A resource of human coronavirus protein-coding sequences in a flexible, multipurpose Gateway Entry clone collection

The COVID-19 pandemic has catalyzed unprecedented scientific data and reagent sharing and collaboration, which enabled understanding the virology of the SARS-CoV-2 virus and vaccine development at record speed. The pandemic, however, has also raised awareness of the danger posed by the family of coronaviruses, of which 7 are known to infect humans and dozens have been identified in reservoir species, such as bats, rodents, or livestock. To facilitate understanding the commonalities and specifics of coronavirus infections and aspects of viral biology that determine their level of lethality to the human host, we have generated a collection of freely available clones encoding nearly all human coronavirus proteins known to date. We hope that this flexible, Gateway-compatible vector collection will encourage further research into the interactions of coronaviruses with their human host, to increase preparedness for future zoonotic viral outbreaks.

Structural characterization of the Aspergillus niger citrate transporter CexA uncovers the role of key residues S75, R192 and Q196

The Aspergillus niger CexA transporter belongs to the DHA1 (Drug-H⁺ antiporter) family. CexA homologs are exclusively found in eukaryotic genomes, and CexA is the sole citrate exporter to have been functionally characterized in this family so far. In the present work, we expressed CexA in Saccharomyces cerevisiae, demonstrating its ability to bind isocitric acid, and import citrate at pH 5.5 with low affinity. Citrate uptake was independent of the proton motive force and compatible with a facilitated diffusion mechanism. To unravel the structural features of this transporter, we then targeted 21 CexA residues for site-directed mutagenesis. Residues were identified by a combination of amino acid residue conservation among the DHA1 family, 3D structure prediction, and substrate molecular docking analysis. S. cerevisiae cells expressing this library of CexA mutant alleles were evaluated for their capacity to grow on carboxylic acid-containing media and transport of radiolabeled citrate. We also determined protein subcellular localization by GFP tagging, with seven amino acid substitutions affecting CexA protein expression at the plasma membrane. The substitutions P200A, Y307A, S315A, and R461A displayed loss-of-function phenotypes. The majority of the substitutions affected citrate binding and translocation. The S75 residue had no impact on citrate export but affected its import, as the substitution for alanine increased the affinity of the transporter for citrate. Conversely, expression of CexA mutant alleles in the Yarrowia lipolytica cex1Δ strain revealed the involvement of R192 and Q196 residues in citrate export. Globally, we uncovered a set of relevant amino acid residues involved in CexA expression, export capacity and import affinity.

A proteome-scale map of the SARS-CoV-2-human contactome

Understanding the mechanisms of coronavirus disease 2019 (COVID-19) disease severity to efficiently design therapies for emerging virus variants remains an urgent challenge of the ongoing pandemic. Infection and immune reactions are mediated by direct contacts between viral molecules and the host proteome, and the vast majority of these virus-host contacts (the 'contactome') have not been identified. Here, we present a systematic contactome map of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with the human host encompassing more than 200 binary virus-host and intraviral protein-protein interactions. We find that host proteins genetically associated with comorbidities of severe illness and long COVID are enriched in SARS-CoV-2 targeted network communities. Evaluating contactome-derived hypotheses, we demonstrate that viral NSP14 activates nuclear factor κB (NF-κB)-dependent transcription, even in the presence of cytokine signaling. Moreover, for several tested host proteins, genetic knock-down substantially reduces viral replication. Additionally, we show for USP25 that this effect is phenocopied by the small-molecule inhibitor AZ1. Our results connect viral proteins to human genetic architecture for COVID-19 severity and offer potential therapeutic targets.

P–773 Infertility treatment and the risk of small for gestational age births: a population-based study in the United States

Study question

What is the association between infertility treatments and small for gestational age (SGA) births?

Summary answer

Women who conceived pregnancies with any infertility treatment had a decreased risk of SGA <10th, <5th and <3rd percentiles compared to naturally conceived pregnancies.

What is known already

Assisted reproductive technology (ART) and other infertility treatments have long been associated with an increased risk of SGA births, which confers a greater risk of perinatal morbidity and mortality compared to appropriate for gestational age births.

