bluuebunny/crossref_metadata_2025 huggingface dataset:
A high-throughput screen for transcription activation domains reveals their sequence characteristics and permits reliable prediction by deep learning
Authors: Erijman Ariel , Kozlowski Lukasz , Sohrabi-Jahromi Salma , Fishburn James , Warfield Linda , Schreiber Jacob , Noble William S. , Söding Johannes , Hahn Steven
Published: December 2019

Transcription activation domains (ADs) are encoded by a wide range of seemingly unrelated amino acid sequences, making it difficult to recognize features that permit their dynamic behavior, fuzzy interactions and target specificity. We screened a large set of random 30-mer peptides for AD function and trained a deep neural network (ADpred) on the AD-positive and negative sequences. ADpred correctly identifies known ADs within protein sequences and accurately predicts the consequences of mutations. We show that functional ADs are (1) located within intrinsically disordered regions with biased amino acid composition, (2) contain clusters of hydrophobic residues near acidic side chains, (3) are enriched or depleted for particular dipeptide sequences, and (4) have higher helical propensity than surrounding regions. Taken together, our findings fit the model of “fuzzy” binding through hydrophobic protein-protein interfaces, where activator-coactivator binding takes place in a dynamic hydrophobic environment rather than through combinations of sequence-specific interactions.
Maternal alum-adjuvanted recombinant HIV Env vaccine does not enhance autologous virus neutralization in HIV-infected pregnant women
Authors: Hompe Eliza D. , Mangold Jesse F. , Eudailey Joshua A. , Giorgi Elena E. , Kumar Amit , McGuire Erin , Haynes Barton F. , Moody M. Anthony , Wright Peter F. , Fouda Genevieve G. , Gao Feng , Permar Sallie R.
Published: December 2019

Preventive strategies beyond ART will be required to end the pediatric HIV epidemic. A maternal vaccine capable of boosting neutralizing antibody (nAb) responses against circulating viruses in HIV-infected pregnant women could effectively decrease mother-to-child transmission of HIV. However, it is not known if an HIV envelope (Env) vaccine administered to infected pregnant women can enhance autologous virus neutralization.

Here, we assessed autologous virus nAb responses in maternal plasma samples obtained from AIDS Vaccine Evaluation Group (AVEG) Protocols 104 and 102, historical Phase I safety and immunogenicity trials of recombinant HIV Env subunit vaccines in HIV-infected pregnant women (NCT00001041). AVEG 104 participants were randomized to receive 300 µg Env subunit MN recombinant gp120 with alum adjuvant or alum alone. AVEG 102 participants were randomized to receive 640 µg Env subunit recombinant gp160 or placebo. HIV Env-specific maternal plasma binding and neutralizing responses were characterized before and after vaccination in 15 AVEG 104 (n=10 vaccinee, n=5 placebo) and 2 AVEG 102 (n=1 vaccinee, n=1 placebo) participants. Single genome amplification (SGA) was used to obtain HIVenvgene sequences from autologous viruses for pseudovirus production in pre- and post-vaccination plasma of HIV-infected pregnant vaccinees (n=6 gp120, n=1 gp160) and placebo recipients (n=3).

We detected an increase in MN gp120-specific IgG binding in the vaccinee group between the first immunization visit and the last visit at delivery (p=0.027, 2-sided Wilcoxon test). However, no difference was observed in the neutralization potency of maternal plasma collected at delivery against autologous viruses isolated from early or late pregnancy. Thus, maternal vaccination with gp120/160 did not boost maternal autologous virus nAb responses. Immunization strategies capable of more potent B cell stimulation will likely be required to effectively boost autologous virus nAb responses in pregnant women and synergize with ART to further reduce infant HIV infections.

Highlights

Prior maternal HIV Env vaccine trial did not assess autologous virus neutralization

Circulating viruses isolated from mothers were tested against autologous plasma

Maternal vaccination with HIV Env gp120/160 increased MN gp120-specific IgG binding

Maternal HIV Env vaccine regimen did not boost autologous virus neutralization

More potent B cell stimulation will be required to elicit autologous nAb responses
Rapid assessment of phytoplankton assemblages using Next Generation Sequencing – Barcode of Life database: a widely applicable toolkit to monitor biodiversity and harmful algal blooms (HABs)
Authors: Ivanova Natalia V. , Watson L. Cynthia , Comte Jérôme , Bessonov Kyrylo , Abrahamyan Arusyak , Davis Timothy W. , Bullerjahn George S. , Watson Susan B.
Published: December 2019

