bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of Bacteroides thetaiotaomicron outer membrane vesicles as a universal, mucosal vaccine for Influenza A virus
Authors: Bentley Eleanor , Al Katy Sanaria , Kipar Anja , Stenz Regis , Carding Simon R , Stewart James
Published: April 2019

Influenza A Virus (IAV) is a zoonotic pathogen which causes seasonal epidemics worldwide, resulting in significant morbidity and mortality. Due to rapid virus evolution, available vaccines/antiviral drugs must be re-formulated and re-administered in most years. There is therefore an unmet need for a ‘universal’ vaccine to provide long-lasting, adaptive immunity to multiple strains of IAV. The aim of this study was to assess outer membrane vesicles (OMVs) produced by Bacteroides thetaiotaomicron (Bt) containing IAV antigens as a candidate universal mucosal vaccine. First, using intranasally-delivered fluorescently-labelled OMVs and FACS we demonstrated good uptake of OMVs by dendritic cells in both secondary and tertiary lymphoid tissue, showing OMVs are efficiently trafficked from the mucosa to the lymphatic system. Immunohistology confirmed this and showed expansion of lymphoid tissues and lymphoid follicles after OMV delivery. The stem/stalk of IAV HA is less variable and will generate antibodies that are cross-protective. Thus, we produced OMVs (termed H5F) that contained the stalk region of HA from strain A/VietNam/1203/04 (H5N1). We inoculated mice intranasally with H5F expressing OMVs or wild type OMVs and assessed antibody production and protection from challenge using a lethal dose of a different strain of influenza (PR8; H1N1). OMV-H5F-inoculted mice produced IgG and IgA in the respiratory tract that recognised both H5 HA and H1 HA. OMV-H5F inoculated mice were also protected from lethal challenge and supported lower virus titres. Our results indicate a strong potential for this approach to generate a universal IAV vaccine.
Post-transcriptional regulation of gene expression in Escherichia coli experiencing sustained nitrogen starvation
Authors: McQuail Josh , Switzer Amy , Wigneshweraraj Ramesh
Published: April 2019

While transcriptional reprogramming is perhaps the most well understood form of controlling gene expression in response to nitrogen starvation in bacteria, how post-transcriptional regulation (PTR) of gene expression contributes to this adaptive response remains elusive. Small regulatory RNAs (sRNAs) are the major post-transcriptional regulators of gene expression in bacteria. They regulate gene expression by base pairing to target mRNAs, leading to enhanced translation or inhibition of translation and/or alteration of mRNA stability. To form productive interactions with target mRNAs, most sRNAs require an RNA chaperone. In many bacteria of diverse lineages, the RNA chaperone Hfq plays a central and integral role in the PTR of gene expression by stabilising sRNAs and promoting their interactions with cognate mRNAs. Comparative analysis of the transcriptomes of Escherichia coli at different stages of nitrogen starvation reveal that levels of sRNA vary throughout starvation. We used Hfq as a surrogate to study sRNA-mediated PTR of gene expression during sustained nitrogen starvation. Our results indicate that sRNAs-mediated PTR of gene expression plays a major role in the adaptive response to sustained nitrogen starvation. Intriguingly, using single-molecule PALM, we reveal that Hfq is involved in the formation of intracellular structures which functionally might resemble processing (P) bodies found in eukaryotic cells involved in mRNA turnover.
Functional characterisation of cell wall proteins that enhance nasal colonisation by Staphylococcus aureus, through binding to host mucin
Authors: Alotaibi Amenah , Clark Simon
Published: April 2019

Human nasal colonization with Staphylococcus aureus sets the stage for subsequent systemic infection. The mechanisms responsible for colonization are not fully understood. This study characterizes S. aureus adhesion to nasal mucosa in vitro and observes the interaction of S. aureus with mucin. S. aureus showed significantly higher binding to mucin during stationary phase in comparison to log-phase cells. Adherence of S. aureus srtA mutant to mucin was not significantly different from wild-type, thus Srt A shows no influence on S. aureus interaction with mucin. Adherence to mucin was saturable in a dose- and time-dependent fashion. Biotin–labelled mucin bound to surface protein (55 kDa) of cell wall extracted S. aureus which is encoded by the sbi gene. These data suggest that adherence factors are present on the surface of S. aureus such as sbi. Purified recombinant Sbi was prepared and the mucin binding capacity of the protein was tested by ELISA. In order to determine the function of specific domains of Sbi in adhesion, Sbi constructs with, without the IgG-domain and with B2-glycoprotein domain were expressed on the surface of E. coli BL21(DE3). The expression of Sbi with the B2-glycoprotein domain on the surface adhesion, emphasizing the role of Sbi in mucin adhesion. A profound binding effect was observed with Sbi incubated in wells coated with host mucin. Therefore, it is proposed to investigate a novel interaction of S. aureus to host mucin in order to control S. aureus nasal colonization.
A CRISPR-associated Rossmann fold (CARF) domain regulates transcription of an RNA repair system in Escherichia coli
Authors: Kotta-Loizou Ioly , Jovanovic Milija , Schaefer Jorrit , Engl Christoph , Zhang Nan , Buck Martin
Published: April 2019