Study design, size, duration

This is a cross-sectional study of 16,836,228 births in the United States (US) between 2015–2019. The exposure group included women who underwent any infertility treatment, including ART and prescribed fertility enhancing medications. The comparison group included those who had naturally conceived pregnancies. The primary outcome was SGA birth, defined as sex-specific birthweight <10th percentile for gestational age. Secondary outcomes included SGA <5th and <3rd percentile births.

Participants/materials, setting, methods

Pregnant subjects (n = 16,836,228) in the US who delivered non-malformed, singleton live births between 24–44 weeks’ gestational age. We estimated risk of SGA births in relation to any infertility treatment from fitting log-linear Poisson regression models with robust variance. Risk ratios (RR) and 95% confidence intervals (CI) were estimated as the effect measure before and after adjusting for confounders. We also performed a sensitivity analysis to correct for potential non-differential exposure misclassification and unmeasured confounding biases.

Main results and the role of chance

During the study period, 1.4% (n = 231,177) of non-malformed singleton live births resulted from infertility treatments (0.8% ART and 0.6% fertility enhancing medications). Of these, 9.4% (n = 21,771) of pregnancies conceived with infertility treatment were complicated by SGA <10th percentile compared to 11.9% (n = 1,755,925) of naturally conceived pregnancies. For pregnancies conceived with infertility treatment versus naturally conceived pregnancies, the adjusted RR for SGA <10th percentile was 1.07 (95% CI 1.06, 1.08). However, after correction for misclassification bias and unmeasured confounding, infertility treatment was found to be protective for SGA and conferred a 27% reduced risk of SGA <10th percentile (bias-corrected RR 0.73, 95% CI 0.53, 0.85). These trends were similar for analyses stratified by exposure to ART and fertility enhancing medications and secondary SGA outcomes, including SGA <5th and <3rd percentile.

Limitations, reasons for caution

All information collected on infertility treatment relies on self-reporting by patients and recording by hospital staff at the time of delivery, which likely resulted in underreporting of infertility treatments. Additionally, we cannot determine the impact of interventions that were not recorded, such as intrauterine insemination (IUI).

Wider implications of the findings: Compared to naturally conceived pregnancies, exposure to infertility treatment is associated with reduction in the risk of SGA births. These findings, which are contrary to some published reports, likely reflect changes in the modern practice of infertility care in the US, and importantly, robust analysis of the national data.

Trial registration number

Not applicable

P–776 Singleton pregnancies conceived with infertility treatments and the risk of
neonatal and infant mortality

Study question

Is maternal infertility treatment associated with an increased risk of neonatal and infant mortality when compared to natural conception?

Summary answer

Infertility treatment is associated with a 70% increased adjusted risk of neonatal mortality. This association is strongly mediated by preterm delivery.

What is known already

The number of assisted reproduction technology (ART) cycles performed in the United States (US) increased by 39% from 142,435 cycles in 2007 to 197,737 in 2016. Within this growing experience, several studies described an increased risk of preterm delivery, low birth weight, congenital malformations, neonatal intensive care unit admission, stillbirth, and perinatal mortality among singletons conceived through ART compared to those conceived naturally. Experts have called for ART patients to be advised of potential increased risk for adverse perinatal outcomes and for obstetricians to manage these pregnancies as high risk.

Study design, size, duration

This is a cross-sectional study of 11,289,466 pregnancies in the United States (US) from 2015–2017 that resulted in a non-malformed singleton live birth. The exposure group includes births resulting from any infertility treatment method, including ART and fertility-enhancing drugs. The control group includes births resulting from natural conceptions. The primary outcomes measured were neonatal (within 1 month), post-neonatal (1 month to a year), and infant (up to 1 year) mortality.

Participants/materials, setting, methods

Pregnancies (n = 11,289,466) resulting in a non-malformed singleton live birth in the US from 2015–2017. Associations were estimated from log-linear Poisson regression models with robust variance. Risk ratio (RR) and 95% confidence interval (CI) were derived as the effect measure with adjustments for confounders. The impact of exposure misclassification and unmeasured confounding biases were assessed. A causal mediation analysis of the infertility treatment-mortality association with preterm delivery (<37 weeks) was performed.

