bluuebunny/crossref_metadata_2025 huggingface dataset:
Fenestrated Scleral Lenses: Back to the Origins? Review of Their Benefits and Fitting Techniques
Authors: Fadel Daddi , Ezekiel Donald F.
Published: September 2020

SIGNIFICANCE

This review illustrates the history of fenestrated scleral lenses, reporting personal communication from one of the present authors; describes their peculiarities and disadvantages; explains the fitting methods so far used; and recommends future fitting methods.

Indications and benefits of scleral lenses are widely described in the literature. The introduction of more advanced gas-permeable materials allowed scleral lenses to spread and be available to patients worldwide. Despite the improvement of the gas-permeable scleral lens' clinical performance, complications associated with corneal hypoxia persist, especially in patients with corneal endothelial abnormalities. Fenestrated scleral lenses may solve different complications caused by hypoxia. Also, fenestrated scleral lenses may be beneficial for several issues such as handling difficulties, midday fogging, lens suction, lens instability, conjunctival compression, and alteration of IOP. There is a need and a benefit to directly comparing fenestrated scleral lenses to sealed gas-permeable scleral lenses. This topical review allows practitioners to understand the fenestration philosophy in scleral lenses, practice better, and obtain information on their indications and fitting process. Industry and patients will benefit from future advances in scleral lens designs.
Quantifying the Optical and Physical Consequences of Daily Cleaning on Conventional and Wavefront-guided Scleral Lenses
Authors: Wilting Sarah M. , Hastings Gareth D. , Nguyen Lan Chi , Kauffman Matthew J. , Bell Elizabeth S. , Hu Chuan , Rijal Sujata , Marsack Jason D.
Published: September 2020

SIGNIFICANCE

An equivalent 12 months of cleaning did not induce significant changes in the optical aberrations or base curves of scleral lenses.

PURPOSE

This study aimed to test whether an equivalent of 12 months of manual cleaning alters the optical and physical properties of conventional and wavefront-guided scleral lenses.

METHODS

Twelve scleral lenses (four repeats of three designs, termed A, B, and C) were manufactured in Boston XO material: design A, −5.00 D defocus; design B, −5.00 D defocus with −0.153-μm vertical coma; and design C, −5.00 D defocus with a full custom wavefront-guided correction (second to fifth Zernike radial orders) of an eye with severe keratoconus. One lens of each design group served as a control and was not cleaned. To simulate a year of cleaning, seven individuals cleaned nine lenses (three from each group) twice a day for 27 days using the palm technique and commercially available cleaners, resulting in 378 cleanings of each lens. Lens aberrations were optically profiled and base curve radii were measured at baseline and after every 42nd cleaning. Differences in higher-order root mean square (HORMS) wavefront error and base curve radii associated with cleaning were compared with clinical benchmarks and using sign tests.

RESULTS

For the experimental lenses, median change in Seidel spherical dioptric power was +0.01 D (maximum, +0.025 D). Median change in HORMS wavefront error was 0.013 μm (maximum, 0.019 μm). All lenses exhibited HORMS changes less than one-eighth equivalent diopters (P = .002). Median percentage change in HORMS wavefront error in the three wavefront-guided lenses was 0.96% (maximum, 1.25%). Median change in base curve radii was 0.00 mm, with all lenses exhibiting changes (P = .002), less than the American National Standards Institute tolerance of 0.05 mm.

CONCLUSIONS

Cleaning over an equivalent 12-month period did not induce clinically significant changes in the optical or base curve properties of conventional or wavefront-guided scleral lenses.
Corneoscleral Topography Measured with Fourier-based Profilometry and Scheimpflug Imaging
Authors: Bandlitz Stefan , Esper Patrick , Stein Magdalena , Dautzenberg Torsten , Wolffsohn James S.
Published: September 2020

SIGNIFICANCE

Precise measurement of corneoscleral topography makes a valuable contribution to the understanding of anterior eye anatomy and supports the fitting process of contact lenses. Sagittal height data, determined by newer noninvasive techniques, are particularly useful for initial scleral lens selection.

PURPOSE

The purpose of this study was to investigate the agreement and repeatability of Fourier-based profilometry and Scheimpflug imaging, in the measurement of sagittal height and toricity of the corneoscleral region.

METHODS

Minimal (Minsag), maximal (Maxsag) sagittal height, toricity (Maxsag − Minsag), and the maximum possible measurement zone diameter of 38 subjects were compared using the Eye Surface Profiler (ESP; Eagle Eye, Houten, the Netherlands) and the corneoscleral profile module of the Pentacam (Oculus, Wetzlar, Germany) at two different sessions. Correlations between the instruments were analyzed using the Pearson coefficient. Differences between sessions and instruments were analyzed using Bland-Altman and paired t tests.

RESULTS

For an equal chord length, the measurement with Pentacam was significantly greater for Minsag (344 μm; 95% confidence interval [CI], 322 to 364 μm; P < .001) and significantly greater for Maxsag (280 μm; 95% CI, 256 to 305 μm; P < .001), but significantly smaller for toricity (−63 μm; 95% CI, −95 to −31 μm; P < .001). Maximum possible measurement zone diameter with ESP (16.4 ± 1.3 mm) was significantly greater than with Pentacam (14.8 ± 1.1 mm) (P < .001). Repeated measurements from session 1 and session 2 were not significantly different for Pentacam and ESP (P = .74 and P = .64, respectively). The 95% CIs around differences indicate good repeatability for Pentacam (mean difference, −0.9 μm; 95% CI, −6.7 to 4.8 μm) and ESP (4.6 μm; −22.4 to 31.6).

