bluuebunny/crossref_metadata_2025 huggingface dataset:
Developmental profile of psychiatric risk associated with voltage-gated cation channel activity
Authors: Clifton Nicholas E , Collado-Torres Leonardo , Burke Emily E , Pardiñas Antonio F , Harwood Janet C , Di Florio Arianna , Walters James TR , Owen Michael J , O’Donovan Michael C , Weinberger Daniel R , Holmans Peter A , Jaffe Andrew E , Hall Jeremy
Published: October 2020

Background

Recent breakthroughs in psychiatric genetics have implicated biological pathways onto which genetic risk for psychiatric disorders converges. However, these studies do not reveal the developmental time point(s) at which these pathways are relevant.

Methods

We aimed to determine the relationship between psychiatric risk and developmental gene expression relating to discrete biological pathways. We used post-mortem RNA sequencing data (BrainSeq and BrainSpan) from brain tissue at multiple pre- and post-natal timepoints and summary statistics from recent genome-wide association studies of schizophrenia, bipolar disorder and major depressive disorder. We prioritised gene sets for overall enrichment of association with each disorder, and then tested the relationship between the association of each of their constituent genes with their relative expression at each developmental stage.

Results

We observed relationships between the expression of genes involved involtage-gated cation channel activityduring Early Midfetal, Adolescence and Early Adulthood timepoints and association with schizophrenia and bipolar disorder, such that genes more strongly associated with these disorders had relatively low expression during Early Midfetal development and higher expression during Adolescence and Early Adulthood. The relationship with schizophrenia was strongest for the subset of genes related to calcium channel activity, whilst for bipolar disorder the relationship was distributed between calcium and potassium channel activity genes.

Conclusions

Our results indicate periods during development when biological pathways related to the activity of calcium and potassium channels may be most vulnerable to the effects of genetic variants conferring risk to psychiatric disorders. Furthermore, they indicate key time points and potential targets for disorder-specific therapeutic interventions.
CellRank for directed single-cell fate mapping
Authors: Lange Marius , Bergen Volker , Klein Michal , Setty Manu , Reuter Bernhard , Bakhti Mostafa , Lickert Heiko , Ansari Meshal , Schniering Janine , Schiller Herbert B. , Pe’er Dana , Theis Fabian J.
Published: October 2020

Computational trajectory inference enables the reconstruction of cell-state dynamics from single-cell RNA sequencing experiments. However, trajectory inference requires that the direction of a biological process is known, largely limiting its application to differentiating systems in normal development. Here, we present CellRank (https://cellrank.org) for mapping the fate of single cells in diverse scenarios, including perturbations such as regeneration or disease, for which direction is unknown. Our approach combines the robustness of trajectory inference with directional information from RNA velocity, derived from ratios of spliced to unspliced reads. CellRank takes into account both the gradual and stochastic nature of cellular fate decisions, as well as uncertainty in RNA velocity vectors. On data from pancreas development, we show that it automatically detects initial, intermediate and terminal populations, predicts fate potentials and visualizes continuous gene expression trends along individual lineages. CellRank also predicts a novel dedifferentiation trajectory during regeneration after lung injury, which we follow up experimentally by confirming the existence of previously unknown intermediate cell states.
Toll-9 interacts with Toll-1 to mediate a feedback loop during apoptosis-induced proliferation inDrosophila
Authors: Shields Alicia , Amcheslavsky Alla , Brown Elizabeth , Nie Yingchao , Tanji Takahiro , Ip Y. Tony , Bergmann Andreas
Published: October 2020

DrosophilaToll-1 and all mammalian Toll-like receptors regulate innate immunity. However, the functions of the remaining eight Toll-related proteins inDrosophilaare not fully understood. Here, we show thatDrosophilaToll-9 is necessary and sufficient for a special form of compensatory proliferation after apoptotic cell loss (undead apoptosis-induced proliferation (AiP)). Mechanistically, for AiP, Toll-9 interacts with Toll-1 to activate the intracellular Toll-1 pathway for nuclear translocation of the NF-κB-like transcription factor Dorsal which induces expression of the pro-apoptotic genesreaperandhid. This activity contributes to the feedback amplification loop that operates in undead cells. Given that Toll-9 also functions in loser cells during cell competition, we define a general role of Toll-9 in cellular stress situations leading to the expression of pro-apoptotic genes which trigger apoptosis and apoptosis-induced processes such as AiP. This work identifies conceptual similarities between cell competition and AiP.
Characteristics and outcomes of clinically diagnosed RT-PCR swab negative COVID-19: a retrospective cohort study
Authors: Middleton Paul , Perez-Guzman Pablo N. , Cheng Alexandra , Kumar Naveenta , Kont Mara D. , Daunt Anna , Mukherjee Sujit , Cooke Graham , Hallett Timothy B. , Hauck Katharina , White Peter J. , Thursz Mark R. , Nayagam Shevanthi
Published: October 2020

