bluuebunny/crossref_metadata_2025 huggingface dataset:
Siamese cat tyrosinase has enhanced proteasome degradation and increased cellular aggregation
Authors: Niesman Ingrid R.
Published: June 2020

Siamese cats are a notable example of a temperature-sensitive partial albinism phenotype. The signature color-pointing pattern is the result of an amino acid substitution – G302R – in the cysteine-rich domain of feline tyrosinase. The precise mechanism for the loss of tyrosinase enzyme activity due to this mutation is unknown.

Objective

We have used a cellular biology approach to begin unravel relationships between feline coloration, behavior and increased risk for feline cognitive dysfunction syndrome. GFP-fusion constructs of wild type domestic short hair tyrosinase and Siamese (G302R) tyrosinase generated to study cellular trafficking, degradation and the propensity for cellular aggregation.

Data Description

C-terminal GFP G302R expression has reduced Golgi localization, increased cytosolic fractions with reduced calnexin co-localization. N-terminal GFP constructs were retained in the ER, with little to no Golgi associated forms. C-terminal and N-terminal GFP G302R TYR is observed to have increased high molecular weight aggregation following proteasome inhibition.
Selective Vulnerability of Senescent Glioblastoma Cells to Bcl-XL Inhibition
Authors: Rahman Masum , Olson Ian , Mansour Moustafa , Carlstrom Lucas P. , Sutiwisesak Rujapope , Saber Rehan , Rajani Karishma , Warrington Arthur E , Howard Adam , Schroeder Mark , Chen Sisi , Decker Paul A. , Sananikone Eliot F. , Zhu Yi , Parney Ian F. , Burma Sandeep , Brown Desmond , Rodriguez Moses , Sarkaria Jann N. , Kirkland James , Burns Terry C.
Published: June 2020

Despite decades of research and numerous basic science advances, there have only marginal gains in improving glioblastoma multiforme survival. Therefore, new ideas and approaches for treating this aggressive disease are essential to drive progress forward. Conventional therapies, such as radiation and Temozolomide (TMZ), function to cause oxidative stress and DNA damage yielding a senescent-like state of replicative arrest in susceptible cells. However, increasing evidence demonstrates malignant cells can escape senescence leading to tumor recurrence. Ablation of non-replicating senescent tumor cells after radiation and chemotherapy may be an avenue to reduce the rates of tumor recurrence. Senolytic agents have been developed that selectively target senescent cells, but it remains unknown whether senolytics might be utilized against senescent-like glioma cells. We employed radiation or TMZ to induce a functionally senescent state in human glioblastoma cells. Viable cells that survive these treatments were then utilized to screen candidate senolytic drugs, to identify those selectively effective at ablating senescent-like cells over naïve non-tumor and proliferative cells. Among 10 candidate senolytic drugs evaluated, only Bcl-XL inhibitors demonstrated reproducible senolytic activity in radiated or TMZ-treated glioma across the majority of GBM cell lines evaluated. Conversely, Bcl-2 inhibitors and other established senolytic drugs failed to show any consistent senolytic activity. In agreement with these data, Bcl-XL knockdown selectively reduced the viability of senescent-like GBM cells, whereas knockdown of Bcl-2 or Bcl-W yielded no senolytic effect. These findings demonstrate the potential to harness radiation-induced biology to ablate latent surviving cells and highlight Bcl-XL dependency as a potential vulnerability of surviving GBM cells after exposure to radiation or TMZ.
pHLARE: A Genetically Encoded Ratiometric Lysosome pH Biosensor
Authors: Webb Bradley A. , Cook Jessica , Wittmann Torsten , Barber Diane L.
Published: June 2020

Many lysosome functions are determined by a lumenal pH of ~5.0, including the activity of resident acid-activated hydrolases. Lysosome pH (pHlys) is increased in neurodegenerative disorders and predicted to be decreased in cancers, making it a potential target for therapeutics to limit the progression of these diseases. Accurately measuring pHlys, however, is limited by currently used dyes that accumulate in multiple intracellular compartments and cannot be propagated in clonal cells for longitudinal studies orin vivodeterminations. To resolve this limitation, we developed a genetically encoded ratiometric pHlys biosensor, pHLARE (pH LysosomalActivityREporter), which localizes predominantly in lysosomes, has a dynamic range of pH 4.0 to 6.5, and can be stably expressed in cells. Using pHLARE we show decreased pHlys with inhibiting activity of the mammalian target of rapamycin complex 1 (mTORC1), in breast and pancreatic cancer cells compared with tissue-matched untransformed cells, and with the activated oncogene H-RasV12. pHLARE is a new tool to accurately measure pHlys, for improved understanding of lysosome dynamics that could be a promising therapeutic target.