CONCLUSIONS

Although both instruments deliver useful data especially for the fitting of scleral and soft contact lenses, the sagittal height and the toricity measurements cannot be considered as interchangeable.
Targeting Metabolic Pathways in Kidney Cancer
Authors: Hoerner Christian R. , Miao Susanna Y. , Hsieh James J. , Fan Alice C.
Published: September 2020

Alterations in cellular sugar, amino acid and nucleic acid, and lipid metabolism, as well as in mitochondrial function, are a hallmark of renal cell carcinoma (RCC). The activation of oncogenes such as hypoxia-inducible factor and loss of the von Hippel-Lindau function and other tumor suppressors frequently occur early on during tumorigenesis and are the drivers for these changes, collectively known as “metabolic reprogramming,” which promotes cellular growth, proliferation, and stress resilience. However, tumor cells can become addicted to reprogrammed metabolism. Here, we review the current knowledge of metabolic addictions in clear cell RCC, the most common form of RCC, and to what extent this has created therapeutic opportunities to interfere with such altered metabolic pathways to selectively target tumor cells. We highlight preclinical and emerging clinical data on novel therapeutics targeting metabolic traits in clear cell RCC to provide a comprehensive overview on current strategies to exploit metabolic reprogramming clinically.
Immune Related Adverse Events
Authors: Zengin Zeynep B. , Salgia Nicholas J. , Chehrazi-Raffle Alexander , Meza Luis , Malhotra Jasnoor , Pal Sumanta K.
Published: September 2020

Recent therapeutic advancements have incorporated immune checkpoint inhibitors (ICIs) into the management of metastatic renal cell carcinoma. Pivotal phase III trials have resulted in Food and Drug Administration approval for anti–programmed death 1/programmed death ligand 1 ICIs, either in combination with anti–cytotoxic T-lymphocyte antigen 4 ICIs or with vascular endothelial growth factor–directed targeted therapies, as standard-of-care frontline regimens. Immune checkpoint inhibitors offer improved clinical outcomes when compared to previous treatment options. However, these agents also present unique toxicity profiles collectively referred to as immune-related adverse events. Common immune-related adverse events include colitis, hepatitis, dermatitis, and thyroiditis. Rare toxicities, such as myocarditis and pneumonitis, have the potential for causing severe harm. Herein, we provide a case-based discussion of how to identify, grade, and manage irAEs in metastatic renal cell carcinoma.
Smartphone-based Assessment of Preoperative Decision Conflict and Postoperative Physical Activity Among Patients Undergoing Cancer Surgery
Authors: Panda Nikhil , Solsky Ian , Cauley Christy E. , Lipsitz Stuart , Desai Eesha V. , Huang Emily J. , Benjamin Evan M. , Lubitz Carrie C. , Onnela Jukka-Pekka , Haynes Alex B.
Published: September 2020

Objective:

To determine the prevalence of clinically significant decision conflict (CSDC) among patients undergoing cancer surgery and associations with postoperative physical activity, as measured through smartphone accelerometer data.

Background:

Patients with cancer face challenging treatment decisions, which may lead to CSDC. CSDC negatively affects patient-provider relationships, psychosocial functioning, and health-related quality of life; however, physical manifestations of CSDC remain poorly characterized.

Methods:

Adult smartphone-owners undergoing surgery for breast, skin-soft-tissue, head-and-neck, or abdominal cancer (July 2017–2019) were approached. Patients downloaded the Beiwe application that delivered the Decision Conflict Scale (DCS) preoperatively and collected smartphone accelerometer data continuously from enrollment through 6 months postop-eratively. Restricted-cubic-spline regression, adjusting for a priori potential confounders (age, type of surgery, support status, and postoperative complications) was used to determine trends in postoperative daily physical activity among patients with and without CSDC (DCS score >25/100).

Results:

Among 99 patients who downloaded the application, 85 completed the DCS (86% participation rate). Twenty-three (27%) reported CSDC. These patients were younger (mean age 48.3 years [standard deviation 14.2]-vs–55.0 [13.3], P = 0.047) and more frequently lived alone (22%-vs–6%, P = 0.042). There were no differences in preoperative physical activity (115.4 minutes [95%CI 90.9, 139.9]-vs–110.8 [95%CI 95.7, 126.0], P = 0.753). Adjusted postoperative physical activity was lower among patients reporting CSDC at 30 days (difference 33.1 minutes [95%CI 5.93,60.2], P = 0.017), 60 days 35.5 [95%CI 8.50, 62.5], P = 0.010 and 90 days 31.8 [95%CI 5.44, 58.1], P = 0.018 postoperatively.