Harmful algal blooms have important implications for the health, functioning and services of aquatic ecosystems. Our ability to detect and monitor these events is often challenged by the lack of rapid and cost-effective methods to identify bloom-forming organisms and their potential for toxin production, Here, we developed and applied a combination of DNA barcoding and Next Generation Sequencing (NGS) for the rapid assessment of phytoplankton community composition with focus on two important indicators of ecosystem health: toxigenic bloom-forming cyanobacteria and impaired planktonic biodiversity. To develop this molecular toolset for identification of cyanobacterial and algal species present in HABs (Harmful Algal Blooms), hereafter called HAB-ID, we optimized NGS protocols, applied a newly developed bioinformatics pipeline and constructed a BOLD (Barcode of Life Data System) 16S reference database from cultures of 203 cyanobacterial and algal strains representing 101 species with particular focus on bloom and toxin producing taxa. Using the new reference database of 16S rDNA sequences and constructed mock communities of mixed strains for protocol validation we developed new NGS primer set which can recover 16S from both cyanobacteria and eukaryotic algal chloroplasts. We also developed DNA extraction protocols for cultured algal strains and environmental samples, which match commercial kit performance and offer a cost-efficient solution for large scale ecological assessments of harmful blooms while giving benefits of reproducibility and increased accessibility. Our bioinformatics pipeline was designed to handle low taxonomic resolution for problematic genera of cyanobacteria such as theAnabaena-Aphanizomenon-Dolichospermumspecies complex, two clusters ofAnabaena(I and II),PlanktothrixandMicrocystis. This newly developed HAB-ID toolset was further validated by applying it to assess cyanobacterial and algal composition in field samples from waterbodies with recurrent HABs events.
Structure of biomolecular condensates from dissipative particle dynamics simulations
Authors: Shillcock Julian C. , Brochut Maelick , Chénais Etienne , Ipsen John H.
Published: December 2019

Phase separation of immiscible fluids is a common phenomenon in polymer chemistry, and is recognized as an important mechanism by which cells compartmentalize their biochemical reactions. Biomolecular condensates are condensed fluid droplets in cells that form by liquid-liquid phase separation of intrinsically-disordered proteins. They have a wide range of functions and are associated with chronic neurodegenerative diseases in which they become pathologically rigid. Intrinsically-disordered proteins are conformationally flexible and possess multiple, distributed binding sites for each other or for RNA. However, it remains unclear how their material properties depend on the molecular structure of the proteins. Here we use coarse-grained simulations to explore the phase behavior and structure of a model biomolecular condensate composed of semi-flexible polymers with attractive end-caps in a good solvent. Although highly simplified, the model contains the minimal molecular features that are sufficient to observe liquid-liquid phase separation of soluble polymers. The polymers condense into a porous, three-dimensional network in which their end-caps reversibly bind at junctions. The spatial separation of connected junctions scales with the polymer backbone length as a self-avoiding random walk over a wide range of concentration with a weak affinity-dependent prefactor. By contrast, the average number of polymers that meet at the junctions depends strongly on the end-cap affinity but only weakly on the polymer length. The regularity and porosity of the condensed network suggests a mechanism for cells to regulate biomolecular condensates. Interaction sites along a protein may be turned on or off to modulate the condensate’s porosity and tune the diffusion and interaction of additional proteins.
Electron transfer proteins in gut bacteria yield metabolites that circulate in the host
Authors: Liu Yuanyuan , Chen Haoqing , Van Treuren William , Hou Bi-Huei , Higginbottom Steven K. , Sonnenburg Justin L. , Dodd Dylan
Published: December 2019

It has long been known that proteolytic Clostridia obtain their energy by coupling oxidative and reductive pathways for amino acid metabolism – the Stickland reaction1. The oxidation of one amino acid is coupled with reduction of another, yielding energy in the former step and re-achieving redox balance with the latter. Here, we find that the gut bacterium,Clostridium sporogenesmetabolizes amino acids through reductive pathways to produce metabolites that circulate within the host. Measurementsin vitroindicate that reductive Stickland pathways are coupled to ATP formation, revealing their role in energy capture by gut bacteria. By probing the genetics ofC. sporogenes, we find that the Rnf complex is involved in reductive amino acid metabolism. Rnf complex mutants are attenuated for growth in the mouse gut, demonstrating the importance of energy capture during reductive metabolism for gut colonization. Our findings reveal that the production of high-abundance molecules by a commensal bacterium within the host gut is linked to an energy yielding redox process.
Molecular Investigations into the Unfoldase Action of Severing Enzymes on Microtubules
Authors: Varikoti Rohith Anand , Macke Amanda C. , Speck Virginia , Ross Jennifer L. , Dima Ruxandra I.
Published: December 2019

Microtubules associated proteins regulate the dynamic behavior of microtubules during cellular processes. Microtubule severing enzymes are the associated proteins which destabilize microtubules by removing subunits from the lattice. One model for how severing enzymes remove tubulin dimers from the microtubule lattice is by unfolding its subunits through pulling on the carboxy-terminal tails of tubulin dimers. This model stems from the fact that severing enzymes are AAA+ unfoldases. To test this mechanism, we apply pulling forces on the carboxy-terminal regions of microtubule subunits using coarse grained molecular simulations. In our simulations we used different microtubule lattices and concentrations of severing enzymes. We compare our simulation results with data fromin-vitrosevering assays and find that the experimental data is best fit by a model of cooperative removal of protofilament fragments by severing enzymes which depends on the severing enzyme concentration and placement on the microtubule lattice.
An allosteric switch regulatesMycobacterium tuberculosisClpP1P2 protease function as established by cryo-EM and methyl-TROSY NMR
Authors: Vahidi Siavash , Ripstein Zev A. , Juravsky Jordan B. , Rennella Enrico , Goldberg Alfred L. , Mittermaier Anthony K. , Rubinstein John L. , Kay Lewis E.
Published: December 2019