Summary Statement

Most lysosome functions require a low lumenal pH, which is dysregulated in many human diseases. We report a new genetically biosensor to accurately measure lysosome pH dynamics, which we use to show decreased lysosome pH in cancer cell lines.
Mercury methylation by metabolically versatile and cosmopolitan marine bacteria
Authors: Lin Heyu , Ascher David B. , Myung Yoochan , Lamborg Carl H. , Hallam Steven J. , Gionfriddo Caitlin M. , Holt Kathryn E. , Moreau John W.
Published: June 2020

Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin in terrestrial and marine food webs. This process requires the gene pairhgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet (SI), British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, includingCalditrichaeota, SAR324 andMarinimicrobia, with the last by far the most active based onhgctranscription levels.Marinimicrobia hgcgenes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicted thatMarinimicrobiaHgcAB proteins contain the highly conserved structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several SI putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognised.
An emerging role ofPrevotella histicolaon estrogen-deficiency induced bone loss through the gut microbiota-bone axis
Authors: Wang Zhongxiang , Chen Kai , Wu Congcong , Chen Junhao , Pan Hao , Liu Yangbo , Wu Peng , Yuan Jiandong , Lang Junzhe , Du Juanjuan , Xu Jiake , Jin Keke , Chen Lei
Published: June 2020

Gut microbiota (GM)-bone axis has emerged as a crucial mediator in the maintenance of bone homeostasis. Estrogen-deficiency induced bone loss is closely associated with an altered GM. However, the underlying mechanisms remain not fully understood. To this end, feces samples collected from the postmenopausal patients with osteoporosis (PMO) and with normal bone mass (PMN) were examined by 16s rRNA gene sequencing. We found that GM in PMO group was featured by a significant decreased proportion of genusPrevotellain comparison with that in the PMN group. Next,Prevotella histicola(P.histicola), a typical specie ofPrevotella, was orally given to the mice following the ovariectomy (OVX) procedure and it significantly prevented OVX induced bone loss. Mechanistically, the protective effects ofP.histicolaon bone mass were found to be associated with the inhibition of osteoclastic resorption by attenuating osteoclastogenic cytokines expression and ameliorating gut permeability. Thus,P.histicolamay prevent estrogen-deficiency induced bone loss through the GM-bone axis.
Peripheral blood immune status at clinical onset correlates with severity of Coronavirus Disease 2019
Authors: Santoro Nathalie , Cignetti Alessandro , Tenace Valerio , Casonato Ines Clotilde , Cosseddu Domenico , Vizzini Margherita , De Rosa Giovanni , Geuna Massimo
Published: June 2020

The Coronavirus Disease 2019 (COVID-19) pandemic is a global threat to healthcare systems, requiring hospitalization in sub intensive and intensive care for respiratory syndrome in 25-30% of patients and accounting for a lethality up to 15%.

In this retrospective study the clinical characteristics of 215 COVID-19 patients were correlated with the peripheral blood immune status.

Different groups of COVID-19 patients may be identified on the basis of clinical behavior and a strong correlation between groups and age and comorbidities as well as with the immune profile is demonstrated. A lower age correlates with a lower severity of the disease differentiating between patients who may be quarantined at home and those requiring hospitalization. An older age (>82 years) together with a higher number of comorbidities is associated to a very severe prognosis. The absolute number of CD3+, CD4+, CD8+ T lymphocytes was progressively decreasing according to the severity of the disease and a CD3+ and CD8+ threshold indicating very severe cases is suggested.
Prevention of COVID-19 in Ghana: Compliance audit of selected transportation stations in the Greater Accra region of Ghana
Authors: Bonful Harriet Affran , Addo-Lartey Adolphina , Aheto Justice MK , Ganle John Kuumouri , Sarfo Bismark , Aryeetey Richmond
Published: June 2020

Globally, as little evidence exists on transmission patterns of COVID-19, recommendations to prevent infection include appropriate and frequent handwashing plus physical and social distancing. We conducted an exploratory observational study to assess compliance with these recommendations in selected transportation stations in Ghana. A one-hour audit of 45 public transport stations in the Greater Accra region was carried out between 27th and 29th March 2020. Using an adapted World Health Organization (WHO) hand hygiene assessment scale, the availability and use of handwashing facilities, social distancing, and ongoing public education on COVID-19 prevention measures were assessed, weighted and scored to determine the level of compliance of stations. Compliance with recommendations was categorized as “inadequate” “basic”, “intermediate” and “advanced” based on the overall score. The majority (80%) of stations in Accra have at least one Veronica Bucket with flowing water and soap but the number of washing places at each station is not adequate. Only a small minority (18%) of stations were communicating the need to wash hands frequently and appropriately, and to practice social/physical distancing while at the station. In most stations (95%), hand washing practice was either not observed or only infrequently. Almost all stations (93%) did not have alcohol-based hand sanitizers for public use, while social distancing was rarely (only 2%) practiced. In over 90% of the stations, face masks were either not worn or only worn by a few passengers. Compliance with COVID-19 prevention measures was inadequate in 13 stations, basic in 16 stations, intermediate in 7 stations, and advanced in 9 stations. Compliance with COVID-19 prevention measures in public transportation stations in the Greater Accra region remains a challenge. Awareness creation should aim to elevate COVID-19 risk perception of transportation operators and clients. Transport operators and stations need support and guidance to enforce hand washing and social distancing.
A Fractal Viewpoint to COVID-19 Infection
Authors: Sotolongo-Costa Oscar , Weberszpil José , Sotolongo-Grau Oscar
Published: June 2020

