Asexual Evolution and Forest Conditions Drive Genetic Parallelism in Phytophthora ramorum

It is commonly assumed that asexual lineages are short-lived evolutionarily, yet many asexual organisms can generate genetic and phenotypic variation, providing an avenue for further evolution. Previous work on the asexual plant pathogen Phytophthora ramorum NA1 revealed considerable genetic variation in the form of Structural Variants (SVs). To better understand how SVs arise and their significance to the California NA1 population, we studied the evolutionary histories of SVs and the forest conditions associated with their emergence. Ancestral state reconstruction suggests that SVs arose by somatic mutations among multiple independent lineages, rather than by recombination. We asked if this unusual phenomenon of parallel evolution between isolated populations is transmitted to extant lineages and found that SVs persist longer in a population if their genetic background had a lower mutation load. Genetic parallelism was also found in geographically distant demes where forest conditions such as host density, solar radiation, and temperature, were similar. Parallel SVs overlap with genes involved in pathogenicity such as RXLRs and have the potential to change the course of an epidemic. By combining genomics and environmental data, we identified an unexpected pattern of repeated evolution in an asexual population and identified environmental factors potentially driving this phenomenon.

Ca2+ Ions Promote Fusion of Middle East Respiratory Syndrome Coronavirus with Host Cells and Increase Infectivity

Fusion with, and subsequent entry into, the host cell is one of the critical steps in the life cycle of enveloped viruses. For Middle East respiratory syndrome coronavirus (MERS-CoV), the spike (S) protein is the main determinant of viral entry. Proteolytic cleavage of the S protein exposes its fusion peptide (FP), which initiates the process of membrane fusion. Previous studies on the related severe acute respiratory syndrome coronavirus (SARS-CoV) FP have shown that calcium ions (Ca²⁺) play an important role in fusogenic activity via a Ca²⁺ binding pocket with conserved glutamic acid (E) and aspartic acid (D) residues. SARS-CoV and MERS-CoV FPs share a high sequence homology, and here, we investigated whether Ca²⁺ is required for MERS-CoV fusion by screening a mutant array in which E and D residues in the MERS-CoV FP were substituted with neutrally charged alanines (A). Upon verifying mutant cell surface expression and proteolytic cleavage, we tested their ability to mediate pseudoparticle (PP) infection of host cells in modulating Ca²⁺ environments. Our results demonstrate that intracellular Ca²⁺ enhances MERS-CoV wild-type (WT) PP infection by approximately 2-fold and that E891 is a crucial residue for Ca²⁺ interaction. Subsequent electron spin resonance (ESR) experiments revealed that this enhancement could be attributed to Ca²⁺ increasing MERS-CoV FP fusion-relevant membrane ordering. Intriguingly, isothermal calorimetry showed an approximate 1:1 MERS-CoV FP to Ca²⁺ ratio, as opposed to an 1:2 SARS-CoV FP to Ca²⁺ ratio, suggesting significant differences in FP Ca²⁺ interactions of MERS-CoV and SARS-CoV FP despite their high sequence similarity.IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) is a major emerging infectious disease with zoonotic potential and has reservoirs in dromedary camels and bats. Since its first outbreak in 2012, the virus has repeatedly transmitted from camels to humans, with 2,468 confirmed cases causing 851 deaths. To date, there are no efficacious drugs and vaccines against MERS-CoV, increasing its potential to cause a public health emergency. In order to develop novel drugs and vaccines, it is important to understand the molecular mechanisms that enable the virus to infect host cells. Our data have found that calcium is an important regulator of viral fusion by interacting with negatively charged residues in the MERS-CoV FP region. This information can guide therapeutic solutions to block this calcium interaction and also repurpose already approved drugs for this use for a fast response to MERS-CoV outbreaks.