The 300-kDa ClpP1P2 protease fromMycobacterium tuberculosiscollaborates with the AAA+ (ATPases associated with a variety of cellular activities) unfoldases, ClpC1 and ClpX, to degrade substrate proteins. Unlike in other bacteria, all the components of the Clp system are essential for growth and virulence of mycobacteria, and their inhibitors show promise as novel antibiotics. MtClpP1P2 is unique in that it contains a pair of distinct ClpP1 and ClpP2 rings and also requires the presence of activator peptides, such as benzoyl-leucyl-leucine (Bz-LL), for function. Understanding the structural basis for this requirement has been elusive but is critical for the rational design and improvement of anti-TB therapeutics that target the Clp system. Here we present a combined biophysical and biochemical study to explore the structure-dynamics-function relationship in MtClpP1P2. Cryo-EM structures of apo and acyldepsipeptide-bound MtClpP1P2 explain their lack of activity by showing loss of a key β-sheet in a sequence known as the handle region that is critical for the proper formation of the catalytic triad. Methyl transverse relaxation-optimized spectroscopy (TROSY)-based NMR, cryo-EM, and biochemical assays show that upon binding Bz-LL or covalent inhibitors, MtClpP1P2 undergoes a conformational change from an inactive compact state to an active extended structure that can be explained by a modified Monod-Wyman-Changeux model. Our study establishes a critical role for the handle region as an on/off switch for function, and shows extensive allosteric interactions involving both intra- and inter-ring communication that regulate MtClpP1P2 activity and that can potentially be exploited by small molecules to targetM. tuberculosis.

Significance Statement

The MtClpP1P2 protease is part of the essential protein degradation machinery that helps maintain protein homeostasis inMycobacterium tuberculosis, the causative agent of TB. Antibiotics that selectively kill both dormant and growing drug-resistant populations ofM. tuberculosisby disrupting MtClpP1P2 function have attracted recent attention. Here we characterize a switch that can control MtClpP1P2 activity through binding of small peptides, leading to a concerted conformational change that potentially can be exploited by drug molecules to interfere with MtClpP1P2 function. Overall, this work highlights the power of a combined NMR and cryo-EM approach to provide detailed insights into the structure-dynamics-function relationship of molecular machines critical to human health.
Quantitative method for estimating stain density in electron microscopy of conventionally prepared biological specimens
Authors: Fera Andrea , He Qianping , Zhang Guofeng , Leapman Richard D.
Published: December 2019

Stain density is an important parameter for optimizing the quality of ultrastructural data obtained from several types of 3D electron microscopy techniques, including serial block-face electron microscopy (SBEM), and focused ion beam scanning electron microscopy (FIB-SEM). Here, we show how some straightforward measurements in the TEM can be used to determine the stain density based on a simple expression that we derive. Numbers of stain atoms per unit volume are determined from the measured ratio of the bright-field intensities from regions of the specimen that contain both pure embedding material and the embedded biological structures of interest. The determination only requires knowledge of the section thickness, which can either be estimated from the microtome setting, or from low-dose electron tomography, and the elastic scattering cross section for the heavy atoms used to stain the specimen. The method is tested on specimens of embedded blood platelets, brain tissue, and liver tissue.
coil: an R package for cytochrome C oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation
Authors: Nugent Cameron M. , Elliott Tyler A. , Ratnasingham Sujeevan , Adamowicz Sarah J.
Published: December 2019

Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation and curation, leading to varying levels of success in the separation of biological variation from experimental error. The five-prime region of cytochrome c oxidase subunit I (COI-5P) is the most common barcode gene for animals, with conserved structure and function that allows for biologically informed error identification. Here, we present coil (https://CRAN.R-project.org/package=coil), an R package for the pre-processing and error assessment of COI-5P animal barcode and metabarcode sequence data. The package contains functions for placement of barcodes into a common reading frame, accurate translation of sequences to amino acids, and highlighting insertion and deletion errors. The analysis of 10,000 barcode sequences of varying quality demonstrated how coil can place barcode sequences in reading frame and distinguish sequences containing indel errors from error-free sequences with greater than 97.5% accuracy. Package limitations were tested through the analysis of COI-5P sequences from the plant and fungal kingdoms as well as the analysis of potential contaminants: nuclear mitochondrial pseudogenes andWolbachiaCOI-5P sequences. Results demonstrated that coil is a strong technical error identification method but is not reliable for detecting all biological contaminants.
Cell-free genetic devices confer autonomic and adaptive properties to hydrogels
Authors: Whitfield Colette J. , Banks Alice M. , Dura Gema , Love John , Fieldsend Jonathan E. , Goodchild Sarah A. , Fulton David A. , Howard Thomas P.
Published: December 2019

