bluuebunny/crossref_metadata_2025 huggingface dataset:
Bilateral sudden sensorineural hearing loss with Sweet syndrome
Authors: You Yeon Seok , Park Sang Woo , Yun Seok Kweon , Lee Eun Jung
Published: September 2020

Introduction:

Sweet syndrome (SS) is an idiopathic autoimmune disease which has been associated with various extracutaneous manifestations. Otologic symptoms secondary to SS are characterized by bilateral, progressive, sensorineural hearing loss, which requires auditory rehabilitation with, for example, cochlear implantation.

Patient concerns:

A 43-year-old woman complaining of bilateral sudden hearing loss visited the Emergency Department of our University. Abrupt onset of fever peaking up to 40°C and vomiting accompanied the hearing loss and other associated symptoms were: tinnitus that sounded like a machine humming, mild dizziness, a painful rash (on the right upper eyelid, chest, back, forearms, and lower extremities), arthralgia in both the hip and knee joints, and vision loss in the right eye. The patient had no history of autoimmune diseases or surgery.

Diagnosis:

Pure tone audiometry and biopsy on the skin lesion were performed. SS with bilateral sudden sensorineural hearing loss was confirmed.

Interventions:

The patient was treated with intravenous prednisolone and topical steroids.

Outcomes:

After a week of treatment, skin lesions had improved. And 3 months after treatment, the hearing test showed full recovery.

Conclusion:

This case emphasizes the point that early diagnosis and timely treatment are essential for hearing recovery in patients with SS who have otologic symptoms.
Synergistic therapeutic actions of antimicrobial peptides to treat multidrug-resistant bacterial infection
Authors: Pervin Zinia , Hassan Md Mehadi
Published: September 2020

Growing antibiotic resistance has been reported as a great health problem throughout the world. The threat of multidrug resistance is significantly exacerbated in biofilm-associated infection as most of the antimicrobials are rarely effective against biofilm and its virulence factors. Consequently, there is a strong demand for developing novel approaches and new materials to treat biofilm-associated bacterial infection. Engineering technology introduces nanoparticle-mediated drug delivery to reduce treatment failure and increase the synergistic effects of the drugs. Cationic antimicrobial peptides (CAMPs) are usually attracted to negatively charged bacterial phospholipid membrane and kill the microbial pathogens by disintegrating their cell membrane with the subsequent collapse of infective pathogenesis. Previous studies have already provided evidence of the success of AMPs to treat the biofilm-associated multidrug-resistant bacterial infection. Although, there are some challenges to use AMPs in clinical practice such as proteolytic degradation, cytotoxicity, instability, low membrane permeability which diminishes the effects of AMPs as a wide spectral antibacterial agent. To enhance the highest therapeutic capacity of AMPs, research should need to be performed on designing a combination strategy to triumph over the difficulties of AMPs in the clinical application. The purpose of this review is to investigate the synergistic relationship of AMPs with a different type of antimicrobial agent including a nanocarrier drug delivery system to accomplish the clinical practice against drug-resistant bacterial infection.
Leclercia adecarboxylata: a rare cause of traumatic wound infections in immunocompetent patients: case reports and review of the literature
Authors: Tilouche Lamia , Ben Dhia Refka , Karaborni Sonia , Chaouch Cherifa , Ketata Soumaya , Bouallegue Olfa , Boujaafar Noureddine
Published: September 2020

Leclercia adecarboxylata is a motile Gram-negative bacilli and a member of the Enterobacteriaceae family. It has been described as an emerging pathogen mostly isolated from immunocompromised patients. We report here, two cases of L. adecarboxylata trauma-related wound infections in two previously healthy patients and give a review of previous reports on wound infections encountered in immunocompetent patient. Both strains were sensitive to most tested antibiotics.
Construction of a recombinant Lactobacillus casei expressing fliC gene fused with guanylyl cyclase C and dendritic cell-binding peptide using CRISPR–Cas9 system: a first step towards design of vaccine against colorectal cancer
Authors: Khosravi Azar Dokht , Teimoori Ali , Seyed-Mohammadi Sakineh
Published: September 2020

Colorectal cancer (CRC) with 1.2 million new cases and 600 000 deaths per year is the 4th leading cause of cancer and the 2nd leading cause of cancer mortality worldwide. Effort to design of safe and efficient vaccines can be a good strategy for the treatment of primary or metastatic CRC. Plasmid pLCNICK was linearized by using restriction enzymes BcuI and ApaI. Unintended fragments were removed from the plasmid and selected genes were cloned in plasmid. Electro-transformation of the two plasmids containing gRNA 1 and gRNA 2 into Lactobacillus casei was performed simultaneously in the following step. The recombinant L. casei was identified by PCR colony. For detection protein of interest was done Western blot. Amplification selected genes by PCR and then clone of fragments into two vectors were done successfully. After electroporation, growth of bacterial colonies on plates supplemented with antibiotic showed that the bacteria have received the plasmid because there was erythromycin resistance gene on plasmid. Also, the production of recombinant L. casei by CRISPR-Cas9D10A nickase-based plasmid, and designed gRNA 1 and gRNA 2 was done successfully, and was confirmed by the presence of a 1126 bp band in agarose gel electrophoresis of colony PCR. Expression of the protein was shown by Western blot. In conclusion, recombinant lactic acid bacteria strains have the capacity to express heterologous proteins. Thus in this study for the first time a recombinant L. casei using CRISPR–Cas9 system as a first step for design of a vaccine against CRC was constructed that expresses fliC gene fused with guanylyl cyclase C and dendritic cell binding peptide.
Complex Fistula Formations After Orbital Fracture Repair With Teflon
Authors: Goslin Krysta N. , Miller Nicholas J. , Nguyen Elizabeth V. , Hassan Adam S.
Published: September 2020

