bluuebunny/crossref_metadata_2025 huggingface dataset:
Plasma-based strategy for inhibiting Candida albicans growth and CaMCA1 gene expression in vitro and reducing fungal pathogenicity in a murine model of vulvovaginal candidiasis
Authors: Ebrahimi-Shaghaghi Fatemeh , Atyabi Seyed-Mohammad , Razzaghi-Abyaneh Mehdi
Published: October 2021

Vulvovaginal candidiasis (VVC) is a common mucosal infection, mainly caused by Candida albicans. The use of common antifungal drugs in treatment of VVC is limited due to emergence of resistant fungal strains and severe side effects. Cold atmospheric plasma (CAP) as a novel therapeutic approach is proven to display strong antifungal activity against C. albicans. In the present study, the effects of CAP treatment on virulence and pathogenicity of C. albicans in a murine model was investigated. Candida albicans was treated with CAP at different time exposures. Fungal cell morphology and the expression profile of CaMCA1 gene in CAP-treated fungus was evaluated using electron microscopy and quantitative RT-PCR. Moreover, the mice model of VVC was developed using CAP-treated and non-treated C. albicans and characterized in terms of vaginal fungal burden, the rate of hyphae formation in the vaginal tissue and fluid and the inflammation degree of mice vaginal tissue. Significant reduction in CaMCA1 expression and remarkable mitochondrial degradation were observed in CAP-treated C. albicans cells. The lowest fungal burden, reduced hyphae formation, poor adherence of yeast cells to vaginal epithelium, and the low degree of inflammation were observed in mice infected with CAP-treated C. albicans. Suppression of CaMCA1 gene and mitochondrial degradation in CAP-treated C. albicans yeast cells may diminish yeast to hyphae transition and reduce fungal pathogenicity in murine model of VVC. CAP treatment can be considered as a novel and efficient therapeutic strategy against C. albicans and related Candida infections in practice.

Lay summary

CAP was successfully used to inhibit fungal growth and CaMCA1 gene expression in C. albicans. It caused morphological alterations in membranous structures of the yeast cells and finally led to the cell death. CAP meaningfully reduced C. albicans virulence and pathogenicity in a murine model of VVC.
Astraeus IV: quantifying the star formation histories of galaxies in the Epoch of Reionization
Authors: Legrand Laurent , Hutter Anne , Dayal Pratika , Ucci Graziano , Gottlöber Stefan , Yepes Gustavo
Published: October 2021

We use the astraeus framework, which couples an N-body simulation with a semi-analytic model for galaxy formation and a semi-numerical model for reionization, to quantify the star formation histories (SFHs) of galaxies in the first billion years. Exploring four models of radiative feedback, we fit the SFH of each galaxy at $z$ > 5 as log(SFR($z$)) = −α(1 + $z$) + β; star formation is deemed stochastic if it deviates from this fit by more than $\Delta _\mathrm{SFR}=0.6\,$dex. Our key findings are as follows: (i) The fraction of stellar mass formed and time spent in the stochastic phase decrease with increasing stellar mass and redshift $z$. While galaxies with stellar masses of $M_\star \sim 10^7\rm M_\odot$ at $z$ ∼ 5 (10) form $\sim 70{{\ \rm per\ cent}}~(20{{\ \rm per\ cent}})$ of their stellar mass in the stochastic phase, this reduces to $\lt 10{{\ \rm per\ cent}}$ at all redshifts for galaxies with $M_\star \gt 10^{10}\rm M_\odot$; (ii) the fractional mass assembled and lifetime spent in the stochastic phase do not significantly change with the radiative feedback model used; and (iii) at all redshifts, α increases (decreases for the strongest radiative feedback model) with stellar mass for galaxies with $M_\star \lesssim 10^{8.5}\rm M_\odot$ and converges to ∼0.18 for more massive galaxies; β always increases with stellar mass. Our proposed fits can reliably recover the stellar masses and mass-to-light ratios for galaxies with $M_\star \sim 10^{8}\!-\!10^{10.5}\,\rm M_\odot$ and ${\it M}_{\rm UV}\sim -17~{\rm to}~-23$ at $z$ ∼ 5–9. This physical model can therefore be used to derive the SFHs for galaxies observed by a number of forthcoming instruments.
MOSS I: Double radio relics in the Saraswati supercluster
Authors: Parekh V , Kincaid R , Thorat K , Hugo B , Sankhyayan S , Kale R , Oozeer N , Smirnov O , Heywood I , Makhathini S , van der Heyden K
Published: October 2021

Superclusters are the largest objects in the Universe, and they provide a unique opportunity to study how galaxy clusters are born at the junction of the cosmic web as well as the distribution of magnetic fields and relativistic particles beyond cluster volume. The field of radio astronomy is going through an exciting and important era of the Square Kilometer Array (SKA). We now have the most sensitive functional radio telescopes, such as the MeerKAT, which offers high angular resolution and sensitivity towards diffuse and faint radio sources. To study the radio environments around supercluster, we observed the (core part of) Saraswati supercluster with the MeerKAT. From our MeerKAT Observation of the Saraswati Supercluster (MOSS) project, the initial results of the pilot observations of two massive galaxy clusters, A2631 and ZwCl2341.1+0000, which are located around the dense central part of the Saraswati supercluster, were discussed. In this paper, we describe the observations and data analysis details, including direction-dependent calibration. In particular, we focus on the ZwCl2341.1+0000 galaxy cluster, which hosts double radio relics and puzzling diffuse radio source in the filamentary network. We have imaged these double radio relics in our high resolution and sensitive L-band MeerKAT observation and a puzzling radio source, located between relics, in the low-resolution image. We also derived the spectra of double radio relics using MeerKAT and archival GMRT observations. The following papers will focus on the formation of radio relics and halo, as well as radio galaxy properties in a supercluster core environment.
Bipolar molecular outflow from M17
Authors: Sofue Yoshiaki
Published: October 2021