Smart materials are able to alter one or more of their properties in response to defined stimuli. Our ability to design and create such materials, however, does not match the diversity and specificity of responses seen within the biological domain. We propose that relocation of molecular phenomena from living cells into hydrogels can be used to confer smart functionality to materials. We establish that cell-free protein synthesis can be conducted in agarose hydrogels, that gene expression occurs throughout the material and that co-expression of genes is possible. We demonstrate that gene expression can be controlled transcriptionally (usingin gelgene interactions) and translationally in response to small molecule and nucleic acid triggers. We use this system to design and build a genetic device that can alter the structural property of its chassis material in response to exogenous stimuli. Importantly, we establish that a wide range of hydrogels are appropriate chassis for cell-free synthetic biology, meaning a designer may alter both the genetic and hydrogel components according to the requirements of a given application. We probe the relationship between the physical structure of the gel andin gelprotein synthesis and reveal that the material itself may act as a macromolecular crowder enhancing protein synthesis. Given the extensive range of genetically encoded information processing networks in the living kingdom and the structural and chemical diversity of hydrogels, this work establishes a model by which cell-free synthetic biology can be used to create autonomic and adaptive materials.

Significance statement

Smart materials have the ability to change one or more of their properties (e.g. structure, shape or function) in response to specific triggers. They have applications ranging from light-sensitive sunglasses and drug delivery systems to shape-memory alloys and self-healing coatings. The ability to programme such materials, however, is basic compared to the ability of a living organism to observe, understand and respond to its environment. Here we demonstrate the relocation of biological information processing systems from cells to materials. We achieved this by operating small, programmable genetic devices outside the confines of a living cell and inside hydrogel matrices. These results establish a method for developing materials functionally enhanced with molecular machinery from biological systems.
Model-driven design allows growth ofMycoplasma pneumoniaeon serum-free media
Authors: Gaspari Erika , Malachowski Antoni , Garcia-Morales Luis , Burgos Raul , Serrano Luis , Santos Vitor A. P. Martins dos , Suarez-Diez Maria
Published: December 2019

Mycoplasma pneumoniaeis a slow-growing, human pathogen that causes atypical pneumonia. Because it lacks a cell wall, many antibiotics are ineffective, and vaccination is required. Due to its reduced genome and dearth of many biosynthetic pathways, this fastidious bacterium depends on rich, undefined medium for growth, which makes large-scale cultivation for vaccine production challenging and expensive.

To understand factors limiting growth, we developed a genome-scale, constraint-based model ofM. pneumoniaecalled iEG158_mpn to describe the metabolic potential of this bacterium. We have put special emphasis on cell membrane formation to identify key lipid components to maximize bacterial growth. We have used this knowledge to predict and validatein vitrotwo serum-free media able to sustain growth.

Our findings also show that glycolysis and lipid metabolism are much less efficient under hypoxia; these findings suggest that factors other than metabolism and membrane formation alone affect the growth ofM. pneumoniae.

Altogether, our modelling approach enabled us to optimize medium composition, capacitated growth in defined media and streamlined operational requirements, thereby providing the basis for stable, reproducible and less expensive vaccine production.
Selection for rapid uptake of scarce or fluctuating resource explains vulnerability of glycolysis to imbalance
Authors: Janulevicius Albertas , van Doorn G. Sander
Published: December 2019

Glycolysis is a conserved central pathway in energy metabolism that converts glucose to pyruvate with net production of two ATP molecules. Because ATP is produced only in the lower part of glycolysis (LG), preceded by an initial investment of ATP in the upper glycolysis (UG), achieving robust start-up of the pathway upon activation presents a challenge: a sudden increase in glucose concentration can throw a cell into a self-sustaining imbalanced state in which UG outpaces LG, glycolytic intermediates accumulate and the cell is unable to maintain high ATP concentration needed to support cellular functions. Such metabolic imbalance can result in “substrate-accelerated death”, a phenomenon observed in prokaryotes and eukaryotes when cells are exposed to an excess of substrate that previously limited growth. Here, we address why evolution has apparently not eliminated such a costly vulnerability and propose that it is a manifestation of an evolutionary trade-off, whereby the glycolysis pathway is adapted to quickly secure scarce or fluctuating resource at the expense of vulnerability in an environment with ample resource. To corroborate this idea, we perform evolutionary simulations of a simplified yeast glycolysis pathway consisting of UG, LG, phosphate transport between a vacuole and a cytosol, and a general ATP demand reaction. The pathway is evolved in constant or fluctuating resource environments by allowing mutations that affect the (maximum) reaction rate constants, reflecting changing expression levels of different glycolytic enzymes. We demonstrate that under limited constant resource, the population evolves to a genotype that is balanced but exhibits strongly imbalanced dynamics under ample resource conditions. Furthermore, when resource availability is fluctuating, the imbalanced phenotype enjoys a fitness advantage over balanced dynamics: when glucose is abundant, imbalanced pathways can quickly accumulate glycolytic intermediate FBP as intracellular storage that is used during periods of starvation to maintain high ATP concentration needed for growth. Our model further predicts that in environments with fluctuating resource, competition for glucose can result in stable coexistence of balanced and imbalanced cells, as well as repeated cycles of population crashes and recoveries that depend on such polymorphism. Overall, we demonstrate the importance of ecological and evolutionary arguments for understanding seemingly maladaptive aspects of cellular metabolism.
FLASH irradiation enhances the therapeutic index of abdominal radiotherapy for the treatment of ovarian cancer
Authors: Levy Karen , Natarajan Suchitra , Wang Jinghui , Chow Stephanie , Eggold Joshua T. , Loo Phoebe , Manjappa Rakesh , Lartey Frederick M. , Schüler Emil , Skinner Lawrie , Rafat Marjan , Ko Ryan , Kim Anna , Rawi Duaa Al , von Eyben Rie , Dorigo Oliver , Casey Kerriann M. , Graves Edward E. , Bush Karl , Yu Amy S. , Koong Albert C. , Maxim Peter G. , Loo Billy W. , Rankin Erinn B.
Published: December 2019