Main results and the role of chance

Any infertility treatment was documented in 1.3% (n = 142,215) of singleton live births during the study period. Any infertility treatment was associated with a 70% increased adjusted risk of neonatal mortality (RR 1.70, 95% CI 1.54–1.88), with an even higher risk for early neonatal (RR 1.82, 95% CI 1.63–2.05) than late neonatal (RR 1.37, 95% CI 1.11–1.69) mortality. These risks were similar among pregnancies conceived through ART and treatment with fertility-enhancing drugs. The mediation analysis showed that 68% (95% CI 59–81) of the total effect of infertility treatment on neonatal mortality was mediated through preterm delivery. In a sensitivity analysis, following corrections for exposure misclassification and unmeasured confounding biases, these risks were higher for early neonatal (bias-corrected RR [RRbc] 2.94 95% CIbc 2.16–4.01), but not for late neonatal (RRbc 1.04, 95% CIbc 0.68–1.59) mortality.

Limitations, reasons for caution

Limitations of the study include the potential underreporting of infertility treatment on birth certificates and potential confounding from sociodemographic characteristics that were not accounted for in this study.

Wider implications of the findings: Pregnancies conceived with infertility treatment are associated with increased neonatal mortality and this association is mediated by the increased risk of preterm delivery. Knowledge of this risk should be shared with prospective couples consulting for fertility care in order to best provide adequate informed consent.

Trial registration number

Not applicable

Efficient conversion of hemicellulose sugars from spent sulfite liquor into optically pure L-lactic acid by Enterococcus mundtii

Spent sulfite liquor (SSL), a waste stream from wood pulp production, has great potential as carbon source for future industrial fermentations. In the present study, SSL was separated into a hemicellulose derived sugar syrup (HDSS) and a lignosulfonic fraction by simulated moving bed chromatography. The recovery of SSL sugars in the HDSS was 89% and the fermentation inhibitors furfural, 5-hydroxymethylfurfural and acetic acid were removed by 98.7%, 60.5% and 75.5%, respectively. The obtained sugars have been converted to L-lactic acid, a building block for bioplastics, by fermentation with the lactic acid bacterium Enterococcus mundtii DSM4838. Batch fermentations on HDSS produced up to 56.3 g/L L-lactic acid. Simultaneous conversion of pentose and hexose sugars during fed-batch fermentation of wildtype E. mundtii led to 87.9 g/L optically pure (>99%) L-lactic acid, with maximum productivities of 3.25 g/L.h and yields approaching 1.00 g/g during feeding phase from HDSS as carbon source.

[Critical aspects of the transmandibular approach to the oral cavity and oropharynx]

BACKGROUND

In the context of tumor surgery, the median mandibulotomy as an access route to the oral cavity and oropharynx provides an excellent overview of the surgical site. However, it is not regarded entirely unproblematic with regard to early and later complications that may arise.

OBJECTIVE

The results and complications of the median mandibulotomy will be presented based on data collected from our own patient collective.

MATERIALS AND METHODS

A total of 21 patients who had undergone a median mandibulotomy as part of tumor surgery at the Department of Otorhinolaryngology of the SRH Zentralklinikum Suhl were examined over a period from 01 January 2010 to 31 December 2020. The patient files were retrospectively evaluated.

RESULTS

A stair-step median mandibulotomy was performed in all 21 patients. Reconstruction was performed using a 2.8 mm thick angled mandibular plate and bicortical locking screws. The mean follow-up period was 29.8 months. In all, 7 patients (33%) had a recurrence at the time of surgery; 5 patients (24%) had already undergone pre-radiation. Furthermore, 18 patients (85.7%) received adjuvant radiotherapy. We found plate loosening or extrusion in 0 of 21 cases. A salivary fistula (4.7%) was observed in 1 patient. Trismus was found in 4 (19%) cases during follow-up. Osteoradionecrosis was found in 2 (9.5%) of 21 cases. Cosmetic deficits were not observed.

CONCLUSION

Our results show that the stair-step median mandibulotomy in combination with a 2.8 mm thick reconstruction plate and bicortical locking screws leads to a stable and safe reconstruction even with pre-irradiated situations. Plate loosening or extrusion did not occur.