Kinematics of the molecular clouds in the star-forming complex M17 is studied using the high-resolution CO-line mapping data at resolution (20 arcsec ∼ 0.2 pc) with the Nobeyama 45-m telescope. The northern molecular cloud of M17, which we call the molecular ‘lobe’, is shown to have an elongated shell structure around a top-covered cylindrical cavity. The lobe is expanding at ∼5 km s−1 in the minor axis direction, and at ∼3/cos  i km s−1 in the major axis direction, where i is the inclination of the major axis. The kinetic energy of the expanding motion is on the order of ∼3 × 1049 erg. We show that the lobe is a backyard structure having the common origin to the denser molecular ‘horn’ flowing out from NGC 6618 toward the south, so that the lobe and horn compose a bipolar outflow. Intensity distributions across the lobe and horn show a double-peak profile typical for a cylinder around a cavity. Position–velocity diagrams (PVD) across the lobe and horn exhibit open-ring structure with the higher and/or lower-velocity side(s) being lacking or faded. This particular PVD behaviour can be attributed to outflow in a conical cylinder with the flow velocity increasing toward the lobe and horn axes.
Radio emission from colliding outflows in high-mass X-ray binaries with strongly magnetized neutron stars
Authors: Chatzis Margaritis , Petropoulou Maria , Vasilopoulos Georgios
Published: October 2021

We present a toy model for radio emission in HMXBs with strongly magnetized NSs where a wind-collision region is formed by the NS outflow and the stellar wind of the massive companion. Radio emission is expected from the synchrotron radiation of shock-accelerated electrons and the free-free emission of the stellar wind. We found that the predicted relation between the GHz luminosity (LR) and the accretion X-ray luminosity (LX) can be written as $L_R \propto L_X^b$ for most parameters. No correlation with X-rays is expected (b = 0) when the thermal emission of the stellar wind dominates in radio. We typically find a steep correlation (b = 12/7) for sub-Eddington X-ray luminosities and a more shallow one (b = 2(p − 1)/7) for super-Eddington X-ray luminosities, where p is the power-law index of accelerated electrons. The maximum predicted radio luminosity is independent of the NS properties, while it depends on the stellar wind momentum, binary separation distance, and the minimum electron Lorentz factor. Using a Bayesian approach we modelled the radio observations of Swift J0243.6+6124 that cover a wide range of mass accretion rates. Our results support a shock origin for the radio detections at sub-Eddington X-ray luminosities. However, no physically meaningful parameters could be found for the super-Eddington phase of the outburst, suggesting a different origin. Future observations with more sensitive instruments might reveal a large number of HMXBs with strongly magnetized NSs in radio, allowing determination of the slope in the LR − LX relation, and putting the wind-collision scenario into test.
m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome
Authors: Ma Jiongming , Song Bowen , Wei Zhen , Huang Daiyun , Zhang Yuxin , Su Jionglong , de Magalhães João Pedro , Rigden Daniel J , Meng Jia , Chen Kunqi
Published: October 2021

5-Methylcytosine (m5C) is one of the most prevalent covalent modifications on RNA. It is known to regulate a broad variety of RNA functions, including nuclear export, RNA stability and translation. Here, we present m5C-Atlas, a database for comprehensive collection and annotation of RNA 5-methylcytosine. The database contains 166 540 m5C sites in 13 species identified from 5 base-resolution epitranscriptome profiling technologies. Moreover, condition-specific methylation levels are quantified from 351 RNA bisulfite sequencing samples gathered from 22 different studies via an integrative pipeline. The database also presents several novel features, such as the evolutionary conservation of a m5C locus, its association with SNPs, and any relevance to RNA secondary structure. All m5C-atlas data are accessible through a user-friendly interface, in which the m5C epitranscriptomes can be freely explored, shared, and annotated with putative post-transcriptional mechanisms (e.g. RBP intermolecular interaction with RNA, microRNA interaction and splicing sites). Together, these resources offer unprecedented opportunities for exploring m5C epitranscriptomes. The m5C-Atlas database is freely accessible at https://www.xjtlu.edu.cn/biologicalsciences/m5c-atlas.
Availability and role of clinical pharmacists in ambulatory neuro-oncology
Authors: Patel Mallika P , Lipp Eric S , Miller Elizabeth S , Healy Patrick N , Herndon James E , Peters Katherine B
Published: October 2021

Background

Outpatient clinics treating neuro-oncology patients are becoming more multidisciplinary. Utilization of all team members is critical for the holistic care of these complex patients. Specifically, the role of clinical pharmacist (CP) in the ambulatory clinic remains undefined and will likely evolve as more therapeutics are developed for CNS malignancies. We queried the Society for Neuro-Oncology (SNO) membership about the availability of a CP in their ambulatory setting and, if present, the role of that CP.

Methods

In an IRB-exempt study, we surveyed the SNO community and analyzed responses to queries about CPs in the ambulatory setting.