One of the central tools to control the COVID-19 pandemics is the knowledge of its spreading dynamics. Here we develop a fractal model capable of describe this dynamics, in term of daily new cases, and provide quantitative criteria for some predictions. We propose a fractal dynamical model using conformed derivative and fractal time scale. A Burr-XII shaped solution of the fractal-like equation is obtained. The model is tested using data from several countries, showing that a single function is able to describe very different shapes of the outbreak. The diverse behavior of the outbreak on those countries is presented and discussed. Moreover, a criterion to determine the existence of the pandemic peak and a expression to find the time to reach herd immunity are also obtained.
Monitoring life expectancy levels during the COVID-19 pandemic: Example of the unequal impact in Spanish regions
Authors: Trias-Llimós Sergi , Riffe Tim , Bilal Usama
Published: June 2020

Background

To provide an interpretable summary of the impact on mortality of the COVID-19 pandemic we estimate weekly and annual life expectancies at birth in Spain and its regions.

Methods

We used daily death count data from the Spanish MoMo, and death counts from 2018, and population on 1 July, 2019 by region (CCAA), age groups, and sex from the Spanish National Statistics Institute. We estimated weekly and annual (2019 and 2020*, the shifted annual calendar period up to June 14th 2020) life expectancies at birth as well as their differences with respect to 2019.

Results

Weekly life expectancies at birth in Spain were lower in weeks 11-20, 2020 compared to the same weeks in 2019. This drop in weekly life expectancy was especially strong in weeks 13 and 14 (March 23rd to April 5th), with national declines ranging between 6.1 and 7.6 years and maximum regional weekly declines of up to 15 years in Madrid. Annual life expectancy differences between 2019 and 2020 also reflected an overall drop in annual life expectancy of 0.8 years for both men and women. These drops ranged between 0 years in several regions (e.g. Canary and Balearic Islands) to 2.7 years among men in Madrid.

Conclusions

Life expectancy is an easy to interpret measure for understanding the heterogeneity of mortality patterns across Spanish regions. Weekly and annual life expectancy are sensitive useful indicators for understanding disparities and communicating the gravity of the situation because differences are expressed in intuitive year units.

Key messages

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Weekly and annual updated life expectancy are valuable indicators of the health impacts of the pandemic in populations.

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The impact of the COVID-19 pandemic in Spain has been severe and highly heterogeneous, with weekly life expectancy falls of up to 15 years in Madrid, and with annual life expectancy falls ranging between 0 and 2.7 years.

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Our results for Spain provide important insights into the magnitude of the pandemic in mortality levels across regions and are easy to interpret and compare.
Solar UV–B/A Radiation is Highly Effective in Inactivating SARS-CoV-2
Authors: Nicastro Fabrizio , Sironi Giorgia , Antonello Elio , Bianco Andrea , Biasin Mara , Brucato John R. , Ermolli Ilaria , Pareschi Giovanni , Salvati Marta , Tozzi Paolo , Trabattoni Daria , Clerici Mario
Published: June 2020

Solar UV-C photons do not reach Earth’s surface, but are known to be endowed with germicidal properties that are also effective on viruses. The effect of softer UV-B and UV-A photons, which copiously reach the Earth’s surface, on viruses are instead little studied, particularly on single-stranded RNA viruses.

Here we combine our measurements of the action spectrum of Covid-19 in response to UV light, Solar irradiation measurements on Earth during the SARS-CoV-2 pandemics, worldwide recorded Covid-19 mortality data and our “Solar-Pump” diffusive model of epidemics to show that (a) UV-B/A photons have a powerful virucidal effect on the single-stranded RNA virus Covid-19 and that (b) the Solar radiation that reaches temperate regions of the Earth at noon during summers, is sufficient to inactivate 63% of virions in open-space concentrations (1.5×103 TCID50/mL, higher than typical aerosol) in less than 2 minutes.

We conclude that the characteristic seasonality imprint displayed world-wide by the SARS-Cov-2 mortality time-series throughout the diffusion of the outbreak (with temperate regions showing clear seasonal trends and equatorial regions suffering, on average, a systematically lower mortality), might have been efficiently set by the different intensity of UV-B/A Solar radiation hitting different Earth’s locations at different times of the year.

Our results suggest that Solar UV-B/A play an important role in planning strategies of confinement of the epidemics, which should be worked out and set up during spring/summer months and fully implemented during low-solar-irradiation periods.
Prevalence and risk factors associated with Anxiety Symptoms and Disorders Among Chronic Kidney Disease patients – A Systematic Review and Meta-analysis of studies
Authors: Huang Caleb Weihao , Wee Poh Hui , Low Lian Leng , Koong Ying Leng Agnes , Htay Htay , Fan Qiao , Foo Wai Yin Marjorie , Seng Jun Jie Benjamin
Published: June 2020

Background

Anxiety is associated with poor health outcomes among chronic kidney disease (CKD) patients. This review summarizes the prevalence and risk factors associated with anxiety symptoms and disorders among CKD patients.