Coronavirus membrane fusion mechanism offers a potential target for antiviral development

The coronavirus disease 2019 (COVID-19) pandemic has focused attention on the need to develop effective therapies against the causative agent, SARS-CoV-2, and also against other pathogenic coronaviruses (CoV) that have emerged in the past or might appear in future. Researchers are therefore focusing on steps in the CoV replication cycle that may be vulnerable to inhibition by broad-spectrum or specific antiviral agents. The conserved nature of the fusion domain and mechanism across the CoV family make it a valuable target to elucidate and develop pan-CoV therapeutics. In this article, we review the role of the CoV spike protein in mediating fusion of the viral and host cell membranes, summarizing the results of research on SARS-CoV, MERS-CoV, and recent peer-reviewed studies of SARS-CoV-2, and suggest that the fusion mechanism be investigated as a potential antiviral target. We also provide a supplemental file containing background information on the biology, epidemiology, and clinical features of all human-infecting coronaviruses, along with a phylogenetic tree of these coronaviruses.

Coronavirus membrane fusion mechanism offers a potential target for antiviral development

The coronavirus disease 2019 (COVID-19) pandemic has focused attention on the need to develop effective therapies against the causative agent, SARS-CoV-2, and also against other pathogenic coronaviruses (CoV) that have emerged in the past or might appear in future. Researchers are therefore focusing on steps in the CoV replication cycle that may be vulnerable to inhibition by broad-spectrum or specific antiviral agents. The conserved nature of the fusion domain and mechanism across the CoV family make it a valuable target to elucidate and develop pan-CoV therapeutics. In this article, we review the role of the CoV spike protein in mediating fusion of the viral and host cell membranes, summarizing the results of research on SARS-CoV, MERS-CoV, and recent peer-reviewed studies of SARS-CoV-2, and suggest that the fusion mechanism be investigated as a potential antiviral target. We also provide a supplemental file containing background information on the biology, epidemiology, and clinical features of all human-infecting coronaviruses, along with a phylogenetic tree of these coronaviruses.

Open-source raspberry Pi-based operant box for translational behavioral testing in rodents

BACKGROUND

Rodents have been used for decades to probe neural circuits involved in behavior. Increasingly, attempts have been developed to standardize training paradigms across labs; and to use visual/auditory paradigms that can be also tested in humans. Commercially available systems are expensive and thus do not scale easily, and are not optimized for electrophysiology.

NEW METHOD

Using the rich open-source technology built around Raspberry Pi, we were able to develop an inexpensive (<$1000) visual-screen based operant chamber with electrophysiological and optogenetic compatibility. The chamber is operated within MATLAB/Simulink, a commonly used scientific programming language allowing for rapid customization.

RESULTS

Here, we describe and provide all relevant details needed to develop and produce these chambers, and show examples of behavior and electrophysiology data collected using these chambers. We also include all of the tools needed to allow readers to build and develop their own boxes (CAD models for 3D printing and laser-cutting; PCB-board design; all bill of materials for required parts and supplies, and some examples of Simulink models to operate the boxes).

COMPARISON WITH EXISTING METHODS

The new boxes are far more cost-effective than commercially available environments and allow for the combination of automated behavioral testing with electrophysiological read-outs with high temporal precision.

CONCLUSION

These open-source boxes can be used for labs interested in developing high-throughput visual/auditory behavioral assays for ∼ 10th the cost of commercial systems.

Rate of colorectal neoplasia in patients with Hodgkin lymphoma

AIM

Survivors of Hodgkin lymphoma (HL) are at increased risk of breast, lung, thyroid, stomach, pancreatic and colon cancer. There is limited information on the utility of endoscopic screening for colon cancer. We aimed to describe the adenoma detection rate (ADR) in patients with HL to determine the appropriate timing of colonoscopy screening.

METHOD

We retrospectively studied patients with HL who underwent colonoscopy between 2000 and 2017.

RESULTS

A total of 251 patients underwent colonoscopy. Eighty (32%) patients had 151 colonic polyps. Thirty per cent of the polyps exhibited high-grade dysplasia, and invasive colon adenocarcinoma was found in 10 patients. Patients with the nodular sclerosing subtype of HL had a significantly lower ADR than others (P = 0.002). The ADR was 5% in patients younger than 35 years (n = 64), 23% in patients between 35 and 40 years of age (n = 22), 39% in patients between 40 and 50 years of age (n = 51) and 46% in patients older than 50 years (n = 114).

