bluuebunny/crossref_metadata_2025 huggingface dataset:
Accurate Distinction of Ovarian Clear Cell From Endometrioid Carcinoma Requires Integration of Phenotype, Immunohistochemical Predictions, and Genotype
Authors: Rodriguez Monica , Kang Eun Young , Farrington Kyo , Cook Linda S. , Le Nhu D. , Karnezis Anthony N. , Lee Cheng-Han , Nelson Gregg S. , Terzic Tatjana , Lee Sandra , Köbel Martin
Published: September 2021

Ovarian clear cell carcinoma (OCCC) and ovarian endometrioid carcinoma (OEC) are both associated with endometriosis but differ in histologic phenotype, biomarker profile, and survival. Our objectives were to refine immunohistochemical (IHC) panels that help distinguish the histotypes and reassess the prevalence of mismatch repair deficiency (MMRd) in immunohistochemically confirmed OCCC. We selected 8 candidate IHC markers to develop first-line and second-line panels in a training set of 344 OCCC/OEC cases. Interobserver reproducibility of histotype diagnosis was assessed in an independent testing cohort of 100 OCC/OEC initially without and subsequently with IHC. The prevalence of MMRd was evaluated using the testing cohort and an expansion set of 844 ovarian carcinomas. The 2 prototypical combinations (OCCC: Napsin A+/HNF1B diffusely+/PR−; OEC: Napsin A−/HNF1B nondiffuse/PR+) occurred in 75% of cases and were 100% specific. A second-line panel (ELAPOR1, AMACR, CDX2) predicted the remaining cases with 83% accuracy. Integration of IHC improved interobserver reproducibility (κ=0.778 vs. 0.882, P<0.0001). The prevalence of MMRd was highest in OEC (11.5%, 44/383), lower in OCCC (1.7%, 5/297), and high-grade serous carcinomas (0.7%, 5/699), and absent in mucinous (0/126) and low-grade serous carcinomas (0/50). All 5 MMRd OCCC were probable Lynch syndrome cases with prototypical IHC profile but ambiguous morphologic features: 3/5 with microcystic architecture and 2/5 with intratumoral stromal inflammation. Integration of first-line and second-line IHC panels increases diagnostic precision and enhances prognostication and triaging for predisposing/predictive molecular biomarker testing. Our data support universal Lynch syndrome screening in all patients with OEC when the diagnosis of other histotypes has been vigorously excluded.
Three-year durable efficacy of dolutegravir plus lamivudine in antiretroviral therapy – naive adults with HIV-1 infection
Authors: Cahn Pedro , Sierra Madero Juan , Arribas José R. , Antinori Andrea , Ortiz Roberto , Clarke Amanda E. , Hung Chien-Ching , Rockstroh Jürgen K. , Girard Pierre-Marie , Sievers Jörg , Man Choy Y. , Urbaityte Rimgaile , Brandon Daisy J. , Underwood Mark , Pappa Keith A. , Curtis Lloyd , Smith Kimberly Y. , Gartland Martin , Aboud Michael , van Wyk Jean , Wynne Brian
Published: September 2021

Objective:

To assess efficacy and safety of dolutegravir (DTG) + lamivudine (3TC) vs. DTG + tenofovir disoproxil fumarate/emtricitabine (TDF/FTC) in treatment-naive adults with HIV-1 in the prespecified 144-week secondary analyses of GEMINI-1 and GEMINI-2.

Design:

Identical, multicenter, phase III, randomized, non-inferiority studies (double-blind through 96 weeks).

Methods:

Participants with HIV-1 RNA ≤500 000 copies/ml and no major viral resistance mutations to nucleoside reverse transcriptase inhibitors, nonnucleoside reverse transcriptase inhibitors, or protease inhibitors were randomized 1:1 to once-daily DTG + 3TC or DTG + TDF/FTC.

Results:

At week 144, DTG + 3TC (N = 716) was noninferior to DTG + TDF/FTC (N = 717) in proportion of participants achieving HIV-1 RNA <50 copies/ml (Snapshot algorithm) in the pooled analysis (82% vs. 84%, respectively; adjusted treatment difference [95% confidence interval (CI)], −1.8% [−5.8, 2.1]), GEMINI-1 (−3.6% [−9.4, 2.1]), and GEMINI-2 (0.0% [−5.3, 5.3]). Twelve DTG + 3TC participants and nine DTG + TDF/FTC participants met protocol-defined confirmed virologic withdrawal (CVW) criteria; none developed treatment-emergent resistance. One DTG + 3TC participant who did not meet CVW criteria developed M184V at week 132 and R263R/K at week 144, conferring a 1.8-fold change in susceptibility to DTG; non-adherence to therapy was reported. Significantly fewer drug-related adverse events occurred with DTG + 3TC vs. DTG + TDF/FTC (20% vs. 27%; relative risk [95% CI], 0.76 [0.63–0.92]). Renal and bone biomarker changes favored DTG + 3TC.

Conclusions:

Three-year durable efficacy, long-term tolerability, and high barrier to resistance support first-line use of DTG + 3TC for HIV-1 treatment (see Supplemental Digital Content 1, http://links.lww.com/QAD/C297; video abstract).
Dose optimisation of antibiotics used for meningitis
Authors: Heffernan Aaron J. , Roberts Jason A.
Published: September 2021

Purpose of review

Central nervous system (CNS) infections such as ventriculitis and meningitis are associated with significant morbidity and mortality. In part, this may be due to increased difficulties in achieving a therapeutic antibiotic concentration at the site of infection due to both the pharmacokinetic (PK) changes observed during critical illness and the reduced antibiotic penetration through the blood brain barrier. This paper reviews the pharmacodynamics (PD) and CNS PKs of antibiotics used for Gram-negative bacterial CNS infections to provide clinicians with practical dosing advice.