Methods

Articles evaluating the prevalence and risk factors associated with anxiety symptoms and disorders among CKD patients, as diagnosed via DSM 4th or 5th edition criteria, clinical interviews or validated questionnaires, were searched in Medline®, Embase®, PsychINFO® and CINAHL®. Using random-effects meta-analyses, prevalence of anxiety was estimated. A narrative review on the risk factors associated with anxiety was presented.

Results

From 4941 articles, 61 studies were included. Pooled prevalence of anxiety disorders (9 studies, n=1071) among CKD patients across studies was 18.9% while that of anxiety symptoms (52 studies, n=10,739) was 42.8%. Across continents, prevalence of anxiety symptoms was highest in Europe and Asia. Between pre-dialysis and dialysis patients, prevalence of anxiety symptoms was statistically comparable at 30.5% and 42.1% respectively. Most commonly studied risk factors associated with anxiety were female gender, increased age, concomitant depression, and increased comorbidities.

Conclusion

Given the high prevalence of anxiety disorders and symptoms, there is a need for developing clinical guidelines on anxiety screening among CKD patients, facilitating early identification of at-risk patients.
Auditory cortex activity measured with functional near-infrared spectroscopy is susceptible to masking by cortical blood stealing
Authors: Steinmetzger Kurt , Shen Zhengzheng , Riedel Helmut , Rupp André
Published: June 2020

To validate the use of functional near-infrared spectroscopy (fNIRS) in auditory perception experiments, combined fNIRS and electroencephalography (EEG) data were obtained from normal-hearing subjects passively listening to speech-like stimuli without linguistic content. The fNIRS oxy-haemoglobin (HbO) results were found to be inconsistent with the deoxy-haemoglobin (HbR) and EEG data, as they were dominated by pronounced cerebral blood stealing in anterior- to-posterior direction. This large-scale bilateral gradient in the HbO data masked the right-lateralised neural activity in the auditory cortex that was clearly evident in the HbR data and EEG source reconstructions. When the subjects were subsequently split into subgroups with more positive or more negative HbO responses in the right auditory cortex, the former group surprisingly showed smaller event-related potentials, less activity in frontal cortex, and increased EEG alpha power, all indicating reduced attention and vigilance. These findings thus suggest that positive HbO responses in the auditory cortex may not necessarily be a favourable result when investigating auditory perception using fNIRS. More generally, the results show that the interpretation of fNIRS HbO signals can be misleading and demonstrate the benefits of combined fNIRS-EEG analyses in resolving this issue.
A monogenic and fast-responding Light-Inducible Cre recombinase as a novel optogenetic switch
Authors: Duplus-Bottin Hélène , Spichty Martin , Triqueneaux Gérard , Place Christophe , Mangeot Philippe Emmanuel , Ohlmann Théophile , Vittoz Franck , Yvert Gaël
Published: June 2020

Optogenetics enables genome manipulations with high spatiotemporal resolution, opening exciting possibilities for fundamental and applied biological research. Here, we report the development of LiCre, a novel light-inducible Cre recombinase. LiCre is made of a single flavin-containing protein comprising the asLOV2 photoreceptor domain ofAvena sativafused to a Cre variant carrying destabilizing mutations in its N-terminal and C-terminal domains. LiCre can be activated within minutes of illumination with blue light, without the need of additional chemicals. When compared to existing photoactivatable Cre recombinases based on two split units, LiCre displayed faster and stronger activation by light as well as a lower residual activity in the dark. LiCre was efficient both in yeast, where it allowed us to control the production ofβ-carotene with light, and in human cells. Given its simplicity and performances, LiCre is particularly suited for fundamental and biomedical research, as well as for controlling industrial bioprocesses.
Use of signals of positive and negative selection to distinguish cancer genes and passenger genes
Authors: Bányai László , Trexler Mária , Kerekes Krisztina , Csuka Orsolya , Patthy László
Published: June 2020

A major goal of cancer genomics is to identify all genes that play critical roles in carcinogenesis. Most approaches focused on genes that are positively selected for mutations that drive carcinogenesis and neglected the role of negative selection. Some studies have actually concluded that negative selection has no role in cancer evolution. In the present work we have re-examined the role of negative selection in tumor evolution through the analysis of the patterns of somatic mutations affecting the coding sequences of human genes. Our analyses have confirmed that tumor suppressor genes are positively selected for inactivating mutations. Oncogenes, however, were found to display signals of both negative selection for inactivating mutations and positive selection for activating mutations. Significantly, we have identified numerous human genes that show signs of strong negative selection during tumor evolution, suggesting that their functional integrity is essential for the growth and survival of tumor cells.
Constitutional activation of BMP4 and WNT signalling in hESC results in impaired mesendoderm differentiation
Authors: Markouli C. , Couvreu De Deckersberg E. , Dziedzicka D. , Regin M. , Franck S. , Keller A. , Gheldof A. , Geens M. , Sermon K. , Spits C.
Published: June 2020