Peritoneal metastases are the leading cause of morbidity and mortality in ovarian cancer. Despite current surgery, chemotherapy and targeted therapies, the majority of patients diagnosed with advanced epithelial ovarian cancer develop recurrent disease and overall survival rates remain poor. It is known that ovarian cancer is a radiosensitive tumor. Historically, total abdominal irradiation (TAI) was used as an effective postsurgical adjuvant therapy in the management of chemotherapy sensitive and resistant ovarian cancer. However, TAI fell out of favor due to high toxicity, particularly of the gastrointestinal tract. We have developed a preclinical irradiation platform that allows for total abdominal ultrahigh dose rate FLASH irradiation. We demonstrate that TAI-FLASH reduces radiation-induced intestinal injury in both healthy and tumor-bearing mice compared to conventional dose rate (CONV) irradiation. Single high dose TAI-FLASH reduced mortality from gastrointestinal syndrome, spared gut function and epithelial integrity, and decreased cell death in crypt base columnar cells. Importantly, FLASH and CONV irradiation had similar efficacy in the reduction of ovarian cancer peritoneal metastases. These findings suggest that FLASH irradiation may be an effective strategy to enhance the therapeutic index of radiotherapy for the treatment of metastatic ovarian cancer in women.
Brain-machine interface learning is facilitated by specific patterning of distributed cortical feedback
Authors: Abbasi A. , Lassagne H. , Estebanez L. , Goueytes D. , Shulz D. E. , Ego-Stengel V.
Published: December 2019

Neuroprosthetics offer great hope for motor-impaired patients. One obstacle is that fine motor control requires near-instantaneous, rich somatosensory feedback. Such distributed feedback may be recreated in a brain-machine interface using distributed artificial stimulation across the cortical surface. Here, we hypothesized that neuronal stimulation must be contiguous in its spatiotemporal dynamics in order to be efficiently integrated by sensorimotor circuits. Using a closed-loop brain-machine interface, we trained head-fixed mice to control a virtual cursor by modulating the activity of motor cortex neurons. We provided artificial feedback in real time with distributed optogenetic stimulation patterns in the primary somatosensory cortex. Mice developed a specific motor strategy and succeeded to learn the task only when the optogenetic feedback pattern was spatially and temporally contiguous while it moved across the topography of the somatosensory cortex. These results reveal new properties of sensorimotor cortical integration and set new constraints on the design of neuroprosthetics.

Teaser

Targeting a brain-machine interface feedback to a cortical map reveals unexpected constraints.
Characterization of the adaptation to visuomotor rotations in the muscle synergies space
Authors: Severini Giacomo , Zych Magdalena
Published: December 2019

The adaptation to visuomotor rotations is one of the most studied paradigms of motor learning. Previous literature has presented evidence of a dependency between the process of adaptation to visuomotor rotations and the constrains dictated by the workspace of the biological actuators, the muscles, and their co-activation strategies, modeled using muscle synergies analysis. To better understand this relationship, we asked a sample of healthy individuals (N =7) to perform two experiments aiming at characterizing the adaptation to visuomotor rotations in terms of rotations of the activation space of the muscle synergies during isometric reaching tasks. In both experiments, subjects were asked to adapt to visual rotations altering the position mapping between the force exerted on a fixed manipulandum and the movement of a cursor on a screen. In the first experiment subjects adapted to three different visuomotor rotation angles (30°, 40° and 50° clockwise) applied to the whole experimental workspace. In the second experiment subjects adapted to a single visuomotor rotation angle (45° clockwise) applied to eight different sub-spaces of the whole workspace, while also performing movements in the rest of the unperturbed workspace. The results from the first experiment confirmed the observation that visuomotor rotations induce rotations in the synergies activation workspace that are proportional to the visuomotor rotation angle. The results from the second experiment showed that rotations affecting limited sub-spaces of the whole workspace are adapted for by rotating only the synergies involved in the movement, with an angle proportional to the distance between the preferred angle of the synergy and the sub-space covered by the rotation. Moreover, we show that the activation of a synergy is only rotated when the sub-space covered by the visual perturbation is applied at the boundaries of workspace of the synergy. We found these results to be consistent across subjects, synergies and sub-spaces. Moreover, we found a correlation between synergies and muscle rotations further confirming that the adaptation process can be well described, at the neuromuscular level, using the muscle synergies model. These results provide information on how visuomotor rotations can be used to induce a desired neuromuscular response.
The lipid transfer function of RDGB at ER-PM contact sites is regulated by multiple interdomain interactions
Authors: Basak Bishal , Krishnan Harini , Raghu Padinjat
Published: December 2019