Patients with strong clinical features of COVID-19 with negative real time polymerase chain reaction (RT-PCR) SARS-CoV-2 testing are not currently included in official statistics. The scale, characteristics and clinical relevance of this group are thus unknown. We performed a retrospective cohort study in two large London hospitals to characterize the demographic, clinical, and hospitalization outcome characteristics of swab-negative clinical COVID-19 patients. We found 1 in 5 patients with a negative swab and clinical suspicion of COVID-19 received a clinical diagnosis of COVID-19 within clinical documentation, discharge summary or death certificate. We compared this group to a similar swab positive cohort and found similar demographic composition, symptomology and laboratory findings. Swab-negative clinical COVID-19 patients had better outcomes, with shorter length of hospital stay, reduced need for >60% supplementary oxygen and reduced mortality. Patients with strong clinical features of COVID-19 that are swab-negative are a common clinical challenge. Health systems must recognize and plan for the management of swab-negative patients in their COVID-19 clinical management, infection control policies and epidemiological assessments.
Tocilizumab is associated with reduction in inflammation and improvement in P/F ratio in critically sick COVID19 patients
Authors: Rana Muhammad Asim , Hashmi Mubashar , Ullah Saif Muhammad Muneeb , Munir Muhammad Faisal , Qayyum Ahad , Pervaiz Rizwan , Hafeez Muhammad Mansoor
Published: October 2020

Introduction

Coronavirus disease 2019 was initially detected in China and has been declared a global pandemic by World Health Organization on March 11, 2020. In the majority of patients, SARS□CoV□2 causes a mild to moderate illness characterized by fever and respiratory symptoms, with or without evidence of pneumonia. The recent studies suggest that anti-cytokine targeted therapies might be associated with benefit for patients with severe COVID-19 especially in improving respiratory failure. Tocilizumab, a monoclonal antibody against interleukin 6 (IL6) receptor, is associated with clinical benefit for COVID-19 patients as it inhibits IL6 and decreases inflammation.

Methods

As Tocilizumab has been an important part of our treatment and a strict criterion was followed to administer Tocilizumab, a retrospective study design used to assess the beneficial effects of Tocilizumab in improvement of ratio partial pressure of arterial Oxygen and fraction of inspired Oxygen (PaO2/FiO2 or P/F ratio) and C-reactive protein (CRP) in COVID19 patients has been done. 60 patients were taken for this study by using convenient sampling technique the data of demographics, laboratory results, and clinical outcomes i.e. improvement of respiratory failure depicted in the form of PF Ratio were obtained from the medical records, Statistical analysis was done with SPSS, version 21.0.

Results

Sixty patients (47 males and 13 females) with COVID□19 were included in this study, the mean age of patients was 53.83 (14□81) years. After administration of Tocilizumab the lab parameters were changed as CRP decreased down to .40 (9.6□73) mg/L but other parameters were not affected. The PF ratio improved in COVID-19 patients after administration of Tocilizumab the median of PF Ratio before treatment was 108 (52□362) and improved up to 128 (37□406) after Tocilizumab therapy.

Conclusion

In summary, Tocilizumab appears to be associated with improvement in P/F Ratio and CRP in COVID19 patients but other markers did not improve in response to Tocilizumab therapy in severely ill COVID-19 patients.
Validation of expert system enhanced deep learning algorithm for automated screening for COVID-Pneumonia on chest X-rays
Authors: Gidde Prashant Sadashiv , Prasad Shyam Sunder , Singh Ajay Pratap , Bhatheja Nitin , Prakash Satyartha , Singh Prateek , Saboo Aakash , Thakar Rohit , Gupta Salil , Saurav Sumeet , Raghunandanan M V , Singh Amritpal , Sardana Viren , Mahajan Harsh , Kalyanpur Arjun , Mandal Atanendu Shekhar , Mahajan Vidur , Agrawal Anurag , Agrawal Anjali , Venugopal Vasantha Kumar , Singh Sanjay , Dash Debasis
Published: October 2020

The coronavirus disease of 2019 (COVID-19) pandemic exposed a limitation of artificial intelligence (AI) based medical image interpretation systems. Early in the pandemic, when need was greatest, the absence of sufficient training data prevented effective deep learning (DL) solutions. Even now, there is a need for Chest-X-ray (CxR) screening tools in low and middle income countries (LMIC), when RT-PCR is delayed, to exclude COVID-19 pneumonia (Cov-Pneum) requiring transfer to higher care. In absence of local LMIC data and poor portability of CxR DL algorithms, a new approach is needed. Axiomatically, it is faster to repurpose existing data than to generate new datasets. Here, we describe CovBaseAI, an explainable tool which uses an ensemble of three DL models and an expert decision system (EDS) for Cov-Pneum diagnosis, trained entirely on datasets from the pre-COVID-19 period. Portability, performance, and explainability of CovBaseAI was primarily validated on two independent datasets. First, 1401 randomly selected CxR from an Indian quarantine-center to assess effectiveness in excluding radiologic Cov-Pneum that may require higher care. Second, a curated dataset with 434 RT-PCR positive cases of varying levels of severity and 471 historical scans containing normal studies and non-COVID pathologies, to assess performance in advanced medical settings. CovBaseAI had accuracy of 87% with negative predictive value of 98% in the quarantine-center data for Cov-Pneum. However, sensitivity varied from 0.66 to 0.90 depending on whether RT-PCR or radiologist opinion was set as ground truth. This tool with explainability feature has better performance than publicly available algorithms trained on COVID-19 data but needs further improvement.
Innate Immune Response Modulation and Resistance to SARS-CoV-2 infection: A Prospective Comparative Cohort Study in High Risk Healthcare Workers
Authors: Jaiswal Sarita Rani , Mehta Anupama , Bhagwati Gitali , Lakhchaura Rohit , Aiyer Hemamalini , Khamar Bakulesh , Chakrabarti Suparno
Published: October 2020