Recent findings

Recent PK studies have shown that currently used intravenous antibiotic dosing regimens may not achieve a therapeutic exposure within the CNS, even for reportedly ‘susceptible’ bacteria per the current clinical meningitis breakpoints. Limited data exist for new β-lactam antibiotic/β-lactamase inhibitor combinations, which may be required for multidrug resistant infections. Intraventricular antibiotic administration, although not a new concept, has further evidence demonstrating improved patient outcomes compared with intravenous therapy alone, despite the ongoing paucity of PK studies guiding dosing recommendations.

Clinicians should obtain the bacterial minimum inhibitory concentration when treating patients with CNS Gram-negative bacterial infections and consider the underlying PK/PD principles when prescribing antibiotics. Therapeutic drug monitoring, where available, should be considered to guide dosing. Intraventricular therapy should also be considered for patients with ventricular drains to optimise clinical outcomes.
Reducing Time and Patient Radiation of Computed Tomography–guided Thoracic Needle Biopsies With Single-rotation Axial Acquisitions
Authors: Goiffon Reece J. , Best Till D. , Wrobel Maria M. , McDermott Shaunagh , Sharma Amita , Chang Connie Y. , Yang Kai , Fintelmann Florian J.
Published: September 2021

Purpose:

To investigate the effect on procedure time and patient radiation indices of replacing helical acquisitions for needle guidance during thoracic needle biopsy (TNB) with intermittent single-rotation axial acquisitions.

Materials and Methods:

This retrospective intervention study included 215 consecutive TNBs performed by a single operator from 2014 to 2018. Characteristics of patients, lesions, and procedures were compared between TNBs guided only by helical acquisitions initiated in the control room (helical group, n=141) and TNBs guided in part by intermittent single-rotation axial computed tomography controlled by foot pedal (single-rotation group, n=74). Procedure time and patient radiation indices were primary outcomes, complications, and radiologist radiation dose were secondary outcomes.

Results:

Patient, lesion, and procedural characteristics did not differ between helical and single-rotation groups. Use of single-rotation axial acquisitions decreased procedure time by 10.5 minutes (95% confidence interval [CI]: 8.2-12.8 min) or 27% (95% CI: 22%-32%; P<0.001). Patient dose in cumulative volume computed tomography dose index decreased by 23% (95% CI: 12%-33%) or 8 mGy (95% CI: 4.3-31.6 mGy; P=0.01). Dose-length product decreased by 50% (95% CI: 40%-60%) or 270 mGy cm (95% CI: 195-345 mGy cm; P<0.001). No operator radiation exposure was detected. Rate of diagnostic result, pneumothorax, hemoptysis, and hemorrhage did not differ between groups.

Conclusions:

Replacing helical acquisitions with intermittent single-rotation axial acquisitions significantly decreases TNB procedure time and patient radiation indices without adversely affecting diagnostic rate, procedural complications, or operator radiation dose.
Comparison of Triple-Rule-Out Prospectively ECG-triggered Systolic and Diastolic Acquisition Protocol in Patients With Acute Chest Pain
Authors: Fusaro Michele , Caruso Damiano , Tessarin Giovanni , de Santis Domenico , Balestriero Giovanni , Bortolanza Carlo , Panvini Nicola , Polidori Tiziano , Laghi Andrea , Morana Giovanni
Published: September 2021

Purpose:

The purpose of this study was to compare image quality and coronary interpretability of triple-rule-out systolic and diastolic protocols in patients with acute chest pain.

Materials and Methods:

From March 2016 to October 2017 the authors prospectively enrolled patients with undifferentiated acute chest pain, who were at low to intermediate cardiovascular risk. Those with heart rate >75 bpm underwent a systolic prospectively triggered acquisition (systolic triggering [ST]), and in those with ≤75 bpm, end-diastolic triggering (DT) was instead performed. Examinations were evaluated for coronary artery disease, aortic dissection, and pulmonary embolism. Image quality was assessed using a Likert scale. Coronary arteries interpretability was evaluated both on a per-vessel and a per segment basis. The occurrence of major adverse cardiovascular events was investigated.

Results:

The final study population was 189 patients. Fifty-two patients (27.5%) underwent systolic acquisition and 137 (72.5%) underwent diastolic acquisition. No significant differences in overall image quality were observed between DT and ST groups (median score 5 [interquartile ranges 4 to 5] vs. 4 [interquartile ranges 4 to 5], P=0.074). Although both DT and ST protocols showed low percentages of noninterpretable coronary arteries on a per-vessel (1.5% and 6.7%, respectively) and per-segment analysis (1% and 4.7%, respectively), these percentages resulted significantly higher for ST groups (P<0.001). Obstructive coronary stenosis was observed in 18 patients. Only one case of pulmonary embolism was diagnosed and no cases of aortic dissection were found in our population. No death or major adverse cardiovascular events were observed during follow-up among the 2 groups.

Conclusions:

Results showed that triple-rule-out computed tomography angiography is a reliable technique in patients with acute chest pain and that an ST acquisition protocol could be considered an alternative acquisition protocol in patients with higher heart rate, reaching a good image quality.
Quantitative Image Analysis at Chronic Lung Allograft Dysfunction Onset Predicts Mortality
Authors: Weigt S. Samuel , Kim Grace-Hyun J. , Jones Heather D. , Ramsey Allison L. , Amubieya Olawale , Abtin Fereidoun , Pourzand Lila , Lee Jihey , Shino Michael Y. , DerHovanessian Ariss , Stripp Barry , Noble Paul W. , Sayah David M. , Saggar Rajan , Britton Ian , Lynch Joseph P. , Belperio John A. , Goldin Jonathan
Published: September 2021

Background.