The authors present 3 unique cases of complex fistula formations because of orbital fracture repair with a Teflon (polytetrafluroethylene) implant. A 26-year-old man presented with dacryocystitis and a cutaneous fistula 8 years after left orbital floor and medial wall fracture repair with a Teflon implant. A 46-year-old woman suffered orbital trauma after a motor vehicle accident as a teenager and the fracture was repaired with Teflon implant. Thirty-two years later, she presented with lower eyelid fistula, ectropion, and retraction. A 65-year-old woman also previously had Teflon implants for the repair of her left inferior and lateral orbital rim after a motor vehicle accident. Twenty-five years later, she presented with chronic infections involving the repaired areas, as well as left lower lid ectropion and fistula formation. The woven material nature of Teflon acted as a nidus for infection, inflammation, and led to complex cutaneous fistula formations in these patients.
Immediate inhibition of spinal secretory phospholipase A2 prevents the pain and elevated spinal neuronal hyperexcitability and neuroimmune regulatory genes that develop with nerve root compression
Authors: Quindlen-Hotek Julia C. , Kartha Sonia , Winkelstein Beth A.
Published: September 2020

Cervical nerve root injury induces a host of inflammatory mediators in the spinal cord that initiate and maintain neuronal hyperexcitability and pain. Secretory phospholipase A2 (sPLA2) is an enzyme that has been implicated as a mediator of pain onset and maintenance in inflammation and neural injury. Although sPLA2 modulates nociception and excitatory neuronal signaling in vitro, its effects on neuronal activity and central sensitization early after painful nerve root injury are unknown. This study investigated whether inhibiting spinal sPLA2 at the time of nerve root compression (NRC) modulates the pain, dorsal horn hyperexcitability, and spinal genes involved in glutamate signaling, nociception, and inflammation that are seen early after injury. Rats underwent a painful C7 NRC injury with immediate intrathecal administration of the sPLA2 inhibitor thioetheramide-phosphorlycholine. Additional groups underwent either injury alone or sham surgery. One day after injury, behavioral sensitivity, spinal neuronal excitability, and spinal cord gene expression for glutamate receptors (mGluR5 and NR1) and transporters (GLT1 and EAAC1), the neuropeptide substance P, and pro-inflammatory cytokines (TNFα, IL1α, and IL1β) were assessed. Treatment with the sPLA2 inhibitor prevented mechanical allodynia, attenuated neuronal hyperexcitability in the spinal dorsal horn, restored the proportion of spinal neurons classified as wide dynamic range, and reduced genes for mGluR5, substance P, IL1α, and IL1β to sham levels. These findings indicate spinal regulation of central sensitization after painful neuropathy and suggest that spinal sPLA2 is implicated in those early spinal mechanisms of neuronal excitability, perhaps via glutamate signaling, neurotransmitters, or inflammatory cascades.
Electroconvulsive Therapy for Depression in Transgender Patients
Authors: Mormando Charles B. , Dalke Katharine , Mikoluk Cezary , Garman John C. , Francis Andrew
Published: September 2020

There is very limited information regarding the effectiveness of electroconvulsive therapy (ECT) as a treatment for major depressive disorder in transgender patients. This population is also at risk for comorbid conditions, such as posttraumatic stress disorder and substance use that could impact the outcome of ECT. We report our experience with the use of ECT in this population. Clinical and response characteristics of 7 consecutive cases are described in this series. All patients had multiple psychiatric diagnoses and were refractory to pharmacologic intervention. Pretreatment Beck Depression Inventory-II scores were 45.5 ± 3.2 SEM and posttreatment scores were 21.2 ± 6.4 [P < 0.01]. Suicidality scores reduced by greater than 60%, whereas remission of depression was obtained for 2 of 7, and 4 of 7 showed greater than 50% reduction in depression scores. Treatments were tolerated well using conventional treatment procedures. This case series suggests that ECT can be effective for depressed transgender patients with multiple clinical comorbidities.
Proportional Relative Hazards Model for Competing Risks Data
Authors: Shen Hanjie , Jeong Jong H. , Mell Loren K.
Published: September 2020

In this article, we propose a Proportional Relative Hazards (PRH) model to differentiate subjects according to their risk for a primary event relative to competing events. The model estimates effects on the baseline ratio of the hazard for a primary event, or set of primary events, relative to the hazard for a competing event, or set of competing events (ω+ ratio). An analogous model is presented to estimate effects on the baseline ratio of the hazard for a primary event (or set of events) relative to the hazard for all events (ω ratio). A weighted regression method is introduced, along with practical presentation of risk-stratification using the PRH model in breast and head and neck cancer data sets.
Tocilizumab in Hospitalized Patients With COVID-19 Pneumonia
Authors: Rosas Ivan O. , Bräu Norbert , Waters Michael , Go Ronaldo , Hunter Bradley D. , Bhagani Sanjay , Skiest Daniel , Aziz Mariam S. , Cooper Nichola , Douglas Ivor S. , Savic Sinisa , Youngstein Taryn , Del Sorbo Lorenzo , Gracian Antonio Cubillo , De La Zerda David J. , Ustianowski Andrew , Bao Min , Dimonaco Sophie , Graham Emily , Matharu Balpreet , Spotswood Helen , Tsai Larry , Malhotra Atul
Published: September 2020

BACKGROUND

COVID-19 is associated with immune dysregulation and hyperinflammation. Tocilizumab is an anti–interleukin-6 receptor antibody.