Results

Of the 65 SNO members who responded, 52 were clinical members. Of these 52 clinicians, the majority were physicians (88.5%, n = 46). Of these physicians, most were in academic practices (93.5%, n = 43). Over half of the 52 clinical respondents (51.9%, n = 27) reported that they saw ≥30 primary brain tumor patients per month, thus typifying busy clinics. Despite having busy clinics, only 12 (28.6%) of 42 providers with access to a CP reported that their CP was solely dedicated to neuro-oncology patients. For the respondents who had access to a CP, only ~two-thirds of those CPs had direct patient interaction. The top 3 roles of the CP included medication review, chemotherapy dosing/modifications, and practice guideline development; none of which involve direct patient interaction.

Conclusions

We found that while our surveyed population of SNO clinical members have demanding outpatient practices, most do not have the support or expertise of dedicated neuro-oncology CPs.
Misregulation of MYB16 expression causes stomatal cluster formation by disrupting polarity during asymmetric cell divisions
Authors: Yang Shao-Li , Tran Ngan , Tsai Meng-Ying , Ho Chin-Min Kimmy
Published: October 2021

Stomatal pores and the leaf cuticle regulate evaporation from the plant body and balance the tradeoff between photosynthesis and water loss. MYB16, encoding a transcription factor involved in cutin biosynthesis, is expressed in stomatal lineage ground cells, suggesting a link between cutin biosynthesis and stomatal development. Here, we show that the downregulation of MYB16 in meristemoids is directly mediated by the stomatal master transcription factor SPEECHLESS (SPCH) in Arabidopsis thaliana. The suppression of MYB16 before an asymmetric division is crucial for stomatal patterning, as its overexpression or ectopic expression in meristemoids increased stomatal density and resulted in the formation of stomatal clusters, as well as affecting the outer cell wall structure. Expressing a cutinase gene in plants ectopically expressing MYB16 reduced stomatal clustering, suggesting that cutin affects stomatal signaling or the polarity setup in asymmetrically dividing cells. The clustered stomatal phenotype was rescued by overexpressing EPIDERMAL PATTERNING FACTOR2, suggesting that stomatal signaling was still functional in these plants. Growing seedlings ectopically expressing MYB16 on high-percentage agar plates to modulate tensile strength rescued the polarity and stomatal cluster defects of these seedlings. Therefore, the inhibition of MYB16 expression by SPCH in the early stomatal lineage is required to correctly place the polarity protein needed for stomatal patterning during leaf morphogenesis.
Knowledge, attitudes and control practices regarding venomous arthropods among staff and students in a Nigerian public university campus
Authors: Ogbusu Vivian Onyinyechukwu , Onyido Angus Ejidikeme , Okechukwu Chidiebere Emmanuel , Okwelogu Izunna Somadina
Published: October 2021

Background

The objectives of this study were to assess the knowledge, attitudes and control practices among the staff and students of Nnamdi Azikiwe University (NAU), Awka, Anambra State, Nigeria, regarding venomous arthropods.

Methods

The knowledge, attitudes and control practices regarding venomous arthropods were assessed in 350 participants.

Results

The respondents were aware of the presence of venomous arthropods at NAU and they had seen them on campus, with spiders (40.44%) being the most common and electric ants (1.39%) being the least common. The control practices applied to limit the activities of these arthropods included keeping the environment clean (40.80%), the use of insecticides (37.33%), the use of repellents (8.68%), spraying houses with kerosene (7.81%), spraying of fuel on the arthropods (3.47%), screening of houses (1.39%) and the use of bed nets (0.52%).

Conclusions

An assessment and determination of knowledge, attitudes and control practices regarding venomous arthropods among the staff and students of NAU is necessary in order to improve the preventive measures to reduce injuries caused by venomous arthropod encounters, which are some of the most underestimated health hazards in tropical regions, including southeastern Nigeria, affecting primarily rural communities. According to the findings of our study, students and staff at NAU are rarely involved in life-threatening incidents as a result of their encounters with venomous arthropods and most apply several globally accepted standard practices for the control of venomous arthropods.
Clinical Transition: RN to BSN Students’ Perceptions of Their Abilities to Meet Program Outcomes
Authors: Connerton Charlotte S. , Hand Mikel W. , Wooton Angela K.
Published: October 2021

The purpose of this study was to analyze RN to BSN students’ perceptions of their abilities to meet program outcomes through their clinical experiences with a clinical teaching associate and after assuming responsibility for planning and directing clinical learning activities. A mixed-methods approach was used. Most students (87 percent) reported achievement of program outcome measures. Students demonstrated real-world learning and application through clinical experiences and successfully met program outcomes.
Preparing for Next Generation NCLEX® Through Team-Based Learning: Student Perspectives
Authors: Rhodes Kathleen A. , Carr Kayla , McElwain Sharon , Stewart Mary W.
Published: October 2021

The Next Generation NCLEX® requires higher levels of understanding for new registered nurses to practice safely. Team-based learning (TBL) offers a rigorous but pragmatic approach to achieve that aim. TBL employs collaborative strategies for structured problem-solving, a key focus of contemporary nurse educators. In this prospective study, a faculty team at a second-degree, accelerated baccalaureate nursing program within the southeast United States evaluated student perspectives of TBL. Overall findings revealed positive student experiences (n = 30, with three students on an alternate plan of study) in all aspects of the method.
Undibacterium baiyunense sp. nov., Undibacterium curvum sp. nov., Undibacterium fentianense sp. nov., Undibacterium flavidum sp. nov., Undibacterium griseum sp. nov., Undibacterium hunanense sp. nov., Undibacterium luofuense sp. nov., Undibacterium nitidum sp. nov., Undibacterium rivi sp. nov., Undibacterium rugosum sp. nov. and Undibacterium umbellatum sp. nov., isolated from streams in China
Authors: Lu Huibin , Liu Fei , Deng Tongchu , Xu Meiying
Published: October 2021