We identified a human embryonic stem cell subline that fails to respond to the differentiation cues needed to obtain mesendoderm derivatives, differentiating into trophoblast-like cells instead. RNA-sequencing analysis showed that the subline has hyperactivation of the WNT and BMP4 signalling. Modulation of these pathways with small molecules confirmed them as the cause of the differentiation impairment. While activation of WNT and BMP4 in control cells resulted in a loss of mesendoderm differentiation and induction of trophoblast markers, inhibition of these pathways in the subline restored its ability to differentiate. Karyotyping and exome sequencing analysis did not identify any changes in the genome that could account for the pathway deregulation. These findings add to the increasing evidence that different responses of stem cell lines to differentiation protocols are based on genetic and epigenetic factors, inherent to the line or acquired during cell culture.
Hierarchical disruption in the cortex of anesthetized monkeys as a new signature of consciousness loss
Authors: Signorelli Camilo Miguel , Uhrig Lynn , Kringelbach Morten , Jarraya Bechir , Deco Gustavo
Published: June 2020

Anesthesia induces a reconfiguration of the repertoire of functional brain states leading to a high function-structure similarity. However, it is unclear how these functional changes lead to loss of consciousness. Here we suggest that the mechanism of conscious access is related to a general dynamical rearrangement of the intrinsic hierarchical organization of the cortex. To measure cortical hierarchy, we applied the Intrinsic Ignition analysis to resting-state fMRI data acquired in awake and anesthetized macaques. Our results reveal the existence of spatial and temporal hierarchical differences of neural activity within the macaque cortex, with a strong modulation by the depth of anesthesia and the employed anesthetic agent. Higher values of Intrinsic Ignition correspond to rich and flexible brain dynamics whereas lower values correspond to poor and rigid, structurally driven brain dynamics. Moreover, spatial and temporal hierarchical dimensions are disrupted in a different manner, involving different hierarchical brain networks. All together suggest that disruption of brain hierarchy is a new signature of consciousness loss.
Quantitative longitudinal predictions of Alzheimer’s disease by multi-modal predictive learning
Authors: Prakash M. , Abdelaziz M. , Zhang L. , Strange B.A. , Tohka J. ,   Alzheimer’s Disease Neuroimaging Initiative
Published: June 2020

Background

Quantitatively predicting the progression of Alzheimer’s disease (AD) in an individual on a continuous scale, such as AD assessment scale-cognitive (ADAS-cog) scores, is informative for a personalized approach as opposed to qualitatively classifying the individual into a broad disease category. We hypothesize that multi-modal data and predictive learning models can be employed for longitudinally predicting ADAS-cog scores.

Methods

Multivariate regression techniques were employed to model baseline multi-modal data (demographics, neuroimaging, and cerebrospinal fluid based markers, and genetic factors) and future ADAS-cog scores. Prediction models were subjected to repeated cross-validation and the resulting mean absolute error and cross-validated correlation of the model assessed.

Results

Prediction models on multi-modal data outperformed single modal data up to 36 months. Incorporating baseline ADAS-cog scores to prediction models marginally improved predictive performance.

Conclusions

Future ADAS-cog scores were successfully estimated via predictive learning aiding clinicians in identifying those at greater risk of decline and apply interventions at an earlier disease stage and inform likely future disease progression in individuals enrolled in AD clinical trials.
Secretion, maturation and activity of a quorum-sensing peptide (GSP) inducing bacteriocins transcription inStreptococcus gallolyticus
Authors: Harrington Anthony , Proutiere Alexis , Dramsi Shaynoor , Tal-Gan Yftah
Published: June 2020

Streptococcus gallolyticussubsp.gallolyticus(Sgg) is an emerging opportunistic pathogen responsible for septicemia and endocarditis in the elderly. Invasive infections bySggare strongly linked to the occurrence of colorectal cancer (CRC). It was previously shown that increased secondary bile salts in CRC-conditions enhances the bactericidal activity of gallocin, a bacteriocin produced bySgg, enabling it to colonize the mouse colon by outcompeting resident enterococci. In a separate study, we have shown thatSggproduces and secretes a 21-mer peptide that activates bacteriocin production. This peptide was named CSP because of its sequence similarity with competence stimulating peptides found in other streptococci. Here we demonstrate that CSP is abona fidequorum-sensing peptide involved in activation of gallocin gene transcription. We therefore refer to CSP as GSP (gallocin stimulating peptide). GSP displays some unique features since itsN-terminal amino-acid lies three residues after the double glycine leader sequence. Herein, we set out to investigate the processing and export pathway that leads to mature GSP. We also conducted the first comprehensive structure-activity relationship (SAR) ofSggGSP to identify its key structural features.