METHODS

Patients hospitalized with severe COVID-19 pneumonia receiving standard care were randomized (2:1) to double-blinded intravenous tocilizumab 8 mg/kg or placebo. The primary outcome measure was clinical status on a 7-category ordinal scale at day 28 (1, discharged/ready for discharge; 7, death).

RESULTS

Overall, 452 patients were randomized; the modified-intention-to-treat population included 294 tocilizumab-treated and 144 placebo-treated patients. Clinical status at day 28 was not statistically significantly improved for tocilizumab versus placebo (P=0.36). Median (95% CI) ordinal scale values at day 28: 1.0 (1.0 to 1.0) for tocilizumab and 2.0 (1.0 to 4.0) for placebo (odds ratio, 1.19 [0.81 to 1.76]). There was no difference in mortality at day 28 between tocilizumab (19.7%) and placebo (19.4%) (difference, 0.3% [95% CI, –7.6 to 8.2]; nominal P=0.94). Median time to hospital discharge was 8 days shorter with tocilizumab than placebo (20.0 and 28.0, respectively; nominal P=0.037; hazard ratio 1.35 [95% CI 1.02 to 1.79]). Median duration of ICU stay was 5.8 days shorter with tocilizumab than placebo (9.8 and 15.5, respectively; nominal P=0.045). In the safety population, serious adverse events occurred in 34.9% of 295 patients in the tocilizumab arm and 38.5% of 143 in the placebo arm.

CONCLUSIONS

In this randomized placebo-controlled trial in hospitalized COVID-19 pneumonia patients, tocilizumab did not improve clinical status or mortality. Potential benefits in time to hospital discharge and duration of ICU stay are being investigated in ongoing clinical trials.

Trial registration

ClinicalTrials.gov NCTG432G615
Seroprevalence of SARS-CoV-2 in Palestine: a cross-sectional seroepidemiological study
Authors: Qutob Nouar , Awartani Faisal , Salah Zaidoun , Asia Mohammad , Khader Imad Abu , Herzallah Khaled , Balqis Nadeen , Sallam Husam
Published: September 2020

Seroprevalence rates are important indicators to the epidemiology of COVID-19 and the extent of the pandemic given the existence of asymptomatic cases. The purpose of this study is to assess the seroprevalence rate in the Palestinian population residing in the West Bank. Blood samples were collected between 15th June 2020 and 30th June 2020 from 1355 adults from Palestinian households in the West Bank and 1136 individuals visiting laboratories between the 1st May 2020 and 9th July 2020 for a routine checkup. Serological tests for the 2491 serum samples were done using an Immunoassay for the qualitative detection of antibodies against SARS-CoV-2. The random sample of Palestinians living in the West Bank yeilded 0% seroprevalence with 95% CI [0,0.0036], while the lab referrals sample yielded an estimated seroprevalence of 0.354% with 95% CI [0.0011,0096]. Our results indicate that as of July 2020, seroprevalence in Palestine persist low and is inadequate to provide herd immunity, emphasizing the need to maintain health measures to keep the outbreak under control. Population-based seroprevalence studies are to be conducted periodically to monitor the SARS-CoV-2 seroprevalence in Palestine and inform policy makers about the efficacy of their surveillance system.
Unraveling Endothelial Cell Phenotypic Regulation By Spatial Hemodynamic Flows With Microfluidics
Authors: Varma Sarvesh , Garcia-Cardena Guillermo , Voldman Joel
Published: September 2020

Human endothelial cells (hECs) experience complex spatiotemporal hemodynamic flows and that directly regulate hEC function and susceptibility to cardiovascular disease. Recent medical imaging studies reveal that helical flows strongly correlate with lowered disease susceptibility, as contrasted to multidirectional disturbed flows. However, a lack of platforms to replicate these spatial profiles of flow (SPF) has prevented biological studies to investigate the role hECs play in tuning the observed SPF-correlated disease susceptibility. Here, we utilize microfluidic devices to apply varying SPF upon hECs for the first time, and discover that these flows can differentially impact hEC morphology, transcription, and polarization. Collectively, our platform and studies significantly advance our ability to delineate flow-regulated hEC function and disease susceptibility.

Significance Statement

In vivo, hECs experience complex hemodynamic flows, including those that are spatially helical or disturbed, which is in stark contrast to the unidirectional flows typically used to study hECsin vitro.Understanding the impact of SPF on hEC function informs our understanding of the pathophysiology of hEC dysfunction and can lead to interventional solutions that specifically perturb SPF to lower disease risk. Here, we leverage microfluidics to apply and discover the specific impact of SPF on hECs for the first time. Broadly, our platform bridges the mutual interests of the vascular biology and interventional cardiology communities to collectively understand how cardiovascular health is tied to the way blood flows upon the endothelium.
Estimating the effect of a scanner upgrade on measures of grey matter structure for longitudinal designs
Authors: Medawar Evelyn , Thieleking Ronja , Manuilova Iryna , Paerisch Maria , Villringer Arno , Witte A. Veronica , Beyer Frauke
Published: September 2020

1

Longitudinal imaging studies are crucial for advancing the understanding of brain development over the lifespan. Thus, more and more studies acquire imaging data at multiple time points or with long follow-up intervals. In these studies changes to magnetic resonance imaging (MRI) scanners often become inevitable which may decrease the reliability of the MRI assessments and introduce biases.