Twelve Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (CY7WT, CY18WT, CY22WT, FT31WT, FT137WT, FT147WT, BYS50W, BYS107WT, LFS511WT, LX15WT, LX22WT and NL8WT) were isolated from streams in China. Comparisons based on 16S rRNA gene sequences indicated that these strains take species of genus

Undibacterium

as close neighbours. The reconstructed phylogenetic and phylogenomic trees also showed that these strains cluster with species of genus

Undibacterium

together. The genome G+C contents of these strains were in the range of 45.3 to 53.3 mol%. The calculated pairwise OrthoANIu values and digital DNA–DNA hybridization values among these strains and related strains were in the range of 70.4 to 94.1% and 19.3 to 55.3% except that the values between strains CY7WT and BYS50W were 99.0 and 91.8 %, respectively. Q-8 was their predominant respiratory quinone. C16 : 1
 ω7c and C16 : 0 were their major fatty acids. Their polar lipids profiles were similar, including phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and two kinds of unidentified aminolipids. Combining polyphasic taxonomic characteristics and phylogenetic relationships, twelve strains should represent eleven independent novel species of genus

Undibacterium

, for which the names Undibacterium baiyunense sp. nov. (type strain BYS107WT=GDMCC 1.2453T=KCTC 82653T), Undibacterium curvum sp. nov. (type strain CY22WT=GDMCC 1.1906T=KACC 21951T), Undibacterium fentianense sp. nov. (type strain FT137WT=GDMCC 1.2456T=KCTC 82656T), Undibacterium flavidum sp. nov. (type strain LX15WT=GDMCC 1.1910T=JCM 34286T), Undibacterium griseum sp. nov. (type strain FT31WT=GDMCC 1.1908T=KACC 21953T), Undibacterium hunanense sp. nov. (type strain CY18WT=GDMCC 1.1904T=KACC 21949T), Undibacterium luofuense sp. nov. (type strain LFS511WT=GDMCC 1.2458T=KCTC 82658T), Undibacterium nitidum sp. nov. (type strain LX22WT=GDMCC 1.1912T=KACC 21957T), Undibacterium rivi sp. nov. (type strain FT147WT=GDMCC 1.2457T=KCTC 82657T), Undibacterium rugosum sp. nov. (type strain CY7WT=GDMCC 1.1903T=KACC 21961T) and Undibacterium umbellatum sp. nov. (type strain NL8WT=GDMCC 1.1915T=KACC 21960T) are proposed.
A novel NS3/4A protease dependent cleavage site within pestiviral NS2
Authors: Walther Thomas , Bruhn Barbara , Isken Olaf , Tautz Norbert
Published: October 2021

Pestiviruses like bovine viral diarrhoea virus (BVDV) and classical swine fever virus (CSFV) belong to the family Flaviviridae. A special feature of the Flaviviridae is the importance of nonstructural (NS) proteins for both genome replication and virion morphogenesis. The NS2-3-4A region and its regulated processing by the NS2 autoprotease and the NS3/4A protease plays a central role in the pestiviral life cycle. We report the identification and characterization of a novel internal cleavage in BVDV NS2, which is mediated by the NS3/4A protease. Further mapping using the NS2 of BVDV-1 strain NCP7 showed that cleavage occurs between L188 and G189. This cleavage site represents a novel sequence motif recognized by the NS3/4A protease and is conserved between the pestivirus species A, B and D. Inhibition of this internal NS2 cleavage by mutating the cleavage site did not cause obvious effects on RNA replication or virion morphogenesis in cultured cell lines. Accordingly, this novel internal NS2 cleavage adds an additional layer to the already complex polyprotein processing of Pestiviruses and might further extend the repertoires of the multifunctional NS2. However, unravelling of the functional relevance of this novel processing event in NS2, therefore, awaits future in vivo studies.
Dysregulation of circulating protease activity in Covid-19-associated superinfection
Authors: Dos Santos Fernando , Li Joyce B. , Juocys Nathalia , Mazor Rafi , Beretta Laura , Coufal Nicole G. , Lam Michael T.Y. , Odish Mazen F. , Irigoyen Maria C. , O’Donoghue Anthony J. , Aletti Federico , Kistler Erik B.
Published: October 2021

Infection by SARS-CoV-2 and subsequent COVID-19 can cause viral sepsis and septic shock. Several complications have been observed in patients admitted to the intensive care unit (ICU) with COVID-19, one of those being bacterial superinfection. Based on prior evidence that dysregulated systemwide proteolysis is associated with death in bacterial septic shock, we investigated whether protease activity and proteolysis could be elevated in COVID-19-induced sepsis with bacterial superinfection. In particular, we sought to assess the possible implications on the regulation of protein systems, such as for instance the proteins and enzymes involved in the clotting cascade.

Blood samples collected at multiple time points during the ICU stay of four COVID-19 patients were analyzed to quantify: a) the circulating proteome and peptidome by mass spectrometry; b) plasma enzymatic activity of trypsin-like substrates and five clotting factors (plasmin, thrombin, factor VII, factor IX, factor X) by a fluorogenic assay.

Of the four patients, one was diagnosed with bacterial superinfection on day 7 after beginning of the study and later died. The other three patients all survived (ICU length-of-stay 11.25±6.55 days, hospital stay of 15.25±7.18 days). Spikes in protease activity (factor VII, trypsin-like activity) were detected on day 7 for the patient who died. Corresponding increases in the total intensity of peptides derived by hydrolysis of plasma proteins, especially of fibrinogen degradation products, and a general reduction of coagulation proteins, were measured as well. A downregulation of endogenous enzymatic inhibitors, in particular trypsin inhibitors, characterized the non-surviving patient throughout her ICU stay. Enzymatic activity was stable in the patients who survived.