Significance

Streptococcus gallolyticussubsp.gallolyticus(Sgg) is an opportunistic pathogen associated with colorectal cancer (CRC) and endocarditis.Sggutilizes quorum-sensing (QS) to regulate the production of a bacteriocin (gallocin) and gain selective advantage in colonizing the colon. In this manuscript, we report 1) the first structure-activty relationship study of theSggQS pheromone that regulates gallocin production; 2) evidence that the active QS pheromone is processed to its mature form by a unique ABC transporter and not processed by an extracellular protease; and 3) supporting evidence of interspecies interactions between streptococci pheromones. Our results revealed the minimal pheromone scaffold needed for gallocin activation and uncovered unique interactions between two streptococci species QS signals that warrant further studies.
Structure and assembly of CAV1 8S complexes revealed by single particle electron microscopy
Authors: Han Bing , Porta Jason C. , Hanks Jessica L. , Peskova Yelena , Binshtein Elad , Dryden Kelly , Claxton Derek P. , Mchaourab Hassane S. , Karakas Erkan , Ohi Melanie D. , Kenworthy Anne K.
Published: June 2020

Highly stable oligomeric complexes of the monotopic membrane protein caveolin serve as fundamental building blocks of caveolae. Current evidence suggests these complexes are disc shaped, but the details of their structural organization and how they assemble are poorly understood. Here, we address these questions using single particle electron microscopy of negatively stained recombinant 8S complexes of human Caveolin-1. We show that 8S complexes are toroidal structures ~15 nm in diameter that consist of an outer ring, an inner ring, and central protruding stalk. Moreover, we map the position of the N- and C-termini and determine their role in complex assembly, and visualize the 8S complexes in heterologous caveolae. Our findings provide critical insights into the structural features of 8S complexes and allow us to propose a new model for how these highly stable membrane-embedded complexes are generated.
Crystal structure of a novel guanine nucleotide exchange factor encoded by the scrub typhus pathogen Orientia tsutsugamushi
Authors: Lim Christopher , Berk Jason M. , Blaise Alyssa , Bircher Josie , Koleske Anthony J. , Hochstrasser Mark , Xiong Yong
Published: June 2020

Rho family GTPases regulate an array of cellular processes and are often modulated by pathogens to promote infection. Here, we identify a cryptic guanine nucleotide exchange factor (GEF) domain in the OtDUB protein encoded by the pathogenic bacterium Orientia tsutsugamushi. A proteomics-based OtDUB interaction screen identified numerous potential host interactors, including the Rho-GTPases Rac1 and Cdc42. We discovered a new domain in OtDUB with Rac1/Cdc42 GEF activity (OtDUBGEF), with higher activity toward Rac1 in vitro. While this GEF bears no obvious sequence similarity to known GEFs, crystal structures of OtDUBGEF alone (3.0 Å) and complexed with Rac1 (1.7 Å) reveal striking convergent evolution, with a distinct topology, on a V-shaped bacterial GEF fold shared with other bacterial GEF domains. Structure-guided mutational analyses identified residues critical for activity and a novel mechanism for nucleotide displacement. Ectopic expression of OtDUB activates Rac1 preferentially in cells, and expression of the OtDUBGEF alone alters cell morphology. Cumulatively, this work reveals a novel bacterial GEF within the multifunctional OtDUB that co-opts host Rac1 signaling to evoke changes in cytoskeletal structure.
Comparative MD simulations and advanced analytics based studies on wild-type and hot-spot mutant A59G HRas
Authors: Sharma Neeru , Sonavane Uddhavesh , Joshi Rajendra
Published: June 2020

The Ras family of proteins is known to play an important role in cellular signal transduction. The oncoprotein Ras is also found to be mutated in ∼90% of the pancreatic cancers, of which G12V, G13V, A59G and Q61L are the known hot-spot mutants. These ubiquitous proteins fall in the family of G-proteins, and hence switches between active GTP bound and inactive GDP bound states, which is hindered in most of its oncogenic mutant counterparts. Moreover, Ras being a GTPase has an intrinsic property to hydrolyze GTP to GDP, which is obstructed due to mutations and lends the mutants stuck in constitutively active state leading to oncogenic behavior. In this regard, the present study aims to understand the dynamics involved in the hot-spot mutant A59G-Ras using long classical MD simulations (∼10µs) and comparing the same with its wild-type counterpart. Advanced analytics using Markov State Model (MSM) based approach has been deployed to comparatively understand the transition path for the wild-type and mutant systems. Roles of crucial residues like Tyr32, Gln61 and Tyr64 have also been established using multivariate PCA analyses. Furthermore, this multivariate PCA analysis also provides crucial features which may be used as reaction coordinates for biased simulations for further studies. The absence of formation of pre-hydrolysis network is also reported for the mutant conformation, using the distance-based analyses (between crucial residues) of the conserved regions. The implications of this study strengthen the hypothesis that the disruption of the pre-hydrolysis network in the mutant A59G ensemble might lead to permanently active oncogenic conformation in the mutant conformers.
A tale of two fish: Comparative transcriptomics of resistant and susceptible steelhead following exposure toCeratonova shastahighlights differences in parasite recognition
Authors: Barrett Damien , Bartholomew Jerri L.
Published: June 2020