We therefore investigated the difference between MRI scanners with subsequent versions (3 Tesla Siemens Verio vs. Skyra fit) on the cortical and subcortical measures of grey matter in 116 healthy, young adults using the well-established longitudinal FreeSurfer stream for T1-weighted brain images. We found excellent between-scanner reliability for cortical and subcortical measures of grey matter structure (intra-class correlation coefficient > 0.8). Yet, paired t-tests revealed statistically significant differences in at least 75% of the regions, with percent differences up to 5%, depending on the outcome measure. Offline correction for gradient distortions only slightly reduced these biases. Further, T1-imaging based quality measures systematically differed between scanners.

We conclude that scanner upgrades during a longitudinal study introduce bias in measures of cortical and subcortical grey matter structure. Therefore, before upgrading a MRI scanner during an ongoing study, researchers should prepare to implement an appropriate correction method for these effects.
Representation of Color, Form, and their Conjunction across the Human Ventral Visual Pathway
Authors: Taylor JohnMark , Xu Yaoda
Published: September 2020

Despite decades of neuroscience research, our understanding of the relationship between color and form processing in the primate ventral visual pathway remains incomplete. Using fMRI multivoxel pattern analysis, this study examined the coding of color with both a simple form feature (orientation) and a mid-level form feature (curvature) in human early visual areas V1 to V4, posterior and central color regions, and shape areas in ventral and lateral occipito-temporal cortex. With the exception of the central color region (which showed color but not form decoding), successful color and form decoding was found in all other regions examined, even for color and shape regions showing univariate sensitivity to one feature. That said, all regions exhibited significant feature decoding biases, with decoding from color and shape regions largely consistent with their univariate preferences. Color and form are thus represented in neither a completely distributed nor a completely modular manner, but abiased distributedmanner. Interestingly, coding of one feature in a brain region was always tolerant to changes in the other feature, indicating relative independence of color and form coding throughout the ventral visual cortex. Although evidence for interactive coding of color and form also existed, the effect was weak and only existed for color and orientation conjunctions in early visual cortex. No evidence for interactive coding of color and curvature was found. The predominant relationship between color and form coding in the human brain appears to be one of anatomical coexistence (in a biased distributed manner), but representational independence.
Comparison of transparency and shrinkage of insect brains using novel and traditional clearing methods
Authors: Bekkouche Bo M. B. , Fritz Helena K. M. , Rigosi Elisa , O’Carroll David C.
Published: September 2020

Improvement of imaging quality has the potential to visualize previously unseen building blocks of the brain and is therefore one of the great challenges in neuroscience. Rapid development of new tissue clearing techniques in recent years have attempted to solve imaging compromises in thick brain samples, particularly for high resolution optical microscopy, where the clearing medium needs to match the refractive index of the objective immersion medium. These problems are exacerbated in insect tissue, where numerous (initially air-filled) tracheal tubes branching throughout the brain increase the scattering of light. To date, surprisingly few studies have systematically quantified the benefits of such clearing methods using objective transparency and tissue shrinkage measurements. In this study we compare a traditional and widely used insect clearing medium, methyl salicylate combined with permanent mounting in Permount (‘MS/P’) with several more recently applied clearing media that offer tunable refractive index (n): 2,2-thiodiethanol (TDE), ‘SeeDB2’ (in variants SeeDB2S & SeeDB2G matched to oil and glycerol immersion,n=1.52 & 1.47 respectively) and Rapiclear (also withn=1.52 & 1.47). We measured transparency and tissue shrinkage by comparing freshly dissected brains with cleared brains from dipteran flies, with or without addition of vacuum or ethanol pre-treatments (dehydration and rehydration) to evacuate air from the tracheal system. The results show that ethanol pre-treatment is very effective for improving transparency, regardless of the subsequent clearing medium, while vacuum treatment offers little measurable benefit. Ethanol pre-treated SeeDB2G and Rapiclear brains show much less shrinkage than using the traditional MS/P method. Furthermore, these newly developed media offer outstanding transparency compared to TDE and MS/P. Rapiclear protocols were less laborious compared to SeeDB2, but both offer sufficient transparency and refractive index tunability to permit super-resolution imaging of local volumes in whole mount brains from large insects, and even light-sheet microscopy. Although long-term permanency of Rapiclear stored samples remains to be established, our samples still showed good preservation of fluorescence after storage for more than a year at room temperature.
Sex-based clinical and immunological differences in COVID-19
Authors: Li Kening , Huang Bin , Cai Yun , Wang Zhihua , Li Lu , Wu Lingxiang , Zhu Mengyan , Li Jie , Wang Ziyu , Wu Min , Li Wanlin , Wu Wei , Zhang Lishen , Xia Xinyi , Wang Shukui , Wang Qianghu
Published: September 2020

Background

Males and females differ in their immunological responses to foreign pathogens. However, most of the current COVID-19 clinical practices and trials do not take sex as consideration.