CRISPR-associated Rossmann fold (CARF) domain signalling underpins the modulation of CRISPR-Cas systems. Unlike the majority of known CARF domains associated with nuclease activity in CRISPR-Cas systems, the CARF domain of the transcriptional regulator RtcR modulates the opposite function by activating an RNA end sealing system. The Rtc RNA repair system in Escherichia coli consists ofthe universally conserved RNA cyclase RtcA and RNA ligase RtcB, and is known to be induced by antibiotics and oxidative stress. We aim to investigate the CARF domain mediated transcriptional regulation of the Rtc system in vivo and in vitro. A reporter based assay confirmed that the RtcR CARF domain has a negative regulatory effect on RtcR activity and subsequent induction of the rtcBA operon. Both predictive modelling and site-directed mutagenesis suggest the Rtc induction is not due to oxidation of cysteines present in the RtcR regulatory CARF domain. Interestingly, the enzymes RtcA and RtcB, products of the actions of RtcR as a transcription regulator, are required for RtcR to stimulate expression of the rtcBA operon and directly bind to the RtcR CARF domain as shown in vivo by two-hybrid and in vitro by gel filtration. Given that CARF domains are known to be activated by RNA binding, a range of RNA molecules linked to the Rtc system or CARF domains in general are currently being investigated as potential inducers in an in vitro transcription system. Together, our data indicate an expanded range for CARF domain signalling, including via protein-protein interactions.
Identification of niche-specific virulence factors via experimental evolution of Streptococcus pneumoniae
Authors: Green Angharad , Neill Daniel , Hinton Jay
Published: April 2019

Streptococcus pneumoniae (the pneumococcus) is an important human pathogen, adept at colonising various ecological niches within the host. Colonisation of the nasopharynx, followed by asymptomatic carriage and non-inflammatory clearance is the predominant outcome of infection, but diverse disease manifestations including pneumonia, septicaemia and meningitis occur in a minority of individuals. Through experimental evolution of pneumococci in mouse disease models, we are investigating the genetic basis of the niche adaptations that enable pneumococci to switch from a commensal lifestyle in the nasopharynx, to a pathogenic phenotype in the lungs, brain or blood. Experimental evolution was carried out via serial passage of pneumococci separately through pneumonia and nasopharyngeal carriage mouse models, to generate lineages adapted to the lung and nasopharyngeal environments, respectively. Starting from a non-passaged (lab adapted) isolate, ten independently-evolved lineages of lung-adapted pneumococci have been generated, each having been passaged 20-times through a mouse pneumonia model. Pneumococci recovered from the infected lungs were used to inoculate further mice for the next passage round. We will present the results from whole genome sequencing and phenotypic analysis of lung-passaged bacterial isolates including growth characteristics, toxin production, adherence and invasion with lung epithelial cells. We will also describe how the acquired pneumococcal adaptations, which facilitate survival in the lung environment, can influence bacterial gene expression during exponential growth. These studies will provide insight into genetic changes associated with pneumococcal commensal to pathogen switch. Identifying such genetic determinants of virulence will be valuable for the development of vaccine candidates and targets for therapeutic intervention.
Effect of metronidazole on microbiomes associated with asymptomatic bacterial vaginosis
Authors: Coudray Makella , Ruiz-Perez Daniel , Colbert Brett , Krupp Karl , Kumari Hansi , Narasimhan Giri , Mathee Kalai , Madhivanan Purnima
Published: April 2019

Asymptomatic Bacterial Vaginosis (BV) damages vaginal epithelium increasing risk of sexually-transmitted infections. Gardnerella vaginalis, Atopobium vaginae, Prevotella amnii, P. bivia and Candida albicans are associated with BV. Presence of Lactobacillus spp. is indicative of a healthy microbiota. Symptomatic BV is treated with metronidazole. The role of microbiota and metronidazole treatment in the recurrence and persistence of asymptomatic BV remains to be elucidated. This study uses whole genome sequencing (WGS) to determine the microbiota changes with metronidazole treatment. DNA from 20 vaginal swabs was obtained at four time points over 12 months from five African American women and was subjected to WGS. The first time point is the untreated baseline. All subjects were tested every 4 months and received a course of metronidazole for each episode of BV during the 12 months period. Nugent scores were used to classify BV status. The microbial profiles were analyzed along with the sociodemographic metadata. Despite treatment, the participants did not recover from BV — two participants experienced persistent BV, and the rest had recurrent BV. WGS analyses show that G. vaginalis was the most abundant organism as compared to Lactobacillus species. The metronidazole treatment resulted in the loss of Lactobacillus and Prevotella species. One participant scored healthy based on Nugent score at one time point, during when Lactobacillus species dominated the microbiome. Based on this pilot longitudinal study, metronidazole may not be an effective treatment for asymptomatic BV. Studies with larger cohorts can lead to statistically significant conclusions to develop alternative interventions for asymptomatic BV.
Tracking plasmid-mediated antibiotic resistance from environmental reservoirs to the food chain
Authors: Murphy Sinéad , Joyce Aoife , Vollenweider Vera , Drissner David , Walsh Fiona
Published: April 2019

