bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanobodies as Probes and Modulators of Cardiovascular G Protein–Coupled Receptors
Authors: Wingler Laura M. , Feld Andrew P.
Published: November 2021

Understanding the activation of G protein-coupled receptors (GPCRs) is of paramount importance to the field of cardiovascular medicine due to the critical physiological roles of these receptors and their prominence as drug targets. Although many cardiovascular GPCRs have been extensively studied as model receptors for decades, new complexities in their regulation continue to emerge. As a result, there is an ongoing need to develop novel approaches to monitor and to modulate GPCR activation. In less than a decade, nanobodies, or recombinant single-domain antibody fragments from camelids, have become indispensable tools for interrogating GPCRs both in purified systems and in living cells. Nanobodies have gained traction rapidly due to their biochemical tractability and their ability to recognize defined states of native proteins. Here, we review how nanobodies have been adopted to elucidate the structure, pharmacology, and signaling of cardiovascular GPCRs, resolving long-standing mysteries and revealing unexpected mechanisms. We also discuss how advancing technologies to discover nanobodies with tailored specificities may expand the impact of these tools for both basic science and therapeutic applications.
Pharmacological Inhibition of Mammalian Target of Rapamycin Attenuates Deoxycorticosterone Acetate Salt–Induced Hypertension and Related Pathophysiology: Regulation of Oxidative Stress, Inflammation, and Cardiovascular Hypertrophy in Male Rats
Authors: Temiz-Resitoglu Meryem , Guden Demet S. , Senol Sefika P. , Vezir Ozden , Sucu Nehir , Kibar Deniz , Yılmaz Sakir N. , Tunctan Bahar , Malik Kafait U. , Sahan-Firat Seyhan
Published: November 2021

The present study aimed to explore the contribution of mammalian target of rapamycin (mTOR) in deoxycorticosterone acetate (DOCA) salt–induced hypertension and related pathophysiological changes in cardiovascular and renal tissues. DOCA salt loading resulted in an increase in systolic blood pressure, diastolic blood pressure, and mean blood pressure along with the activity of ribosomal protein S6, the effector protein of mTOR. Treatment with rapamycin, the selective inhibitor of mTOR, initiated at the fourth week of DOCA- salt administration normalized the systolic blood pressure and attenuated ribosomal protein S6 activity in the heart, aorta, and kidney. Cardiac and vascular hypertrophy, oxidative stress, and infiltration of macrophages (CD68+), the marker of inflammation, were also reduced in rapamycin-treated, DOCA-salt, hypertensive rats. In addition, renal hypertrophy and dysfunction were also reduced with rapamycin-treated hypertensive rats. Moreover, these pathophysiological changes in DOCA-salt hypertensive rats were associated with increased NADPH oxidase (NOX) activity, gp91phox (formerly NOX2) expression, ERK1/2, and p38 MAPK activities in the heart, aorta, and kidney were minimized by rapamycin. These data indicate that mTOR plays an important role in regulating blood pressure and the development of cardiovascular and renal pathophysiological changes, most likely due to increased NOX expression/activity, ERK1/2, and p38 MAPK activity with macrophages infiltration in the heart, kidney, and aorta. Pharmacological inhibition of mTOR and related signaling pathways could serve as a novel target for the treatment of hypertension.
Immunological Biomarkers in Blood to Monitor the Course and Therapeutic Outcomes of COVID-19
Authors: Wieland Eberhard
Published: November 2021

Background:

The COVID-19 pandemic has posed a great challenge to the medical community because little is known about its clinical course, therapeutic options, and laboratory monitoring tools for diagnosis, prognosis, and surveillance. This review focuses on immune biomarkers that can be measured in peripheral blood in a clinical laboratory under routine conditions to monitor the innate immune system response in the acute phase, as well as the adaptive immune response established both after infection and vaccination.

Methods:

A PubMed search was performed covering January 2020 to June 2021 to extract biomarkers suitable for monitoring the immune response and outcome of COVID-19 and therapeutic interventions, including vaccination.

Results:

To monitor the innate immune response, cytokines such as interleukin-6 or acute phase reactants such as C-reactive protein or procalcitonin can be measured on autoanalyzers complemented by automated white blood cell differential counts. The adaptive immune response can be followed by commercially available enzyme-linked immune spot assays to assess the specific activation of T cells or by monitoring immunoglobulin A (IgA), IgM, and IgG antibodies in serum to follow B-cell activation. As antigens of the SARS-CoV-2 virus, spike and nucleocapsid proteins are particularly suitable and allow differentiation between the immune response after infection or vaccination.

Conclusions:

Routine immune monitoring of COVID-19 is feasible in clinical laboratories with commercially available instruments and reagents. Strategies such as whether biomarkers reflecting the response of the innate and adaptive immune system can be used to make predictions and assist in individualizing therapeutic interventions or vaccination strategies need to be determined in appropriate clinical trials. Promising preliminary data are already available based on single-center reports and completed or ongoing vaccination trials.
A Systematic Review of Health State Utility Values in the Plastic Surgery Literature
Authors: Christopher Adrienne N. , Morris Martin P. , Patel Viren , Klifto Kevin , Fischer John P.
Published: November 2021

Background:

Cost-utility analyses assess health gains acquired by interventions by incorporating weighted health state utility values (HSUVs). HSUVs are important in plastic and reconstructive surgery (PRS) because they include qualitative metrics when comparing operative techniques or interventions. We systematically reviewed the literature to identify the extent and quality of existing original utilities research within PRS.