Chronic lung allograft dysfunction (CLAD) phenotype determines prognosis and may have therapeutic implications. Despite the clarity achieved by recent consensus statement definitions, their reliance on radiologic interpretation introduces subjectivity. The Center for Computer Vision and Imaging Biomarkers at the University of California, Los Angeles (UCLA) has established protocols for chest high-resolution computed tomography (HRCT)-based computer-aided quantification of both interstitial disease and air-trapping. We applied quantitative image analysis (QIA) at CLAD onset to demonstrate radiographic phenotypes with clinical implications.

Methods.

We studied 47 first bilateral lung transplant recipients at UCLA with chest HRCT performed within 90 d of CLAD onset and 47 no-CLAD control HRCTs. QIA determined the proportion of lung volume affected by interstitial disease and air-trapping in total lung capacity and residual volume images, respectively. We compared QIA scores between no-CLAD and CLAD, and between phenotypes. We also assigned radiographic phenotypes based solely on QIA, and compared their survival outcomes.

Results.

CLAD onset HRCTs had more lung affected by the interstitial disease (P = 0.003) than no-CLAD controls. Bronchiolitis obliterans syndrome (BOS) cases had lower scores for interstitial disease as compared with probable restrictive allograft syndrome (RAS) (P < 0.0001) and mixed CLAD (P = 0.02) phenotypes. BOS cases had more air-trapping than probable RAS (P < 0.0001). Among phenotypes assigned by QIA, the relative risk of death was greatest for mixed (relative risk [RR] 11.81), followed by RAS (RR 6.27) and BOS (RR 3.15).

Conclusions.

Chest HRCT QIA at CLAD onset appears promising as a method for precise determination of CLAD phenotypes with survival implications.
Liver or Kidney Transplantation After SARS-CoV-2 Infection: Prevalence, Short-term Outcome, and Kinetics of Serum IgG Antibodies
Authors: Verbeek Jef , Vrij Casper , Vermeersch Pieter , Van Elslande Jan , Vets Sofie , Lagrou Katrien , Vos Robin , van Cleemput Johan , Jochmans Ina , Monbaliu Diethard , Pirenne Jacques , Kuypers Dirk , Nevens Frederik
Published: September 2021

Background.

There is a paucity of data on the prevalence, adequate timing, and outcome of solid organ transplantation after severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and the kinetics of immunoglobulin G (IgG) antibodies in these patients.

Methods.

SARS-CoV-2 antinucleocapsid (N) IgG and polymerase chain reaction via a nasopharyngeal swab were analyzed in all patients within 24 h before liver or kidney transplantation. Kinetics of IgG antibodies were analyzed and compared with an immunocompetent cohort.

Results.

Between May 1, 2020, and March 18, 2021, 168 patients underwent liver or kidney transplantation in our center, of which 11 (6.54%) patients with a previous SARS-CoV-2 infection were identified. The median interval between SARS-CoV-2 infection and transplantation was 4.5 mo (range, 0.9–11). After a median posttransplant follow-up of 4.9 mo, 10 out of 11 patients were alive without clinical signs of viral shedding or recurrent or active infection. One patient without symptom resolution at time of transplantation died after combined liver-kidney transplantation. In 9 out of 11 patients with previously polymerase chain reaction-confirmed infection, SARS-CoV-2 anti-N and antispike (S) IgG were detectable at day of transplantation. Absolute levels of anti-N and anti-S IgG were positively correlated, declined over time in all patients, and were significantly lower compared with immunocompetent individuals. All patients remained anti-S IgG positive until the last posttransplant follow-up, whereas 3 patients became anti-N negative.

Conclusions.

We observed an uncomplicated course of liver or kidney transplantation after SARS-CoV-2 infection in selected patients. Although having lower absolute IgG antibody levels than immunocompetent individuals, all seroconverted patients remained anti-S IgG positive. These encouraging data need validation in larger studies.
Anopheles salivary antigens as serological biomarkers of vector exposure and malaria transmission: A systematic review with multilevel modelling
Authors: Kearney Ellen A , Agius Paul A , Chaumeau Victor , Cutts Julia C , Simpson Julie A , Fowkes Freya JI
Published: September 2021

Background

Entomological surveillance for malaria is inherently resource-intensive and produces crude population-level measures of vector exposure which are insensitive in low-transmission settings. Antibodies against Anopheles salivary proteins measured at the individual-level may serve as proxy biomarkers for vector exposure and malaria transmission, but their relationship is yet to be quantified.

Methods

A systematic review of studies measuring antibodies against Anopheles salivary antigens (PROSPERO: CRD42020185449). Multilevel modelling estimated associations between seroprevalence with Anopheles human biting rate (HBR) and malaria transmission measures.

Results

From 3981 studies identified in literature searches, 42 studies across 16 countries were included contributing 393 meta-observations of anti-Anopheles salivary antibodies determined in 42,764 samples. A positive non-linear association between HBR and seroprevalence was found; overall a 50% increase in HBR was associated with a 13% increase in odds of seropositivity (OR: 1.13, 95%CI: 1.06-1.20, p<0.001). The association between HBR and Anopheles salivary antibodies was strongest with concordant, rather than discordant Anopheles species. Seroprevalence was also significantly positively associated with established epidemiological measures of malaria transmission: entomological inoculation rate, Plasmodium spp. prevalence, and malarial endemicity class.