It has been well documented that antibiotic resistance (AR) is a clinical concern that affects both human and animal health but AR in the environment and food-chain is not as well understood. AR bacteria can occur naturally in soil, water and organic fertilizers used in agriculture so there is a risk that AR can pass to humans via the food-chain. This study focuses on lettuce cultivation undergoing four treatments (Normal irrigation water+normal soil, normal irrigation water+manure, UV irrigation water+normal soil, UV irrigation water+manure)to determine the mechanisms by which the AR is transferred to the plants over the growth period of the lettuce (7 time-points – week 0 to week 6). Plasmids (n=318) have been isolated from irrigation water (n=36), soil (n=45) and lettuce (n=42) samples using the exogenous isolation method for week 0 and week 6 initially. Antibiotic susceptibility testingto amikacin, cefotaxime, ciprofloxacin, imipenem, kanamycin, tetracycline has been carried out. Multi-drug resistance profiles were established for soil taken at timepoint 0 and lettuce taken at timepoint 6. Extracted plasmid DNA was sent for metagenomic analysis to determine which genes are involved in the transfer of AR at the interfaces. The results of the sequencing showed that there are multiple AR genespresent, including Tet, Sme, Cmy, Oxa and ANT(4’)-Ib, that confer resistance to bacteria. The identification of multi-drug resistance in soil and lettuce samples is concerning and highlights the need to determine the mechanisms leading to antibiotic resistance in food.
Spatiotemporal dynamics of host cell modification caused by herpesvirus infection
Authors: Scherer Katharina M. , Soh Timothy , Manton James D. , Mascheroni Luca , Crump Colin M. , Kaminski Clemens F.
Published: April 2019

Herpesviruses are large and complex DNA viruses that are composed of an icosahedral capsid, a proteinaceous layer termed the tegument, and a glycoprotein rich lipid envelope. One important area of host-pathogen interaction that is still poorly understood is the extensive change to intracellular organelles and cellular morphology that occur within the infected cell during active virus replication. In order to characterise the spatiotemporal dynamics of host cell remodelling caused by herpesvirus infection, we use novel multiparametric fluorescence microscopy methods compatible with live-cell imaging. In addition, we apply expansion microscopy to map 3D rearrangement in great detail. The remodelling of the host cell is correlated to the stage of virus replication which can highly vary between individual cells. Therefore, we have constructed a recombinant reporter virus that expresses eYFP-tagged ICP0, a multifunctional immediate early tegument protein, as well as mCherry-tagged glycoprotein C (gC), a late protein that is a major component of the viral envelope. The sequential expression of these two viral proteins provides us with an intrinsic time stamp for the stage of virus infection in each cell. With this fluorescent reporter virus, we are able to describe the remodeling of- the three-dimensional architecture of microtubules and the actin network,- compartments of the secretory and endocytic pathways which are intimately linked to viral envelope protein synthesis, maturation and transport,- and key antiviral and inflammatory signalling platforms (mitochondria and peroxisomes).
A liposomal drug delivery system for improved eradication of Helicobacter pylori
Authors: Osborne Nicola , Catania Rosa , Stolnik-Trenkic Snow , Falcone Franco H. , Robinson Karen
Published: April 2019

Helicobacter pylori is the leading cause of peptic ulcers and gastric cancer. Eradicating H. pylori infections is becoming more difficult due to increasing antibiotic resistance and poor patient compliance. We aim to develop a novel liposomal drug delivery system that encapsulates antibiotics and the antimicrobial fatty acid linolenic acid (LLA). We hypothesise that H. pylori will have much lower resistance rates to this dual formulation. Liposomes consisting of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), sphingomyelin, and cholesterol were produced using the thin film hydration method. The size of our liposomes was assessed using dynamic light scattering (DLS), and their antimicrobial activity was assessed using a viable count assay. The liposomes had a particle size ranging from 95 to 150 nm. We have successfully loaded LLA up to 20 % of total lipid composition, and shown stability of the particles in storage at 4 °C for up to 3 months. The LLA liposomes achieved complete eradication of H. pylori
in vitro at 150 µg ml−1, whereas control liposomes containing no LLA had no antimicrobial effect. We have recently formulated liposomes encapsulating LLA and amoxicillin at 2.2 mg ml−1 and 0.99 mg ml−1 respectively, and are currently assessing their antimicrobial activity against H. pylori. In conclusion, it is possible to prepare LLA- and amoxicillin-containing liposomes and LLA has antimicrobial activity against H. pylori. In future work we will utilise strategies to enhance gastric retention which will provide local bactericidal activity, improving on inefficient systemic uptake mechanisms with current therapies.
Investigating the interferon antagonistic abilities of louping ill virus, a neglected animal pathogen endemic to the UK
Authors: Clark Jordan , Goertz Giel , Schnettler Esther , McInnes Colin , Biek Roman , Kohl Alain
Published: April 2019