Diseases caused by myxozoan parasites represent a significant threat to the health of salmonids in both the wild and aquaculture setting, and there are no effective therapeutants for their control. The myxozoanCeratonova shastais an intestinal parasite of salmonids that causes severe enteronecrosis and mortality. Most fish populations appear genetically fixed as resistant or susceptible to the parasite, offering an attractive model system for studying the immune response to myxozoans. We hypothesized that early recognition of the parasite is a critical factor driving resistance and that susceptible fish would have a delayed immune response. RNA-seq was used to identify genes that were differentially expressed in the gills and intestine during the early stages ofC. shastainfection in both resistant and susceptible steelhead(Oncorhynchus mykiss).This revealed a downregulation of genes involved in the IFN-γ signaling pathway in the gills of both phenotypes. Despite this, resistant fish quickly contained the infection and several immune genes, including two innate immune receptors were upregulated. Susceptible fish, on the other hand, failed to control parasite proliferation and had no discernible immune response to the parasite, including a near-complete lack of differential gene expression in the intestine. Further sequencing of intestinal samples from susceptible fish during the middle and late stages of infection showed a vigorous yet ineffective immune response driven by IFN-γ, and massive differential expression of genes involved in cell adhesion and the extracellular matrix, which coincided with the breakdown of the intestinal structure. Our results suggest that the parasite may be suppressing the host’s immune system during the initial invasion, and that susceptible fish are unable to recognize the parasite invading the intestine or mount an effective immune response. These findings improve our understanding of myxozoan-host interactions while providing a set of putative resistance markers for future studies.
Combination of favorable gene haplotypes plays an important role in rice hybrid grain quality traits based on genome-wide association analysis
Authors: Li Lanzhi , Zheng Xingfei , Zhang Xueli , Xu Kai , Song Shufeng , Su Jing , Wu Chao , Li Zirong , Tang Wenbang , Diao Ying , Tang Zhonghai , Yuan Zheming , Hu Zhongli
Published: June 2020

Yield level and grain quality determine the commercial potential of rice (Oryza sativaL.) varieties. Mining and using genes that control important rice grain quality characteristics are major tasks for plant breeders. Here, a genome-wide association study was conducted to determine the genetic bases of 12 rice grain quality traits in 113 varieties and 565 testcross hybrids. A total of 56 significant SNPs were associated with 9 of the traits in variety phenotypic, general combining ability, testcross hybrid phenotypic and mid-parental heterotic datasets, from which 45 novel loci were identified. The cumulative effects of superior alleles or favorable haplotypes of genes closest to significant quality trait-associated loci were found in the four datasets. Additionally, the favorable gene haplotypes performed better than those of superior alleles in the variety and testcross hybrid datasets. Pyramiding the favorable haplotypes of five cloned rice grain quality genes resulted in a very low amylose content and high yield in the latter. These testcross hybrids had rice grain qualities similar to their parental lines but with much higher yields. The amylose content, grain width and grain length predictions for potential hybrids among the 113 varieties using genomic selection based on the BayesB method revealed a performance trend similar to those the testcross hybrids in our study. Thus, the selection of combination of favorable rice quality-related gene haplotypes is recommended to breed hybrids with high yields and elite grain qualities.
2D or Not 2D? An FMRI Study of How Dogs Visually Process Objects
Authors: Prichard Ashley , Chhibber Raveena , Athanassiades Kate , Chiu Veronica , Spivak Mark , Berns Gregory S.
Published: June 2020

Given humans’ habitual use of screens, they rarely consider potential differences when viewing two dimensional (2D) stimuli and real-world versions of dimensional stimuli. Dogs also have access to many forms of screens and touch pads, with owners even subscribing to dog-directed content. Humans understand that 2D stimuli are representations of real-world objects, but do dogs? In canine cognition studies, 2D stimuli are almost always used to study what is normally 3D, like faces, and may assume that both 2D and 3D stimuli are represented in the brain the same way. Here, we used awake fMRI of 15 dogs to examine the neural mechanisms underlying dogs’ perception of two- and three-dimensional objects after the dogs were trained on either a two- or three-dimensional version of the objects. Activation within reward processing regions and parietal cortex of the dog brain to 2D and 3D versions of objects was determined by their training experience, as dogs trained on one dimensionality showed greater activation to the dimension on which they were trained. These results show that dogs do not automatically generalize between two- and three-dimensional stimuli and caution against implicit assumptions when using pictures or videos with dogs.
Is Overfishing the Main or Only Factor in Fishery Resource Decline? The Case of The Magdalena River Fishery and Its Correlation with Anthropic Pressures
Authors: Hernández-Barrero Sandra , Barco Mauricio Valderrama , Barreto Reyes Carlos Guillermo , Sierra Luis Sierra , Stotz Wolfgang
Published: June 2020