Conclusions:

CSDC was prevalent among patients who underwent cancer surgery and associated with lower postoperatively daily physical activity. These data highlight the importance of addressing modifiable decisional needs of patients through enhanced shared decision-making.
Alternative Strategies for Evaluating General Surgery Residency Applicants and an Interview Limit for MATCH 2021
Authors: Rajesh Aashish , Asaad Malke
Published: September 2020

The COVID-19 pandemic has posed unique challenges for evaluating general surgery residency applicants to MATCH 2021. In the absence of away rotations, programs are likely to afford greater importance to objective data to stratify the applicant pool and medical students are likely to experience difficulty in thoroughly assessing each program. Virtual rotations, meet-and-greet events conducted before the application submission deadline, personality testing before extending interviews, standardized letters of recommendation, and skills testing can serve as valuable adjuncts for determining the best applicant-program fit. Finally, an interview limit which sets the bar for the maximum number of accepted interviews per applicant per specialty can offer a level playing field in the absence of time and cost limitations associated with travel.
Genetic impact of ZNF804A on cognitive function in patients with bipolar I disorder
Authors: Shi Bo , Zhang Chengcheng , Zhao Junxiong , Tang Wei , Lu Weihong , Zhang Chen
Published: September 2020

Our previous genetic study identified a variant rs1344706 in the zinc finger protein 804A (ZNF804A) gene conferring susceptibility to bipolar disorder subtype I (BD-I) in Han Chinese. Literature documented that this variant may affect brain structure and function. As such, we attempted to identify whether the rs1344706 polymorphism influences cognitive function in patients with bipolar disorder I. We recruited 177 patients with bipolar disorder in remission period. Cognitive function was evaluated using the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). The single nucleotide polymorphisms (SNP) rs1344706 was genotyped using TaqMan assays. Analysis of covariance (ANCOVA) analysis showed a significant genotypic effect on RBANS immediate memory (P = 0.002) and total score (P = 0.001). Post hoc analysis showed that the patients with T/T genotype have lower RBANS immediate memory and total scores than those with T/G or G/G genotypes. When the patients were stratified by sex, such significances are only seen in male patients, but not female patients. Our findings suggested a sex-specific effect of ZNF804A rs1344706 polymorphism on cognitive function in patients with bipolar disorder-I.
Unraveling the Developmental Dynamic of Visual Exploration of Social Interactions in Autism
Authors: Kojovic Nada , Cekic Sezen , Castañón Santiago Herce , Franchini Martina , Sperdin Holger Franz , Sandini Corrado , Jan Reem Kais , Zöller Daniela , Ben Hadid Lylia , Bavelier Daphné , Schaer Marie
Published: September 2020

Atypical deployment of social gaze is present early on in toddlers with autism spectrum disorders (ASDs). Yet, studies characterizing the developmental dynamic behind it are scarce. Here we used a data-driven method to delineate the developmental change in visual exploration of social interaction over childhood years in autism. Longitudinal eye-tracking data were acquired as children with ASD and their typically developing (TD) peers freely explored a short cartoon movie. We found divergent moment-to-moment gaze patterns in children with ASD compared to their TD peers. This divergence was particularly evident in sequences that displayed social interactions between characters and even more so in children with lower developmental and functional levels. The basic visual properties of the animated scene did not account for the enhanced divergence. Over childhood years, these differences dramatically increased to become more idiosyncratic. These findings suggest that social attention should be targeted early in clinical treatments.
Targeted Proteomics Reveals Quantitative Differences in Low Abundance Glycosyltransferases of Patients with Congenital Disorders of Glycosylation
Authors: Sakson Roman , Beedgen Lars , Bernhard Patrick , Alp Keziban M. , Lübbehusen Nicole , Röth Ralph , Niesler Beate , Mayer Matthias P. , Thiel Christian , Ruppert Thomas
Published: September 2020

Protein glycosylation is essential in all domains of life and its mutational impairment in humans can result in severe diseases named Congenital Disorders of Glycosylation (CDGs). Studies on molecular level are however challenging, because many glycosyltransferases in the endoplasmic reticulum (ER) are low abundance membrane proteins. We established a comprehensive multiple reaction monitoring (MRM) assay to quantify most human glycosyltransferases involved in the processes ofN-glycosylation,O- andC-mannosylation in the ER. To increase reproducibility, a membrane protein fraction of isotopically labeled HEK 293T cells was used as an internal standard. With this internal standard the MRM assay is easily transferable between laboratories. 22 glycosyltransferases could be reliably quantified from whole cell lysates of HEK 293T cells, HeLa cells and skin fibroblast cell lines. We then analyzed fibroblasts derived from CDG type I patients with mutations in theALG1,ALG2orALG11gene. Mutations inALG1orALG2gene strongly reduced the levels of the ALG1 and ALG2 protein, respectively. In contrast, the levels of all other glycosyltransferases remained unchanged, which was unexpected given evidence that the ALG1, ALG2 and ALG11 proteins form a stable complex. This study describes an efficient workflow for the development of MRM assays for low abundance proteins, establishes a ready-to-use tool for the comprehensive quantification of ER-localized glycosyltransferases and provides new insight into the organization of disease-relevant glycosylation processes.
Distinctive properties of cones in the retinal clock and the circadian system
Authors: Sandu Cristina , Wongchitrat Prapimpun , Mazzaro Nadia , Jaeger Catherine , Calligaro Hugo , Mendoza Jorge , Hicks David , Felder-Schmittbuhl Marie-Paule
Published: September 2020

The circadian system is a hierarchical network of cell and tissue-specific oscillators synchronized to the environmental light/dark cycle. Entrainment is mediated by the retina through diverse photosensitive cells and pigments. The retina is itself a complex circadian system whose cellular constitutive elements have not been fully characterized. By using theNrl-/-cone gain-of-function mouse model we here show that the retinal network comprises an autonomous oscillator harbored in cones. We further provide novel evidence for an input from cones to the master clock, as revealed under constant light condition.
Conductance-Based Structural Brain Connectivity in Aging and Dementia
Authors: Frau-Pascual Aina , Augustinak Jean , Varadarajan Divya , Yendiki Anastasia , Salat David H. , Fischl Bruce , Aganj Iman ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: September 2020

Background

Structural brain connectivity has been shown to be sensitive to the changes that the brain undergoes during Alzheimer’s disease (AD) progression.