Our study highlights the potential of multiomics approaches, combined with quantitative analysis of enzymatic activity, to i) shed light on proteolysis as a possible pathological mechanism in sepsis and septic shock, including COVID-19-induced sepsis; ii) provide additional insight into malfunctioning protease-mediated systems, such as the coagulation cascade; and iii) describe the progression of COVID-19 with bacterial superinfection.
Diamond Raman Laser and Yb Fiber Amplifier for In Vivo Multiphoton Fluorescence Microscopy
Authors: Engelmann Shaun A. , Zhou Annie , Hassan Ahmed M. , Williamson Michael R. , Jarrett Jeremy W. , Perillo Evan P. , Spence David J. , Jones Theresa A. , Dunn Andrew K.
Published: October 2021

Here we introduce a fiber amplifier and a diamond Raman laser that output high powers (6.5 W, 1.3 W) at valuable wavelengths (1060 nm, 1250 nm) for multiphoton excitation of red-shifted fluorophores. These custom excitation sources are both simple to construct and cost-efficient in comparison to similar custom and commercial alternatives. Furthermore, they operate at a repetition rate (80 MHz) that allows fast image acquisition using resonant scanners. We demonstrate our system’s compatibility with fast resonant scanning, the ability to acquire neuronal images, and the capability to image vasculature at deep locations (>1 mm) within the mouse cerebral cortex.
Plasticity of Neural Connections Underlying Oxytocin-mediated Parental Behaviors of Male Mice
Authors: Inada Kengo , Hagihara Mitsue , Tsujimoto Kazuko , Abe Takaya , Konno Ayumu , Hirai Hirokazu , Kiyonari Hiroshi , Miyamichi Kazunari
Published: October 2021

The adult brain can flexibly adapt behaviors to specific life-stage demands. For example, while sexually naïve male mice are aggressive to the conspecific young, they start to provide caregiving to infants around the time when their own young are expected. How such behavioral plasticity is implemented at the level of neural connections remains poorly understood. Using viral-genetic approaches, here we establish hypothalamic oxytocin neurons as key regulators of parental caregiving behaviors of male mice. We then used rabies virus-mediated unbiased screen to identify excitatory neural connections originating from the lateral hypothalamus to the oxytocin neurons to be drastically strengthened when male mice become fathers. These connections are functionally relevant, as their activation suppresses pup-directed aggression in virgin males. These results demonstrate the life-stage associated, long-distance, and cell-type-specific plasticity of neural connections in the hypothalamus, the brain region classically assumed to be hard-wired.

Highlight

–

OT is indispensable for parental caregiving behavior of male mice

–

Activation of OT neurons triggers paternal caregiving behavior in otherwise infanticidal sexually-naïve male mice partly via OT ligand

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Unbiased rabies virus-mediated screening reveals enhanced connectivity originated from excitatory LHA neurons to OT neurons in fathers.

–

This structural plasticity can support behavioral plasticity
GAMES: A dynamic model development workflow for rigorous characterization of synthetic genetic systems
Authors: Dray Kate E. , Muldoon Joseph J. , Mangan Niall M. , Bagheri Neda , Leonard Joshua N.
Published: October 2021

Mathematical modeling is invaluable for advancing understanding and design of synthetic biological systems. However, the model development process is complicated and often unintuitive, requiring iteration on various computational tasks and comparisons with experimental data. Ad hoc model development can pose a barrier to reproduction and critical analysis of the development process itself, reducing potential impact and inhibiting further model development and collaboration. To help practitioners manage these challenges, we introduceGAMES: a workflow forGeneration andAnalysis ofModels forExploringSynthetic systems that includes both automated and human-in-the-loop processes. We systematically consider the process of developing dynamic models, including model formulation, parameter estimation, parameter identifiability, experimental design, model reduction, model refinement, and model selection. We demonstrate the workflow with a case study on a chemically responsive transcription factor. The generalizable workflow presented in this tutorial can enable biologists to more readily build and analyze models for various applications.

Graphical Abstract
Escherichia coli ribosomal protein S1 enhances the kinetics of ribosome biogenesis and RNA decay
Authors: Duval Mélodie , Prévost Karine , Bandyra Katarzyna J. , Helfer Anne Catherine , Korepanov Alexey , Bakhti Latifa , Kuhn Lauriane , Springer Mathias , Romby Pascale , Luisi Ben F. , Massé Eric , Marzi Stefano
Published: October 2021

Escherichia coli ribosomal protein S1 is essential for translation initiation of mRNAs and for cellular viability. Two oligonucleotide binding (OB)-fold domains located in the C-terminus of S1 are dispensable for growth, but their deletion causes a cold-shock phenotype, loss of motility and deregulation of RNA mediated stress responses. Surprisingly, the expression of the small regulatory RNA RyhB and one of its repressed target mRNA, sodB, are enhanced in the mutant strain lacking the two OB domains. Using in vivo and in vitro approaches, we show that RyhB retains its capacity to repress translation of target mRNAs in the mutant strain but becomes deficient in triggering rapid turnover of those transcripts. In addition, the mutant is defective in of the final step of the RNase E-dependent maturation of the 16S rRNA. This work unveils an unexpected function of S1 in facilitating ribosome biogenesis and RyhB-dependent mRNA decay mediated by the RNA degradosome. Through its RNA chaperone activity, S1 participates to the coupling between ribosome biogenesis, translation, and RNA decay.
SiglecFhigh neutrophils in lung tumor tissues suppress local CD8 T cell responses and limit the efficacy of anti PD-L1 antibodies
Authors: Simoncello Francesca , Piperno Giulia Maria , Caronni Nicoletta , Battini Tiziana , Cappelletto Ambra , Bicciato Silvio , Benvenuti Federica
Published: October 2021