Conclusions

Anopheles salivary antibody biomarkers can serve as a proxy measure for HBR and malaria transmission, and could monitor vectorial capacity and malaria receptivity of a population to sustain malaria transmission. Validation of Anopheles species-specific biomarkers are important given the global heterogeneity in the distribution of Anopheles species. Salivary biomarkers have the potential to transform surveillance by replacing impractical, inaccurate entomological investigations, especially in areas progressing towards malaria elimination.

Funding

Australian National Health and Medical Research Council, Wellcome Trust.
Inhibition of sodium conductance by cannabigerol contributes to a reduction of neuronal dorsal root ganglion excitability
Authors: Ghovanloo Mohammad-Reza , Estacion Mark , Zhao Peng , Dib-Hajj Sulayman , Waxman Stephen G.
Published: September 2021

Cannabigerol (CBG), a non-psychotropic phytocannabinoid, is a precursor for cannabis derivatives, Δ9-tetrahydrocannabinol and cannabidiol (CBD). Like CBD, CBG has been suggested as an analgesic. A previous study reported CBG (10 μM) blocks voltage-gated sodium (Nav) currents in CNS neurons. However, the manner in which CBG inhibits Nav channels, and whether this effect contributes to CBG’s potential analgesic behavior remain unknown. Genetic and functional studies have validated Nav1.7 as an opportune target for analgesic drug development. The efforts to develop therapeutic selective Nav1.7 blockers have been unsuccessful thus far, possibly due to issues in occupancy; drugs have been administered at concentrations many folds above IC50, resulting in loss of isoform-selectivity, and increasing off-target effects. We reasoned that an alternative approach could use compounds possessing 2 important properties: ultra-hydrophobicity and functional selectivity. Hydrophobicity could enhance absorption into neuronal cells especially with local administration. Functional selectivity could reduce likelihood of side-effects. As CBG is ultra-hydrophobic (cLogD=7.04), we sought to determine whether it also possesses functional selectivity against Nav channels that are expressed in dorsal root ganglion (DRG). We found that CBG is a ~10-fold state-dependent Nav inhibitor (KI-KR: ~2-20 μM) with an average Hill-slope of ~2. We determined that at lower concentrations, CBG predominantly blocks sodium Gmax and slows recovery from inactivation; however, as concentration is increased, CBG also hyperpolarizes Nav inactivation curves. Our modeling and multielectrode array recordings suggest that CBG attenuates DRG excitability, which is likely linked with Nav inhibition. As most Nav1.7 channels are inactivated at DRG resting membrane potential, they are more likely to be inhibited by lower CBG concentrations, suggesting functional selectivity against Nav1.7 compared to other Navs (via Gmax block).
Neurotransmitter regulation rather than cell-intrinsic properties shape the high-pass filtering properties of olfactory bulb glomeruli
Authors: Zak Joseph D. , Schoppa Nathan E.
Published: September 2021

GABAergic periglomerular (PG) cells in the olfactory bulb are proposed to mediate an intraglomerular “high-pass” filter through inhibition targeted onto a glomerulus. With this mechanism, weak stimuli (e.g., an odor with a low affinity for an odorant receptor) mainly produce PG cell-driven inhibition but strong stimuli generate enough excitation to overcome inhibition. PG cells may be particularly susceptible to being activated by weak stimuli due to their intrinsically small size and high input resistance. Here, we used dual-cell patch-clamp recordings and imaging methods in bulb slices obtained from wild-type and transgenic rats with labeled GABAergic cells to test a number of predictions of the high-pass filtering model. We first directly compared the responsiveness of PG cells with that of external tufted cells (eTCs), which are a class of excitatory interneurons that reside in a parallel but opposing position in the glomerular circuitry. PG cells were in fact found to be no more responsive than eTCs at low levels of sensory neuron activity. While PG cells required smaller currents to be excited, this advantage was offset by the fact that a given level of sensory neuron activity produced much smaller synaptic currents. We did however identify other factors that shaped the excitation/inhibition balance in a manner that would support a high-pass filter, including glial glutamate transporters and presynaptic metabotropic glutamate receptors. We conclude that a single glomerulus may act as a high-pass filter to enhance the contrast between different olfactory stimuli through mechanisms that are largely independent cell intrinsic properties.

Key Points Summary

GABAergic periglomerular (PG) cells in the olfactory bulb are proposed to mediate a “high-pass” filter at a single glomerulus that selectively blocks weak stimulus signals. Their efficacy may reflect their intrinsically small size and high input resistance, which allows them to be easily excited.

We found that PG cells were in fact no more likely to be activated by weak stimuli than excitatory neurons. PG cells spiked more readily in response to a fixed current input, but this advantage for excitability was offset by small synaptic currents.

Glomeruli nevertheless display an excitation/inhibition balance that can support a high pass filter, becoming much more favorable with increasing stimulus strength. Factors shaping the filter include glial glutamate transporters and presynaptic metabotropic glutamate receptors.

We conclude that a single glomerulus may act as a high-pass filter to enhance stimulus contrast through mechanisms that are largely independent of cell-intrinsic properties.
Zika Virus Infection of Murine and Human Neutrophils and their Function as Trojan Horses to the Placenta
Authors: Zanluqui NG , Oliveira LG , Polonio CM , França TT , De Souza GP , Muraro SP , Amorim MR , Carregari VC , Brandão-Teles C , da Silva Patrick , de Oliveira MG , França RFO , Cunha MP , Nogueira ML , Martins-de-Souza D , Condino-Neto A , Proença-Modena JL , Peron JPS
Published: September 2021