Methods:

A systematic review of articles with original PRS utility data was conducted in accordance with the Preferred Reporting Items for a Systematic Review and Meta-Analysis guidelines. Subspecialty, survey sample size, and respondent characteristics were extracted. For each HSUV, the utility measure [direct (standard gamble, time trade off, visual analog scale) and/or indirect], mean utility score, and measure of variance were recorded. Similar HSUVs were pooled into weighted averages based on sample size if they were derived from the same utility measure.

Results:

In total, 348 HSUVs for 194 disease states were derived from 56 studies within seven PRS subspecialties. Utility studies were most common in breast (n = 17, 30.4%) and hand/upper extremity (n = 15, 26.8%), and direct measurements were most frequent [visual analog scale (55.4%), standard gamble (46.4%), time trade off (57.1%)]. Studies surveying the general public had more respondents (n = 165, IQR 103–299) than those that surveyed patients (n = 61, IQR 48–79) or healthcare professionals (n = 42, IQR 10–109). HSUVs for 18 health states were aggregated.

Conclusions:

The HSUV literature within PRS is scant and heterogeneous. Researchers should become familiar with these outcomes, as integrating utility and cost data will help illustrate that the impact of certain interventions are cost-effective when we consider patient quality of life.
Corneal Densitometry After Uneventful Descemet Membrane Endothelial Keratoplasty—5-Year Outcomes
Authors: Droutsas Konstantinos , Kappos Nikolaos , Giallouros Eleftherios , Schroeder Frank Michael , Sekundo Walter , Kandarakis Stylianos , Lazaridis Apostolos
Published: November 2021

Purpose:

The purpose of this study is to analyze the course of corneal densitometry (CD), endothelial cell density (ECD), best-corrected visual acuity (BCVA), and central corneal thickness (CCT) 5 years after uneventful Descemet membrane endothelial keratoplasty (DMEK).

Methods:

Sixty uneventful cases (51 patients) with a minimum follow-up of 5 years were included. CD of various corneal layers (anterior, central, posterior, and total layer) and zones (0–2 mm, 2–6 mm, and 6–10 mm) were measured with Scheimpflug tomography. ECD, BCVA, and CCT were also evaluated.

Results:

Total CD at 0 to 2 mm and 2 to 6 mm zones significantly decreased from 33 ± 10 and 27.8 ± 8 grayscale units (GSU) preoperatively to 21.8 ± 3.1 and 22.2 ± 4.2 GSU at 5 years, respectively (P < 0.001). On the contrary, total CD at the 6 to 10 mm zone significantly increased from 30 ± 8.3 GSU preoperatively to 34.6 ± 7.8 GSU at 5 years (P < 0.001). ECD significantly decreased from 2496 ± 267 cells/mm2 preoperatively to 1063 ± 470 cells/mm2 at 5 years (P < 0.001). Similarly, CCT significantly decreased from 686 ± 109 μm preoperatively to 557 ± 37 μm at 5 years (P < 0.001). Postoperative BCVA was significantly better after DMEK for every examination time point.

Conclusions:

Despite a slight CD increase at all layers of all corneal zones from the second to the fifth postoperative year, the excellent visual outcome was maintained throughout 5-year follow-up. Thus, DMEK seems to effectively treat corneal endothelial disease in the long term.
Comparison of Donor Corneal Endothelial Cell Density Determined by Eye Banks and by a Central Image Analysis Reading Center Using the Same Image Analysis Method
Authors: Huang Heidi , Benetz Beth Ann , Clover Jameson M. , Titus Michael , O'Brien Robert C. , Menegay Harry J. , Lass Jonathan H.
Published: November 2021

Purpose:

The purpose of this study was to evaluate agreement between eye banks (EBs) and an image analysis reading center on endothelial cell density (ECD) determinations using the same image analysis method.

Methods:

The Cornea Image Analysis Reading Center (CIARC) determined ECD with a single experienced analyst on EB-obtained central endothelial images from donors intended for keratoplasty from 2 eye banks, Eversight and Lions VisionGift, using the Konan center analysis method. The EBs performed ECD determination on their respective sets of images using the same analysis method with experienced eye bank technicians.

Results:

The mean age of the 200 donors was 54 years (range 30–75 years). Seventy (35%) of the 200 patients were women, and 57 (29%) were diabetic. The mean ECD was 10 cells/mm2 greater by the EBs than by CIARC (P = 0.39), with 95% limits of agreement of [−304 to 323 cells/mm2]. The mean difference was not substantially changed when the difference between EBs and CIARC ECD was adjusted for sex, donor age, donor diabetes, CV, HEX, number of cells analyzed, and EBs as a random effect (estimated mean difference of 20 cells/mm2 after adjustment in a linear mixed model; P = 0.73). The EB-determined preoperative ECD was within 10% of the CIARC-determined ECD for 178 (89%) image sets, with 15 (8%) higher by >10% and 7 (3%) lower by >10%.