Publisher Correction: Extensive signal integration by the phytohormone protein network

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Successful development of methodology for detection of hapten-specific contact hypersensitivity (CHS) memory in swine

Hapten contact hypersensitivity (CHS) elicits a well-documented inflammation response that can be used to illustrate training of immune cells through hapten-specific CHS memory. The education of hapten-specific memory T cells has been well-established, recent research in mice has expanded the “adaptive” characteristic of a memory response from solely a function of the adaptive immune system, to innate cells as well. To test whether similar responses are seen in a non-rodent model, we used hapten-specific CHS to measure the ear inflammation response of outbred pigs to dinitrofluorobenzene (DNFB), oxazolone (OXA), or vehicle controls. We adapted mouse innate memory literature protocols to the domestic pig model. Animals were challenged up to 32 days post initial sensitization exposure to the hapten, and specific ear swelling responses to this challenge were significant for 7, 21, and 32 days post-sensitization. We established hapten-specific CHS memory exists in a non-rodent model. We also developed a successful protocol for demonstrating these CHS responses in a porcine system.

Incorporation studies of clickable ceramides in Jurkat cell plasma membranes

The incorporation properties of ceramide analogues for click chemistry in Jurkat T cells were investigated. The analogues varied in the acyl chain length and the position of the functional group for click chemistry. Fluorescence microscopy studies including anisotropy and quenching experiments showed significant differences in the accessibility of the functional group indicating different incorporation properties into the plasma membrane.

OmoMYC blunts promoter invasion by oncogenic MYC to inhibit gene expression characteristic of MYC-dependent tumors

MYC genes have both essential roles during normal development and exert oncogenic functions during tumorigenesis. Expression of a dominant-negative allele of MYC, termed OmoMYC, can induce rapid tumor regression in mouse models with little toxicity for normal tissues. How OmoMYC discriminates between physiological and oncogenic functions of MYC is unclear. We have solved the crystal structure of OmoMYC and show that it forms a stable homodimer and as such recognizes DNA in the same manner as the MYC/MAX heterodimer. OmoMYC attenuates both MYC-dependent activation and repression by competing with MYC/MAX for binding to chromatin, effectively lowering MYC/MAX occupancy at its cognate binding sites. OmoMYC causes the largest decreases in promoter occupancy and changes in expression on genes that are invaded by oncogenic MYC levels. A signature of OmoMYC-regulated genes defines subgroups with high MYC levels in multiple tumor entities and identifies novel targets for the eradication of MYC-driven tumors.

[Human papillomavirus and squamous cell cancer of the head and neck region : Prognostic, therapeutic and prophylactic implications]

Human papilloma viruses (HPV) are responsible for approximately half of all oropharyngeal squamous cell carcinomas (OPSCC) and incidence rates of HPV-associated OPSCC continue to increase substantially. The defined viral carcinogenesis permits development of specific diagnostic, therapeutic, and prophylactic approaches. Laboratory identification of HPV-associated OPSCC may be achieved by p16(INK4a) immunohistochemistry combined with HPV DNA detection by polymerase chain reaction (PCR) using tumor tissue. Patients with HPV-associated OPSCC have a relatively good prognosis; therefore, the HPV status plays an important role in patient guidance. Due to the relatively favorable prognosis, ongoing studies are evaluating whether less rigorous therapy for HPV-positive patients results in equally good cure rates. The criteria for patient selection are, however, still uncertain. Particularly markers for detection of HPV-positive patients with a high risk of treatment failure are lacking. Besides tumor stage and comorbidities, distinct genomic, epigenetic, and immunologic alterations are prognostically relevant for HPV-associated OPSCC, and might be of predictive value. Furthermore, the characteristic molecular alterations suggest the possibility of novel vigilant and specific therapy approaches. These may be inhibitors of the phosphatidylinositol 3‑kinase (PI3K) pathway, which is frequently activated in HPV-associated OPSCC, and immunotherapeutic methods, e. g., therapeutic vaccination. Although prophylactic HPV vaccinations may also prevent development of HPV-associated OPSCC, foreseeable effects on OPSCC incidence will be low, given the low vaccination rates in Germany. This highlights the fact that interdisciplinary research networks should enhance the necessary activities related to HPV-associated OPSCC.