Louping ill virus (LIV; Flavivirus, Flaviviridae) is an important—but poorly characterized—animal pathogen of significant economic concern within the UK. Transmitted by ticks, LIV predominantly causes disease in ruminants and grouse, resulting in heavy losses. LIV is closely related to another flavivirus—tick-borne encephalitis virus (TBEV) which, unlike LIV, is a significant human pathogen. The molecular mechanisms that underpin host restriction in these viruses are poorly understood however, previously it has been shown that the TBEV non-structural (NS) proteins do not act as type-I interferon (IFN) antagonists, unlike many other Flavivirus NS proteins. Therefore, to facilitate comparison with LIV we investigated the possible antagonistic actions of the LIV NS proteins using a luciferase-based IFN reporter assay. Utilising this assay we identified six LIV NS proteins that function as antagonists throughout the IFN induction cascade. We also identified and modelled a subgenomic flavivirus RNA (sfRNA) that is produced during LIV infection and is similar in structure to TBEV sfRNA. We found that the LIV and TBEV sfRNAs antagonise RIG-I, indicating that the IFN antagonistic ability of sfRNA is not limited to mosquito-borne flaviviruses. Finally, we established the first LIV reverse genetics system using circular polymerase extension reaction (CPER). This powerful tool can be used to produce chimeric viruses which will allow further investigation into the factors governing host restriction and virulence in tick-borne flaviviruses. Investigating the mechanisms that underlie LIV infection aids our understanding of interferon antagonism in flaviviruses and the molecular determinants of host restriction.
Deciphering the secretion mechanism and novel protein-protein interactions of TecA, a Burkholderia cenocepacia toxin
Authors: Monjaras-Feria Julia , Bisaro Fabiana , Valvano Miguel
Published: April 2019

Burkholderia cenocepacia (Bc) is an environmental opportunistic pathogen that causes persistent, often severe, lung infections in individuals with cystic fibrosis and other underlying diseases. Rho GTPases are central molecular switches that regulate cytoskeletal dynamics, trafficking, immune responses and cell proliferation in eukaryotic cells. Many microbes produce proteins that target Rho GTPase signalling. Bc employs a type VI secretion system (T6SS) to survive in macrophages by disarming Rho GTPases and causing actin cytoskeletal defects. Bc protein TecA is a non-VgrG T6SS effector that is responsible for actin disruption. TecA and other bacterial homologs bear a cysteine protease-like catalytic triad, which inactivates Rho GTPases by deamidating a conserved asparagine in the GTPase switch-I region. RhoA deamidation induces Pyrin inflammasome activation1. Our goal is to determine the detailed TecA secretion mechanism and the interacting partners inside the bacterial cytoplasm and inside the macrophages. In this study, we found by Co-IP/MS analysis that TecA interacts with the T6SS tube protein HcP, the membrane anchored TssM and with the elongation factor Tu. We also found that TecA is secreted in the absence of HcP and the secretion mechanism is discussed. 1. Aubert, D.F., X. Hao, J. Yang, X. Shi, W. Gao, L. Li, F. Bisaro, S. Chen, M.A. Valvano, and F. Shao. 2016. A Burkholderia Type VI Effector Deamidates Rho GTPases to Activate the Pyrin Inflammasome. Cell Host and Microbe 19 : 664–674.
Genomic analysis reveals the re-emergence of a nosocomial outbreak caused by multidrug resistant Klebsiella pneumoniae
Authors: Nguyen Thi Nguyen To , Baker Stephen
Published: April 2019

Multidrug resistant (MDR) K. pneumoniae is listed among the most urgent public health threats due to its virulence and insusceptibility to a wide range of antimicrobials. Infection with this pathogen frequently leads to fatal outcomes, especially in low-income hospital settings. Patan Hospital is a 450-bed government hospital located within the Kathmandu Valley, Nepal. The hospital has previously witnessed multiple outbreaks caused by MDR K. pneumoniae in the neonatal intensive care unit (NICU). Particularly, a carbapenemase producing sequence type (ST) 15 K. pneumoniae clone was responsible for an outbreak with mortality rate up to 75 % in 2012. Recently in 2015, this same NICU suffered again from an MDR K. pneumoniae outbreak. In this study, using whole genome sequencing (WGS) and state-of-the-art analytic approaches, we aimed to define the nature of this recent outbreak. We found that the 2015 outbreak in Patan Hospital was caused by the same MDR ST15 K. pneumoniae reported in 2012. Albeit genetically similar, these recent strains were susceptible to carbapenems due to deletion of the blaNDM-1 cassette. Using Bayesian phylogenetic inference, we determined the outbreak strain was introduced to Patan Hospital in late 2010 and subsequently caused major outbreaks in NICU in 2012 and again in 2015. This clone acquired four different plasmids encoding resistance to numerous therapeutic antimicrobials, and this may underlie its successful propagation and associated high mortality. Insights provided through this study are invaluable in tailoring infection control strategies as well as raising public awareness
Generalized locomotion of brittle stars with a flexible number of arms
Authors: Wakita Daiki , Kagaya Katsushi , Aonuma Hitoshi
Published: April 2019

Typical brittle stars have five radially symmetrical arms, which coordinate to move their body in a certain direction. However, some species of them show individual difference in the number of arms. We found this trait unique since intact legged animals each own a fixed number of limbs in general. How does a single species manage such different numbers of motile organs to realize adaptive locomotion? We here described four-, five-, six-, and seven-armed locomotion with the aim to generalize a common rule which is flexible with arm numbers in brittle stars. We mechanically stimulated an arm inOphiactis brachyaspisto analyze escape direction and arm movements. Gathering quantitative indices and employing Bayesian statistical modeling, we figured out an average locomotion: regardless of the total number of arms, a front position emerges at one of the second neighboring arms to a mechanically stimulated arm, while side arms adjacent to the front synchronously work as left and right rowers. We suggest a model where some afferent signal runs either clockwise or anticlockwise along the nerve ring while linearly counting how many arms it passes. This idea would explain how ‘left and right’ emerges in a radially symmetrical body via a decentralized system.
Angiocrine FSTL1 insufficiency leads to atrial and vein wall fibrosis via SMAD3 activation
Authors: Jiang Haijuan , Zhang Luqing , Liu Xuelian , Sun Wei , Kato Katsuhiro , Chen Chuankai , Li Xiao , Han Wencan , Zhang Fujing , Xiao Qi , Yang Zhongzhou , Qin Zhihai , Adams Ralf H. , Gao Xiang , He Yulong
Published: April 2019