ZIKV is a 11Kb positive stranded flavivirus transmitted by infected Aedes aegypti and by sexual intercourse. After a short period of viremia of 5-7 days, the virus is cleared, and infection resolved in 80% of individuals. However, around 27% of the fetuses from pregnant infected mothers may develop several fetal brain and ocular pathology. Here we show that murine and peripheral blood human neutrophils support ZIKV infection and replication both in vitro and in vivo, which may correlate to the facilitation of vertical transmission. ZIKV did not interfere with cell viability, neither induced ROS production nor the release of NETs by infected neutrophils. Also, ZIKV infection of neutrophils did not trigger a pro-inflammatory profile, as evidenced by qPCR and proteomic analysis. Interestingly, ZIKV-infected neutrophils were isolated from the placenta were highly infected. The transference of in vitro ZIKV-infected neutrophils to pregnant female mice favored the transference of viral particles to the fetus. Conversely, neutrophil depletion with monoclonal antibodies reduced fetal viral loads whereas the treatment with recombinant G-CSF has the opposite effect. In summary, although it has already been shown that circulating monocytes harbor ZIKV, to our knowledge, this is the first report demonstrating the role of neutrophils during ZIKV infection, and most important, that it may act as a trojan horse to placental tissue directly impacting the pathogenesis of congenital syndrome.
An outbreak of Rift Valley fever among peri-urban dairy cattle in northern Tanzania, 2018
Authors: de Glanville William A. , Allan Kathryn J. , Nyarobi James M. , Thomas Kate. M. , Lankester Felix , Kibona Tito , Claxton John R. , Brennan Benjamin , Carter Ryan W. , Crump John A. , Halliday Jo E.B. , Ladbury Georgia , Mmbaga Blandina T. , Mramba Furaha , Nyasebwa Obed M. , Rubach Matthew P. , Rostal Melinda K. , Sanka Paul , Swai Emmanuel S. , Szemiel Agnieszka M. , Willett Brian J. , Cleaveland Sarah
Published: September 2021

Undetected Rift Valley fever (RVF) outbreaks are expected in endemic countries but little is known about their size or frequency. We describe a previously unreported RVF outbreak involving dairy cattle that appeared to be limited to the edge of the town of Moshi, Tanzania and occurred from May through August, 2018. The outbreak was detected retrospectively using samples collected as part of a cohort study investigating the causes of livestock abortion across northern Tanzania. A total of 14 RVF-associated cattle abortions were identified using a combination of serology and quantitative reverse transcription PCR (RT-qPCR). Milk samples from three (21%) of 14 cases were also RT-qPCR positive. Genotyping revealed circulation of RVF viruses from two lineages. The occurrence of an RVF outbreak among peri-urban dairy cattle, and evidence for RVF viral shedding in milk, highlights the potential for emerging zoonotic risks associated with the growth of urban and peri-urban livestock populations.
Seasonal temporal dynamics of marine protists communities in tidally mixed coastal waters
Authors: Caracciolo Mariarita , Rigaut-Jalabert Fabienne , Romac Sarah , Mahé Frédéric , Forsans Samuel , Gac Jean-Philippe , Arsenieff Laure , Manno Maxime , Chaffron Samuel , Cariou Thierry , Hoebeke Mark , Bozec Yann , Goberville Eric , Gall Florence Le , Guilloux Loïc , Baudoux Anne-Claire , de Vargas Colomban , Not Fabrice , Thiébaut Eric , Henry Nicolas , Simon Nathalie
Published: September 2021

Major seasonal community reorganizations and associated biomass variations are landmarks of plankton ecology. However, the processes determining marine species and community turnover rates have not been fully elucidated so far. Here, we analyse patterns of planktonic protist community succession in temperate latitudes, based on quantitative taxonomic data from both microscopy counts and ribosomal DNA metabarcoding from plankton samples collected biweekly over 8 years (2009-2016) at the SOMLIT-Astan station (Roscoff, Western English Channel). Considering the temporal structure of community dynamics (creating temporal correlation), we elucidated the recurrent seasonal pattern of the dominant species and OTUs (rDNA-derived taxa) that drive annual plankton successions. The use of morphological and molecular analyses in combination allowed us to assess absolute species abundance while improving taxonomic resolution, and revealed a greater diversity. Overall, our results underpinned a protist community characterised by a seasonal structure, which is supported by the dominant OTUs. We detected that some were partly benthic as a result of the intense tidal mixing typical of the French coasts in the English Channel. While the occurrence of these microorganisms is driven by the physical and biogeochemical conditions of the environment, internal community processes, such as the complex network of biotic interactions, also play a key role in shaping protist communities.
Interactive, visual simulation of a spatio-temporal model of gas exchange in the human alveolus
Authors: Schmid Kerstin , Knote Andreas , Mück Alexander , Pfeiffer Keram , von Mammen Sebastian , Fischer Sabine C.
Published: September 2021

In interdisciplinary fields such as systems biology, close collaboration between experimentalists and theorists is crucial for the success of a project. Theoretical modeling in physiology usually describes complex systems with many interdependencies. On one hand, these models have to be grounded on experimental data. On the other hand, experimenters must be able to penetrate the model in its dependencies in order to correctly interpret the results in the physiological context. When theorists and experimenters collaborate, communicating results and ideas is sometimes challenging. We promote interactive, visual simulations as an engaging way to communicate theoretical models in physiology and to thereby advance our understanding of the process of interest. We defined a new spatio-temporal model for gas exchange in the human alveolus and implemented it in an interactive simulation software namedAlvin. InAlvin, the course of the simulation can be traced in a three-dimensional rendering of an alveolus and dynamic plots. The user can interact by configuring essential model parameters.Alvinallows to run and compare multiple simulation instances simultaneously. The mathematical model was developed with the aim of visualization and the simulation software was engineered based on a requirements analysis. Our work resulted in an integrative gas exchange model and an interactive application that exceed the current standards. We exemplified the use ofAlvinfor research by identifying unknown dependencies in published experimental data. Employing a detailed questionnaire, we showed the benefits ofAlvinfor education. We postulate that interactive, visual simulation of theoretical models, as we have implemented withAlvinon respiratory processes in the alveolus, can be of great help for communication between specialists and thereby advancing research.
Tomato Prosystemin is much more than a simple Systemin precursor
Authors: Molisso Donata , Coppola Mariangela , Buonanno Martina , Di Lelio Ilaria , Monti Simona Maria , Melchiorre Chiara , Amoresano Angela , Corrado Giandomenico , Delano Frier John Paul , Becchimanzi Andrea , Pennacchio Francesco , Rao Rosa
Published: September 2021