Hoarseness revealing Ortner's syndrome

Hoarseness is a common phenomenon that can be caused by uncommon pathology. One seldom cause is Ortner's syndrome, a rare cardiovocal disease that can lead to hoarseness due to left recurrent laryngeal nerve palsy induced by mechanical compression of the nerve by cardiovascular structures. This case report describes a case of a 41-year-old woman with sudden onset of hoarseness. The patient had known pulmonary hypertension and Eisenmenger's syndrome.

Consensus of German transplant centers on hematopoietic stem cell transplantation in Fanconi anemia

Allogeneic hematopoietic stem cell transplantation (HSCT) is currently the only curative therapy for the severe hematopoietic complications associated with Fanconi anemia (FA). In Germany, it is estimated that 10-15 transplants are performed annually for FA. However, because FA is a DNA repair disorder, standard conditioning regimens confer a high risk of excessive regimen-related toxicities and mortality, and reduced intensity regimens are linked with graft failure in some FA patients. Moreover, development of graft-versus-host disease is a major contributing factor for secondary solid tumors. The relative rarity of the disorder limits HSCT experience at any single center. Consensus meetings were convened to develop a national approach for HSCT in FA. This manuscript outlines current experience and knowledge about HSCT in FA and, based on this analysis, general recommendations reached at these meetings.

Measurement uncertainty of isotopologue fractions in fluxomics determined via mass spectrometry

Metabolic flux analysis implies mass isotopomer distribution analysis and determination of mass isotopologue fractions (IFs) of proteinogenic amino acids of cell cultures. In this work, for the first time, this type of analysis is comprehensively investigated in terms of measurement uncertainty by calculating and comparing budgets for different mass spectrometric techniques. The calculations addressed amino acids of Pichia pastoris grown on 10% uniformly (13)C labeled glucose. Typically, such experiments revealed an enrichment of (13)C by at least one order of magnitude in all proteinogenic amino acids. Liquid chromatography-time-of-flight mass spectrometry (LC-TOFMS), liquid chromatography-tandem mass spectrometry (LC-MS/MS) and gas chromatography-mass spectrometry (GC-MS) analyses were performed. The samples were diluted to fit the linear dynamic range of the mass spectrometers used (10 μM amino acid concentration). The total combined uncertainties of IFs as well as the major uncertainty contributions affecting the IFs were determined for phenylalanine, which was selected as exemplary model compound. A bottom-up uncertainty propagation was performed according to Quantifying Uncertainty in Analytical Measurement and using the Monte Carlo method by considering all factors leading to an IF, i.e., the process of measurement and the addition of (13)C-glucose. Excellent relative expanded uncertainties (k = 1) of 0.32, 0.75, and 0.96% were obtained for an IF value of 0.7 by LC-MS/MS, GC-MS, and LC-TOFMS, respectively. The major source of uncertainty, with a relative contribution of 20-80% of the total uncertainty, was attributed to the signal intensity (absolute counts) uncertainty calculated according to Poisson counting statistics, regardless which of the mass spectrometry platforms was used. Uncertainty due to measurement repeatability was of importance in LC-MS/MS, showing a relative contribution up to 47% of the total uncertainty, whereas for GC-MS and LC-TOFMS the average contribution was lower (30 and 15%, respectively). Moreover, the IF actually present also depends on the isotopic purity of the carbon sources. Therefore, in the uncertainty calculation a carbon source purity factor was introduced and a minor contribution to the total uncertainty was observed. The results obtained by uncertainty calculation performed according to the Monte Carlo method were in agreement with the uncertainty value of the Kragten approach and showed a Gaussian distribution.

[Intrathoracic goitre--undiagnosed--nevertheless operated]

A case review of a female patient, who was indicated for surgery for a goitre with minor bilateral retrosternal spread. The procedure included bilateral thyroidectomy during which the surgeon noticed unusual intrathoracic pathology in the left hemithorax, under the removed lobe. Postoperative chest x-ray and CT examinations revealed intrathoracic goitre, which was then removed during a following procedure. In the article, the authors discuss this uncommon pathology. Because of its uncommon location, the pathology was not detected on standard preoperative endocrinological examination. It was the follow up, postoperative examination, based on which the correct treatment was initiated.