Methods

We performed an unbiased sex-based comparative analysis for the clinical outcomes, peripheral immune cells, and SARS-CoV-2 specific antibody levels of 1,558 males and 1,499 females COVID-19 patients from a single center. The lymphocyte subgroups were measured by Flow cytometry. Total antibody, Spike protein (S)-, receptor binding domain (RBD)-, and nucleoprotein (N)-specific IgM and IgG levels were measured by chemiluminescence.

Results

We found that the mortality and ICU admission rates were approximately 2-fold higher in males than that in females (P<0.005). Survival analysis revealed that sex is an independent prognostic factor for COVID-19 (Hazard ratio=2.2, P=0.003). The concentration of inflammatory factors in peripheral blood was significantly higher in males. Besides, the renal and hepatic abnormality induced by COVID-19 was more common in males during the hospitalization. The analysis of lymphocyte subsets revealed that the percentage of CD19+ B cell and CD4+ T cell was significantly higher in females (P<0.001) during hospitalization, indicating the stronger humoral immunity in females than males. Notably, the protective IgG sharply increased and reached a peak in the fourth week after symptom onset in females, while gradually increased and reached a peak in the seventh week in males.

Conclusions

The unfavorable prognosis of male COVID-19 patients may result from the weak humoral immunity and indolent antibody responses during SARS-CoV-2 infection and recovery. Early medical intervention and close monitoring are important, especially for male COVID-19 patients. Hormonal or convalescent plasma therapy may help improve the immunity of males to fight against SARS-CoV-2 infection.
Poorly differentiated XX/XY sex chromosomes are widely shared across skink radiation
Authors: Kostmann Alexander , Kratochvíl Lukáš , Rovatsos Michail
Published: September 2020

Differentiated sex chromosomes are believed to be evolutionarily stable, and their emergence was suggested to lead to a remarkable increase in the diversification rate and in disparity in such groups as birds, mammals and snakes. On the other hand, poorly differentiated sex chromosomes are considered to be prone to turnovers. With around 1.700 currently known species formingc. 15% of reptile species diversity, skinks (family Scincidae) are a very diverse group of squamates known for their large ecological and morphological variability. Skinks generally have poorly differentiated and cytogenetically hardly distinguishable sex chromosomes and their sex determination was suggested to be highly variable. Here, we determined X-linked genes in the common sandfish (Scincus scincus) and demonstrate that skinks have shared the same homologous XX/XY sex chromosomes across their wide phylogenetic spectrum for at least 85 million years, approaching the age of the highly differentiated ZZ/ZW sex chromosomes of birds and advanced snakes. Skinks thus demonstrate that even poorly differentiated sex chromosomes can be evolutionarily stable and that large diversity can emerge even in groups with poorly differentiated sex chromosomes. The conservation of sex chromosomes across skinks allows us to introduce the first molecular sexing method widely applicable in this group.
ASHIC: Hierarchical Bayesian modeling of diploid chromatin contacts and structures
Authors: Ye Tiantian , Ma Wenxiu
Published: September 2020

The recently developed Hi-C technique has been widely applied to map genome-wide chromatin interactions. However, current methods for analyzing diploid Hi-C data cannot fully distinguish between homologous chromosomes. Consequently, the existing diploid Hi-C analyses are based on sparse and inaccurate allele-specific contact matrices, which might lead to inaccurate modeling of diploid genome architecture.

Here, we present ASHIC, a hierarchical Bayesian framework to model allele-specific chromatin organizations in diploid genomes. We developed two models under this Bayesian framework: the Poisson-multinomial (ASHIC-PM) model and the zero-inflated Poisson-multinomial (ASHIC-ZIPM) model. The proposed ASHIC methods impute allele-specific contact maps from diploid Hi-C data and simultaneously infer allelic 3D structures. Through simulation studies, we demonstrated that our methods outperformed existing approaches, especially under low coverage and low SNP density conditions. Additionally, we applied ASHIC-ZIPM to a published diploid mouse Hi-C data and studied the active/inactive X chromosomes and theH19/Igf2imprinting region. In both cases, our method produced fine-resolution diploid chromatin maps and 3D structures, and provided insights into the allelic chromatin organizations and functions. To summarize, our work provides a statistically rigorous framework for investigating fine-scale allele-specific chromatin conformations.

The ASHIC software is publicly available athttps://github.com/wmalab/ASHIC.
Bacillus subtilisspore surface display of photodecarboxylase for the transformation of lipids to hydrocarbons
Authors: Karava Marianna , Gockel Peter , Kabisch Johannes
Published: September 2020

The display of enzymes on the surface of spores allows the rapid and very simple biotechnological production of immobilized enzymes. Here we describe the development of aBacillus subtilisspore display platform and its application to produce hydrocarbons from lipids obtained from the oleaginous yeastsYarrowia lipolytica, Cutaneotrichosporon oleaginosusas well as olive oil.