Conclusions:

Well-trained eye bank technicians achieve comparable results for ECD determination with an experienced image analyst from an image analysis reading center when the same image analysis method is used.
Mortality Rates of Severe Dengue Viral Infection Before and After Implementation of a Revised Guideline for Severe Dengue
Authors: Laoprasopwattana Kamolwish , Khantee Puttichart , Saelim Kantara , Geater Alan
Published: November 2021

Objectives:

To compare the mortality rate of severe dengue (SD) before and after implementation of a revised SD guideline.

Methods:

Medical records of SD patients <15 years of age hospitalized during 1998–2020 were reviewed. The revised SD guidelines were implemented in 2016, including intensive monitoring of vital signs and intra-abdominal pressure, the release of intra-abdominal pressure in cases of abdominal compartment syndrome (ACS) and the use of N-acetyl cysteine in cases of acute liver failure.

Results:

On initial admission, organ failure including severe bleeding, acute respiratory failure, acute kidney injury and acute liver failure was not significantly different between 78 and 23 patients treated in the pre- and postrevised guideline periods, respectively. After hospitalization, the proportions of patients who developed profound shock (68.8% vs. 41.2%), multiorgan failures (60.4% vs. 73.3%), ACS (37.2% vs. 26.1%) and fatal outcome (33.3% vs. 13.0%) were also not significantly different between the pre- and postrevised guideline periods, respectively. In subgroup analysis, the mortality rates in patients with multiorgan failure (44.1% vs. 15.8%), acute respiratory failure and active bleeding (78.1% vs. 37.5%) and ACS (82.8% vs. 33.3%), respectively, were significantly higher in the pre- than the postrevised guideline periods. The durations of time before the liver function tests returned to normal levels, and the mortality rates in acute liver failure patients treated with and without N-acetyl cysteine were not significantly different.

Conclusions:

Although following the revised guidelines could not prevent organ failure, the mortality rates in patients with multiorgan failure and/or ACS decreased significantly when following the revised guidelines.
Experience of African American Surrogate Decision Makers of Patients With Dementia
Authors: Hart Alysha S. , Matthews Alicia K. , Arslanian-Engoren Cynthia , Patil Crystal L. , Krassa Teresa J. , Bonner Gloria J.
Published: November 2021

Dementia cases are expected to grow for African Americans and surrogate decision makers (SDMs) will have a significant role at the end of life (EOL). This qualitative exploratory case study used Cognitive Task Analysis and an integrated conceptual framework to understand the EOL decision experience of African American SDMs for patients with advanced dementia. Using a holistic multiple-case design, 8 African American SDMs were interviewed about their experiences with the decision-making process, including role acceptance, role enactment, and emotional outcomes of decision making. Thirteen themes germane to understanding the EOL decision experience of African American SDMs were identified. Findings suggest African American SDMs often lack sufficient knowledge of disease prognosis and intervention options to make informed treatment choices at EOL. In particular, African Americans extend the caregiver role to SDM for patients with dementia at EOL without being fully aware of the role and decision-making responsibilities. Surrogates lacked a general understanding of EOL options resulting in underutilization of hospice and palliative care and subsequent regret, and few interventions exist to improve the uptake of EOL care services. There is a need to develop culturally appropriate role preparation, education, and decision support to improve EOL treatment decisions and emotional adjustment of surrogates of patients with advanced dementia, which should be rendered early and throughout the illness trajectory.
A Standardization Protocol for the In Situ Detection of SARS-CoV2 RNA and Proteins
Authors: Nuovo Gerard J. , Suster David , Tili Esmerina , Awad Hamdy , Magro Cynthia
Published: November 2021

This manuscript details a stringent protocol for the in situ detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) RNA and 4 different viral proteins: envelope, spike, membrane, and nucleocapsid. Key aspects of the protocol are: (1) analysis of adjacent (serial) sections for viral RNA and at least 2 viral proteins; (2) cytologic alterations in the cells scored as virus positive based on an hematoxylin and eosin stain; (3) in situ demonstration of a host response in the cells scored as virus positive; (4) co-labeling experiments that show that the viral RNA and/or proteins co-localize with each other and the angiotensin converting enzyme 2 (ACE2) receptor; and (5) lack of signal in equivalent tissues obtained before the pandemic. Optimization conditions for the four viral proteins as well as the ACE2 receptor were each antigen retrieval in an EDTA solution which facilitates co-expression analyses. It is recommended not to use either electron microscopy or qRTPCR as methods to corroborate in situ SARS-CoV2 detection. This stringent protocol, that relies on sequentially labeled serial sections and can be completed in one working day, demonstrated the following: (1) infectious SARS-CoV2 is abundant in the lung in fatal coronavirus disease-2019 and is seen primarily in macrophages and endothelial cells; (2) circulating viral capsid proteins (spike, envelope, membrane without RNA) are evident in multiple organs including the skin and brain where it is endocytosed by ACE2+ cells and induce an endothelialitis; (3) both the infectious virus and circulating spike protein induce complement activation and cytologic changes in the viral positive cells.
Calculated functional joint center positions are highly variable in individuals with unilateral transtibial amputation walking with identical prosthetic ankle-foot devices
Authors: De Asha Alan R. , Barnett Cleveland T.
Published: November 2021

Background:

Biomechanical modeling of the lower limbs, including prosthetic componentry, makes a number of assumptions that influence the data obtained and their subsequent interpretation. Calculated prosthetic ankle functional joint center (FJC) positions vary between devices and have been suggested as a possible method of comparing device function.