Systemin (Sys) is an octadecapeptide which, upon wounding, is released from the carboxy terminus of its precursor, prosystemin(ProSys) to promote plant defenses. Recent findings on the disordered structure of ProSysprompted us to investigate a putative biological role of the whole precursor deprived of Sys peptide. We produced transgenic tomato plants expressing a truncatedProSysgene in which the exon coding for Sys was removed and compared their defense response with that induced by the exogenous application of the recombinant deleted ProSys[ProSys(1-178)].By combining protein structure analyses, transcriptomic analysis, gene expression profiling and bioassays with different pests we demonstrate that the truncated ProSys, that does not induce the endogenousProSysgene, promotes defense barriers in tomato plants through a hormone independent defense pathway, likely associated with the production of oligogalacturonides (OGs). Both transgenic and plants treated with the recombinant protein showed the modulation of the expression of genes linked with defense responses and resulted protected against the lepidopteran pestSpodoptera littoralisand the fungusBotrytis cinerea. Our results suggest that the overall function of the wild type prosystemin is more complex than previously shown as it might activate at least two tomato defense pathways: the well-known Sys-dependent pathway connected with the induction of JA biosynthesis and the successive activation of a set of defense-related genes and the ProSys(1-178)-dependent pathway associated with OGs production leading to the OGs mediate plant immunity.
Ecdysteroid kinase-like (EcKL) paralogs confer developmental tolerance to caffeine in Drosophila melanogaster
Authors: Scanlan Jack L. , Battlay Paul , Robin Charles
Published: September 2021

A unique aspect of metabolic detoxification in insects compared to other animals is the presence of xenobiotic phosphorylation, about which little is currently understood. Our previous work raised the hypothesis that members of the taxonomically restricted ecdysteroid kinase-like (EcKL) gene family encode the enzymes responsible for xenobiotic phosphorylation in the model insect Drosophila melanogaster (Diptera: Ephydroidea)—however, candidate detoxification genes identified in the EcKL family have yet to be functionally validated. Here, we test the hypothesis that EcKL genes in the rapidly evolving Dro5 clade are involved in the detoxification of plant and fungal toxins in D. melanogaster. The mining and reanalysis of existing data indicated multiple Dro5 genes are transcriptionally induced by the plant alkaloid caffeine and that adult caffeine susceptibility is associated with a novel naturally occurring indel in CG31370 (Dro5-8) in the Drosophila Genetic Reference Panel (DGRP). CRISPR-Cas9 mutagenesis of five Dro5 EcKLs substantially decreased developmental tolerance of caffeine, while individual overexpression of two of these genes—CG31300 (Dro5-1) and CG13659 (Dro5-7)—in detoxification-related tissues increased developmental tolerance. In addition, we found Dro5 loss-of-function animals also have decreased developmental tolerance of the fungal secondary metabolite kojic acid. Taken together, this work provides the first compelling functional evidence that EcKLs encode detoxification enzymes and suggests that EcKLs in the Dro5 clade are involved in the metabolism of multiple ecologically relevant toxins in D. melanogaster. We also propose a biochemical hypothesis for EcKL involvement in caffeine detoxification and highlight the many unknown aspects of caffeine metabolism in D. melanogaster and other insects.

Highlights

Phosphorylation is an under-characterised detoxification reaction in insects

Dro5 EcKL genes are good detoxification candidate genes in Drosophila melanogaster

Knockout and misexpression of some Dro5 genes modulated tolerance to caffeine

Dro5 genes may also confer tolerance to the fungal toxin kojic acid

Caffeine tolerance could be adaptive for Drosophila associating with Citrus fruits
An Intersection between Iron Availability and Candida albicans Invasive Filamentation
Authors: Junier Ashlee , Weeks Anne , Alcaraz Ysabella , Kumamoto Carol A.
Published: September 2021

Candida albicans filamentation, the ability to convert from oval yeast cells to elongated hyphal cells, is a key factor in its pathogenesis. Previous work has shown that the integral membrane protein Dfi1 is required for filamentation in cells grown in contact with a semi-solid surface. Investigations into the downstream targets of the Dfi1 pathway revealed potential links to two transcription factors – Sef1 and Czf1. Sef1 regulates iron uptake and iron utilization genes in low iron conditions, leading us to hypothesize that there exists a link between iron availability and contact-dependent invasive filamentation. Here, we showed that Sef1 was not required for contact dependent filamentation, but it was required for WT expression levels of a number of genes during growth in contact conditions. Czf1 is required for contact-dependent filamentation and for WT levels of expression of several genes. Constitutive expression and activation of either Sef1 or Czf1 individually in a dfi1 null strain resulted in a complete rescue of the dfi1 null filamentation defect. Because Sef1 is normally activated in low-iron environments, we embedded WT and dfi1 null cells in iron-free agar medium supplemented with various concentrations of Ferrous Ammonium Sulfate (FAS). dfi1 null cells embedded in media with a low concentration of iron (20uM FAS) showed increased filamentation in comparison to mutant cells embedded in higher concentrations of iron (50-500uM). WT cells produced filamentous colonies in all concentrations. Together, this data indicates that Dfi1, Czf1, Sef1, and environmental iron regulate C. albicans contact-dependent filamentation.