To evaluate ability of modulated innate immune response to provide resistance to development of symptomatic RT-PCR confirmed COVID-19, 96 inpatient front line health care workers (HCW) were cohorted in 1:2 ratio to receive TLR2 agonist (heat killed Mycobacterium w, Mw; n=32) as innate immune response modulator or observation (n=64). All were followed up for 100 days. The incidence of COVID-19 was 31 (32.3%) for the entire cohort, with only one developing COVID-19 in Mw group (3.1% vs 46.8%. protective efficacy - 93.33%, p=0.0001; 95% CI 53.3-99.1). Self-limiting local injection site reaction was the only side effect and was seen in 14 HCW. Findings from the study suggest the potential for providing resistance against novel pathogen like SARS-CoV-2 by modulating innate immune response.
Depiction of Mental Illness in Film and Association with Financial and Critical Success
Authors: Kamal Shaan , El-Gabalawy Osama , Zhao Nathan , MacLeod Jelena
Published: October 2020

Film and cinema are an important part of American culture and discourse. In recent years, there have been increasing discussions around the media portrayal of suicide and psychiatric illness and its subsequent impact on prejudice towards individuals with mental health issues. To date, there is no published work quantifying the depiction of mental illness in film. In this work we use movie plot descriptions to identify movies that depict mental illness and compare their financial and critical success to all movies released during the same time period.
Challenges Faced by Dialysis Unit Staff during COVID −19 times-A Qualitative Study
Authors: RaviKumar P. , Dongre Amol
Published: October 2020

Introduction

The novel SARS COV2-Covid −19 has become a global pandemic since January 2020 and has been spreading exponentially. Dialysis patients with lowered immunity are at high risk. The dialysis patients come for repeated treatment. Hence the dialysis staffs are also at great risk of contracting COVID-19.

Objective

To study the challenges faced by the dialysis staff during the COVID-19 pandemic in a rural hemodialysis unit.

Material and Methods

The study was conducted in the hemodialysis unit of Sri ManakulaVinayagar Medical College Hospital, Puducherry, India. We did free list and pile sorting to understand the salient problems and its structure as perceived by the team members. We found Smith’s S value for free list. Multidimensional scaling and Hierarchical cluster analysis were done to pile sort data. Data was analyzed using Anthropac 4.983/X. In addition, group interview was done to get in-depth information and validate the findings obtained from the free list and pile sort exercise.

Results

Twelve salient items were generated from the free list. In pile sort, we got three broad domains-the shortage of personal safety equipment, the lack of personal safety and presence of logistical and operational problems. Relative to other items, testing by RT-PCR was surprisingly not perceived to be important for them.

Conclusion

Addressing the shortage of personal safety equipment, impediments to personal safety and giving credence to the feelings, fears and needs of the dialysis staff in a dialysis unit during COVID −19 pandemic are paramount in ensuring their safety and improving working dynamics.
Associations between COVID-19 transmission rates, park use, and landscape structure
Authors: Johnson Thomas F. , Hordley Lisbeth A. , Greenwell Matthew P. , Evans Luke C.
Published: October 2020

The COVID-19 pandemic has had severe impacts on global public health. In England, social distancing measures and a nationwide lockdown were introduced to reduce the spread of the virus. Green space accessibility may have been particularly important during this lockdown, as it could have provided benefits for physical and mental wellbeing. However, the associations between public green space use and the rate of COVID-19 transmission are yet to be quantified, and as the size and accessibility of green spaces vary within England’s local authorities, the risks and benefits to the public of using green space may be context-dependent. To evaluate how green space affected COVID-19 transmission across 299 local authorities (small regions) in England, we calculated a daily case rate metric, based upon a seven-day moving average, for each day within the period June 1st- November 30th2020 and assessed how baseline health and mobility variables influenced these rates. Next, looking at the residual case rates, we investigated how landscape structure (e.g. area and patchiness of green space) and park use influenced transmission. We first show that reducing mobility is associated with a decline in case rates, especially in areas with high population clustering. After accounting for known mechanisms behind transmission rates, we found that park use (showing a preference for park mobility) was associated with decreased residual case rates, especially when green space was low and contiguous (not patchy). Our results support that a reduction in overall mobility may be a good strategy for reducing case rates, endorsing the success of lockdown measures. However, if mobility is necessary, outdoor park use may be safer than other forms of mobility and associated activities (e.g. shopping or office-based working).
Spinal Anesthesia is Safe and Cost-effective for Laparoscopic Appendectomy in Children: A Case-Control Study
Authors: Hannan Md Jafrul , Parveenl Mosammat Kohinoor , Nandy Alak , Hasan Md Samiul
Published: October 2020

STRUCTURED ABSTRACT

Background

Owing to the widespread use of general anesthesia, administration of spinal anesthesia in pediatrics is not widely practiced. Yet there is ample positive evidence demonstrating its safety, effectiveness and success.

Objective

The objective of this study is to demonstrate that laparoscopic appendectomies are successful under spinal anesthesia and elicit clear advantages over general anesthesia.