Background

Tumor infiltrating neutrophils generally correlates to worst prognosis and refractoriness to immunotherapy yet the complexity and significance of diverse subsets resident in tumor tissues has just begun to emerge. In lung tumors, a network of neutrophils states with graded protumorigenic properties is conserved between mouse and humans and include a subset of mature, long lived cells expressing the sialic-acid-binding protein SiglecF (SiglecFhigh neu). The mechanism of recruitment of SiglecFhigh neu into tumor tissues and the impact on local anti-tumor T cell responses and interference with immunotherapy is still elusive.

Methods

We used an immunogenic model of KrasG12D Tp53 null adenocarcinoma of the lung to screen for factors inducing the recruitment of SiglecFhigh neu, followed by gene editing to delete selected candidates. We analyzed frequencies and effector functions of endogenous CD8 T cell responses in controls and SiglecFhigh neu depleted tumors by flow cytometry and functional assays. Tissues fluorescence and confocal imaging of lung sections was used to explore the relative distribution of neu and CD8 T cells. To establish the impact of SiglecFhigh neu on anti-tumoral immune responses we treated cohort of animals with anti-PD-L1 antibodies to evaluate tumor growth in control conditions and under therapy.

Results

We found that tumor tissues express high levels of CXCL5, mapping to cancer cells. Upon deletion of chemokine expression by gene editing, the recruitment of SiglecFhigh neu was almost entirely abrogated. In tumors depleted of SiglecFhigh neu, the density of tumor specific endogenous CD8 T cells was 3-fold higher than in controls and showed significantly enhanced activation and effector functions. Importantly, checkpoint blockade with anti PD-L1 antibodies was ineffective in control tumors but showed a significant benefit in SiglecFhigh neu depleted tumors.

Conclusion

This study demonstrates that SiglecFhigh neu differentiating in lung tumor tissues inhibit local CD8 T cell responses and interfere with the success of checkpoint blockade. These data suggest that blocking selectively tissue resident neu may promote better responses to immunotherapy.
Cytometric Analysis of Diverse Glaucophyte Species Reveals Distinctive Signals Useful for Fluorescence-Based Detection and Sorting
Authors: Calvaruso Rossella , Lawrence Janice , Reyes-Prieto Adrian
Published: October 2021

Glaucophytes, red algae and viridiplants (green algae and land plants) are formally united in the supergroup Archaeplastida. Although diverse molecular and genomic evidence suggest the common origin of the three Archaeplastida lineages, the lack of a robust glaucophyte knowledgebase has limited comprehensive evaluations of competing hypotheses. Glaucophytes are rare and apparently confined to freshwater habitats. However, the distribution and diversity of these algae have not been thoroughly explored owing to challenges with detecting and isolating novel specimens. Here we examined the cytometric signatures of representative species of the genera Cyanophora, Cyanoptyche, Glaucocystis and Gloeochaete for a distinctive signal that would aid identification. Most glaucophytes analyzed presented a relatively high red fluorescence signal due to the presence of the blue phycobiliproteins C-phycocyanin and allophycocyanin. Cell-size differences and the concurrent presence of the red phycobiliprotein phycoerythrin in other algal lineages, such as red algae and cryptophytes, allowed us to distinguish glaucophytes from other photosynthetic cells containing blue phycobiliproteins. Our results indicate that the peculiar autofluorescence signal of glaucophytes will facilitate further identification and isolation on novel specimens of this scarce but important algal group.
De novo motor learning of a bimanual control task over multiple days of practice
Authors: Haith Adrian M. , Yang Christopher , Pakpoor Jina , Kita Kahori
Published: October 2021

Although much research on motor learning has focused on how we adapt our movements to maintain performance in the face of imposed perturbations, in many cases we must learn new skills from scratch, or de novo. In comparison to adaptation, relatively little is known about de novo learning. In part, this is because learning a new skill can involve many challenges, including learning to recognize new patterns of sensory input and generate new patterns of motor output. However, even with familiar sensory cues and well-practiced movements, the problem of quickly selecting the appropriate actions in response to the current state is challenging. Here, we devised a bimanual hand-to-cursor mapping which isolates this control problem. We find that participants initially struggled to control the cursor under this bimanual mapping, despite explicit knowledge of the mapping. Performance improved steadily over multiple days of practice, however. Participants exhibited no aftereffects when reverting to a veridical cursor, confirming that participants learned the new task de novo, rather than through adaptation. Corrective responses to mid-movement perturbations of the target were initially weak, but with practice, participants gradually became able to respond rapidly and robustly to these perturbations. After four days of practice, participants’ behavior under the bimanual mapping almost matched performance with a veridically mapped cursor. However, there remained a small but persistent difference in performance level. Our findings illustrate the dynamics and limitations of learning a novel controller and introduce a promising paradigm for tractably investigating this aspect of motor skill learning.
Structural anther mimics improve reproductive success through dishonest signalling that enhances both attraction and the morphological fit of pollinators with flowers
Authors: Newman Ethan L , Khoury Katharine L , van Niekerk Sandy E , Peter Craig I
Published: October 2021

Numerous studies have identified traits associated with pollen mimicry, however, the processes underlying floral deception remains poorly documented for these structures. We studied the importance of attraction and mechanical fit of anther mimics inTritonia laxifolia(Iridaceae) and their relative contributions to reproductive success.