Objectives:

The study aimed to assess the variability of joint center position estimates, calculated using an FJC methodology, in all three planes. This was assessed in participants with unilateral transtibial amputation using an identical prosthetic ankle-foot device during walking on a flat surface.

Study design:

Case series.

Technique:

Three-dimensional motion capture recorded the position of markers placed on the shank and ankle-foot device of five individuals with unilateral transtibial amputation, as they completed 10 trials of level walking using the same ankle-foot device. The FJC between the prosthetic foot and shank segments were calculated for each trial.

Results:

The calculated FJC positions were highly variable across individual participants and within each individual. This variability was observed across all three planes of movement and resulted in calculated joint center positions created beyond the physical boundaries of the prosthetic device.

Conclusions:

Biomechanical data are affected by lower limb and prosthetic device modeling assumptions. Definition of a prosthetic “ankle” joint using an FJC method results in highly variable “ankle” joint center positions when applied to a prosthetic ankle-foot device. Their use should be discouraged to avoid misleading interpretations of data.
Rectal chlamydia infections: implications for reinfection risk, screening, and treatment guidelines
Authors: Lau Andrew , Hocking Jane S. , Kong Fabian Y.S.
Published: November 2021

Purpose of review

Rectal chlamydia is a prevalent sexually transmissible infection in both men who have sex with men (MSM) and in women. Screening is recommended for MSM but remains controversial for women. The optimal treatment for rectal chlamydia is now conclusive but interpreting and managing positive results remains challenging. Infections among MSM are increasing and strategies are needed to reduce incident infections. This review summarizes recent developments for the screening and management of rectal chlamydia and its implications on reinfection.

Recent findings

Reinfections in MSM may be occurring due to resumption of sex soon after treatment whereas repeat infections in women may occur due to autoinoculation in the absence of sex. Doxycycline is now first-line treatment but its role in chemoprophylaxis remains unclear. False positive results remain an issue, but the development of viability assays may prove useful in future to determine true infections.

Doxycycline is the first-line treatment for rectal chlamydia and in women may prevent infections at the urogenital site. Viability assays can help to reduce antibiotic use once developed. The role of routine screening of rectal chlamydia in women remains unclear and this debate may soon include asymptomatic infections in MSM.
Error reduction in trauma care: Lessons from an anonymized, national, multicenter mortality reporting system
Authors: Hamad Doulia M. , Mandell Samuel P. , Stewart Ronald M. , Patel Bhavin , Guttman Matthew P. , Williams Phillip , Thomas Arielle , Jerath Angela , Bulger Eileen M. , Nathens Avery B.
Published: November 2021

BACKGROUND

Twenty years ago, the landmark report To Err Is Human illustrated the importance of system-level solutions, in contrast to person-level interventions, to assure patient safety. Nevertheless, rates of preventable deaths, particularly in trauma care, have not materially changed. The American College of Surgeons Trauma Quality Improvement Program developed a voluntary Mortality Reporting System to better understand the underlying causes of preventable trauma deaths and the strategies used by centers to prevent future deaths. The objective of this work is to describe the factors contributing to potentially preventable deaths after injury and to evaluate the effectiveness of strategies identified by trauma centers to mitigate future harm, as reported in the Mortality Reporting System.

METHODS

An anonymous structured web-based reporting template based on the Joint Commission on Accreditation of Healthcare Organizations taxonomy was made available to trauma centers participating in the Trauma Quality Improvement Program to allow for reporting of deaths that were potentially preventable. Contributing factors leading to death were evaluated. The effectiveness of mitigating strategies was assessed using a validated framework and mapped to tiers of effectiveness ranging from person-focused to system-oriented interventions.

RESULTS

Over a 2-year period, 395 deaths were reviewed. Of the mortalities, 33.7% were unanticipated. Errors pertained to management (50.9%), clinical performance (54.7%), and communication (56.2%). Human failures were cited in 61% of cases. Person-focused strategies like education were common (56.0%), while more effective system-based strategies were seldom used. In 7.3% of cases, centers could not identify a specific strategy to prevent future harm.

CONCLUSION

Most strategies to reduce errors in trauma centers focus on changing the performance of providers rather than system-level interventions such as automation, standardization, and fail-safe approaches. Centers require additional support to develop more effective mitigations that will prevent recurrent errors and patient harm.

LEVEL OF EVIDENCE

Therapeutic/Care Management, level V.
Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria
Authors: Weisberg Alexandra J. , Miller Marilyn , Ream Walt , Grünwald Niklaus J. , Chang Jeff H.
Published: November 2021

Members of the agrobacteria–rhizobia complex (ARC) have multiple and diverse plasmids. The extent to which these plasmids are shared and the consequences of their interactions are not well understood. We extracted over 4000 plasmid sequences from 1251 genome sequences and constructed a network to reveal interactions that have shaped the evolutionary histories of oncogenic virulence plasmids. One newly discovered type of oncogenic plasmid is a mosaic with three incomplete, but complementary and partially redundant virulence loci. Some types of oncogenic plasmids recombined with accessory plasmids or acquired large regions not known to be associated with pathogenicity. We also identified two classes of partial virulence plasmids. One class is potentially capable of transforming plants, but not inciting disease symptoms. Another class is inferred to be incomplete and non-functional but can be found as coresidents of the same strain and together are predicted to confer pathogenicity. The modularity and capacity for some plasmids to be transmitted broadly allow them to diversify, convergently evolve adaptive plasmids and shape the evolution of genomes across much of the ARC.