Lipid hydrolysis was examined in a bienzymatic one-pot cascade using a commercially immobilized lipase (RO lipase) as well as spores with and without additional heterologous lipase expression. Decarboxylation of the released fatty acids was achieved displaying a photodecarboxylase (CvFAP) on the spore surface. Differences in composition of the formed hydrocarbons were observed depending on the lipids source. Using 3D printed lighting equipment titers of up to 64.0 ± 5.6 mg/L hydrocarbons were produced.
A Kinematic Index for Estimation of Metabolic Rate Reduction in Running withI-RUN
Authors: Aftabi Hamidreza , Nasiri Rezvan , Ahmadabadi Majid Nili
Published: September 2020

In this paper, we target multiple goals related to our passive running assistive device, calledI-RUN. The major goals are: (1) finding the main reason behind individual differences in benefiting from our assistive device at the muscles level, (2) devising a simple measure for on-lineI-RUNstiffness tuning, and creating a lab-free simple kinematic measure for (3) estimating metabolic rate reduction as well as (4) training subjects to maximize their benefit fromI-RUN. Our approach is using some extensive data-driven OpenSim simulation results employing a generic lower limb model with 92-muscles and 29-DOF.

It is observed that there is a significant relation between the hip joints kinematic and changes in the metabolic rate in the presence ofI-RUN. Accordingly, a simple kinematic index is devised to estimate metabolic rate reduction. This index not only explains individual differences in metabolic rate reduction but also provides a quantitative measure for training subjects to maximize their benefits fromI-RUN.

The simulation results also re-confirm our hypothesis that “reducing the forces of two antagonistic mono-articular muscles is sufficient for involved muscles’ total effort reduction”. Consequently, we introduce a two-muscles EMG-based metric for the on-line tuning ofI-RUN.
Investigating equations for measuring dissolved inorganic nutrient uptake in oligotrophic conditions
Authors: Stukel Michael R.
Published: September 2020

Multiple different equations have been used to quantify nutrient uptake rates from stable isotope tracer label incorporation experiments. Each of these equations implicitly assumes an underlying model for phytoplankton nutrient uptake behavior within the incubation bottle and/or pelagic environment. However, the applicability of different equations remains in question and uncertainty arising from subjective choices of which equation to use is never reported. In this study, I use two approaches to investigate the conditions under which different nutrient uptake equations should be used. First, I utilized a moderate-complexity pelagic ecosystem model that explicitly models the δ15N values of all model compartments (NEMURO+15N) to conduct simulated nitrate uptake and ammonium uptake incubations and quantify the accuracy of different nutrient uptake equations. Second, I used results of deckboard diel nutrient uptake experiments to quantify the biases of 24-h incubations relative to six consecutive 4-h incubations. Using both approaches, I found that equations that account for nutrient regeneration (i.e., isotope dilution) are more accurate than equations that do not, particularly when nutrient concentrations are low but uptake is relatively high. Furthermore, I find that if the goal is to estimatein situuptake rates it is appropriate to use anin situcorrection to standard equations. I also present complete equations for quantifying uncertainty in nutrient uptake experiments using each nutrient uptake equation and make all of these calculations available as Excel spreadsheets and Matlab scripts.
Transcription factor-target relationships complicated by knockout analysis
Authors: Dai Zhiming
Published: September 2020

Knockout analysis is a common tool to reveal transcription factor (TF) functions. However, such a reverse genetic analysis based on observed phenotype changes in mutant cell may lead to a misunderstanding of TF wild-type functions. Here, a model was proposed, in which the knockout-observed TF-target regulatory relationships might only occur in mutant cell, and they do not reflect TF normal functions in wild-type cell. Actually, the knockout of one TF might release another TF which is the protein-protein interaction partner of the deleted TF. The free TF could bind its new target genes and cause their significant expression changes. These seemingly TF knockout affected genes are thus not directly regulated by the deleted TF, but are gain-of-regulated genes of the latter TF in mutant cell. Based on this model, multiple sources of genome-wide data were used to identify 20 such TF pairs, and one pair was validated using other independent data. TF wild-type regulatory genes are not associated with their gain-of-regulated genes. My findings revealed TF-target relationships complicated by TF knockout analysis.
ZNF410 represses fetal globin by devoted control of CHD4/NuRD
Authors: Vinjamur Divya S. , Yao Qiuming , Cole Mitchel A. , McGuckin Connor , Ren Chunyan , Zeng Jing , Hossain Mir , Luk Kevin , Wolfe Scot A. , Pinello Luca , Bauer Daniel E.
Published: September 2020

Major effectors of adult-stage fetal globin silencing include the transcription factors (TFs) BCL11A and ZBTB7A/LRF and the NuRD chromatin complex, although each has potential on-target liabilities for rationalβ-hemoglobinopathy therapeutic inhibition. Here through CRISPR screening we discover ZNF410 to be a novel fetal hemoglobin (HbF) repressing TF. ZNF410 does not bind directly to theγ-globin genes but rather its chromatin occupancy is solely concentrated atCHD4, encoding the NuRD nucleosome remodeler, itself required for HbF repression.CHD4has two ZNF410-bound regulatory elements with 27 combined ZNF410 binding motifs constituting unparalleled genomic clusters. These elements completely account for ZNF410’s effects onγ-globin repression. Knockout of ZNF410 reduces CHD4 by 60%, enough to substantially de-repress HbF while avoiding the cellular toxicity of complete CHD4 loss. Mice with constitutive deficiency of the homolog Zfp410 are born at expected Mendelian ratios with unremarkable hematology. ZNF410 is dispensable for human hematopoietic engraftment potential and erythroid maturation unlike known HbF repressors. These studies identify a new rational target for HbF induction for theβ-hemoglobin disorders with a wide therapeutic index. More broadly, ZNF410 represents a special class of gene regulator, a conserved transcription factor with singular devotion to regulation of a chromatin subcomplex.
Singing-related reorganization of the song motor circuit is accompanied by a shift in hormonal modulation of song
Authors: Rocha Mariana D. , Dreier Jes , Brewer Jonathan , Gahr Manfred , Vellema Michiel
Published: September 2020