Methods

In this work, we used our recently proposed structural connectivity quantification measure derived from diffusion MRI, which accounts for both direct and indirect pathways, to quantify brain connectivity in dementia. We analyzed data from the ADNI-2 and OASIS-3 datasets to derive relevant information for the study of the changes that the brain undergoes in AD. We also compared these datasets to the HCP dataset, as a reference, and eventually validated externally on two cohorts of the EDSD database.

Results

Our analysis shows expected trends of mean conductance with respect to age and cognitive scores, significant age prediction values in aging data, and regional effects centered among sub-cortical regions, and cingulate and temporal cortices.

Discussion

Results indicate that the conductance measure has prediction potential, especially for age, that age and cognitive scores largely overlap, and that this measure could be used to study effects such as anti-correlation in structural connections.

Impact statement

This work presents a methodology and a set of analyses that open new possibilities in the study of healthy and pathological aging. The methodology used here is sensitive to direct and indirect pathways in deriving brain connectivity measures from dMRI, and therefore provides information that many state-of-the-art methods do not account for. As a result, this technique may provide the research community with ways to detect subtle effects of healthy aging and AD.
Contemporary risk of extinction in an extreme environment
Authors: Vincenzi Simone
Published: September 2020

The increased frequency and intensity of extreme events are recognized among the most worrisome aspects of climate change. However, despite increased attention from scientists and conservationists, developing and testing general theories and hypotheses on the effects of extreme events on natural populations remains intrinsically challenging.

Using numerical simulations with general—but realistic for moderately fast-leaving species—parameter values, I tested some of the hypotheses on risk of extinction and population and genetic dynamics in an environment in which both climate (e.g., temperature, rainfall) and point (e.g., fires, floods) extremes occur. In the simulations, a quantitative trait is selected for by a climate variable, but point extremes cause trait-independent massive mortalities.

I found additive effects between age at first reproduction and fecundity on risk of extinction. The extent of population bottlenecks (operationally, the number of years in which a population was at low numbers) was a good predictor of allelic richness for the quantitative trait selected for by the climate. Simple models including basic demographic and vital rates information of the species, along with climate/environmental measures, provided excellent predictions of contemporary risk of population extinction. Mean and minimum population size measured in a 10-year “observation window” were largely the most important predictors of risk of population extinction in the following 10-year “prediction window”.
Evaluations of CRC2631 toxicity, tumor colonization, and genetic stability in the TRAMP prostate cancer model
Authors: Kazmierczak Robert A. , Dhagat-Mehta Bakul , Gulden Elke , Lee Li , Ma Lixin , Davis-Stober Clintin P. , Barnett Austen A. , Chabu Yves C.
Published: September 2020

Conventional cancer chemotherapies are not fully efficacious and do not target tumors, leading to significant treatment-related morbidities. A number of genetically attenuated cancer-targeting bacteria are being developed to safely target tumorsin vivo. Here we report the toxicological, tumor-targeting, and efficacy profiles ofSalmonella entericaserovar Typhimurium CRC2631 in a syngeneic and autochthonous TRAMP model of aggressive prostate cancer. CRC2631 preferentially colonize primary and metastatic tumors in the TRAMP animals. In addition, longitudinal whole genome sequencing studies of CRC2631 recovered from prostate tumor tissues demonstrate that CRC2631 is genetically stable. Moreover, tumor-targeted CRC2631 generates an anti-tumor immune response. Combination of CRC2631 with checkpoint blockade reduces metastasis burden. Collectively, these findings demonstrate a potential for CRC2631 in cancer immunotherapy strategies.
Phase Separation Can Increase Enzyme Activity by Concentration and Molecular Organization
Authors: Peeples William , Rosen Michael K.
Published: September 2020

Biomolecular condensates concentrate macromolecules into discrete cellular foci without an encapsulating membrane. Condensates are often presumed to increase enzymatic reaction rates through increased concentrations of enzymes and substrates (mass action), although this idea has not been widely tested and other mechanisms of modulation are possible. Here we describe a synthetic system where the SUMOylation enzyme cascade is recruited into engineered condensates generated by liquid-liquid phase separation of multidomain scaffolding proteins. SUMOylation rates can be increased up to 36-fold in these droplets compared to the surrounding bulk, depending on substrate KM. This dependency produces substantial specificity among different substrates. Analyses of reactions above and below the phase separation threshold lead to a quantitative model in which reactions in condensates are accelerated by mass action and by changes in substrate KM, likely due to scaffold-induced molecular organization. Thus, condensates can modulate reaction rates both by concentrating molecules and by physically organizing them.
Bromelain Inhibits SARS-CoV-2 Infection in VeroE6 Cells
Authors: Sagar Satish , Rathinavel Ashok Kumar , Lutz William E. , Struble Lucas R. , Khurana Surender , Schnaubelt Andy T , Mishra Nitish Kumar , Guda Chittibabu , Broadhurst Mara J. , Reid St. Patrick M. , Bayles Kenneth W. , Borgstahl Gloria E. O. , Radhakrishnan Prakash
Published: September 2020