Differentiation of ruminant transmissible spongiform encephalopathy isolate types, including bovine spongiform encephalopathy and CH1641 scrapie

With increased awareness of the diversity of transmissible spongiform encephalopathy (TSE) strains in the ruminant population, comes an appreciation of the need for improved methods of differential diagnosis. Exposure to bovine spongiform encephalopathy (BSE) has been associated with the human TSE, variant Creutzfeldt-Jakob disease, emphasizing the necessity in distinguishing low-risk TSE types from BSE. TSE type discrimination in ruminants such as cattle, sheep, goats and deer, requires the application of several prion protein (PrP)-specific antibodies in parallel immunochemical tests on brain homogenates or tissue sections from infected animals. This study uses in a single incubation step, three PrP-specific antibodies and fluorescent Alexa dye-labelled anti-mouse Fabs on a Western blot. The usual amount of brain tissue needed is 0.5 mg. This multiplex application of antibodies directed towards three different PrP epitopes enabled differential diagnosis of all established main features of classical scrapie, BSE and Nor98-like scrapie in sheep and goats, as well as the currently known BSE types C, H and L in cattle. Moreover, due to an antibody-dependent dual PrP-banding pattern, for the first time CH1641 scrapie of sheep can be reliably discriminated from the other TSE isolate types in sheep.

Real-time computation of subdiffraction-resolution fluorescence images

In the recent past, single-molecule based localization or photoswitching microscopy methods such as stochastic optical reconstruction microscopy (STORM) or photoactivated localization microscopy (PALM) have been successfully implemented for subdiffraction-resolution fluorescence imaging. However, the computational effort needed to localize numerous fluorophores is tremendous, causing long data processing times and thereby limiting the applicability of the technique. Here we present a new computational scheme for data processing consisting of noise reduction, detection of likely fluorophore positions, high-precision fluorophore localization and subsequent visualization of found fluorophore positions in a super-resolution image. We present and benchmark different algorithms for noise reduction and demonstrate the use of non-maximum suppression to quickly find likely fluorophore positions in high depth and very noisy images. The algorithm is evaluated and compared in terms of speed, accuracy and robustness by means of simulated data. On real biological samples, we find that real-time data processing is possible and that super-resolution imaging with organic fluorophores of cellular structures with approximately 20 nm optical resolution can be completed in less than 10 s.

Postoperative development of aspirin resistance following coronary artery bypass

BACKGROUND

Aspirin therapy is known to substantially reduce mortality and the rate of ischaemic complications after coronary artery bypass grafting (CABG). Rates of perioperative aspirin resistance cited in the literature are up to 50% and could be influenced by extracorporeal circulation. Thus, aspirin resistance after CABG may have a significant clinical relevance.

MATERIALS AND METHODS

In 59 patients undergoing CABG (on-pump, off-pump and combined procedures) aspirin resistance was investigated by arachidonic acid induced platelet aggregometry. Clinical relevance was assessed with 12-month follow up.

RESULTS

Two types of resistance were observed: A preoperative resistance (despite oral aspirin or in vitro addition) was present in 29% and a postoperative developing type was seen in 49% resulting in only 22% of patients with a 'normal' reaction to aspirin. If patients were already on oral aspirin at admission, the rate of resistance was significantly reduced. Off-pump surgery or pump-times exceeding 120 min had no significant impact on resistance. During the 12-month follow up (98.3%), there were three deaths (one stroke, one intestinal ischaemia, one mediastinitis after postoperative delirium) in patients with the perioperative resistance and none in other patients (P = 0.345). In none of those patients who presented with perioperative aspirin resistance, could this aspirin resistance be demonstrated when tested again after 12 months?

CONCLUSIONS

Aspirin resistance is a transient phenomenon present in the majority of patients undergoing CABG. The three deaths in the resistant group may - although not statistically significant - indicate the possibility of a worse outcome for patients with aspirin resistance.