Importance

Candida albicans is an opportunistic pathogen responsible for a larger proportion of candidiasis and candidemia cases than any other Candida species (CDC). The ability of C. albicans cells to invade and cause disease is linked to their ability to filament and form hyphae. Despite this, there are gaps in our knowledge of the environmental cues and intracellular signaling that triggers the switch from commensal organism to filamentous pathogen. Here we identified a link between contact-dependent filamentation and iron availability. Over the course of tissue invasion, C. albicans cells encounter a number of different iron microenvironments, from the iron-rich gut to iron-poor tissues. Increased expression of Sef1-depndent iron uptake genes as a result of contact-dependent signaling will promote the adaptation of C. albicans cells to a low iron availability environment.
Isolation and characterization of a highly specific monoclonal antibody targeting the botulinum neurotoxin type E exposed SNAP-25 neoepitope
Authors: Mechaly Adva , Diamant Eran , Alcalay Ron , Ben-David Alon , Dor Eyal , Torgeman Amram , Barnea Ada , Girshengorn Meni , Levin Lilach , Epstein Eyal , Tennenhouse Ariel , Fleishman Sarel J. , Zichel Ran , Mazor Ohad
Published: September 2021

Botulinum neurotoxin type E (BoNT/E), the fastest acting toxin of all BoNTs, cleaves the 25 kDa synaptosomal associated protein (SNAP-25) in motor neurons, leading to flaccid paralysis. Specific detection and quantification of BoNT/E-cleaved SNAP-25 neoepitope is essential for diagnosis of BoNT/E intoxication as well as for characterization of anti-BoNT/E antibody preparations. In order to isolate highly specific monoclonal antibodies suitable for in vitro immuno-detection of the exposed neoepitope, mice and rabbits were immunized with an eight amino acid peptide composed of the C-terminus of the cleaved SNAP-25. Immunized rabbits developed a specific and robust polyclonal antibody response, whereas immunized mice mostly demonstrated a weak antibody response that could not discriminate between the two forms of SNAP-25. An immune scFv phage-display library was constructed from the immunized rabbits and a panel of antibodies was isolated. Sequence alignment of the isolated clones revealed high similarity between both heavy and light chains, with exceptionally short HCDR3 sequences. A chimeric scFv-Fc antibody was further expressed and characterized, exhibiting a selective, ultra-high affinity (pM) towards the SNAP-25 neoepitope. Moreover, this antibody enabled sensitive detection of the cleaved SNAP-25 in BoNT/E treated SiMa cells with no cross reactivity with the intact SNAP-25. This novel antibody can be further used to develop an in vitro cell-based assay to diagnose BoNT/E intoxication and to characterize antitoxin preparations, thus eliminating the use of animals in the standard mouse bioassay.
Surface marker expression in small and medium/large mesenchymal stromal cell-derived extracellular vesicles in naïve or apoptotic condition using orthogonal techniques
Authors: Skovronova Renata , Grange Cristina , Dimuccio Veronica , Deregibus Maria Chiara , Camussi Giovanni , Bussolati Benedetta
Published: September 2021

Extracellular vesicles released by mesenchymal stromal cells (MSC EVs) are a promising resource for regenerative medicine. In particular, small MSC EVs represent the active EV fraction for therapeutic applications. A bulk analysis is applied to characterize MSC EVs identity and purity, coupled with the assessment of single EV morphology, size and integrity using electron microscopy. We here applied different orthogonal methods to provide a quantitative analysis of size and surface marker expression in medium/large and small fractions, namely 10k and 100k fractions, of MSC EVs obtained by sequential ultracentrifugations. Bone marrow, adipose tissue, and umbilical cord MSC EVs were compared, in naïve and apoptotic conditions. The 100k EV size <100 nm, as detected by electron microscopy, was confirmed by super-resolution microscopy and ExoView. Quantitative single-vesicle imaging using super-resolution microscopy revealed heterogeneous patterns of tetraspanin expressions, being all MSC EV fractions single, double and triple positive, in variable proportions, for CD63, CD81 and CD9. Moreover, ExoView analysis allowed a comparative multiplex screening of single MSC EV tetraspanin and mesenchymal marker levels. Finally, a semiquantitative bead based cytofluorimetric analysis showed the segregation of immunological and pro-coagulative markers on the 10k MSC EV fraction. Apoptotic MSC EVs were released in higher number, without significant differences from the naïve fractions in surface marker expression. These results indicate that a consistent profile of MSC EV fractions among the different MSC sources, and a safer profile of the 100k MSC EV population for clinical application. Finally, our study identified suitable applications for different EV analytical techniques.
Paving the way towards understanding the inflammatory pathways triggered by giant viruses in mammalian cells: effect of mimivirus-cell interactions on IκBα degradation
Authors: Oliveira Juliana dos Santos , Oliveira Dahienne Ferreira , Essus Victor Alejandro , Nunes Gabriel Henrique Pereira , Honorato Leandro , Oliveira Leandro , Nimrichter Leonardo , Peralta José Mauro , Guimaraes Allan Jefferson , Foguel Debora , Cortines Juliana Reis
Published: September 2021