InDrosophilaphotoreceptors, following Phospholipase C-β activation, the phosphatidylinositol transfer protein (PITP) RDGB, is required to maintain lipid homeostasis at endoplasmic reticulum (ER) plasma membrane (PM) membrane contact sites (MCS). Depletion or mis-localization of RDGB results in multiple defects in photoreceptors. Previously, interaction between the FFAT motif of RDGB with the integral ER protein dVAP-A was shown to be important for its localization at ER-PM MCS. Here, we report that in addition to FFAT motif, a large unstructured region (USR1) of RDGB is required to support the RDGB/dVAP-A interaction. However, interaction with dVAP-A alone is insufficient for accurate localization of RDGB: this also requires association of RDGB with apical PM, through its C-terminal LNS2 domain. Deletion of LNS2 domain results in complete mis-localisation of RDGB and also induces large mis-regulated interdomain movements abrogating RDGB function. Thus, multiple independent interactions between individual domains of RDGB supports its function at ER-PM MCS.
A modular RNA interference system for multiplexed gene regulation
Authors: Dwijayanti Ari , Storch Marko , Stan Guy-Bart , Baldwin Geoff S.
Published: December 2019

The rational design and realisation of simple-to-use genetic control elements that are modular, orthogonal and robust is essential to the construction of predictable and reliable biological systems of increasing complexity. To this effect, we introducemodularArtificialRNAinterference (mARi), a rational, modular and extensible design framework that enables robust, portable and multiplexed post-transcriptional regulation of gene expression inEscherichia coli. The regulatory function of mARi was characterised in a range of relevant genetic contexts, demonstrating its independence from other genetic control elements and the gene of interest, and providing new insight into the design rules of RNA based regulation inE. coli, while a range of cellular contexts also demonstrated it to be independent of growth-phase and strain type. Importantly, the extensibility and orthogonality of mARi enables the simultaneous post-transcriptional regulation of multi-gene systems as both single-gene cassettes and poly-cistronic operons. To facilitate adoption, mARi was designed to be directly integrated into the modular BASIC DNA assembly framework. We anticipate that mARi-based genetic control within an extensible DNA assembly framework will facilitate metabolic engineering, layered genetic control, and advanced genetic circuit applications.
A novel system for maintaining Varroa destructor mites on artificial diets and its application for studying mites as a vector for honey bee viruses
Authors: Posada-Florez Francisco , Ryabov Eugene V. , Heerman Matthew C. , Chen Yanping , Evans Jay D. , Cook Steven C. , Sonenshine Daniel E.
Published: December 2019

The mite Varroa destructor is one of the most destructive parasites of the honey bee (Apis mellifera) and the primary cause of colony collapse in most regions of the world. These mites cause serious injury to their hosts, especially during the larval and pupal stages, and serve as the vector for several viruses, which affect honey bee health causing colony death. Attempts by beekeepers to control these mites have yielded limited success. The inability to rear populations of mites in vitro that excludes contact with their honey bee hosts has stymied research of Varroa biology. Previous attempts to rear and/or maintain Varroa mites in vitro by feeding them on artificial diets have had limited success. Several methods were plagued by mechanical failures including leaking membranes and, thus far, none have been widely adopted. Here we report a robust system for maintaining Varroa mites that includes an artificial diet, which does not contain honey bee tissue-derived components, thus making it particularly valuable in studying mite vectoring of honey bee viruses. With our system we demonstrated for the first time that Varroa mites maintained on an artificial diet supplemented with the particles of honey bee viruses, cDNA clone-derived genetically tagged Varroa destructor virus-1 and wild-type Deformed wing virus, can acquire and later transmit these viruses to recipient honey bee pupae. Along with providing an opportunity to study parasites and pathogens in the absence of honey bee hosts, this in vitro system for Varroa mite maintenance is both scalable and consistent. These features can be used to better understand mite nutritional needs, metabolic activity, responses to chemicals and other biological functions.
Human intestinal tissue-resident memory CD8+ T cells comprise transcriptionally and functionally distinct subsets
Authors: FitzPatrick Michael E.B. , Provine Nicholas M. , Garner Lucy C. , Powell Kate , Amini Ali , Irwin Sophie , Ferry Helen , Ambrose Tim , Friend Peter , Vrakas Georgios , Reddy Srikanth , Soilleux Elizabeth , Klenerman Paul , Allan Philip J.
Published: December 2019

Tissue-resident memory T (TRM) cells provide key adaptive immune responses in infection, cancer, and autoimmunity. However transcriptional heterogeneity of human intestinal TRM cells remains undefined, and definitive markers of CD103-TRM cells are lacking. Here, we investigated transcriptional and functional heterogeneity of human TRM cells through the study of donor-derived intestinal TRM cells from intestinal transplant recipients. Single-cell transcriptional profiling identified four conventional TRM populations, with two distinct transcriptional states of CD8+ TRM cells, delineated by ITGAE and ITGB2 expression. We defined a transcriptional signature discriminating the two CD8+ populations, including differential expression of key residency-associated genes and cytotoxic molecules. Flow cytometry of recipient-derived cells infiltrating the graft and intestinal lymphocytes from healthy gut confirmed the two CD8+ TRM phenotypes, with β2-integrin acting as a CD103-CD8+ TRM marker. CD103+ CD8+ TRM cells produced IL-2, and demonstrated greater polyfunctional cytokine production, while β2-integrin+ CD69+ CD103-TRM cells had higher granzyme expression. Phenotypic and functional analysis of intestinal CD4+ T cells identified many parallels, including a distinct β2-integrin+ population. Together, these results describe the transcriptional, phenotypic, and functional heterogeneity of human intestinal TRM cells, and suggest a role for β2-integrin in TRM development.