Methods

This was a retrospective analysis of 77 pediatric (5-8 year old) laparoscopic appendectomies that took place in a Hospital in Chittagong, Bangladesh in 2019. Approximately half of the patients underwent spinal anesthesia while the other half underwent general anesthesia. Variables such as surgery and operation theatre times, pain score, incidence of post-surgery vomiting, analgesic usage, discharge times and hospital costs were recorded. Statistical analysis was used to analyze the data as a function of form of anesthesia.

Results

The probability of vomiting when using spinal compared to general anesthesia was much lower within the first 5 hours (P < .001) and after 6 hours (P = .008) of operation. Highly significant difference (P < .001) was observed in the total costs of the procedures. A significantly higher likelihood of patients being discharged the same day of the procedure was noted if spinal anesthesia was used (P = .008).

Conclusions

Spinal anesthesia is superior to general anesthesia for pediatric laparoscopic appendectomies. Patient comfort is improved through a significant decrease in vomiting. This enables more rapid hospital discharges and a significant cost saving, without compromising the outcome of the procedure.

MINI-ABSTRACT

Spinal anesthesia is seldom used for laparoscopy in children. This retrospective case-controlled study compared spinal anesthesia with general anesthesia in children between 5 and 8 years of age. Spinal anesthesia proved to be safer and cost-effective for laparoscopy in children.
Sleep disturbances and related factors among preschool children in rural areas of China: a cross-sectional study
Authors: Zhao Tianming , Xuan Kun , Liu Haixia , Chen Xin , Qu Guangbo , Wu Yile , Zhang Jian , Sun Yehuan
Published: October 2020

Objective

Sleep disturbances have been serious since they are believed to be associated with various health problems in preschool children. In this study, we aimed to explore the prevalence of sleep disturbances amongst preschool children in rural areas of China and examine the underlying associated factors.

Methods

A cross-sectional study was conducted in rural areas of Anhui province, China from September 2019 to January 2020. To explore the potential associated factors comprehensively, caregivers of children completed a structured questionnaire, the Children’s Sleep Habits Questionnaire (CSHQ), the Strengths and Difficulties Questionnaire (SDQ), Self-rating Anxiety Scale (SAS) and the Chinese version of the adapted Identification and Management of Feeding Difficulties (IMFeD). One-way ANOVA and hierarchical multiple regression are conducted to explore the potential influencing factors of sleep disturbances in preschool children.

Results

About 89.3% of the preschool children aged from 3 to 6 years had potential sleep disturbances (scored above the cutoff value). Besides, ages of children, discipline attitudes of father and mother, main educational methods, caregivers of children, caregiver anxiety and hyperactivity/inattention, prosocial behavior, conduct problems, emotional symptoms, peer problems, food preference, fear of feeding, parental misperception and organic disease all contributed significantly to CSHQ total score by accounting for approximately 27.4% (R2=0.274) of the variation.

Conclusions

Our study indicated that the prevalence of sleep disturbances among preschool children in rural area of China is quite high. Furthermore, the potential risk factors are complicated which include factors related to both children and caregivers especially their parents.
Prognosis of stage IV bone cancer based on pattern of metastasis: a retrospective survival analysis of patients from the Surveillance, Epidemiology, and End Results (SEER) database
Authors: Ayaz Talha , Panchbhavi Megna A. , Kashif Muhammad T. , Abdullah Mohammed S. , Akhtar Zahra
Published: October 2020

Background

Prognosis in bone cancer patients with metastatic disease is believed to vary based on site/pattern of spread. In 2003, the American Joint Committee on Cancer (AJCC) incorporated this observation into the TNM Staging System by subclassifying metastatic disease into M1a or M1b. We conducted a retrospective survival analysis of patients with primary bone cancer to characterize prognosis and assess outcomes in M1a versus M1b disease.

Methods

The Surveillance, Epidemiology and End Results (SEER) database was searched for cases of primary bone cancer presenting with metastasis from 2010 to 2015. Cases were grouped using AJCC metastatic staging as metastasis to the lung only (M1a) or other pattern of metastasis (M1b). Overall survival and cause-specific survival were assessed using Kaplan-Meier analysis and multivariate cox regression models. Multivariate models adjusted for multiple demographic, tumor characteristic, and treatment covariates.

Results

Five hundred and twenty-six cases met the inclusion criteria for this study. Two hundred and forty-eight were staged as M1a, and 278 were staged as M1b. Mean follow-up time for the cohort was 18.21 months (SD = 16.76). Fifty percent (124 of 248) of M1a and 59.4% (165 of 278) of M1b patients had died by the end of the study. Overall (P = .003) and cause-specific survival (P = .010) times were significantly lower for M1b patients via log-rank test. Adjusted analysis showed that M1b patients had poorer overall survival (HR, 1.505; 95% CI, 1.138-1.989; P = .004) and cause-specific survival (HR, 1.446; 95% CI, 1.091-1.918; P = .010) compared to M1a patients.

Conclusion

Metastasis pattern is an independent predictor of survival. M1a metastatic disease tends to have a better prognosis compared to M1b. This study supports the decision of the AJCC to subclassify metastatic disease for the purposes of staging and highlights the differences in prognosis between these two patterns of disease.
Differential Impact of Mitigation Policies and Socioeconomic Status on COVID-19 Prevalence and Social Distancing in the United States
Authors: Chang Hsien-Yen , Tang Wenze , Hatef Elham , Kitchen Christopher , Weiner Jonathan P. , Kharrazi Hadi
Published: October 2020

Background

The spread of COVID-19 has highlighted the long-standing health inequalities across the U.S. as neighborhoods with fewer resources were associated with higher rates of COVID-19 transmission. Although the stay-at-home order was one of the most effective methods to contain its spread, residents in lower-income neighborhoods faced barriers to practicing social distancing. We aimed to quantify the differential impact of stay-at-home policy on COVID-19 transmission and residents’ mobility across neighborhoods of different levels of socioeconomic disadvantage.