Angiocrine factors, mediating the endothelial-mural cell interaction in vascular wall construction as well as maintenance, are incompletely characterized. Here we show that loss of follistatin-like protein 1 (FSTL1) in endothelial cells (Fstl1ECKO) led to an increase of pulmonary vascular resistance, resulting in the heart regurgitation especially with tricuspid valves. However, this abnormality was not detected in mutant mice withFstl1deletion in smooth muscle cells or hematopoietic cells. We further showed that there was excessive alpha-smooth muscle actin (αSMA) associated with atrial endocardia, heart valves, veins and microvessels after the endothelial FSTL1 deletion. Consistently, there was an increase of collagen deposition as demonstrated in livers ofFstl1ECKOmutants. The SMAD3 phosphorylation was significantly enhanced and pSMAD3 staining was colocalized with αSMA in vein walls, suggesting the activation of TGFβ signaling in vascular mural cells ofFstl1ECKOmice. The findings imply that endothelial FSTL1 is critical for the homeostasis of atria and veins and its insufficiency may favor cardiovascular fibrosis leading to heart failure.
Human biting Culex pipiens bioform molestus is spread in several areas in south Sweden
Authors: Nafula Luande Verah , Eklöf Disa , Lindström Anders , Nyanjom Steven Ger , Evander Magnus , Lilja Tobias
Published: April 2019

The mosquito species Culex pipiens is a potential vector of several pathogens infecting humans and occurs in two distinct bioforms, pipiens and molestus. Traditional morphological identification fails to separate the bioforms of Cx. pipiens despite their behavioural differences since they are morphologically indistinguishable. However, molecular methods can identify the two bioforms. The bioform molestus thrives in urban environments and bite all kinds of vertebrates, whereas bioform pipiens is more rural and mainly feed on birds.

Mosquito samples submitted in a citizen science project from people experiencing mosquito problems in South Sweden were analyzed to determine the geographical distribution of the molestus bioform of Cx. pipiens. Mosquito specimens were identified to species by DNA barcoding of the cytochrome C oxidase subunit I (COI) gene and the bioforms were determined with the CQ11 microsatellite marker. To establish other differences between the bioforms, part of the CPIJ001674 gene was sequenced. Culex pipiens f molestus, was present both within and outside of urban areas in several sites in southern Sweden. In one site, hybrids between the two bioforms were found. Culex pipiens f molestus has previously been found in urban areas in Sweden, but the detection of the bioform in several rural areas was surprising, indicating that it may be more widely spread than previously thought.
Three-dimensional Monolayer Stress Microscopy
Authors: Serrano Ricardo , Aung Aereas , Yeh Yi-Ting , Varghese Shyni , Lasheras Juan C. , del Álamo Juan C.
Published: April 2019

Many biological processes involve the collective generation and transmission of mechanical stresses across cell monolayers. In these processes, the monolayer undergoes lateral deformation and bending due to the tangential and normal components of the cell-generated stresses. Monolayer Stress Microscopy (MSM) methods have been developed to measure the intracellular stress distribution in cell monolayers. However, current methods assume plane monolayer geometry and neglect the contribution of bending to the intracellular stresses.

This work introduces a three-dimensional (3D) MSM method that calculates monolayer stress from measurements of the 3D traction stresses exerted by the cells on a flexible substrate. The calculation is carried out by imposing equilibrium of forces and moments in the monolayer, subject to external loads given by the 3D traction stresses. The equilibrium equations are solved numerically, and the algorithm is validated for synthetic loads with known analytical solutions.

We present 3D-MSM measurements of monolayer stress in micropatterned islands of endothelial cells of different sizes and shapes. These data indicate that intracellular stresses caused by lateral deformation emerge collectively over long distances; they increase with the distance from the island edge until they reach a constant value that is independent of island size. On the other hand, bending-induced intracellular stresses are more concentrated spatially and remain confined to within 1-2 cell lengths of bending sites. The magnitude of these bending stresses is highest at the edges of the cell islands, where they can exceed the intracellular stresses caused by lateral deformations. Our data from non-patterned monolayers suggests that biomechanical perturbations far away from monolayer edges also cause significant localized alterations in bending tension. The localized effect of bending-induced stresses may be important in processes like cellular extravasation, which are accompanied by significant normal deflections of a cell monolayer (i.e. the endothelium), and which require localized changes in monolayer permeability.
The identification of temporal communities through trajectory clustering correlates with single-trial behavioural fluctuations in neuroimaging data
Authors: Thompson William Hedley , Wright Jessey , Shine James M. , Poldrack Russell A.
Published: April 2019