Establishing normative data for the Functional Dexterity Test in typically developing children aged 3-5 years

STUDY DESIGN

Cross-sectional.

INTRODUCTION

The Functional Dexterity Test (FDT) is a timed pegboard hand dexterity test. Normative data have been developed primarily in adults with some studies in the pediatric population. The present study will complement the existing pediatric data and make the FDT a stronger assessment for use in this population.

PURPOSE OF THE STUDY

The primary aim of this study was to collect normative data in typically developing children aged 3-5 years in the Greater Montreal area; the secondary aim was to evaluate the intrarater and interrater reliabilities of the FDT.

METHODS

The FDT was administered to typically developing children aged 3-5 years, who were recruited from various geographical locations and socioeconomic status levels across the Greater Montreal area. Descriptive statistics, t-tests, and analysis of variance were used to compare age-gender groups. The intraclass correlation coefficient (ICC) was calculated to determine intrarater and interrater reliabilities.

RESULTS

Normative data were collected from 267 children (137 females) from 18 daycares. Statistically significant differences in FDT scores were found across all age bands (P < .01). Total time decreased with increasing age (P < .01). No significant differences were found between genders. The FDT showed excellent interrater (ICC = 0.89-0.98) and intrarater (ICC = 0.83-0.99) reliabilities.

CONCLUSIONS

The clear and standardized pediatric instructions, scoring sheet, and normative data table developed in this study provide health care professionals with quick and easy tools to facilitate scoring and clinical interpretation of hand dexterity in preschool-aged children. Future studies should include school-aged children and adolescents from a larger geographic area.

[Comparison the clinical efficacy of 3D versus 2D total laparoscopic thyroidectomy for thyroid cancer by via-breast approach]

Objective:To summarize and analyze the clinical efficacy of 3D and 2D laparoscopic surgery in thyroidectomy for thyroid cancer. Method: Thirty-seven patients with early-differentiated thyroid cancer underwent laparoscopic surgery from August 2016 to November 2018. Their clinical data were retrospectively analyzed. They were divided into 3D laparoscopic group and 2D laparoscopic group based on laparoscopic imaging systems. The perioperative clinical indicators and postoperative complications of the two groups were compared. Result: Compared with the 2D laparoscopic group, the 3D laparoscopic group had shorter operation time and less bleeding, and the incidence of postoperative complications was less, but the differences between the two groups were not statistically significant(P>0.05). Conclusion: Compared with the 2D laparoscopic thyroidectomy, 3D laparoscopic thyroidectomy for thyroid cancer allows higher surgical precision, shorter operation time, lower operation risk and smoother surgical procedure, thus improves surgical efficiency.

Quantum Quench and Nonequilibrium Dynamics in Lattice-Confined Spinor Condensates

We present an experimental study on nonequilibrium dynamics of a spinor condensate after it is quenched across a superfluid to Mott insulator (MI) phase transition in cubic lattices. Intricate dynamics consisting of spin-mixing oscillations at multiple frequencies are observed in time evolutions of the spinor condensate localized in deep lattices after the quantum quench. Similar spin dynamics also appear after spinor gases in the MI phase are suddenly moved away from their ground states via quenching magnetic fields. We confirm these observed spectra of spin-mixing dynamics can be utilized to reveal atom number distributions of an inhomogeneous system, and to study transitions from two-body to many-body dynamics. Our data also imply the nonequilibrium dynamics depend weakly on the quench speed but strongly on the lattice potential. This enables precise measurements of the spin-dependent interaction, a key parameter determining the spinor physics.

Successful therapeutic rechallenge after a severe episode of high dose methotrexate-induced choreoathetosis: A case report

Methotrexate (MTX) is an essential chemotherapy drug used in the treatment of malignancies, but it is known to cause complications to the central nervous system. We report a case of severe MTX neurotoxicity in an adult presenting with choreoathetosis despite a normal clearance of MTX. High dose-MTX has been successfully rechallenged without any neurological sequelae. We reviewed the relevant literature of similar manifestations and summarized their clinical data, magnetic resonance imaging features and treatment given. None of them has recurrence of neurotoxicity. We concluded that it is safe to persist with MTX even after a previous episode of toxic leukoencephalopathy.