Overfishing has been historically considered as the main cause of fish stock depletion worldwide. This paradigm has oriented fishery management towards a classical approach, under which externalities to fisheries were not considered as they were difficult to assess and measure. The aim of this study is to describe the dynamics of different environmental, economic, and demographic variables (water flow, forest cover, gold production, population growth, stored water volume, and sediments) in relation to the behavior of the fishery production in the Magdalena-Cauca river basin from 1980 to 2015. Generalized Additive Models were used to determine the variables that best explain fishery production. The findings confirmed that environmental deterioration of the Magdalena River basin explained at least 60% of the reduction in fishery production. Thus, we concluded that the traditional approach of making fishers responsible for the decline of fish production was a misguided argument, and before implementing restrictions on fishing activity, a better understanding of the overall system is crucial. Hence, fishery management should involve the economic and social sectors that affect the offer of ecosystem services within the basin, including fishing.
Biosynthesis of silver nanoparticles and exopolysaccharide using novel Thermophilic strain (Ts-1) ofBacillus amyloliquefaciens
Authors: Thota Sharath Chandra , Sreelatha Bathini
Published: June 2020

In the developing world, Nanotechnology became an efficient method in therapeutics, antimicrobials, diagnostics, catalysis, microelectronics, and high sensitivity biomolecular detection. As well as on the other hand, Exopolysaccharides are biopolymers which are also widely used in food formulation, bio- flocculants, bio-absorbents, drug delivery agents. As the chemical methods of synthesizing nanoparticles and polymers are environmentally risky, costly, and toxic. In the present study, we focused on production, purification, and characterization of silver nanoparticles (AgNPs) and exopolysaccharide (EPS) by eco-friendly, extracellular biosynthetic methods using novel thermophilicBacillus amyloliquefaciensstrain Ts-1. This strain was isolated from soil samples by employing pour and spread plate techniques. After obtaining pure culture, the bacterium was used for the synthesis of AgNPs and EPS. Nanoparticles were synthesized from AgNO3by using reducing agents secreted by bacteria, and Exopolysaccharide biosynthesis is carried out in three steps by the organism in the presence of a carbon source. Synthesis of colloidal AgNPs and EPS was monitored by UV-Visible spectroscopy and Visual observation, respectively. SEM, Edax and FTIR were performed for the characterization of the AgNPs and EPS such as their size, morphology and composition and we also showed the catalytic activity of AgNps in degradation of methylene blue.
Evaluation of Mosaicism and Off Target Mutations in CRISPR-Mediated Genome Edited Bovine Embryos
Authors: Hennig Sadie L. , Owen Joseph R. , Lin Jason C. , Young Amy E. , Ross Pablo J. , Van Eenennaam Alison L. , Murray James D.
Published: June 2020

The CRISPR/Cas9 genome editing tool has the potential to improve the livestock breeding industry by allowing for the introduction of desirable traits. Although an efficient and targeted tool, the CRISPR/Cas9 system can have some drawbacks, including off-target mutations and mosaicism, particularly when used in developing embryos. Here, we introduced genome editing reagents into single-cell bovine embryos to compare the effect of Cas9 mRNA and protein on the mutation efficiency, level of mosaicism, and evaluate potential off-target mutations utilizing next generation sequencing. We designed guide-RNAs targeting three loci (POLLED, H11, and ZFX) in the bovine genome and saw a significantly higher rate of mutation in embryos injected with Cas9 protein (84.2%) vs. Cas9 mRNA (68.5%). In addition, the level of mosaicism was higher in embryos injected with Cas9 mRNA (100%) compared to those injected with Cas9 protein (94.2%), with little to no unintended off-target mutations detected. This study demonstrates that the use of Cas9 protein, rather than Cas9 mRNA, results in a higher editing efficiency in bovine embryos while lowering the level of mosaicism. However, further optimization must be carried out for the CRISPR/Cas9 system to become feasible for single-step embryo editing in a commercial system.
Biomarker-assessed passive smoking in relation to cause-specific mortality: pooled data from 12 prospective cohort studies comprising 36 584 individuals
Authors: Kvaavik Elisabeth , Tverdal Aage , Batty G. David
Published: June 2020

Aims

While investigators have typically quantified the health risk of passive smoking by utilising self-reported exposure, prospective studies with objective ascertainment, which are less liable to measurement error, are rare. Using data pooling, we examined the relation of a biochemical assessment of passive smoking, salivary cotinine, with mortality from a range of causes.

Methods

We combined data from twelve cohort studies from England and Scotland initiated between 1998 and 2008. Study members were linked to national death registries. A total of 36 584 men and women aged 16 to 85 years of age reported that they were non-smoking at baseline, provided baseline salivary cotinine, and consented to mortality record linkage.

Results

A mean of 8.1 years of mortality follow-up of 36 584 non-smokers (16 792 men and 19 792 women) gave rise to 2367 deaths (775 from cardiovascular disease, 780 from all cancers, and 289 from smoking-related cancers). After controlling for a range of covariates, a 10 ng/ml increase in salivary cotinine level was related to an elevated risk of total (hazard ratios; 95% confidence interval: 1.46; 1.16, 1.83), cardiovascular (1.41; 0.96, 2.09), cancer (1.49; 1.00, 2.22) and smoking-related cancer mortality (2.92; 1.77, 4.83).

Conclusions

Passive smoking assessed biomedically was a risk factor for a range of health outcomes known to be causally linked to active smoking.