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The initial interaction between Transmembrane Serine Protease 2 (TMPRSS2) primed SARS-CoV-2 spike (S) protein and host cell receptor angiotensin-converting enzyme 2 (ACE-2) is a pre-requisite step for this novel coronavirus pathogenesis. Here, we expressed a GFP-tagged SARS-CoV-2 S-Ectodomain in Tni insect cells. That contained sialic acid-enriched N- and O-glycans. Surface resonance plasmon (SPR) and Luminex assay showed that the purified S-Ectodomain binding to human ACE-2 and immunoreactivity with COVID-19 positive samples. We demonstrate that bromelain (isolated from pineapple stem and used as a dietary supplement) treatment diminishes the expression of ACE-2 and TMPRSS2 in VeroE6 cells and dramatically lowers the expression of S-Ectodomain. Importantly, bromelain treatment reduced the interaction between S-Ectodomain and VeroE6 cells. Most importantly, bromelain treatment significantly diminished the SARS-CoV-2 infection in VeroE6 cells. Altogether, our results suggest that bromelain or bromelain rich pineapple stem may be used as an antiviral against COVID-19.

Highlights

Bromelain inhibits / cleaves the expression of ACE-2 and TMPRSS2

Bromelain cleaves / degrades SARS-CoV-2 spike protein

Bromelain inhibits S-Ectodomain binding and SARS-CoV-2 infection
Shared and distinct genetic influences between cognitive domains and psychiatric disorder risk based on genome-wide data
Authors: Carey CE , Huang Y , Strong RW ,   23andMe Research Team, Aslibekyan S , Gentleman RC , Smoller JW , Wilmer JB , Robinson EB , Germine L
Published: September 2020

Group-level cognitive performance differences are found in psychiatric disorders ranging from depression to autism to schizophrenia. To investigate the genetics of individual differences in fluid and crystallized cognitive abilities and their associations with psychiatric disorder risk, we conducted genome-wide association studies (GWAS) of a total of 335,227 consented 23andMe customers of European descent between the ages of 50 and 85, who completed at least one online test of crystallized cognitive ability (vocabulary knowledge, N=188,434) and/or fluid cognitive ability (visual change detection, N=158 888; digit-symbol substitution, N=132,807). All cognitive measures were significantly heritable (h2=0.10-0.16), and GWAS identified 25 novel genome-wide significant loci. Genetic correlation analyses highlight variable profiles of genetic relationships across tasks and disorders. While schizophrenia had moderate negative genetic correlations with tests of fluid cognition (visual change detectionrg=−0.27, p<9.2e-24; digit-symbol substitutionrg=−0.26, p<5.2e-27), it was only weakly negatively associated with crystalized cognition (vocabulary knowledgerg=−0.07, p<0.004). Autism, in contrast, showed a robust positive genetic correlation with vocabulary knowledge (rg=0.30, p<5.6e-13) and little to no genetic correlation with either fluid cognition task (rg’s<0.08, p’s>0.005). Crystalized and fluid cognitive abilities thus have correlated but distinct genetic architectures that relate to those of psychiatric disorders. Understanding the genetic underpinnings of specific cognitive abilities, and their relationships to psychiatric disorder risk, can inform the understanding of disease biology nosology and etiology.
Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors
Authors: Staritzbichler René , Sarti Edoardo , Yaklich Emily , Aleksandrova Antoniya , Stamm Markus , Khafizov Kamil , Forrest Lucy R
Published: September 2020

The alignment of primary sequences is a fundamental step in the analysis of protein structure, function, and evolution. Integral membrane proteins pose a significant challenge for such sequence alignment approaches, because their evolutionary relationships can be very remote, and because a high content of hydrophobic amino acids reduces their complexity. Frequently, biochemical or biophysical data is available that informs the optimum alignment, for example, indicating specific positions that share common functional or structural roles. Currently, if those positions are not correctly aligned by a standard pairwise alignment procedure, the incorporation of such information into the alignment is typically addressed in an ad hoc manner, with manual adjustments. However, such modifications are problematic because they reduce the robustness and reproducibility of the alignment. An alternative approach is the use of restraints, or anchors, to incorporate such position-matching explicitly during alignment. Here we introduce position anchoring in the alignment tool AlignMe as an aid to pairwise sequence alignment of membrane proteins. Applying this approach to realistic scenarios involving distantly-related and low complexity sequences, we illustrate how the addition of even a single anchor can dramatically improve the accuracy of the alignments, while maintaining the reproducibility and rigor of the overall alignment.
SeqRepo: A system for managing local collections biological sequences
Authors: Hart Reece K. , Prlić Andreas
Published: September 2020

Motivation

Access to biological sequence data, such as genome, transcript, or protein sequence, is at the core of many bioinformatics analysis workflows. The National Center for Biotechnology Information (NCBI), Ensembl, and other sequence database maintainers provide methods to access sequences through network connections. For many users, the convenience and currency of remotely managed data are compelling, and the network latency is non-consequential. However, for high-throughput and clinical applications, local sequence collections are essential for performance, stability, privacy, and reproducibility.