Methods

This was a comparative interrupted time-series analysis at the county level. We included 2,087 counties from 38 states which both implemented and lifted the state-wide stay-at-home order. Every county was assigned to one of four equally-sized groups based on its levels of disadvantage, represented by the Area Deprivation Index. Prevalence of COVID-19 was calculated by dividing the daily number of cumulative confirmed COVID-19 cases by the number of residents from the 2010 Census. We used the Social Distancing Index, derived from the COVID-19 Impact Analysis Platform, to measure the social distancing practice. For the evaluation of implementation, the observation started from Mar 1St2020 to one day before lifting; and, for lifting, it ranged from one day after implementation to Jul 5th2020. We calculated a comparative change of daily trends in COVID-19 prevalence and Social Distancing Index between counties with three highest disadvantage levels and those with the least level before and after the implementation and lifting of the stay-at-home order, separately.

Results

On both stay-at-home implementation and lifting dates, COVID-19 prevalence was much higher among counties with the highest or lowest disadvantage level, while mobility decreased as the disadvantage level increased. Mobility of the most disadvantaged counties was least impacted by stay-at-home implementation and relaxation compared to counties with the most resources; however, disadvantaged counties experienced the largest relative increase in COVID-19 infection after both stay-at-home implementation and relaxation.

Conclusions

Neighborhoods with varying levels of socioeconomic disadvantage reacted differently to the implementation and relaxation of COVID-19 mitigation policies. Policymakers should consider investing more resources in disadvantaged counties as the pandemic may not stop until most neighborhoods have it under control.
The cell cycle state defines TACC3 as a regulator gene in glioblastoma
Authors: Briggs Holly , Polson Euan S. , Irving Bronwyn K. , Zougman Alexandre , Mathew Ryan K. , Gendoo Deena M.A. , Wurdak Heiko
Published: October 2020

Overexpression and mitosis-promoting roles of Transforming acidic coiled-coil containing protein 3 (TACC3) are well-established in many cancers, including glioblastoma (GBM). However, the effector gene networks downstream of TACC3 remain poorly defined, partly due to an incomplete understanding of TACC3 cell lineage specificity and its dynamic role during the cell cycle. Here, we use a patient-derived GBM model to report that TACC3 predominantly resides in the GBM cell cytoplasm, while engaging in gene regulation temporally as defined by the cell cycle state. TACC3 loss-of-function, cell cycle stage-specific transcriptomics, and unsupervised self-organizing feature maps revealed pathways (including Hedgehog signalling) and individual genes (including HOTAIR) that exhibited anticorrelated expression phenotypes across interphase and mitosis. Furthermore, this approach identified a set of 22 TACC3-dependent transcripts in publicly-available clinical databases that predicted poor overall and progression-free survival in 162 GBM and 514 low-grade glioma patient samples. These findings uncover TACC3-dependent genes as a function of TACC3 cell cycle oscillation, which is important for TACC3-targeting strategies, and for predicting poor outcomes in brain cancer patients.
A Novel Design of Transcriptional Factor-mediated Dynamic Control of DNA Recombination
Authors: Li Jiayang , Zhang Yihao , Zong Yeqing
Published: October 2020

Genetic regulation is achieved by monitoring multiple levels of gene expression, from transcription to protein interaction. Unlike common temporary transcriptional regulation methods such as the use of inducible promoters, integrases permanently edit DNA sequences. Integrases, however, require especially strict regulation when implemented in synthetic genetic systems because of the irreversible result. Here we propose to improve the regulation of site-specific integrase-based genetic system by dynamically hiding one of the attB/P sites that are essential for recombination with transcriptional factors. After effectively suppressing excessive recombination, we also validated the necessity of each of the essential components in our transcriptional factor-controlled recombination (TFCR) system. The system applied transcriptional-level regulators directly on controlling the activity of existing non-transcriptional-level trans-factor proteins by inhibiting its binding to the cis-regulatory elements. We anticipate my results to provide greater robustness for integrase components to enable safer use in systems as well as be a starting point for future cross-expression level gene regulations.
An amplified derepression controller with multisite inhibition and positive feedback
Authors: Drobac Gorana , Waheed Qaiser , Heidari Behzad , Ruoff Peter
Published: October 2020