Response of maize photosynthesis to high temperature: Implications for modeling the impact of global warming

Negative impacts of increased temperature on maize yield are anticipated using simulation models. However, some temperature functions are parameterized with partial information. There is limited information on photosynthesis response to high temperature in modern maize hybrids. Improved photosynthesis-temperature functions are key for realistic yield simulations. Our experiment was aimed at building a functional relationship between photosynthesis and air temperature exploring temperature ranges relevant for global warming simulations. Maize hybrids from cold, temperate, and subtropical regions were included in the study to assess genetic adaptation. Results showed a trilinear response to temperature with an optimum of 40 °C. No genetic adaptation was observed among the diverse set of hybrids evaluated. Results contrast with common temperature-limiting functions indicating a decline in carbon assimilation above 30-33 °C. Our results suggest possible overestimations of negative impacts of global warming on maize yield due to the use of inadequate response functions relating carbon assimilation to temperature.

[Surgical treatment of uremic secondary hyperparathyroidism complicated with thyroid nodules]

Objective:To investigate the surgical treatment of secondary hyperparathyroidism(SHPT) with thyroid nodule(TN) in uremic patients.Method:The clinical data of 26 patients diagnosed as SHPT combined with TN were retrospectively analyzed.Result:The patients underwent total parathyroidectomy and parathyroid granuless were transplanted subcutaneously into the forearm. The levels of parathyroid hormone,alkaline phosphatase,serum calcium,serum phosphorus and calcium-phosphorus product in 6 months and 12 months after operation were significantly lower than those before operation(P<0.01).The quality of life assessed by KDQOL-SF scale was significantly higher than that before operation(P<0.01). Concomtiant TN was operated simultaneously, and gravel calcification was significantly associated with papillary thyroid carcinoma(P<0.01).Conclusion:Total parathyroidectomy plus subcutaneous minimal forearm autograft and concurrent surgery with TN are feasible, and can not only properly treat TN, but also significantly improve SHPT-related prognosis and quality of life. We should be alert to the possibility of malignant TN in SHPT background, especially those with grit calcification.

[Post-marketing multi-center safety surveillance of inactivated enterovirus A71 vaccine (Vero cell)]

Objective: To evaluate the post-marketing safety profiles of the inactivated enterovirus type 71 (EV-A71) vaccine (Vero cell) after routine inoculation. Methods: Eleven cities of Zhejiang Province, Fengtai district of Beijing, Qinnan district, two counties as Pingle and Pingguo of Guangxi Zhuang Autonomous Region, and Dongtai city of Jiangsu Province were selected as the field sites. A total of 45 239 subjects were enrolled in this study from children who seeked the vaccination of EV-A71 vaccine during the period from July, 2016 to June, 2018. Different sampling method were adopted in different sites. All vaccinated children were invited to participate in the study in Fengtai and Dongtai, however, systematic sampling method were adopted in other sites. Active surveillance was conducted and information about adverse reactions (ARs) occurred in 30 min, 3 d and 30 d following each dose of EV-A71 immunization was collected by field observation, phone-call or face-to-face interview. The incidence of ARs in different types, symptoms and grades were described. Results: In total, there were 45 239 children who received 71 243 doses EV-A71 vaccine. The overall incidence of ARs was 1.079% (769 doses), with the highest incidence of 1.182% (177/14 973) in 5-11 month group and the lowest incidence of 0.849% (18/2 119) in ≥ 36 month group among different age groups. There was a higher incidence in solicited ARs, which was 1.047% (746 doses). The incidences of grade 1 and grade 2 ARs were also higher, which were 0.404% (288 doses) and 0.554% (395 doses), respectively. No grade 4 ARs occurred. The doses of the first and the second vaccination was 40 736 and 30 507, respectively, and the incidences of ARs were 1.281% (522 doses) and 0.810% (247 doses). Also, the incidences of ARs were 0.091% (37 doses) and 0.043% (13 doses) in local, and 1.168% (476 doses) and 0.760% (232 doses) in system. The symptoms of ARs after the two doses of vaccination were basically the same. Redness at the injection site was the most common local ARs after each dose vaccination, with doses of 24 and 11, while fever was the most common systemic ARs, with doses of 362 and 190. Moreover, ARs mainly occurred in 30 min to 3 d after each dose vaccination, with incidence of 1.016% (414 doses) and 0.698% (213 doses) in the first and second dose, respectively. Conclusion: The ARs had a low incidence after vaccination in children and most were mild or moderate. EV-A71 vaccine with good safety is suitable for inoculation in a large scale.