Sex hormones are essential modulators of birdsong. Testosterone, and its active androgenic and estrogenic metabolites, 5α-dihydrotestosterone (DHT) and estradiol, can re-shape the brain circuits responsible for song learning and production. The differential mechanisms of action of these different hormones during song development and song maintenance are, nonetheless, not fully understood. Here we demonstrate that unlike testosterone, DHT treatment does not induce singing behavior in naïve adult female canaries that have never previously produced song. However, in birds with previous testosterone-induced singing experience, DHT alone is enough to promote the re-acquisition of high quality songs, even after months of silence. In addition, we show that the synaptic reorganization that accompanies vocal motor skill development requires more than DHT-induced androgen receptor activation. These results indicate that vocal motor practice will persistently modify the hormone-sensitive brain circuit responsible for song production, suggesting a mechanistic differentiation in the hormone-dependent regulation of the initial vocal motor skill acquisition and later re-acquisition.
UHRF1 suppresses viral mimicry through both DNA methylation-dependent and -independent mechanisms
Authors: Irwin RE , Scullion CA , Thursby SJ , Sun ML , Thakur A , Rothbart SB , Xu GL , Walsh CP
Published: September 2020

Some chemotherapeutic agents which cause loss of DNA methylation have been recently shown to induce a state of “viral mimicry” involving upregulation of endogenous retroviruses (ERV) and a subsequent innate immune response. This approach may be useful in combination with immune checkpoint cancer therapies, but relatively little is known about normal cellular control of ERV suppression. The UHRF1 protein can interact with the maintenance methylation protein DNMT1 and is known to play an important role in epigenetic control in the cell. To examine potential roles of this protein in differentiated cells, we first established stable knockdowns in normal human lung fibroblasts. While these knockdown cells showed the expected loss of DNA methylation genome-wide, transcriptional changes were instead dominated by a single response, namely activation of innate immune signalling, consistent with viral mimicry. We confirmed using mechanistic approaches that activation of interferons and interferon-stimulated genes involved in double-stranded RNA detection was crucial to the response. ERVs were demethylated and transcriptionally activated in UHRF1 knockdown cells. As in these normal cell lines, ERV activation and interferon response also occurred following the transient loss of UHRF1 in both melanoma and colon cancer cell lines. Restoring UHRF1 in either transient- or stable knockdown systems abrogated ERV reactivation and interferon response, but without substantial restoration of DNA methylation. Rescued cell lines were hypersensitive to depletion of SETDB1, implicating H3K9me3 as crucial to UHRF1-mediated repression in the absence of DNA methylation. Confirming this, cells rescued with UHRF1 containing point mutations affecting H3K9me3 binding could not mediate silencing of ERV transcription or the innate immune response. Finally, by introducing similar point mutations in the mouse homologue, we could show that this pathway is conserved in mice. Our results therefore implicate UHRF1 as a key regulator of ERV suppression and strengthen the basis for cancer cell hypomethylation therapy.
Differential pathogenesis of Usutu virus isolates in mice
Authors: Kuchinsky Sarah C. , Hawks Seth A. , Mossel Eric , Coutermarsh-Ott Sheryl , Duggal Nisha K.
Published: September 2020

Usutu virus (USUV;Flavivirus), a close phylogenetic and ecological relative of West Nile virus, is a zoonotic virus that can cause neuroinvasive disease in humans. USUV is maintained in an enzootic cycle betweenCulexmosquitoes and birds. Since the first isolation in 1959 in South Africa, USUV has spread throughout Africa and Europe. Reported human cases have increased over the last few decades, primarily in Europe, with symptoms ranging from mild febrile illness to severe neurological effects. In this study, we investigated whether USUV has become more pathogenic during emergence in Europe. Interferon α/β receptor knockout (Ifnar1-/-) mice were inoculated with recent USUV isolates from Africa and Europe, as well as the historic 1959 South African strain. The three tested African strains and one European strain from Spain caused 100% mortality in inoculated mice, with similar survival times and histopathology in tissues. Unexpectedly, a European strain from the Netherlands caused only 12% mortality and significantly less histopathology in tissues from mice compared to mice inoculated with the other strains. Viremia was highest in mice inoculated with the recent African strains and lowest in mice inoculated with the Netherlands strain. Based on phylogenetics, the USUV isolates from Spain and the Netherlands were derived from separate introductions into Europe, suggesting that disease outcomes may differ for USUV strains circulating in Europe. These results also suggest that while more human USUV disease cases have been reported in Europe recently, circulating African USUV strains are still a potential major health concern.