Interacting sets of nodes and fluctuations in their interaction are important properties of a dynamic network system. In some cases the edges reflecting these interactions are directly quantifiable from the data collected. However, in many cases (such as functional magnetic resonance imaging (fMRI) data), the edges must be inferred from statistical relations between the nodes. Here we present a new method, Temporal Communities through Trajectory Clustering (TCTC), that derives time-varying communities directly from time-series data collected from the nodes in a network. First, we verify TCTC on resting and task fMRI data by showing that time-averaged results correspond with expected static connectivity results. We then show that the time-varying communities correlate and predict single-trial behaviour. This new perspective on temporal community detection of node-collected data identifies robust communities revealing ongoing spatiotemporal community configurations during task performance.
Molecular mapping of transmembrane mechanotransduction through the β1 integrin-CD98hc-TRPV4 axis
Authors: Potla Ratnakar , Hirano-Kobayashi Mariko , Wu Hao , Chen Hong , Mammoto Akiko , Matthews Benjamin D. , Ingber Donald E.
Published: April 2019

One of the most rapid (< 4 msec) transmembrane cellular mechanotransduction events involves activation of Transient Receptor Potential Vanilloid 4 (TRPV4) ion channels by mechanical forces transmitted across β1 integrin receptors in endothelial cells, and the transmembrane Solute Carrier family 3 member 2 (CD98hc) protein has been implicated in this response. Here, we show that β1 integrin, CD98hc, and TRPV4 all tightly associate and co-localize in focal adhesions where mechanochemical conversion takes place. CD98hc knock down inhibits TRPV4-mediated calcium influx induced by mechanical forces, but not by chemical activators, thus confirming the mechanospecificity of this signaling response. Molecular analysis revealed that forces applied to β1 integrin must be transmitted from its cytoplasmic C-terminus to the CD98hc cytoplasmic tail, and from there to the ankyrin repeat domain of TRPV4 in order to produce ultra-rapid, force-induced, channel activation within the focal adhesion.

Abstract Figure

Graphical abstract

A direct path of mechanical signal transfer between β1 integrin, CD98hc, and TRPV4 channels is identified that mediates ultra-rapid transmembrane mechanochemical conversion within focal adhesions.
A low cost, open source Turbidostat design for in-vivo control experiments in Synthetic Biology
Authors: Guarino Agostino , Shannon Barbara , Marucci Lucia , Grierson Claire , Savery Nigel , Bernardo Mario di
Published: April 2019

To characterise the dynamics of new engineered systems in Synthetic biology, continuous culture platforms are required. In this paper, after a brief review of the existing machines present in literature, we describe the design and the implementation of a new flexible and low cost turbidostat for in-vivo control experiments. Then, the results of a 3 hours long experiment of control of the Optical Density is reported. Since the foundation of our design is flexibility, in this work we also discuss some possible extensions of our design, with particular attention to their application to validate in-vivo multicellular control design.
Efficient use of genomic information for sustainable genetic improvement in small cattle populations
Authors: Obšteter J. , Jenko J. , Hickey J. M. , Gorjanc G.
Published: April 2019

This paper compares genetic gain, genetic variation, and the efficiency of converting variation into gain under different genomic selection scenarios with truncation or optimum contribution selection in a small dairy population by simulation. Breeding programs have to maximize genetic gain but also ensure sustainability by maintaining genetic variation. Numerous studies showed that genomic selection increases genetic gain. Although genomic selection is a well-established method, small populations still struggle with choosing the most sustainable strategy to adopt this type of selection. We developed a simulator of a dairy population and simulated a model after the Slovenian Brown Swiss population with ~10,500 cows. We compared different truncation selection scenarios by varying i) the method of sire selection and their use on cows or bull-dams, and ii) selection intensity and the number of years a sire is in use. Furthermore, we compared different optimum contribution selection scenarios with optimization of sire selection and their usage. We compared the scenarios in terms of genetic gain, selection accuracy, generation interval, genetic and genic variance, the rate of coancestry, effective population size, and the conversion efficiency. The results show that early use of genomically tested sires increased genetic gain compared to progeny testing as expected from changes in selection accuracy and generation interval. A faster turnover of sires from year to year and higher intensity increased the genetic gain even further but increased the loss of genetic variation per year. While maximizing intensity gave the lowest conversion efficiency, a faster turn-over of sires gave an intermediate conversion efficiency. The largest conversion efficiency was achieved with the simultaneous use of genomically and progeny tested sires that were used over several years. Compared to truncation selection optimizing sire selection and their usage increased the conversion efficiency by either achieving comparable genetic gain for a smaller loss of genetic variation or achieving higher genetic gain for a comparable loss of genetic variation. Our results will help breeding organizations to implement sustainable genomic selection.
The knockout of the HMG domain of the porcine SRY gene causes sex reversal in gene-edited pigs
Authors: Kurtz Stefanie , Lucas-Hahn Andrea , Schlegelberger Brigitte , Göhring Gudrun , Niemann Heiner , Mettenleiter Thomas C. , Petersen Björn
Published: April 2019