Real world experience of R-CHOP with or without consolidative radiotherapy vs DA-EPOCH-R in the first-line treatment of primary mediastinal B-cell lymphoma

Primary mediastinal large B‐cell lymphoma (PMBCL) is a distinct clinico‐pathological subtype of diffuse large B‐cell lymphoma with unclear prognostic factors and limited clinical data. Optimal treatment and role for radiotherapy is not fully defined. We performed a multicenter retrospective review of 124 patients with newly diagnosed PMBCL between 2001 and 2016. Treatment regimens were R‐CHOP (n = 41), R‐CHOP + RT (n = 37), and DA‐EPOCH‐R (n = 46). 6% (n = 3) in the DA‐EPOCH‐R group received RT. With a median follow up of 45 months, the overall 5‐year OS and PFS was 89.4% and 82.4%, respectively. The type of chemo‐radiotherapy regimen, B symptoms and Ann‐Arbor staging showed a significant association with OS on univariate analysis but only B symptoms remained prognostic (P = 0.012) after multivariate analysis. The chemo‐radiotherapy regimen, Japanese IPI and Ann‐Arbor stage was significantly associated with PFS in univariate analysis, but only chemo‐radiotherapy regimen remained significant (P = 0.02) after multivariate analysis. Patients who received R‐CHOP + RT or DA‐EPOCH‐R had better PFS than those receiving R‐CHOP alone, with 5‐year PFS of 90% vs 88.5% vs 56%, respectively (P = 0.02). In the subgroup analysis of patients with bulk (n = 71), R‐CHOP alone (n = 21) had inferior 5‐year PFS 56.6% compared to those who received R‐CHOP + RT (n = 23) 91.3% or DA‐EPOCH‐R (n = 27) 92.6% (P = 0.007). In contrast, in patients without bulk (n = 42), there was no impact of treatment regimen on PFS (P = 0.25). In conclusion, R‐CHOP + RT and DA‐EPOCH‐R provide excellent outcomes in patients with PMBCL. In patients with bulky disease, the use of DA‐EPOCH‐R may be preferable as it allows omission of RT without reduction in efficacy.

[Comparison of commercial HIV-1 viral load tests by using proficiency test results in China, 2013- 2015]

Objective: To compare the bio-equivalence among commercial HIV-1 viral load tests, including EasyQ HIV-1 v2.0 (EasyQ) from bioMerieux NucliSens of France; VERSANT HIV-1 RNA 3.0 assay (bDNA) from Siemens Healthcare Diagnostics of USA; COBAS AmpliPrep/COBAS TaqMan HIV-1 test (Taqman) from Roche Molecular Diagnosis of USA; Abbott Real Time HIV-1 Kit (M2000) from Abbott Molecular of USA and two domestic HIV-1 viral load test kits (domestic kit) from DaAn Gene Company of Sun Yat-Sen University and Liaoning Bio-Pharmaceutical company of Northeast pharmaceutical group, by using proficiency test results in China from 2013 to 2015. Methods: A total of 2 954 proficiency test results, obtained from 22 positive samples of 6 proficiency tests in 155 laboratories conducted by China CDC were analyzed during 2013-2015. The results from each sample were first logarithmic transformed and then grouped according to the method used, the mean value of logarithmic results was calculated. Subsequently, 22 clusters of mean values were analyzed by Bland-Altman analysis for the consistency, and linear regression analysis for the interdependency. Results: The results indicated that, by taking Taqman as the reference, EasyQ, M2000, bDNA and domestic kit had good consistency (90%-100%) and interdependency. Conclusion: All the viral load tests were bio-equivalent. Moreover, according to the conversion formula derived from domestic proficiency test results, all the viral load results could be converted, which is critical for epidemiological analysis.