How organisms are able to maintain robust homeostasis has in recent years received increased attention by the use of combined control engineering and kinetic concepts, which led to the discovery of robust controller motifs. While these motifs employ kinetic conditions showing integral feedback and homeostasis for step-wise perturbations, the motifs’ performance differ significantly when exposing them to time dependent perturbations. One type of controller motifs which are able to handle exponentially and even hyperbolically growing perturbations are based on derepression. In these controllers the compensatory reaction, which neutralizes the perturbation, is derepressed, i.e. its reaction rate is increased by the decrease of an inhibitor acting on the compensatory flux. While controllers in this category can deal well with different time-dependent perturbations they have the disadvantage that they break down once the concentration of the regulatory inhibitor becomes too low and the compensatory flux has gained its maximum value. We wondered whether it would be possible to bypass this restriction, while still keeping the advantages of derepression kinetics. In this paper we show how the inclusion of multisite inhibition and the presence of positive feedback loops lead to an amplified controller which is still based on derepression kinetics but without showing the breakdown due to low inhibitor concentrations. By searching for the amplified feedback motif in natural systems, we found it as a part of the plant circadian clock where it is highly interlocked with other feedback loops.
Contact-dependent traits in Pseudomonas syringae B728a
Authors: Hernandez Monica N. , Lindow Steven E.
Published: October 2020

Production of the biosurfactant syringafactin by the plant pathogen Pseudomonas syringae B728a is a surface contact-dependent trait. Expression of syfA, as measured using a gfp reporter gene fusion was low in planktonic cells in liquid cultures but over 4-fold higher in cells immobilized on surfaces as varied as glass, plastic, paper, parafilm, agar, membrane filters, and leaves. Induction of syfA as measured by GFP fluorescence was rapid, occurring within two hours after immobilization of cells on surfaces. Comparison of the global transcriptome by RNA sequencing of planktonic cells in a nutrient medium with that of cells immobilized for 2 hours on filters placed on this solidified medium revealed that, in addition to syfA, 3156 other genes were differentially expressed. Genes repressed in immobilized cells included those involved in quaternary ammonium compound (QAC) metabolism and transport, compatible solute production, carbohydrate metabolism and transport, organic acid metabolism and transport, phytotoxin synthesis and transport, amino acid metabolism and transport, and secondary metabolism. Genes induced in immobilized cells included syfA plus those involved in translation, siderophore synthesis and transport, nucleotide metabolism and transport, flagellar synthesis and motility, lipopolysaccharide (LPS) synthesis and transport, energy generation, transcription, chemosensing and chemotaxis, replication and DNA repair, iron-sulfur proteins, peptidoglycan/cell wall polymers, terpenoid backbone synthesis, iron metabolism and transport, and cell division. That many genes are rapidly differentially expressed upon transfer of cells from a planktonic to an immobilized state suggests that cells experience the two environments differently. It seems possible that surface contact initiates anticipatory changes in P. syringae gene expression, which enables rapid and appropriate physiological responses to the new environmental conditions. Such responses could help cells survive transitions from aquatic habitats fostering planktonic traits to attachment on surfaces, conditions that alternatively occur on leaves.
Mechanism of bacterial adhesion and embedment in a DNA biofilm matrix: Evidence that binding of outer membrane lipopolysaccharide (LPS) to HU is key
Authors: Thakur Bhishem , Arora Kanika , Gupta Archit , Guptasarma Purnananda
Published: October 2020

In biofilms, bacteria are embedded within a matrix of extracellular DNA (e-DNA). Since bacterial cells and e-DNA are both negatively-charged, a positively-charged substance must act like a ‘glue’ to allow bacteria to be embedded within the DNA matrix. Here we show that HU (a highly-abundant, histone-like, nucleoid-associated, DNA-binding protein) facilitates bacterium-bacterium and bacterium-DNA interactions by binding to lipopolysaccharide (LPS), a bacterial outer membrane component. We demonstrate that LPS binds to both the canonical and non-canonical DNA-binding sites on HU. We propose that the hexose sugar-terminal phosphate moieties present in the lipid A head-group of LPS bind to the same lysine/arginine residues that are involved in binding of the pentose sugar-phosphate groups in DNA. Alternate binding of LPS and DNA by HU’s DNA-binding sites could allow HU to bind to bacterial cells surfaces and thus elicit bacterium-bacterium and bacterium-DNA interactions in biofilms.
Isolation of cross-reactive monoclonal antibodies against divergent human coronaviruses that delineate a conserved and vulnerable site on the spike protein
Authors: Wang Chunyan , van Haperen Rien , Gutiérrez-Álvarez Javier , Li Wentao , Okba Nisreen M.A. , Albulescu Irina , Widjaja Ivy , van Dieren Brenda , Fernandez-Delgado Raul , Sola Isabel , Hurdiss Daniel L. , Daramola Olalekan , Grosveld Frank , van Kuppeveld Frank J.M. , Haagmans Bart L. , Enjuanes Luis , Drabek Dubravka , Bosch Berend-Jan
Published: October 2020

The coronavirus spike glycoprotein, located on the virion surface, is the key mediator of cell entry. As such, it is an attractive target for the development of protective antibodies and vaccines. Here we describe two human monoclonal antibodies, 1.6C7 and 28D9, that display a remarkable cross-reactivity against distinct species from threeBetacoronavirussubgenera, capable of binding the spike proteins of SARS-CoV and SARS-CoV-2, MERS-CoV and the endemic human coronavirus HCoV-OC43. Both antibodies, derived from immunized transgenic mice carrying a human immunoglobulin repertoire, blocked MERS-CoV infection in cells, whereas 28D9 also showed weak cross-neutralizing potential against HCoV-OC43, SARS-CoV and SARS-CoV-2 in a neutralization-sensitive virus pseudotyping system, but not against authentic virus. Both cross-reactive monoclonal antibodies were found to target the stem helix in the spike protein S2 fusion subunit which, in the prefusion conformation of trimeric spike, forms a surface exposed membrane-proximal helical bundle, that is antibody-accessible. We demonstrate that administration of these antibodies in mice protects from a lethal MERS-CoV challenge in both prophylactic and/or therapeutic models. Collectively, these antibodies delineate a conserved, immunogenic and vulnerabe site on the spike protein which spurs the development of broad-range diagnostic, preventive and therapeutic measures against coronaviruses.
Direct observation of the mechanical role of bacterial chaperones in protein folding
Authors: Chaudhuri Deep , Banerjee Souradeep , Chakraborty Soham , Haldar Shubhasis
Published: October 2020