1

The sex-determining region on the Y chromosome (SRY) is thought to be the central genetic element of male sex development. Mutations within the SRY gene are associated with a male-to-female sex reversal syndrome in humans and other mammalian species such as mice and rabbits. However, the underlying mechanisms are largely unknown. To understand the biological function of the SRY gene, a site-directed mutational analysis is required to investigate associated phenotypic changes at the molecular, cellular and morphological level. In our study, we successfully generated a knockout of the porcine SRY gene by microinjection of two clustered regularly interspaced short palindromic repeats (CRISPR) – associated protein - 9 nuclease (Cas9) ribonucleoprotein (RNP) complexes targeting the centrally located “high mobility group” (HMG) domain of the SRY gene. Mutations within this region resulted in the development of complete external and internal female genitalia in genetically male pigs. The internal female genitalia including uteri, ovaries, and oviducts, revealed substantial size differences in 9-months old SRY-knockout pigs compared to age-matched female wild type controls. In contrast, a deletion within the 5’ flanking region of the HMG domain was not associated with sex reversal. Results of this study demonstrates for the first time the central role of the HMG domain of the SRY gene in male sex determination in pigs. Moreover, quantitative analysis by digital PCR revealed evidence for a duplication of the porcine SRY locus. Our results pave the way towards the generation of boars exclusively producing phenotypically female offspring to avoid surgical castration without anesthesia in piglets. Moreover, the study establishes a large animal model that is much more similar to humans in regard of physiology and anatomy and pivotal for longitudinal studies.
FOXP2 exhibits projection neuron class specific expression, but is not required for multiple aspects of cortical histogenesis
Authors: Kast Ryan J , Lanjewar Alexandra L , Smith Colton D , Levitt Pat
Published: April 2019

The expression patterns of the transcription factor FOXP2 in the developing mammalian forebrain have been described, and some studies have tested the role of this protein in the development and function of specific forebrain circuits by diverse methods and in multiple species. Clinically, mutations in FOXP2 are associated with severe developmental speech disturbances, and molecular studies indicate that impairment of Foxp2 may lead to dysregulation of genes involved in forebrain histogenesis. Here, anatomical and molecular phenotypes of the cortical neuron populations that express FOXP2 were characterized in mice. Additionally, Foxp2 was removed from the developing mouse cortex at different prenatal ages using two Cre-recombinase driver lines. Detailed molecular and circuit analyses were undertaken to identify potential disruptions of development. Surprisingly, the results demonstrate that Foxp2 function is not required for many functions that it has been proposed to regulate, and therefore plays a more limited role in cortical development than previously thought.
Differences of endogenous polyamines and putative genes associated with paraquat resistance in goosegrass (Eleusine indica L.)
Authors: Luo Qiyu , Wei Jiping , Dong Zhaoxia , Shen Xuefeng , Chen Yong
Published: April 2019

Background

Paraquat is one of the most effective herbicides used to control weeds in agricultural management, while the pernicious weed goosegrass (Eleusine indica) has evolved resistance to herbicides, including paraquat. Polyamines provide high-level paraquat resistance in many plants. In the present study, we selected three polyamines, namely, putrescine, spermidine, and spermine, as putative genes to investigate their correlation with paraquat resistance by using paraquat-resistant (R) and paraquat-susceptible (S) goosegrass populations.

Results

There was no significant difference in the putrescine nor spermine content between the R and S biotypes. However, 30 and 90 min after paraquat treatment, the spermidine concentration was 346.14-fold and 421.04-fold (P < 0.001) higher in the R biotype than in the S biotype, but the spermidine concentration was drastically reduced to a marginal level after 90 min. Since the transcript level ofPqEwas low while the spermidine concentration showed a transient increase, thePqEgene was likely involved in the synthesis of the paraquat resistance mechanism, regulation of polyamine content, and synthesis of spermidine and spermine.PqTS1,PqTS2,andPqTS3encode transporter proteins involved in the regulation of paraquat concentration but showed different transcription patterns with synchronous changes in polyamine content.

Conclusion

Endogenous polyamines (especially spermidine) play a vital role in paraquat resistance in goosegrass.PqE, PqTS1, PqTS2, andPqTS3were speculated on the relationship between polyamine metabolism and paraquat resistance. To validate the roles ofPqE, PqTS1, PqTS2, andPqTS3in polyamine transport systems, further research is needed.
Floral volatiles and visitors: A meta‐network of associations in a natural community
Authors: Kantsa Aphrodite , Raguso Robert A. , Lekkas Themistokles , Kalantzi Olga‐Ioanna , Petanidou Theodora
Published: April 2019

Chemosensory communication between flowers and pollinators is a fundamental component of terrestrial biodiversity, given the importance of olfaction to foraging animals. In this respect, exploring chemically mediated interspecific interactions in natural assemblies may provide novel insights into the ecofunctional significance of volatile organic compounds (VOCs) for plant–insect co‐evolution. However, multispecies datasets of associations between plant semiochemicals and arthropods are still very rare and tend to lack community context. Here, we present the first insect–floral VOC meta‐network using plant–pollinator visitation data and the plants’ floral scent blends, collected in a Mediterranean scrubland.

We assembled the insect–VOC meta‐network by substituting each plant species in the plant–pollinator network with the blend of VOCs it emits. Furthermore, we identified the modules of the network that is the most densely connected insect–VOC groups. After describing the role of the species in the network, we focused on the bees of the community, and by building phylogenetically informed GLS models, we found the species traits predicting the degree of chemical specialization.