This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
Hidden diversity of double-stranded DNA phages in symbiotic
Rhizobium
species
Authors: Santamaría Rosa I. , Bustos Patricia , Van Cauwenberghe Jannick , González Víctor
Published: November 2021

In this study, we addressed the extent of diversification of phages associated with nitrogen-fixing symbiotic
Rhizobium
species. Despite the ecological and economic importance of the
Rhizobium
genus, little is known about the diversity of the associated phages. A thorough assessment of viral diversity requires investigating both lytic phages and prophages harboured in diverse
Rhizobium
genomes. Protein-sharing networks identified 56 viral clusters (VCs) among a set of 425 isolated phages and predicted prophages. The VCs formed by phages had more proteins in common and a higher degree of synteny, and they group together in clades in the associated phylogenetic tree. By contrast, the VCs of prophages showed significant genetic variation and gene loss, with selective pressure on the remaining genes. Some VCs were found in various
Rhizobium
species and geographical locations, suggesting that they have wide host ranges. Our results indicate that the VCs represent distinct taxonomic units, probably representing taxa equivalent to genera or even species. The finding of previously undescribed phage taxa indicates the need for further exploration of the diversity of phages associated with
Rhizobium
species.

This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
Experimental evolution of the megaplasmid pMPPla107 in
Pseudomonas stutzeri
enables identification of genes contributing to sensitivity to an inhibitory agent
Authors: Smith Brian A. , Dougherty Kevin , Clark Meara , Baltrus David A.
Published: November 2021

Horizontally transferred elements, such as plasmids, can burden host cells with various metabolic and fitness costs and may lead to other potentially detrimental phenotypic effects. Acquisition of the
Pseudomonas syringae
megaplasmid pMPPla107 by various Pseudomonads causes sensitivity to a growth-inhibiting substance that is produced in cultures by Pseudomonads during growth under standard laboratory conditions. After approximately 500 generations of laboratory passage of
Pseudomonas stutzeri
populations containing pMPPla107, strains from two out of six independent passage lines displayed resistance to this inhibitory agent. Resistance was transferable and is, therefore, associated with mutations occurring on pMPPla107. Resequencing experiments demonstrated that resistance is likely due to a large deletion on the megaplasmid in one line, and to a nonsynonymous change in an uncharacterized megaplasmid locus in the other strain. We further used allele exchange experiments to confirm that resistance is due to this single amino acid change in a previously uncharacterized megaplasmid protein, which we name SkaA. These results provide further evidence that costs and phenotypic changes associated with horizontal gene transfer can be compensated through single mutational events and emphasize the power of experimental evolution and resequencing to better understand the genetic basis of evolved phenotypes.

This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
Asymmetric and adaptive reward coding via normalized reinforcement learning
Authors: Louie Kenway
Published: November 2021

Learning is widely modeled in psychology, neuroscience, and computer science by prediction error-guided reinforcement learning (RL) algorithms. While standard RL assumes linear reward functions, reward-related neural activity is a saturating, nonlinear function of reward; however, the computational and behavioral implications of nonlinear RL are unknown. Here, we show that nonlinear RL incorporating the canonical divisive normalization computation introduces an intrinsic and tunable asymmetry in prediction error coding. At the behavioral level, this asymmetry explains empirical variability in risk preferences typically attributed to asymmetric learning rates. At the neural level, diversity in asymmetries provides a computational mechanism for recently proposed theories of distributional RL, allowing the brain to learn the full probability distribution of future rewards. This behavioral and computational flexibility argues for an incorporation of biologically valid value functions in computational models of learning and decision-making.
Increasing Animal Cognition Research in Zoos
Authors: Garcia-Pelegrin Elias , Clark Fay E. , Miller Rachael
Published: November 2021

Animal cognition covers various mental processes including perception, learning, decision-making and memory, and animal behavior is often used as a proxy for measuring cognition. Animal cognition/behavior research has multiple benefits; it provides fundamental knowledge on animal biology and evolution but can also have applied conservation and welfare applications. Zoos provide an excellent yet relatively untapped resource for animal cognition research, because they house a wide variety of species - many of which are under threat - and allow close observation and relatively high experimental control compared to the wild. Multi-zoo collaboration leads to increased sample size and species representation, which in turn leads to more robust science. However, there are salient challenges associated with zoo-based cognitive research, which are subject-based (e.g., small sample sizes at single zoos, untrained/unhabituated subjects, site effects) and human-based (e.g., time restrictions, safety concerns, and perceptions of animals interacting with unnatural technology or apparatus). We aim to increase the understanding and subsequent uptake of animal cognition research in zoos, by transparently outlining the main benefits and challenges. Importantly, we use our own research (1) a study on novelty responses in hornbills, and (2) a multi-site collaboration called the ‘ManyBirds’ project to demonstrate how challenges may be overcome. These potential options include using ‘drop and go’ apparatuses that require no training, close human contact or animal separation. This article is aimed at zoo animal care and research staff, as well as external researchers interested in zoo-based studies.