Heterogeneity within human tissue-resident memory T (TRM) cells is poorly understood. We show that transcriptionally, phenotypically, and functionally distinct CD4+ and CD8+ TRM subsets exist in the human intestine, and that β2-integrin expression identifies a distinct population of CD8+ TRM cells.
Dimensions of anxiety and depression and neurophysiological indicators of error-monitoring: Relationship with delta and theta oscillatory power and error-related negativity amplitude
Authors: Muir Alexandra M. , Hedges-Muncy Ariana , Clawson Ann , Carbine Kaylie A. , Larson Michael J.
Published: December 2019

Error-monitoring processes may be affected by transdiagnostic dimensions of psychopathology symptoms including trait anxiety, worry, and severity of depressive symptoms. We tested the relationship between continuous measures of anxiety and depressive symptomology and neural correlates of error-monitoring as measured by time-frequency domain delta and theta oscillatory power and time domain error-related negativity (ERN) amplitude extracted from the electroencephalogram (EEG). Secondary analyses tested for diagnostic group differences in error-related neural responses in individuals with generalized anxiety disorder (GAD), major depressive disorder (MDD), and comorbid psychiatric disorders. 178 participants (104 female,M[SD]age= 21.7[4.6]) with a wide range of psychopathology symptoms completed a modified version of the Eriksen flanker task and symptom questionnaires. Residualized difference values between correct and error trials for delta/theta power and error/correct ERN amplitude were dependent variables. Linear regression analyses adjusted for age and sex showed nonsignificant associations of symptom dimension measures with error-related residualized delta/theta power or residualized ERN amplitude. Subset analyses on those with confirmed psychopathology diagnoses also did not predict residualized error-related delta/theta power nor ERN amplitude. Exploratory analyses with only error trial delta/theta power and ERN amplitude also revealed nonsignificant relationships. Taken in the context of previous literature, results suggest a heterogeneous relationship between depressive and anxiety symptom dimensions and neurophysiological indices of error-monitoring.

Impact Statement

In line with the RDoC framework, we tested the relationship between anxiety and depressive symptom dimensions and neural indices of error-processing (delta and theta power, error-related negativity ERP amplitude) in 178 participants with a range of pathology symptoms. A non-significant relationship emerged between neural and symptom measures suggesting anxiety and depressive symptomology have a nuanced relationship with error-monitoring in a large sample across a range of anxiety and depression symptoms.
FGF9 and FGF10 use distinct signaling pathways to direct lung epithelial specification and branching
Authors: Yin Yongjun , Ornitz David M.
Published: December 2019

Fibroblast Growth Factors (FGFs) 9 and 10 are essential during the pseudoglandular stage of lung development. Mesothelial produced FGF9 is principally responsible for mesenchymal growth, whereas epithelial produced FGF9 and mesenchymal produced FGF10 guide lung epithelial development, and loss of either of these ligands affects epithelial branching. Because FGF9 and FGF10 activate distinct FGF receptors (FGFRs), we hypothesized that they would control distinct developmental mechanisms. Here, we show that FGF9 signaled through epithelial FGF receptor 3 (FGFR3) to directly promote distal epithelial fate specification and inhibit epithelial differentiation. By contrast, FGF10 signaled through epithelial FGFR2b to promote epithelial proliferation and differentiation. Furthermore, FGF9-FGFR3 signaling functionally opposed FGF10-FGFR2b signaling, and FGFR3 preferentially used downstream PI3K pathways, whereas FGFR2b relied on downstream RAS-MAPK pathways. These data demonstrate that within lung epithelial cells, different FGFRs function independently; they bind receptor-specific ligands and direct unique developmental functions through activation of distinct downstream signaling pathways.
Examining US business undergraduates’ use of career information sources during career exploration
Authors: Chin Mun Yuk , Blackburn Cohen Chelsea A. , Hora Matthew T.
Published: December 2019

Purpose

Campus career services are increasingly scrutinized as the primary career development resource for undergraduates. The purpose of this paper is to use Career Construction Theory to examine all sources of career information used by undergraduate business students and their contributions toward career exploration and development.

Design/methodology/approach

Using a mixed-methods design, a survey was first administered to 372 university students enrolled in an undergraduate business school in the USA. Focus group interviews were conducted with 35 students from the survey sample. Descriptive statistics are reported, and inductive themes and causal networks were derived from qualitative data.