Production of Pseudotyped Particles to Study Highly Pathogenic Coronaviruses in a Biosafety Level 2 Setting

The protocol aims to generate coronavirus (CoV) spike (S) fusion protein pseudotyped particles with a murine leukemia virus (MLV) core and luciferase reporter, using a simple transfection procedure of the widely available HEK-293T cell line. Once formed and released from producer cells, these pseudovirions incorporate a luciferase reporter gene. Since they only contain the heterologous coronavirus spike protein on their surface, the particles behave like their native coronavirus counterparts for entry steps. As such, they are the excellent surrogates of native virions for studying viral entry into host cells. Upon successful entry and infection into target cells, the luciferase reporter gets integrated into the host cell genome and is expressed. Using a simple luciferase assay, transduced cells can be easily quantified. An important advantage of the procedure is that it can be performed in biosafety level 2 (BSL-2) facilities instead of BSL-3 facilities required for work with highly pathogenic coronaviruses such as Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV). Another benefit comes from its versatility as it can be applied to envelope proteins belonging to all three classes of viral fusion proteins, such as the class I influenza hemagglutinin (HA) and Ebola virus glycoprotein (GP), the class II Semliki forest virus E1 protein, or the class III vesicular stomatitis virus G glycoprotein. A limitation of the methodology is that it can only recapitulate virus entry steps mediated by the envelope protein being investigated. For studying other viral life cycle steps, other methods are required. Examples of the many applications these pseudotype particles can be used in include investigation of host cell susceptibility and tropism and testing the effects of virus entry inhibitors to dissect viral entry pathways used.

Abstract P6-13-03: Not presented

This abstract was not presented at the conference.

Citation Format: Glaspy J, Tang T, Rutty D, Yan X, Bondarenko I, Burdaeva O. Not presented [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-13-03.

Beyond first-line non-anthracycline-based chemotherapy for extranodal NK/T-cell lymphoma: clinical outcome and current perspectives on salvage therapy for patients after first relapse and progression of disease

Background

Current standard treatment, including non-anthracycline-based chemotherapy and optimal combining of radiotherapy, has dramatically improved outcomes of patients with extranodal natural killer/T-cell lymphoma (ENKTL) during the last decade. This study was conducted to investigate the clinical outcome of ENKTL patients with relapsed or progressive disease after initial current standard therapy.

Patients and methods

We retrospectively reviewed patients diagnosed with ENKTL at six centers in four countries (China, France, Singapore, and South Korea) from 1997 to 2015 and analyzed 179 patients who had relapsed or progressed after initial current standard therapy.

Results

After a median follow-up of 58.6 months (range 27.9-89.2), the median second progression-free survival (PFS) was 4.1 months [95% confidence interval (CI) 3.04-5.16] and overall survival (OS) was 6.4 months (95% CI 4.36-8.51). Multivariate Cox-regression analysis revealed that elevated lactate dehydrogenase, multiple extranodal sites (≥2), and presence of B symptoms were associated with inferior OS (P < 0.05). OS and PFS were significantly different according to both prognostic index of natural killer lymphoma (PINK) and PINK-E (Epstein-Barr virus) models. Salvage chemotherapy with l-asparaginase (l-Asp)-based regimens showed a significantly better clinical benefit to response rate and PFS, although it did not lead to OS improvement. First use of l-Asp in the salvage setting and l-Asp rechallenge at least 6 months after initial treatment were the best candidates for salvage l-Asp containing chemotherapy.

Conclusions

Most patients with relapsed or refractory ENKTL had poor prognosis with short survival. Further studies are warranted to determine the optimal treatment of patients with relapsed or refractory ENKTL.