To determine anther mimics role in pollinator attraction, we offered bees’ binary preferences to flowers painted with UV absorbent and reflecting paint. We also conducted preference experiments between flowers with excised anther mimics and unmanipulated controls, from which mechanical fit was assessed using single visits. Anther mimics effects on female reproductive success was determined using similar treatments, but on rooted plants.

Bees preferred UV absorbent over UV reflecting anther mimics. Preference for flowers with and without the three-dimensional structures was equal. Single visits resulted in more pollen deposition on unmanipulated controls over flowers with their anther mimics excised, which was directly linked to pollen-collecting behaviour. Controls with unmanipulated anther mimics experienced more seed set than those with their anther mimics excised.

This study provides insights into pollinator-mediated selection on deceptive floral signals and shows that three-dimensional anther mimics increases reproductive success through both attraction and pollen collecting behaviours that improves the fit between flowers and pollinators.
DNA-PK Promotes DNA End Resection at DNA Double Strand Breaks in G0 cells
Authors: Fowler Faith C. , Chen Bo-Ruei , Zolnerowich Nicholas , Wu Wei , Pavani Raphael , Paiano Jacob , Peart Chelsea , Nussenzweig André , Sleckman Barry P. , Tyler Jessica K.
Published: October 2021

DNA double-strand break (DSB) repair by homologous recombination is confined to the S and G2 phases of the cell cycle partly due to 53BP1 antagonizing DNA end resection in G1 phase and non-cycling quiescent (G0) cells where DSBs are predominately repaired by non-homologous end joining (NHEJ). Unexpectedly, we uncovered extensive MRE11- and CtIP-dependent DNA end resection at DSBs in G0 mammalian cells. A whole genome CRISPR/Cas9 screen revealed the DNA-dependent kinase (DNA-PK) complex as a key factor in promoting DNA end resection in G0 cells. In agreement, depletion of FBXL12, which promotes ubiquitylation and removal of the KU70/KU80 subunits of DNA-PK from DSBs, promotes even more extensive resection in G0 cells. In contrast, a requirement for DNA-PK in promoting DNA end resection in proliferating cells at the G1 or G2 phase of the cell cycle was not observed. Our findings establish that DNA-PK uniquely promotes DNA end resection in G0, but not in G1 or G2 phase cells, and has important implications for DNA DSB repair in quiescent cells.
Cytotoxic CD4+ T cells driven by T-cell intrinsic IL-18R/MyD88 signaling predominantly infiltrate Trypanosoma cruzi-infected hearts
Authors: Barbosa Carlos-Henrique. D. , Canto Fábio B. , Gomes Ariel , Brandão Layza M. , Lima Jéssica R. , Melo Guilherme A. , Granato Alessandra , Neves Eula G.A. , Dutra Walderez O. , Oliveira Ana C. , Nóbrega Alberto , Bellio Maria
Published: October 2021

Increasing attention has been directed to cytotoxic CD4+ T cells (CD4CTLs) in different pathologies, both in humans and mice. The impact of CD4CTLs in immunity and the mechanisms controlling their generation, however, remain poorly understood. Here, we show that CD4CTLs abundantly differentiate during mouse infection with the intracellular parasite Trypanosoma cruzi. CD4CTLs display parallel kinetics to Th1 cells in the spleen, mediate specific cytotoxicity against cells presenting pathogen-derived antigens and express immunoregulatory and/or exhaustion markers. We demonstrate that CD4CTL absolute numbers and activity are severely reduced in both Myd88-/- and Il18ra-/- mice. Of note, the infection of mixed-bone marrow chimeras revealed that WT but not Myd88-/- cells transcribe the CD4CTL gene signature and that Il18ra-/- and Myd88-/- CD4+ T cells phenocopy each other. Moreover, adoptive transfer of WT CD4+GzB+ T cells to infected Il18ra-/- mice extended their survival. Importantly, cells expressing the CD4CTL phenotype predominate among CD4+ T cells infiltrating the infected mouse cardiac tissue and are increased in the blood of Chagas patients, in which the frequency of CD4CTLs correlates with the severity of cardiomyopathy. Our findings describe CD4CTLs as a major player in immunity to a relevant human pathogen and disclose T-cell intrinsic IL-18R/MyD88 signaling as a key pathway controlling the magnitude of the CD4CTL response.
Defining Cardiac Cell Populations and Relative Cellular Composition of the Early Fetal Human Heart
Authors: Dewing Jennifer M. , Saunders Vinay , O’Kelly Ita , Wilson David I.
Published: October 2021