RESEARCH HIGHLIGHTS

Zoos are an excellent yet relatively untapped resource for animal cognition research.

Zoo cognition research has historically been challenging, and traditional laboratory paradigms often do not translate well to the majority of zoos.

Salient challenges of zoo-based cognitive research can be overcome by using less restrictive test apparatuses, limiting animal training and isolation, and subscribing to multi-zoo collaborative programs.
Partial lockdown on unvaccinated individuals promises breaking of fourth COVID-19 wave in Bavaria
Authors: Krebs Tobias , Moeckel Michael J.
Published: November 2021

Purpose of this report

The aim of this rapid communication is a projection of the development of the fourth COVID-19 wave in the federal state of Bavaria in Germany, taking into account different lockdown scenarios especially for unvaccinated individuals. In particular, the number of infections and the occupancy of intensive care facilities are considered.

Applied Methods

We use the agent-based epidemiological simulator Covasim for discussing various epidemiological scenarios. Firstly, we adapt and calibrate our model to reproduce the historical course of the COVID-19 pandemic in Bavaria. For this, we model and integrate numerous public health interventions imposed on the local population. As for some of the political actions rigorous quantification is currently not available, we fit those unknown (free) model parameters to published data on the measured epidemiological dynamics. Finally, we define and analyse scenarios of different lockdown scenarios with restrictions for unvaccinated individuals in different areas of life.

Key message

The results of our simulations show that in all scenarios considered, the number of infections, but also the number of severe cases, exceed previous maximum values. Interventions, especially restrictions on contacts of unvaccinated persons, can still mitigate the impact of the fourth COVID-19 wave on populations substantially. Excluding unvaccinated students from attending classes has only a small impact on the public health burden. However, many severe cases can be prevented by reducing community and/or work related contacts of unvaccinated people, e.g, by achieving high home office rates.
A conserved long intergenic non-coding RNA containing snoRNA sequences, lncCOBRA1, affects Arabidopsis germination and development
Authors: Kramer Marianne C. , Kim Hee Jong , Palos Kyle R. , Garcia Benjamin A. , Lyons Eric , Beilstein Mark A. , Nelson Andrew D.L. , Gregory Brian D.
Published: November 2021

Long non-coding RNAs (lncRNAs) are an increasingly studied group of non-protein-coding transcripts with a wide variety of molecular functions gaining attention for their roles in numerous biological processes. Nearly 6,000 lncRNAs have been identified in Arabidopsis thaliana but many have yet to be studied. Here, we examine a class of previously uncharacterized lncRNAs termed CONSERVED INBRASSICA RAPA (lncCOBRA) transcripts that were previously identified for their high level of sequence conservation in the related crop species Brassica rapa, their nuclear-localization and protein-bound nature. In particular, we focus on lncCOBRA1 and demonstrate that its abundance is highly tissue and developmental specific, with particularly high levels early in germination. lncCOBRA1 contains two snoRNAs domains within it, making it the first sno-lincRNA example in a non-mammalian system, though we find that it is processed differently than its mammalian counterparts. We further show that plants lacking lncCOBRA1 display patterns of delayed gemination and are overall smaller than wild-type plants. Lastly, we identify the proteins that interact with lncCOBRA1 and examine the protein-protein interaction network of lncCOBRA1-interacting proteins.
Intrathecal sc-AAV9-CB-GFP: Systemic Distribution Predominates Following Single-Dose Administration in Cynomolgus Macaques
Authors: Meseck Emily K. , Guibinga Ghiabe , Wang Stephen , McElroy Cameron , Hudry Eloise , Mansfield Keith
Published: November 2021

Biodistribution of self-complementary adeno-associated virus-9 (scAAV9)–chicken β promoter–green fluorescent protein (GFP) was assessed in juvenile cynomolgus macaques infused intrathecally via lumbar puncture or the intracisterna magna (1.0×1013 or 3.0×1013 vg/animal), with necropsy 28 days later. Our results characterized central nervous system biodistribution compared with systemic organs/tissues by droplet digital polymerase chain reaction for DNA and in situ hybridization. GFP expression was characterized by Meso Scale Discovery electrochemiluminescence immunosorbent assay and immunohistochemistry (IHC). Biodistribution was widespread but variable, with vector DNA and GFP expression greatest in the spinal cord, dorsal root ganglia (DRG), and certain systemic tissues (e.g., liver), with low concentrations in many brain regions despite direct cerebrospinal fluid administration. Transduction and expression were observed primarily in perivascular astrocytes in the brain, with a paucity in neurons. Greater GFP expression was observed in hepatocytes, striated myocytes, cardiomyocytes, spinal cord lower motor neurons, and DRG sensory neurons by IHC. These results suggest caution for use of scAAV9-based intrathecal delivery with the current expression cassette as a modality for neurologic diseases that require widespread brain neuronal expression. This capsid/expression cassette combination may be better suited for diseases that express a secreted protein and/or do not require widespread brain neuronal transduction.
Convergent evolution of “genome guardian” functions in a parasite-specific p53 homolog
Authors: Wendt George , Shiroor Divya A. , Adler Carolyn E. , Collins James J.
Published: November 2021