Modularity analysis of the meta‐network revealed tight associations between several classes of VOCs and pollinator groups. Linkage patterns suggest positive associations between (a) Megachilidae bees and sesquiterpenes, (b) Apidae and Andrenidae bees and benzenoids/phenylpropanoids, and (c) wasps, C6 green‐leaf volatiles and specific terpenoids. Benzenoids were found to be the least influential and most specialized chemical class in the community, whereas sesquiterpenes represented the most influential one. Furthermore, the degree of chemical generalization of the bees in the meta‐network was significantly associated with their ecological generalization, body mass and phenology, whereas their contribution to the network's structure was related to their level of sociality.

Synthesis. Our findings help to disclose the ecofunctional significance of the floral volatile landscape and contribute novel testable hypotheses on the behavioural trends and chemical niches of pollinators in a natural community. The insect–volatilome meta‐network is thus shown to be advantageous for detecting and visualizing patterns of chemically mediated interspecific interactions. Given the ubiquity of chemosensory biocommunication, our approach can be applied for investigating various types of ecological interactions in community contexts.
‘Man of the Mountain’: Seeing Jefferson at Monticello
Authors: Tietze Larson Victoria S.
Published: April 2019

Jefferson's ‘retirement’ at Monticello – built, exceptionally for a Virginia plantation house, on top of a mountain – provided the requisite audience for a carefully fashioned self‐image. Its inspiration lay in classical descriptions of country living and mountain‐top villas, which had been appropriated by eighteenth‐century polite literature as part of the imaginary of the British landed gentleman. Although conceived as part of a process of righteous self‐distancing from Europe, Jefferson's retirement nevertheless situated him in a cosmopolitan, elite and genteel company, a fact that complicated his quest to meet republican ideals.
Precipitation and prey abundance influence food habits of an invasive carnivore
Authors: Parsons Mitchell A. , Bridges Andrew S. , Biteman Daniel S. , Garcelon David K.
Published: April 2019

Invasive predators threaten biodiversity worldwide, and generalist invasive predators are often more successful due to their broad diets. Predation patterns can be influenced by prey abundance, prey preference, and climate, and understanding these relationships is integral to conserving native prey species. We examined stomach contents of 2882 feral cats Felis catus from San Clemente Island, California, to assess how their diets varied annually and seasonally, and how precipitation and prey abundance influenced predation patterns. Rodents were found in 95% (n = 2589) of stomachs containing prey. The endemic San Clemente deer mouse Peromyscus maniculatus clementis was the most prevalent prey species and was found in 85% (n = 2589) of stomachs containing prey. Consumption of rodents, lizards, and birds varied annually. In years following dry winters, consumption of rodents decreased and consumption of lizards increased. This had a particularly strong effect on endemic night lizards Xantusia riversiana reticulata with 20.4% (n = 1952) of non‐empty cat stomachs containing night lizards following normal years, and 43.7% (n = 602) following dry years. Consumption of rodents peaked in fall, while consumption of lizards and birds peaked in spring. Using rodenticide removed from bait stations as an index of rodent abundance, we found a positive correlation between bait removal and the number of rodents consumed by cats, and a negative correlation between bait removal and the number of lizards consumed by cats. These results suggest that feral cats use rodents as primary prey and lizards as secondary prey, particularly during droughts when rodent abundance is low. Understanding how weather patterns affect invasive species predation patterns will help conservation biologists predict and manage for the effects of invasive species as climate change continues. Furthermore, identifying and quantifying diet pattern seasonality can help managers identify times when sensitive species are vulnerable and plan interventions accordingly.
Parvalbumin‐immunoreactive cells in the olfactory bulb of the pigeon: Comparison with the rat
Authors: Lee Tae‐Kyeong , Park Joon Ha , Ahn Ji Hyeon , Park Young Eun , Park Cheol Woo , Lee Jae‐Chul , Choi Jung Hoon , Hwang In Koo , Kim Sunhyo , Shim Jaeho , Go Seokmin , Lee Eunji , Seo Kangmoon , Won Moo‐Ho
Published: April 2019

The olfactory bulb (OB) shows special characteristics in its phylogenetic cortical structure and synaptic pattern. In the OB, gamma‐aminobutyric acid (GABA), as an inhibitory neurotransmitter, is secreted from GABAergic neurons which contain parvalbumin (a calcium‐binding protein). Many studies on the distribution of parvalbumin‐immunoreactive neurons in the rodent OB have been published but poorly reported in the avian OB. Therefore, in this study, we compared the structure of the OB and distribution of parvalbumin‐immunoreactive neurons in the OB between the rat and pigeon using cresyl violet staining and immunohistochemistry for parvalbumin, respectively. Fundamentally, the pigeon OB showed layers like those of the rat OB; however, some layers were not clear like in the rat OB. Parvalbumin‐immunoreactive neurons in the pigeon OB were predominantly distributed in the external plexiform layer like that in the rat OB; however, the neurons did not have long processes like those in the rat. Furthermore, parvalbumin‐immunoreactive fibres were abundant in some layers; this finding was not shown in the rat OB. In brief, parvalbumin‐immunoreactive neurons were found like those in the rat OB; however, parvalbumin‐immunoreactive fibres were significantly abundant in the pigeon OB compared to those in the rat OB.