Even after two decades since the identification of the first giant virus, the Acanthamoeba polyphaga mimivirus (APMV), it still elude scientists. Their gigantic size and genome are unique in the whole virosphere, and many aspects of their biology are still unknown, including their possible hosts. They are cultivated in laboratories using Acanthamoeba cells as hosts, but little is known about the infectivity of these giant viruses in vertebrate cells. However, there is evidence of the possible involvement of APMV in pneumonia and activation of inflammatory pathways. Among the hundreds of prospected giant viruses members is Tupanvirus, isolated in Brazil. Its particles have a characteristically large size varying between 1.2 to 2 μm and are covered by fibrils. In the present work, we aim to study the consequences of the incubation of APMV and Tupanvirus with mammalian cells. These cells express Toll-like receptors (TLR) that are capable of recognizing lipopolysaccharides, favoring the internalization of the antigen and activation of the inflammatory system. We used a lineage of human lung adenocarcinoma cells (A549) to evaluate possible effects of TLR activation by the giant viruses and if we could detect the probable cause of the said giant-virus dependent pneumonia. Our results show that APMV and Tupanvirus (TPV) activate cellular receptors related to the Toll-like 4 type-induced inflammatory response and that the A549 cells are capable of internalizing the latter virus. Therefore, this study brings new insights into the possible interactions established between mimiviruses (here represented by APMV and Tupanvirus) and members of the innate cellular immune response.
MyD88 Mediates Colitis- and RANKL-induced Microfold Cell Differentiation
Authors: Li Yang , Yang Shanshan , Huang Xin , Yang Ning , Wang Caiying , Zhao Jing , Jing Zhizhong , Willems Luc , Liu Guangliang
Published: September 2021

Intestinal microfold (M) cells are critical for sampling antigen in the gut and initiating the intestinal mucosal immune response. In this study, we found that the differentiation efficiency of M cells was closely related to the colitis severity. The expression levels of M cells differentiation-related genes were synchronized with the kinetics of pro-inflammatory cytokines expression originated from dextran sulfate sodium (DSS) induction and Salmonella infection. Compared with wild-type (WT) mice, MyD88-/- mice exhibited significantly lower expression levels of M cells differentiation-related genes. However, DSS could induce colitis in MyD88-/- mice but failed to promote M cells differentiation. Furthermore, the receptor activator of the Nuclear Factor-κB ligand (RANKL) induced M cells differentiation in murine intestinal organoids prepared from both WT and MyD88-/- mice. However, less M cells differentiation were found in MyD88-/- mice as compared with WT mice. Hence, we concluded that myeloid differentiation factor 88 (MyD88) is an essential molecule for colitis- and RANKL-related M cells differentiation.
A gut microbial metabolite of dietary polyphenols reverses obesity-driven hepatic steatosis
Authors: Osborn Lucas J. , Schultz Karlee , Massey William , DeLucia Beckey , Choucair Ibrahim , Varadharajan Venkateshwari , Fung Kevin , Horak Anthony J. , Orabi Danny , Nemet Ina , Nagy Laura E. , Wang Zeneng , Allende Daniela S. , Sangwan Naseer , Hajjar Adeline M. , McDonald Christine , Ahern Philip P. , Hazen Stanley L. , Brown J. Mark , Claesen Jan
Published: September 2021

The molecular mechanisms by which dietary fruits and vegetables confer cardiometabolic benefits remain poorly understood. Historically, these beneficial properties have been attributed to the antioxidant activity of flavonoids. Here, we reveal that the host metabolic benefits associated with flavonoid consumption actually hinge on gut microbial metabolism. We show that a single gut microbial flavonoid catabolite is sufficient to reduce diet-induced cardiometabolic disease burden in mice. Dietary supplementation with elderberry extract attenuated obesity and continuous delivery of the catabolite 4-hydroxphenylacetic acid was sufficient to reverse hepatic steatosis. Analysis of human gut metagenomes revealed that under one percent contains a flavonol catabolic pathway, underscoring the rarity of this process. Our study will impact the design of dietary and probiotic interventions to complement traditional cardiometabolic treatment strategies.

One-Sentence Summary

Select gut microbes can metabolize flavonoids from a fruit and vegetable diet to monophenolic acids, which improve fatty liver disease.

Graphical abstract
Determination of m6A frequency utilizing 4SedTTP-RT Ligation Assisted PCR (SLAP) in viral and cellular long non-coding RNAs
Authors: Martin Sarah E , Gan Huachen , Sztuba-Solinska Joanna
Published: September 2021

N6-methyladenosine is one of the most abundant epitranscriptomic signatures that can affect every aspect of RNA biology, from structure and stability to intra- and intermolecular interactions. The accurate quantitative assessment of RNA stoichiometry at single-nucleotide resolution is a prerequisite to evaluate the biological significance of m6A in the context of specific RNA. We have developed a new method, termed 4-Selenothymidine 5’-triphosphate reverse transcription and Ligation Assisted PCR analysis (SLAP), for quantitative and unbiased assessment of the m6A fraction on target RNA. The inclusion of thymidine triphosphate derivative during reverse transcription discourages base pair formation with m6A resulting in the reaction’s cessation, while maintaining normal A-T base pairing. The site-specific ligation of the resulting cDNAs with adapters, followed by amplification, generates two distinct products that reflect the modified and unmodified fraction of the analyzed RNA. These PCR products are subsequently separated by gel electrophoresis and quantified using densitometric analysis. We applied the SLAP to verify the position and assess the frequency of m6A sites present on two exemplary long non-coding RNAs. We assessed the SLAP specificity, accuracy, and sensitivity, proving the applicability of this method for the m6A analysis on less abundant transcripts. Overall, this method constitutes an extension of the bird’s-eye view of RNA m6A landscape provided by epitranscriptome-wide analyses by delivering quantitative assessment of modification frequency and can therefore aid the understanding of the consequences of m6A on biological processes.

Graphical Abstract