Results

Here we describe SeqRepo, a novel system for building a local, high-performance, non-redundant collection of biological sequences. SeqRepo enables clients to use primary database identifiers and several digests to identify sequences and sequence alises. SeqRepo provides a native Python interface and a REST interface, which can run locally and enables access from other programming languages. SeqRepo also provides an alternative REST interface based on the GA4GH refget protocol.

SeqRepo provides fast random access to sequence slices. We provide results that demonstrate that a local SeqRepo sequence collection yields significant performance benefits of up to 1300-fold over remote sequence collections. In our use case for a variant validation and normalization pipeline, SeqRepo improved throughput 50-fold relative to use with remote sequences. SeqRepo may be used with any species or sequence type. Regular snapshots of Human sequence collections are available.

It is often convenient or necessary to use a computed digest as a sequence identifier. For example, a digest-based identifier may be used to refer to proprietary reference genomes or segments of a graph genome, for which conventional identifiers will not be available. Here we also introduce a convention for the application of the SHA-512 hashing algorithm with Base64 encoding to generate URL-safe identifiers. This convention,sha512t24u, combines a fast digest mechanism with a space-efficient representation that can be used for any object. Our report includes an analysis of timing and collision probabilities forsha512t24u. SeqRepo enables clients to use sha512t24u as identifiers, thereby seamlessly integrating public and private sequence sets.

Availability

SeqRepo is released under the Apache License 2.0 and is available on github and PyPi. Docker images and database snapshots are also available. Seehttps://github.com/biocommons/biocommons.seqrepo.
AlphaImpute2: Fast and accurate pedigree and population based imputation for hundreds of thousands of individuals in livestock populations
Authors: Whalen Andrew , Hickey John M
Published: September 2020

In this paper we present a new imputation algorithm, AlphaImpute2, which performs fast and accurate pedigree and population based imputation for livestock populations of hundreds of thousands of individuals. Genetic imputation is a tool used in genetics to decrease the cost of genotyping a population, by genotyping a small number of individuals at high-density and the remaining individuals at low-density. Shared haplotype segments between the high-density and low-density individuals can then be used to fill in the missing genotypes of the low-density individuals. As the size of genetics datasets have grown, the computational cost of performing imputation has increased, particularly in agricultural breeding programs where there might be hundreds of thousands of genotyped individuals. To address this issue, we present a new imputation algorithm, AlphaImpute2, which performs population imputation by using a particle based approximation to the Li and Stephens which exploits the Positional Burrows Wheeler Transform, and performs pedigree imputation using an approximate version of multi-locus iterative peeling. We tested AlphaImpute2 on four simulated datasets designed to mimic the pedigrees found in a real pig breeding program. We compared AlphaImpute2 to AlphaImpute, AlphaPeel, findhap version 4, and Beagle 5.1. We found that AlphaImpute2 had the highest accuracy, with an accuracy of 0.993 for low-density individuals on the pedigree with 107,000 individuals, compared to an accuracy of 0.942 for Beagle 5.1, 0.940 for AlphaImpute, and 0.801 for findhap. AlphaImpute2 was also the fastest software tested, with a runtime of 105 minutes a pedigree of 107,000 individuals and 5,000 markers was 105 minutes, compared to 190 minutes for Beagle 5.1, 395 minutes for findhap, and 7,859 minutes AlphaImpute. We believe that AlphaImpute2 will enable fast and accurate large scale imputation for agricultural populations as they scale to hundreds of thousands or millions of genotyped individuals.
Transcriptome analysis of EPO and GFP HEK293 Cell-lines Reveal Shifts in Energy and ER Capacity Support Improved Erythropoietin Production in HEK293F Cells
Authors: Saghaleyni Rasool , Malm Magdalena , Zrimec Jan , Razavi Ronia , Wistbacka Num , Chotteau Veronique , Hatton Diane , Grassi Luigi , Zelezniak Aleksej , Svensson Thomas , Nielsen Jens , Robinson Jonathan L. , Rockberg Johan
Published: September 2020

Higher eukaryotic cell lines like HEK293 are the preferred hosts for production of therapeutic proteins requiring human post translational processing. However, recombinant protein production can result in severe stress on the cellular machinery, resulting in limited titre and product quality. To investigate the cellular and metabolic characteristics associated with these limitations, we compared erythropoietin (secretory) and GFP (non-secretory) protein producer HEK293 cell-lines using transcriptomics analysis. Despite the high demand for ATP in all protein producer clones, a significantly higher capacity for ATP production was observed with erythropoietin producers as evidenced by the enrichment of upregulated genes in the oxidative phosphorylation pathway. In addition, ribosomal genes exhibited specific patterns of expression depending on the recombinant protein and the production rate. In a clone displaying a dramatically increased erythropoietin secretion, we detected higher ER stress, including upregulation of the ATF6B gene. Our results are significant in recognizing key pathways for recombinant protein production and identifying potential target genes for further development of secretory power in mammalian cell factories.