Protein folding under force is an integral source of generating mechanical energy in various cellular processes, ranging from protein translation to degradation. Although chaperones are well known to interact with proteins under mechanical force, how they respond to force and control cellular energetics remains unknown.

To address this question, we introduce novel real-time magnetic-tweezers technology to mimic physiological force environment on client proteins, keeping the chaperones unperturbed. We studied two structurally distinct client proteins with seven different chaperones, independently and in combination, and proposed novel mechanical activity of chaperones. We found chaperones behave differently, while these client proteins are under force than its previously known functions. For instance, tunnel associated chaperones (DsbA and trigger factor), otherwise working as holdase without force, assist folding under force. This process generates an additional mechanical energy up to ∼147 zJ to facilitate translation or translocation. However, well-known cytoplasmic foldase chaperones (PDI, thioredoxin, or DnaKJE), does not possess the mechanical folding ability under force. Notably, the transferring chaperones (DnaK, DnaJ, SecB), act as unfoldase and slow down folding process, both in the presence and absence of force, to prevent misfolding of the client proteins. This provides an emerging insight of mechanical roles of chaperones: they can generate or consume energy by shifting energy landscape of the client proteins towards folded or unfolded state; suggesting an evolutionary mechanism to minimize the energy consumption in various biological processes.
Temporal prediction elicits rhythmic pre-activation of relevant sensory cortices
Authors: Barne Louise Catheryne , Cravo André Mascioli , de Lange Floris P. , Spaak Eelke
Published: October 2020

Being able to anticipate events before they happen facilitates stimulus processing. The anticipation of the contents of events is thought to be implemented by the elicitation of prestimulus templates in sensory cortex. In contrast, the anticipation of the timing of events is typically associated with entrainment of neural oscillations. It is so far unknown whether and in which conditions temporal expectations interact with feature-based expectations, and, consequently, whether entrainment modulates the generation of content-specific sensory templates. In this study, we investigated the role of temporal expectations in a sensory discrimination task. We presented participants with rhythmically interleaved visual and auditory streams of relevant and irrelevant stimuli while measuring neural activity using magnetoencephalography. We found no evidence that rhythmic stimulation induced prestimulus feature templates. However, we did observe clear anticipatory rhythmic pre-activation of the relevant sensory cortices. This oscillatory activity peaked at behaviourally relevant, in-phase, intervals. Our results suggest that temporal expectations about stimulus features do not behave similarly to explicitly cued, non-rhythmic, expectations; yet elicit a distinct form of modality-specific pre-activation.

Graphical abstract

The brain extracts temporal regularities from the environment to anticipate upcoming events. Furthermore, with prior knowledge about their contents, the brain is thought to leverage this by instantiating anticipatory sensory templates. We investigated if sensory templates occur in response to a rhythmic stimulus stream with predictable temporal structure. We found that temporal rhythmic predictions did not induce sensory templates, but rather modulated the excitability in early sensory cortices.
Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis
Authors: Gong Shanzhong , Kirmizialtin Serdal , Chang Adrienne , Mayfield Joshua E. , Zhang Yan Jessie , Johnson Kenneth A.
Published: October 2020

We examined the roles of Mg2+ions in DNA polymerization by kinetic analysis of single nucleotide incorporation catalyzed by HIV reverse transcriptase and by molecular dynamics simulation of Mg2+binding. Binding of the Mg-nucleotide complex induces a conformational change of the enzyme from open to closed states in a process that is independent of free Mg2+concentration. Subsequently, the second Mg2+binds weakly to the closed state of the enzyme-DNA-Mg.dNTP complex with an apparentKd= 3.7 mM and facilitates the catalytic reaction. This weak binding of the catalytic Mg2+is important to maintain fidelity in that the Mg2+samples the correctly aligned substrate without perturbing the equilibrium at physiological Mg2+concentrations. The binding of the catalytic Mg2+increases nucleotide specificity (kcat/Km) by increasing the rate of the chemistry and decreasing the rate of enzyme opening allowing nucleotide release. Changing the free Mg2+concentration from 0.25 to 10 mM increased nucleotide specificity (kcat/Km) by 12-fold. Mg2+binds very weakly to the open state of the enzyme in the absence of nucleotide (Kd≈ 34 mM) and competes with Mg.dNTP. Analysis based on publish crystal structures showed that HIV RT binds only two metal ions during incorporation of a correct base-pair. MD simulations support the kinetic studies suggesting weak binding of the catalytic Mg2+in open and closed states. They also support the two-metal ion mechanism, although the polymerase may bind a third metal ion in the presence of a mismatched nucleotide.
Mycobacterium abscessus biofilms have viscoelastic properties which may contribute to their recalcitrance in chronic pulmonary infections
Authors: Gloag Erin S. , Wozniak Daniel J. , Stoodley Paul , Hall-Stoodley Luanne
Published: October 2020