Significance

P53 is a widely studied tumor suppressor that is found throughout metazoans, including invertebrates that do not develop malignancies. The prevailing theory for why this is the case is that P53 originally evolved to protect the germline of early metazoans from genotoxic stress such as UV radiation. In this study, we examine the function of two P53 homologs in the parasitic flatworm Schistosoma mansoni. The first is orthologous to canonical P53, and regulates stem cell maintenance and differentiation. The second P53 gene is a parasite-specific paralog that is required for the normal response to genotoxic stress. This implies that the ability to respond to genotoxic stress in parasitic flatworms may have arisen from convergent evolution.
Deep proteome profiling with reduced carry over using superficially porous microfabricated nanoLC columns
Authors: Stejskal Karel , de Beeck Jeff Op , Matzinger Manuel , Dürnberger Gerhard , Boychenko Alexander , Jacobs Paul , Mechtler Karl
Published: November 2021

In the field of LC-MS based proteomics, increases in sampling depth and proteome coverage have mainly been accomplished by rapid advances in mass spectrometer technology. The comprehensiveness and quality of data that can be generated do however also depend on the performance provided by nano liquid chromatography (nanoLC) separations. Proper selection of reversed-phase separation columns can be important to provide the MS instrument with peptides at the highest possible concentration and separated at the highest possible resolution. In the current contribution, we evaluate the use of prototype generation 2 μPAC nanoLC columns which use C18 functionalized superficially porous micro pillars as a stationary phase. When comparing to traditionally used fully porous silica stationary phases, more precursors could be characterized when performing single shot data-dependent LC-MS/MS analyses of a human cell line tryptic digest. Up to 30% more protein groups and 60% more unique peptides were identified for short gradients (10 min) and limited sample amounts (10-100 ng of cell lysate digest). With LC-MS gradient times of 10, 60, 120 and 180 min, we respectively identified 2252, 6513, 7382 and 8174 protein groups with 25, 500, 1000 and 2000 ng of sample loaded on column. Reduction of sample carry over to the next run (up to 2 to 3%) and decreased levels of methionine oxidation (up to 3-fold) were identified as additional figures of merit. When analyzing a disuccinimidyl dibutyric urea (DSBU) crosslinked synthetic library, 29 to 59 more unique crosslinked peptides could be identified at a experimentally validated false discovery rate (FDR) of 1-2%.
Less is worse than none: ineffective adaptive foraging can destabilise food webs
Authors: Ho Hsi-Cheng , Pawar Samraat , Tylianakis Jason M.
Published: November 2021

Consumers can potentially adjust their diet in response to changing resource abundances, thereby achieving better foraging payoffs. Although previous work has explored how such adaptive foraging scales up to determine the structure and dynamics of food webs, consumers may not be able to perform perfect diet adjustment due to sensory or cognitive limitations. Whether the effectiveness of consumers’ diet adjustment alters food-web consequences remains unclear.

Here, we study how adaptive foraging, specifically the effectiveness (i.e. rate) with which consumers adjust their diet, influences the structure, dynamics, and overall species persistence in synthetic food webs.

We model metabolically-constrained optimal foraging as the mechanistic basis of adaptive diet adjustment and ensuing population dynamics within food webs. We compare food-web dynamical outcomes among simulations sharing initial states but differing in the effectiveness of diet adjustment.

We show that adaptive diet adjustment generally makes food-web structure resilient to species loss. Effective diet adjustment that maintains optimal foraging in the face of changing resource abundances facilitates species persistence in the community, particularly reducing the extinction of top consumers. However, a greater proportion of intermediate consumers goes extinct as optimal foraging becomes less-effective and, unexpectedly, slow diet adjustment leads to higher extinction rates than no diet adjustment at all. Therefore, food-web responses cannot be predicted from species’ responses in isolation, as even less-effective adaptive foraging benefits individual species (better than non-adaptive) but can harm species’ persistence in the food web as a whole (worse than non-adaptive).

Whether adaptive foraging helps or harms species coexistence has been contradictory in literature Our finding that it can stabilise or destabilise the food web depending on how effectively it is performed help reconcile this conflict. Inspired by our simulations, we deduce that there may exist a positive association between consumers’ body size and adaptive-foraging effectiveness in the real world. We also infer that such effectiveness may be higher when consumers cognise complete information about their resources, or when trophic interactions are driven more by general traits than by specific trait-matching. We thereby suggest testable hypotheses on species persistence and food-web structure for future research, in both theoretical and empirical systems.
DUAL FUNCTION OF ZIKA VIRUS NS2B-NS3 PROTEASE
Authors: Shiryaev Sergey A. , Cieplak Piotr , Cheltsov Anton , Liddington Robert C. , Terskikh Alexey V.
Published: November 2021