In Brief

Although the protein secretion process has been widely studied, the complexity of it leaves many questions with regards to defining bottlenecks for successful protein secretion to be answered. By investigating the transcriptomic profiles of different HEK293 clones with varying translational rates producing either the secreted protein erythropoietin or the intracellular GFP, we reveal that high ATP production and improved capacity of specific post-translational pathways are key factors associated with boosting erythropoietin production.

Highlights

Transcriptomics analysis of a panel of HEK293 stable cell lines expressing GFP or erythropoietin (EPO) at varying translational rates

Expression of mitochondrial ribosomal genes is positively correlated with EPO secretion

Expression of different cytosolic ribosomal genes are correlated with productivity in a recombinant-protein specific manner

High EPO producing clones have significant upregulation of ATF6B, potentially enabling a beneficial ER stress response to cope with high protein secretion

Graphical Abstract
Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques
Authors: Hoang Timothy N. , Pino Maria , Boddapati Arun K. , Viox Elise G. , Starke Carly E. , Upadhyay Amit A. , Gumber Sanjeev , Busman-Sahay Kathleen , Strongin Zachary , Harper Justin L. , Tharp Gregory K. , Pellegrini Kathryn L. , Kirejczyk Shannon , Zandi Keivan , Tao Sijia , Horton Tristan R. , Beagle Elizabeth N. , Mahar Ernestine A. , Lee Michelle YH , Cohen Joyce , Jean Sherrie M. , Wood Jennifer S. , Connor-Stroud Fawn , Stammen Rachelle L. , Delmas Olivia M. , Wang Shelly , Cooney Kimberly A. , Sayegh Michael N. , Wang Lanfang , Weiskopf Daniela , Filev Peter D. , Waggoner Jesse , Piantadosi Anne , Kasturi Sudhir P. , Shakhshir Hilmi Al- , Ribeiro Susan P. , Sekaly Rafick P. , Levit Rebecca D. , Estes Jacob D. , Vanderford Thomas H. , Schinazi Raymond F. , Bosinger Steven E. , Paiardini Mirko
Published: September 2020

Effective therapeutics aimed at mitigating COVID-19 symptoms are urgently needed. SARS-CoV-2 induced hypercytokinemia and systemic inflammation are associated with disease severity. Baricitinib, a clinically approved JAK1/2 inhibitor with potent anti-inflammatory properties is currently being investigated in COVID-19 human clinical trials. Recent reports suggest that baricitinib may also have antiviral activity in limiting viral endocytosis. Here, we investigated the immunologic and virologic efficacy of baricitinib in a rhesus macaque model of SARS-CoV-2 infection. Viral shedding measured from nasal and throat swabs, bronchoalveolar lavages and tissues was not reduced with baricitinib. Type I IFN antiviral responses and SARS-CoV-2 specific T cell responses remained similar between the two groups. Importantly, however, animals treated with baricitinib showed reduced immune activation, decreased infiltration of neutrophils into the lung, reduced NETosis activity, and more limited lung pathology. Moreover, baricitinib treated animals had a rapid and remarkably potent suppression of alveolar macrophage derived production of cytokines and chemokines responsible for inflammation and neutrophil recruitment. These data support a beneficial role for, and elucidate the immunological mechanisms underlying, the use of baricitinib as a frontline treatment for severe inflammation induced by SARS-CoV-2 infection.
The flexibility of ACE2 in the context of SARS-CoV-2 infection
Authors: Barros E. P. , Casalino L. , Gaieb Z. , Dommer A. C. , Wang Y. , Fallon L. , Raguette L. , Belfon K. , Simmerling C. , Amaro R. E.
Published: September 2020

The COVID-19 pandemic has swept over the world in the past months, causing significant loss of life and consequences to human health. Although numerous drug and vaccine developments efforts are underway, many questions remain outstanding on the mechanism of SARS-CoV-2 viral association to angiotensin-converting enzyme 2 (ACE2), its main host receptor, and entry in the cell. Structural and biophysical studies indicate some degree of flexibility in the viral extracellular Spike glycoprotein and at the receptor binding domain-receptor interface, suggesting a role in infection. Here, we perform all-atom molecular dynamics simulations of the glycosylated, full-length membrane-bound ACE2 receptor, in both an apo and spike receptor binding domain (RBD) bound state, in order to probe the intrinsic dynamics of the ACE2 receptor in the context of the cell surface. A large degree of fluctuation in the full length structure is observed, indicating hinge bending motions at the linker region connecting the head to the transmembrane helix, while still not disrupting the ACE2 homodimer or ACE2-RBD interfaces. This flexibility translates into an ensemble of ACE2 homodimer conformations that could sterically accommodate binding of the spike trimer to more than one ACE2 homodimer, and suggests a mechanical contribution of the host receptor towards the large spike conformational changes required for cell fusion. This work presents further structural and functional insights into the role of ACE2 in viral infection that can be exploited for the rational design of effective SARS-CoV-2 therapeutics.