Author Summary

Usutu virus (USUV) is an emerging mosquito-borne virus that causes severe neuroinvasive disease in humans. USUV was first detected in Africa in 1959, and cases of human disease have increased in recent years. Most USUV disease cases are now reported in Europe, where the virus currently circulating. One possibility for the increase in case numbers is that USUV strains have become more pathogenic over time during its spread from Africa into Europe. We compared the pathogenesis of five USUV isolates from Africa and Europe in a mouse model. Three isolates from Africa and one isolate from Europe caused 100% mortality in mice. Surprisingly, one isolate from Netherlands caused only 12% motality. Significantly less histopathology was observed in tissues from mice inoculated with the Netherlands strain compared to mice inoculated with the other four strains. Our results suggest that, even though more human USUV disease cases have been reported in Europe recently, African USUV strains are also highly pathogenic.
Reduction of Glut1 in retinal neurons but not the RPE alleviates polyol accumulation and normalizes early characteristics of diabetic retinopathy
Authors: Holoman Nicholas C. , Aiello Jacob J. , Trobenter Timothy D. , Tarchick Matthew J. , Kozlowski Michael R. , Makowski Emily R. , De Vivo Darryl C. , Singh Charandeep , Sears Jonathan E. , Samuels Ivy S.
Published: September 2020

Hyperglycemia is a key determinant for development of diabetic retinopathy (DR). Inadequate glycemic control exacerbates retinopathy, while normalization of glucose levels delays its progression. In hyperglycemia, hexokinase is saturated and excess glucose is metabolized to sorbitol by aldose reductase via the polyol pathway. Therapies to reduce retinal polyol accumulation for the prevention of DR have been elusive due to low sorbitol dehydrogenase levels in the retina and inadequate inhibition of aldose reductase. Using systemic and conditional genetic inactivation, we targeted the primary facilitative glucose transporter in the retina, Glut1, as a preventative therapeutic in diabetic male and female mice. Unlike wildtype diabetics, diabeticGlut1+/−mice did not display elevated Glut1 levels in the retina. Furthermore, diabeticGlut1+/−mice exhibited ameliorated ERG defects, inflammation and oxidative stress, which was correlated with a significant reduction in retinal sorbitol accumulation. RPE-specific reduction of Glut1 did not prevent an increase in retinal sorbitol content or early hallmarks of DR. However, like diabeticGlut1+/−mice, reduction of Glut1 specifically in retinal neurons mitigated polyol accumulation and completely prevented retinal dysfunction and the elevation of markers for oxidative stress and inflammation associated with diabetes. These results suggest that modulation of retinal polyol accumulation via Glut1 in photoreceptors can circumvent the difficulties in regulating systemic glucose metabolism and be exploited to prevent DR.

Significance

Diabetic retinopathy (DR) affects one third of diabetic patients and is the primary cause of vision loss in adults aged 20-74. While anti-VEGF and photocoagulation treatments for the late-stage vision threatening complications can prevent vision loss, a significant proportion of patients do not respond to anti-VEGF therapies and mechanisms to stop progression of early-stage symptoms remain elusive. Glut1 is the primary facilitative glucose transporter for the retina. We determined that a moderate reduction in Glut1 levels, specifically in retinal neurons, but not the RPE, was sufficient to prevent retinal polyol accumulation and the earliest functional defects to be identified in the diabetic retina. Our study defines modulation of Glut1 in retinal neurons as a targetable molecule for prevention of DR.
Toxoplasma gondiisecreted effectors co-opt host repressor complexes to inhibit necroptosis
Authors: Rosenberg Alex , Sibley L. David
Published: September 2020

During infection,Toxoplasma gondiitranslocates effector proteins directly into its host cell to subvert various signaling pathways. Here we characterize a novel secreted effector that localizes to the host cell nucleus where it modulates NCoR/SMRT repressor complex levels to repress interferon regulated genes involved in cell death. Type I and type II interferons upregulate many genes including protein kinase R (PKR), inducing formation of the necrosome complex that activates Mixed Lineage Kinase Domain Like Pseudokinase (MLKL) to execute necrotic cell death. Toxoplasma NCoR/SMRT modulator (TgNSM) acts together with another secreted effector TgIST, previously shown to down-modulate IFN-γ signaling to block immune functions. Together TgNSM and TgIST block IFN driven expression of PKR and MLKL, thus preventing host cell necroptotic death. The mechanism of action of TgNSM highlights a previously unappreciated role of NCoR/SMRT in regulation of necroptosis, assuring survival of intracellular cysts, and maintenance of chronic infection.
Preparing GST-, His-, or MBP-Fusion Proteins from Bacteria
Authors: Greenfield Edward A. , DeCaprio James , Brahmandam Mohan
Published: September 2020

An excellent source of antigens is to overexpress cloned genes in bacteria. A wide variety of coding regions can be expressed in bacteria either on their own or as fusion proteins. Indeed, it is often convenient to use vectors that express the antigen fused to an affinity tag, such as glutathione-S-transferase (GST), maltose-binding protein (MBP), or poly-histidine (e.g., 6×His). Each of these tags reliably binds to a specific affinity column enabling the antigen to be conveniently eluted under appropriate conditions. It should be noted that GST adds ∼25 kDa and MBP adds 40 kDa to the expressed protein. Because bacteria will reliably express proteins that are <80 kDa, the mass of the affinity tag should be included when designing your recombinant protein construct.
Sarkosyl Preparation of Antigens from Bacterial Inclusion Bodies
Authors: Greenfield Edward A. , DeCaprio James , Brahmandam Mohan
Published: September 2020

In many cases, solubility and proper folding of fusion proteins expressed in bacteria pose a major challenge in protein purification and crystallization. This is especially true when the fusion proteins are of eukaryotic origin. They form aggregates or become packaged into inclusion bodies, which makes protein purification extremely difficult. Sarkosyl is widely used to extract misfolded proteins from inclusion bodies in soluble form.