Findings

In order of prominence, students endorsed using sociocultural (e.g. family) and institutional (e.g. career services center) resources, and exploratory activities (e.g. work experience) as career information sources. These sources contributed toward students’ vocational development by enhancing their psychological readiness for work, building social capital and facilitating decisions.

Research limitations/implications

Participants were sampled from one undergraduate business school in the USA and were self-selected into the study.

Practical implications

Career services and higher education professionals should think of the career-related information sources available to students as a complex ecosystem of advice instead of singular resources that exist in isolation. Professionals should also attend to students existing sources of career information and consider ways to support students’ development of social and professional networks and opportunities. Furthermore, universities should consider the potential for integrating career exploration into course curricula as opposed to tasking career services offices to be fully responsible for students’ career-related outcomes.

Originality/value

This study is the first to examine undergraduate business students’ sources of career information and their contributions to career development. Its insights offer evidence for ways to tailor interventions to support students’ use of available information sources beyond campus career services.
Rethinking competition-based entrepreneurship education in higher education institutions
Authors: Watson Kayleigh , McGowan Pauric
Published: December 2019

Purpose

The purpose of this paper is to focus with the university-based business plan competition (BPC) and proposes how the theory of effectuation might inform a new model. Such a purpose is timely given the under-challenged nature of the BPC methodology.

Design/methodology/approach

Extant literature pertaining to business planning and the business plan within entrepreneurship education and effectuation is reviewed; numerous conceptual issues which undermine BPC provision in its traditional form are then identified. In response to these identified issues, a series of principles which could underpin the introduction of an effectuation-led business coopetition (EBC) are outlined.

Findings

Strong emphasis on business plan production within a conventional BPC model raises questions about its capacity to release the entrepreneurial potential of the higher education institution student and provide them with an authentic and relevant entrepreneurial learning experience. Through using the ideas of effectuation to rethink provision, the action of business plan production can usefully be replaced with the action of business implementation. As well as facilitate a beneficial shift from competition to coopetition-based entrepreneurship education.

Originality/value

This paper valuably critiques the efficacy of a commonly employed yet under-challenged methodology for entrepreneurship education; the BPC. The propositions offered can guide competition provision in a more authentic, realistic and relevant way that is potentially better suited to inspiring and supporting entrepreneurial new venturing amongst students and graduates now rather than in the future. The paper thus has practical value to those designing and delivering competition-based entrepreneurship education.
Learning from design-prototyping interaction for engineering innovation from a cross-functional perspective
Authors: Lee Demei
Published: December 2019

Purpose

Novel engineering designs are usually infeasible for manufacturing or fail to meet the required performance. The dissimilar functionalities and mindsets between design and manufacturing pose challenges, as well as opportunities for innovation projects. This paper aims to report the innovation process that prototyped a novel engineering design of a haptic device in an engineering research lab. The innovation process went through several design generations. Interaction between design and manufacturing drove the innovation toward both better and worse directions between generations.

Design/methodology/approach

Using the case research method, the steps of theoretical proposition development, case selection, data collection, data analysis and theory modification were followed. By interviewing the key persons, the characteristics, issues and recommendations for improvement of the innovation process were identified.

Findings

It was found that technical issues were not the hurdles in the innovation process. Instead, managing the inter-organizational mechanism proved critical to its eventual success. The educational gap between the design and manufacturing groups gave rise to communicational and perceptional distance, while the gap in terms of work experience between the two groups enlarged that distance.

Research limitations/implications

The research results may be limited to cases with similar organizational and technological contexts.

Practical implications

Within an organization, the design and the manufacturing divisions are separated by a functional gap. The functional gap should be managed with multiple views, namely, technical, personal and organizational perspectives. The identified innovation process could help bridge such a gap and facilitate innovative engineering designs in research institutes.

Originality/value

The effectiveness of the innovation process was, thus, found to be determined by the positive or negative reinforcement of these two gaps between the design and manufacturing of the research institute.
An integrated Grey-DEMATEL approach for evaluating ICT adoption barriers in manufacturing SMEs
Authors: Singh Amit , Thakkar Jitesh , Jenamani Mamata
Published: December 2019

Purpose

The purpose of this paper is to propose an integrated gray-decision making trial and evaluation laboratory (Grey-DEMATEL) framework to evaluate the ICT adoption barriers in manufacturing small and medium enterprises (MSMEs) running in developing countries. The proposed model is also tested for Indian MSMEs.

Design/methodology/approach

The model consists of 16 potential ICT adoption barriers selected from existing literature and refined based on discussion with domain experts. While DEMATEL analyses causal relationship and prioritizes them, Grey approach tackles individual biases and data insufficiency.

Findings

The authors conclude that lack of awareness about benchmarking and lack of management vision are the most critical ICT adoption barriers in the case of Indian MSMEs.

Research limitations/implications

Outcomes of the present research are based on the experts’ inputs which are subject to the biases related to their experience and exposure. In India practices adopted by SMEs have geographical and political influence that is also neglected.

Originality/value

This study provides a model consisting of 16 ICT adoption barriers for MSMEs in developing country and a framework to analyze causal relationships among the barriers with the flexibility of data input from their own domain experts. The framework is also capable of dealing with expert biases and data insufficiency.