Statement of Significance

As the host receptor of SARS-CoV-2, ACE2 has been the subject of extensive structural and antibody design efforts in aims to curtail COVID-19 spread. Here, we perform molecular dynamics simulations of the homodimer ACE2 full-length structure to study the dynamics of this protein in the context of the cellular membrane. The simulations evidence exceptional plasticity in the protein structure due to flexible hinge motions in the head-transmembrane domain linker region and helix mobility in the membrane, resulting in a varied ensemble of conformations distinct from the experimental structures. Our findings suggest a dynamical contribution of ACE2 to the spike glycoprotein shedding required for infection, and contribute to the question of stoichiometry of the Spike-ACE2 complex.
Inhibition ofStreptococcus pneumoniaeautolysins highlight distinct differences between chemical and genetic inactivation
Authors: Haubrich Brad A , Nayyab Saman , Williams Caroline , Whitman Andrew , Zimmerman Tahl , Li Qiong , Chen Yuxing , Zhou Cong-Zhao , Basu Amit , Reid Christopher W
Published: September 2020

Despite renewed interest, development of chemical biology methods to study peptidoglycan metabolism has lagged in comparison to the glycobiology field in general. To address this, a panel of diamides were screened against the Gram-positive pathogenStreptococcus pneumoniaeto identify inhibitors of bacterial growth. The screen identified the diamidefgkcas a narrow spectrum bacteriostatic inhibitor ofS. pneumoniaegrowth with an MIC of 7.8 μM. The diamide inhibited detergent-induced autolysis in a concentration dependent manner indicating peptidoglycan degradation as the mode-of-action. Genetic screening of autolysin mutants suggested LytB, an endo-N-acetylglucosaminidase, involved in cell division as the potential target. Surprisingly, biochemical, and phenotypic analysis contradicted the genetic screen results. Phenotypic studies with theΔlytbstrain illustrate the difference between genetic and chemical inactivation of autolysins. These findings suggest that meta-phenotypes including autolytic activity, cell morphology, and genetic screening can be the result of the complex interaction of one or more possible pathways that are connected to cell wall metabolism.
The Wnt effector TCF7l2 promotes oligodendroglial differentiation by repressing autocrine BMP4-mediated signaling
Authors: Zhang Sheng , Wang Yan , Zhu Xiaoqing , Song Lanying , Zhan Xinhua , Ma Edric , McDonough Jennifer , Fu Hui , Cambi Franca , Grinspan Judith , Guo Fuzheng
Published: September 2020

Promoting oligodendrocyte differentiation represents a promising option for remyelination therapy for treating the demyelinating disease multiple sclerosis (MS). The Wnt effector TCF7l2 was upregulated in MS lesions and had been proposed to inhibit oligodendrocyte differentiation. Recent data suggest the opposite yet underlying mechanisms remain elusive. Here we unravel a previously unappreciated function of TCF7l2 in controlling autocrine bone morphogenetic protein (BMP4)-mediated signaling. Disrupting TCF7l2 results in oligodendroglial-specific BMP4 upregulation and canonical BMP4 signaling activationin vivo. Mechanistically, TCF7l2 binds toBmp4gene regulatory element and directly represses its transcriptional activity. Functionally, enforced TCF7l2 expression promotes oligodendrocyte differentiation by reducing autocrine BMP4 secretion and dampening BMP4 signaling. Importantly, compound genetic disruption demonstrates that oligodendroglial-specific BMP4 deletion rescues arrested oligodendrocyte differentiation elicited by TCF7l2 disruptionin vivo. Collectively, our study reveals a novel connection between TCF7l2 and BMP4 in oligodendroglial lineage and provides new insights into augmenting TCF7l2 for promoting remyelination in demyelinating disorders such as MS.

Significance Statement

Incomplete or failed myelin repairs, primarily resulting from the arrested differentiation of myelin-forming oligodendrocytes from oligodendroglial progenitor cells, is one of the major reasons for neurological progression in people affected by multiple sclerosis (MS). Usingin vitroculture systems andin vivoanimal models, this study unraveled a previously unrecognized autocrine regulation of BMP4-mediated signaling by the Wnt effector TCF7l2. We showed for the first time that TCF7l2 promotes oligodendroglial differentiation by repressing BMP4-mediated activity, which is dysregulated in MS lesions. Our study suggests that elevating TCF7l2 expression may be possible in overcoming arrested oligodendroglial differentiation as observed in MS patients.
Development of a structure-analysis pipeline using multiple-solvent crystal structures of barrier-to-autointegration factor
Authors: Agarwal Sorabh , Smith Mychal , De La Rosa Indhira , Verba Kliment A. , Swartz Paul , Segura-Totten Miriam , Mattos Carla
Published: September 2020

The multiple-solvent crystal structure (MSCS) approach uses high concentrations of organic solvents to characterize the interactions and effects of solvents on proteins. Here, the method has been further developed and an MSCS data-handling pipeline is presented that uses the Detection of Related Solvent Positions (DRoP) program to improve data quality. DRoP is used to selectively model conserved water molecules, so that an advanced stage of structural refinement is reached quickly. This allows the placement of organic molecules more accurately and convergence on high-quality maps and structures. This pipeline was applied to the chromatin-associated protein barrier-to-autointegration factor (BAF), resulting in structural models with better than average statistics. DRoP and Phenix Structure Comparison were used to characterize the data sets and to identify a binding site that overlaps with the interaction site of BAF with emerin. The conserved water-mediated networks identified by DRoP suggested a mechanism by which water molecules are used to drive the binding of DNA. Normalized and differential B-factor analysis is shown to be a valuable tool to characterize the effects of specific solvents on defined regions of BAF. Specific solvents are identified that cause stabilization of functionally important regions of the protein. This work presents tools and a standardized approach for the analysis and comprehension of MSCS data sets.