Zika virus (ZIKV) serine protease, indispensable for viral polyprotein processing and replication, is composed of the membrane-anchored NS2B polypeptide and the N-terminal domain of the NS3 polypeptide (NS3pro). The C-terminal domain of the NS3 polypeptide (NS3hel) is necessary for helicase activity and contains an ATP-binding site. We discovered that ZIKV NS2B-NS3pro can bind single-stranded RNA with a Kdof ∼0.3 μM, suggesting a novel function. We tested various structural modifications of NS2B-NS3pro and observed that constructs stabilized in the recently discovered “super-open” conformation do not bind RNA. Likewise, stabilization of NS2B-NS3pro in the “closed” (proteolytically active) conformation using substrate inhibitors abolished RNA binding. We posit that RNA binding occurs when ZIKV NS2B-NS3pro adopts the “open” conformation, which we modeled using highly homologous dengue NS2B-NS3pro crystallized in the open conformation. We identified two positively charged fork-like structures present only in the open conformation of NS3pro. These forks are conserved acrossFlaviviridaefamily and could be aligned contiguously with the positively charged grove on NS3hel that binds RNA. This led us to propose the “reverse inchworm” model for a tightly intertwined NS2B-NS3 helicase-protease machinery, which suggests that the cycles of NS2B-NS3pro binding and releasing RNA enable the unlimited processivity of NS3hel. The transition to the closed conformation, likely induced by the substrate, enables the classical protease activity of NS2B-NS3pro.
Importance of Molecular Dynamics Equilibrium Protocol on Protein-lipid Interactions near Channel Pore
Authors: Jiang Wenjuan , Lacroix Jerome , Luo Yun Lyna
Published: November 2021

Multiscale molecular dynamics (MD) simulations using Martini coarse-grained (CG) and all-atom (AA) forcer fields are commonly used in membrane protein studies. In particular, reverse-mapping an equilibrated CG model to an AA model offers an efficient way for preparing large membrane protein systems with complex protein shapes and lipid compositions. Here, we report that this hybrid CG-equilibrium-AA-production protocol may artificially increase lipid density and decrease hydration in ion channel pores walled with transmembrane gaps. To understand the origin of this conundrum, we conducted replicas of CG, AA, and reverse-mapped AA simulations of the pore domain of the mechanosensitive Piezo1 channel in a non-conducting conformation. Lipid/water density analysis and free energy calculations reveal that the lack of initial pore hydration allows adjacent lipids to enter the pore lumen through gaps between pore helices during CG simulation. Due to the mismatch between CG and AA lipid kinetics, these pore lipids remain trapped in the subsequent AA simulations, despite unfavorable binding free energy. We tested several CG equilibrium protocols and found that a protocol restraining the whole lipid produces pore hydration consistent with AA results, thus eliminating this artifact for further studies of lipid gating and protein-lipid interactions.

WHY IT MATTERS

Membrane-embedded proteins constantly interact with lipid molecules. Computational molecular dynamics simulations have become an indispensable tool for investigating the role of such protein-lipid interactions. Using mechanosensitive Piezo1 channel as model, we found that subtle differences in solvation and equilibrium protocols between coarse-grained and all-atom MD simulations can result in different lipid densities inside the channel pore. We identify the underlying cause of this discrepancy and propose alternative protocols to avoid this artifact.
Incretin hypersecretion in gestational diabetes mellitus
Authors: Fritsche Louise , Heni Martin , Eckstein Sabine S. , Hummel Julia , Schuermann Annette , Haering Hans-Ulrich , Preissl Hubert , Birkenfeld Andreas L. , Peter Andreas , Fritsche Andreas , Wagner Robert
Published: November 2021

Background
Incretins are crucial stimulators of insulin secretion after food intake. We investigated the incretin response during an oral glucose tolerance test in pregnant women with and without gestational diabetes.
Methods
Subjects underwent a 5-point OGTT with 75 g glucose. We assessed insulin secretion and levels of total GLP-1, GIP, glicentin and glucagon during the OGTT.
Findings
We examined 167 women (33 with GDM) during gestational week 26.95 (2.15 SD). Insulin secretion was significantly lower in women with GDM (p<0.001). Postprandial GLP-1 and GIP were ~20% higher in women with GDM (all p<0.05) independent from age, BMI and gestational age. GLP-1 increase associated with insulin secretion only in GDM, but not in NGT. Postprandial GLP-1 levels associated negatively with birth weight.
Interpretation
The more pronounced GLP-1 increase in women with GDM could be part of a compensatory mechanism counteracting GLP-1 resistance. Higher GLP-1 levels might be protective against fetal overgrowth.
Asgard ESCRT-III and VPS4 reveal evolutionary conserved chromatin binding properties of the ESCRT machinery
Authors: Nachmias Dikla , Melnikov Nataly , Zorea Alvah , De-picchoto Yasmin , Zarivach Raz , Mizrahi Itzhak , Elia Natalie
Published: November 2021

The ESCRT machinery drive membrane remodeling in numerous processes in eukaryotes. Genes encoding for ESCRT proteins have been identified in Asgard archaea, a newly discovered superphylum, currently recognized as the ancestor of all eukaryotes. This begs the question of the functional evolutionary origin of this machinery and its conservation across lineages. Here, we find that Asgard-ESCRT’s exhibit conserved DNA-binding properties, which is derived from recruitment of specific members. We show that Asgard-ESCRT-III/VPS4 homologs interact with one another inside mammalian cells, associate with chromatin, and recruit their counterparts to organize in discrete foci in the mammalian nucleus. This is congruent with human-ESCRT-III homologs. We find that human- and Asgard-ESCRT-IIIs associate with chromatin via the same N terminal domain, and that human-ESCRT-III can recruit Asgard-VPS4 to the nucleus to form foci. Therefore, ESCRTs possess chromatin binding properties that were preserved through the billion years of evolution that separate Asgard and human cells.