The human heart is primarily composed of cardiomyocytes, fibroblasts, endothelial and smooth muscle cells. Reliable identification of fetal cardiac cell types using protein markers is important for understanding cardiac development and delineating the cellular composition of the human heart during early development, which remains largely unknown. The aim of this study was to use immunohistochemistry (IHC), flow cytometry and RT-PCR analyses to investigate the expression and specificity of commonly used cardiac cell markers in the early human fetal heart (8-12 post-conception weeks). The expression of previously reported protein markers for the detection of cardiomyocytes (Myosin Heavy Chain (MHC) and Troponin I (cTnI)), fibroblasts (DDR2, Thy1, Vimentin), endothelial cells (CD31) and smooth muscle cells (α-SMA) were assessed. Flow cytometry revealed two distinct populations of cTnI expressing cells based on fluorescence intensity: cTnIHigh and cTnILow. MHC positive cardiomyocytes were cTnIHigh, whereas MHC negative non-myocyte cells were cTnILow. cTnI expression in non-myocytes was further confirmed by IHC and RT-PCR analyses, suggesting troponins are not cardiomyocyte-specific and may play distinct roles in non-muscle cells during early development. Vimentin was confirmed to be enriched in cultured fibroblast populations and flow cytometry revealed VimHigh and VimLow cell populations in the fetal heart. MHC positive cardiomyocytes were VimLow whilst CD31 positive endothelial cells were VimHigh. Based on the markers investigated, we estimate fetal human cardiomyocyte populations comprise 75-80% of total cardiac cells and exhibit the following marker profile: α-MHC+/cTnIHigh/VimLow. For the non-cardiomyocyte population, we estimate they comprise 20-25% of total cardiac cells and exhibit the following marker profile: α-MHC-/cTnILow/VimHigh. Our study suggests the marker profiles and proportions of fetal cardiac populations are distinct from that of the adult heart.
Probing behavior of the corn leafhopperDalbulus maidison susceptible and resistant maize hybrids
Authors: Carpane Pablo Daniel , Catalano María Inés
Published: October 2021

The corn leafhopperDalbulus maidisis the main vector of the pathogens that cause corn stunt, a major disease of maize in the Americas. As host resistance is an efficient tool to control diseases, the findings of a previous report showed that some corn hybrids are resistant toD. maidis. In this work, we assessed the probing behavior ofD. maidison susceptible and resistant corn hybrids using EPG (Electrical Penetration Graph) technology. Fifteen-day-old females were monitored for 20 hours, with access to hybrids DK390, DK670, DK79-10, and DK72-10. Hybrids DK390 and DK72-10 showed resistance toD. maidisin phloem, since insects feeding on these hybrids presented more salivation events in phloem without subsequent ingestion, which are seen as failed attempts to ingest. A reduction of the total duration of phloem ingestion was observed, and accordingly of the time spent by insects with access to these hybrids on xylem ingestion. The hybrid DK390 also had mesophyll resistance, seen as less probing time and a higher number of probes of short duration. These findings support and are consistent with previous research, providing useful information to characterize maize hybrids resistant toD. maidis, and so to corn stunt.
Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis
Authors: Liu Chang , Li Rui , Li Young , Lin Xiumei , Wang Shuowen , Liu Qun , Zhao Kaichen , Yang Xueqian , Shi Xuyang , Ma Yuting , Pei Chenyu , Wang Hui , Bao Wendai , Hui Junhou , Berberoglu Michael Arman , Sahu Sunil Kumar , Esteban Miguel A. , Ma Kailong , Fan Guangyi , Li Yuxiang , Liu Shiping , Chen Ao , Xu Xun , Dong Zhiqiang , Liu Longqi
Published: October 2021

Vertebrate embryogenesis is a remarkably dynamic process during which numerous cell types of different lineages generate, change, or disappear within a short period of time. A major challenge in understanding this process is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell fate decisions. Here, we employed Stereo-seq, a high-definition spatially resolved transcriptomic technology, to dissect the spatiotemporal dynamics of gene expression and regulatory networks in the developing zebrafish embryos. We profiled 91 embryo sections covering six critical time points during the first 24 hours of development, obtaining a total of 139,391 spots at cellular size (∼100 μm2) with spatial coordinates. Meanwhile, we identified spatial modules and co-varying genes for specific tissue organizations. By performing the integrative analysis of the Stereo-seq and scRNA-seq data from each time point, we reconstructed the spatially resolved developmental trajectories of cell fate transitions and molecular changes during zebrafish embryogenesis. We further investigated the spatial distribution of ligand-receptor pairs for major signaling pathways and identified novel interactions that potentially crosstalk with the Notch signaling pathway during zebrafish development. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development.
ChemChaste: Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks
Authors: Johnson Connah G. M. , Fletcher Alexander G. , Soyer Orkun S.
Published: October 2021

Motivation

Spatial organisation plays an important role in the function of many biological systems, from cell fate specification in animal development to multi-step metabolic conversions in microbial communities. The study of such systems benefits from the use of spatially explicit computational models that combine a discrete description of cells with a continuum description of one or more chemicals diffusing within a surrounding bulk medium. These models allow thein silicotesting and refinement of mechanistic hypotheses. However, most existing models of this type do not account for concurrent bulk and intracellular biochemical reactions and their possible coupling.

Results

Here, we describe ChemChaste, an extension for the open-source C++ computational biology library Chaste. ChemChaste enables the spatial simulation of both multicellular and bulk biochemistry by expanding on Chaste’s existing capabilities. In particular, ChemChaste enables: (i) simulation of an arbitrary number of spatially diffusing chemicals; (ii) spatially heterogeneous chemical diffusion coefficients; and (iii) inclusion of both bulk and intracellular biochemical reactions and their coupling. ChemChaste also introduces a file-based interface that allows users to define the parameters relating to these functional features without the need to interact directly with Chaste’s core C++ code. We describe ChemChaste and demonstrate its functionality using a selection of chemical and biochemical exemplars, with a focus on demonstrating increased ability in modelling bulk chemical reactions and their coupling with intracellular reactions.

Availability and implementation

ChemChaste is a free, open-source C++ library, available via GitHub athttps://github.com/OSS-Lab/ChemChasteunder the BSD license.

Contact

O.Soyer@warwick.ac.ukora.g.fletcher@sheffield.ac.uk