and a fourth was determined to be a BoHV-1.2b respiratory isolate. Recovery of BoHV-1.1 that is very closely related to an MLV vaccine virus from a herd not receiving vaccines in an extended period prior to its isolation suggests that MLV viruses may remain latent or circulate within herds for long periods.
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