Mycobacterium abscessus is emerging as a cause of recalcitrant chronic pulmonary infections, particularly in people with cystic fibrosis (CF). Biofilm formation has been implicated in the pathology of this organism, however the role of biofilm formation in infection is unclear. Two colony-variants of M. abscessus are routinely isolated from CF samples, smooth (MaSm) and rough (MaRg). These two variants display distinct colony morphologies due to the presence (MaSm) or absence (MaRg) of cell wall glycopeptidolipids (GPLs). We hypothesized that MaSm and MaRg variant biofilms might have different biophysical and mechanical properties, including stiffness, viscosity and elasticity. To test this hypothesis, we performed uniaxial mechanical indentation, and shear rheometry on MaSm and MaRg colony-biofilms. We identified that MaRg biofilms were significantly stiffer than MaSm under a normal force, while MaSm biofilms were more pliant compared to MaRg, under both normal and shear forces. Furthermore, using theoretical indices of mucociliary and cough clearence, we identified that M. abscessus biofilms may be more resistant to mechanical forms of clearance from the lung, compared to other common pulmonary pathogens, such as P. aeruginosa. Thus, the mechanical properties of M. abscessus biofilms may contribute to the persistent nature of pulmonary infections caused by this organism.
Enteric viruses evoke broad host immune responses resembling bacterial microbiome
Authors: Simone Dallari , Thomas Heaney , Adriana Rosas-Villegas , Neil Jessica A. , Serre-Yu Wong , Brown Judy J. , Kelly Urbanek , Dermody Terence S. , Ken Cadwell
Published: October 2020

Contributions of the viral component of the microbiome, the virome, to the development of innate and adaptive immunity are largely unknown. Here, we systematically defined the host response in mice to a panel of eukaryotic enteric viruses representing six different families. Most of these viruses asymptomatically infected the mice, the magnitude and duration of which was dependent on the microbiota. Flow cytometric and transcriptional profiling of mice mono-associated with these viruses unveiled general adaptations by the host, such as lymphocyte differentiation and IL-22 signatures in the intestine as well as numerous viral strain-specific responses that persist. Comparison with a dataset derived from analogous bacterial mono-association mice identified bacterial species that evoke an immune response comparable to the viruses we examined. These results expand an understanding of the immune space occupied by the enteric virome and underscore the importance of viral exposure events.
In vivoimaging of retrovirus infection reveals a role for Siglec-1/CD169 in multiple routes of transmission
Authors: Haugh Kelsey A. , Ladinsky Mark S. , Ullah Irfan , Pi Ruoxi , Gilardet Alexandre , Kumar Priti , Bjorkman Pamela J. , Mothes Walther , Uchil Pradeep D.
Published: October 2020

Early events in retrovirus transmission are determined by interactions between incoming viruses and frontline cells near entry sites. Despite their importance for retroviral pathogenesis, very little is known about these events. We developed a bioluminescence imaging (BLI)-guided multiscale imaging approach to study these eventsin vivo. Engineered murine leukemia reporter viruses allowed us to monitor individual stages of the retrovirus life cycle including virus particle flow, virus entry into cells, infection and spread for retroorbital, subcutaneous and oral routes. BLI permitted temporal tracking of orally administered retroviruses along the gastrointestinal tract as they traversed the lumen through Peyer’s Patch to reach the draining mesenteric sac. Importantly, capture and acquisition of lymph-, blood- and milk-borne retroviruses spanning three routes, was promoted by a common host factor, the I-type lectin CD169, expressed on sentinel macrophages. These results highlight how retroviruses co-opt the immune surveillance function of tissue resident sentinel macrophages for establishing infection.
Targeted modulation of protein liquid-liquid phase separation by evolution of amino-acid sequence
Authors: Lichtinger Simon M. , Garaizar Adiran , Collepardo-Guevara Rosana , Reinhardt Aleks
Published: October 2020

Rationally and efficiently modifying the amino-acid sequence of proteins to control their ability to undergo liquid-liquid phase separation (LLPS) on demand is not only highly desirable, but can also help to elucidate which protein features are important for LLPS. Here, we propose an innovative computational method that couples a genetic algorithm to a sequence-dependent coarse-grained protein model to evolve the amino-acid sequences of phase-separating intrinsically disordered protein regions (IDRs), and purposely enhance or inhibit their capacity to phase-separate. We apply it to the phase-separating IDRs of three naturally occurring proteins, namely FUS, hnRNPA1 and LAF1, as prototypes of regions that exist in cells and undergo homotypic LLPS driven by different types of intermolecular interaction. We find that the evolution of amino-acid sequences towards enhanced LLPS is driven in these three cases, among other factors, by an increase in the average size of the amino acids. However, the direction of change in the molecular driving forces that enhance LLPS (such as hydrophobicity, aromaticity and charge) depends on the initial amino-acid sequence: the critical temperature can be enhanced by increasing the frequency of hydrophobic and aromatic residues, by changing the charge patterning, or by a combination of both. Finally, we show that the evolution of amino-acid sequences to modulate LLPS is strongly coupled to the composition of the medium (e.g. the presence or absence of RNA), which may have significant implications for our understanding of phase separation within the many-component mixtures of biological systems.