bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial dysfunction and autophagy responses to skeletal muscle stress
Authors: Nichenko Anna S. , Southern W. Michael , Qualls Anita E. , Flemington Alexandra B. , Mercer Grant H. , Yin Amelia , Yin Hang , Call Jarrod A.
Published: April 2019

Autophagy plays an important role in mitochondrial maintenance, yet many details of skeletal muscle autophagic activity are unresolved in the context of muscle stress and/or damage. Skeletal muscles from mice were stressed either by fatiguing contractions, eccentric contraction-induced injury (ECCI), or freeze injury (FI) to establish a timeline of mitochondrial function and autophagy induction after different forms of muscle stress. Only FI was sufficient to elicit a reduction in mitochondrial function (−88%, p=0.006), yet both ECCI and FI resulted in greater autophagy-related protein content (28-fold, p≤0.008) suggesting a tunable autophagic response. Muscles from another cohort of mice were used to determine specific forms of autophagy, i.e., flux and mitochondrial-specific, in response to muscle damage. Mitochondrial-specific autophagy was evident by accumulation of autophagy-related proteins in mitochondrial-enriched muscle fractions following FI (37-fold, p=0.017); however, autophagy flux, assessed by LC3II accumulation with the lysosomal inhibitor chloroquine, was insignificant suggesting a physiological bottleneck in the clearance of dysfunctional organelles following FI. Ulk1 muscle-specific knockout (Ulk1 MKO) mice were used to determine if autophagy is necessary for the recovery of mitochondrial function after muscle damage. Ulk1 MKO mice were weaker (−12%, p=0.012) and demonstrated altered satellite cell dynamics (e.g., proliferation) during muscle regeneration after FI compared to littermate control mice, but determination of autophagy necessity for the recovery of mitochondrial function was inconclusive. This study concludes that autophagy is a tunable cellular response to muscle damaging stress and may influence muscle fiber regeneration through interaction with satellite cells.

Key Points Summary

Muscle contractility dysfunction is well characterized after many different types of muscle stress however, the timing and magnitude of mitochondrial dysfunction and autophagy induction after different types of muscle stress is largely unknown.

In this study we found that only traumatic freeze injury causes mitochondria dysfunction compared to fatigue contractions and eccentric contraction-induced injury, and that the autophagic response to muscle stress scales to the magnitude of muscle damage, i.e., freeze vs. eccentric contraction-induced injury.

We determined that total autophagy-related protein content has a greater response to muscle fiber damage compared to autophagy flux likely reflecting a bottleneck of autophagosomes awaiting degradation following muscle injury.

Using a skeletal gmuscle-specific autophagy knockout mouse (Ulk1), we found that muscle contractility and satellite cell activity might be influenced by cellular events within the adult muscle fiber following muscle damage.
Detection of Ovarian Cancer Using Samples Sourced from the Vaginal Microenvironment
Authors: Galey Melissa M. , Young Alexandria N. , Petukhova Valentina Z. , Wang Mingxun , Wang Jian , Burdette Joanna E. , Sanchez Laura M.
Published: April 2019

Mass spectrometry (MS) offers high levels of specificity and sensitivity in clinical applications, and we have previously been able to demonstrate that matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS is capable of distinguishing two-component biological mixtures at low limits of detection. Ovarian cancer is notoriously difficult to detect due to the lack of any screening methods for early detection. By sampling a local microenvironment, such as the vaginal fluids, a MS based method is presented that was capable of monitoring disease progression from vaginally collected, local samples from tumor bearing mice. A murine xenograft model of high grade serous ovarian carcinoma (HGSOC) was used for this study and vaginal lavages were obtained from mice on a weekly basis throughout disease progression and subjected to our MALDI-TOF MS workflow followed by statistical analyses. Proteins in the 4-20 kDa region of the mass spectrum could consistently be measured to yield a fingerprint that correlated with disease progression over time. These fingerprints were found to be statistically stable across all mice with the protein fingerprint converging towards the end point of the study. MALDI-TOF MS serves as a unique analytical technique for measuring a sampled vaginal microenvironment in a specific and sensitive manner for the detection of HGSOC in a murine model.
New β-Lactamase Inhibitors Nacubactam and Zidebactam Improve the In Vitro Activity of β-Lactam Antibiotics Against Mycobacterium abscessus Complex Clinical Isolates
Authors: Kaushik Amit , Ammerman Nicole C. , Parrish Nicole M. , Nuermberger Eric L.
Published: April 2019

The new diazabicyclooctane-based β-lactamase inhibitors avibactam and relebactam improve the in vitro activity of β-lactam antibiotics against Mycobacterium abscessus complex (MABC). Here, we evaluated the in vitro activity of two newer diazabicyclooctane-based β-lactamase inhibitors in clinical development, nacubactam and zidebactam, with β-lactams against clinical isolates of MABC. Both inhibitors lowered the MICs of their partner β-lactams, meropenem (eight-fold) and cefepime (two-fold), and those of other β-lactams, similar to prior results with avibactam and relebactam.
Malaria vaccine candidates displayed on novel virus-like particles are immunogenic and induce transmission-blocking activity
Authors: Chan Jo-Anne , Wetzel David , Reiling Linda , Miura Kazutoyo , Drew Damien , Gilson Paul R , Anderson David A , Richards Jack S , Long Carole A , Suckow Manfred , Jenzelewski Volker , Tsuboi Takafumi , Boyle Michelle J , Piontek Michael , Beeson James G
Published: April 2019

The development of effective malaria vaccines remains a global health priority. Currently, the most advanced vaccine, known as RTS,S, has only shown modest efficacy in clinical trials. Thus, the development of more efficacious vaccines by improving the formulation of RTS,S for increased efficacy or to interrupt malaria transmission are urgently needed. The RTS,S vaccine is based on the presentation of a fragment of the sporozoite antigen on the surface of virus-like particles (VLPs) based on human hepatitis B virus (HBV). In this study, we have developed and evaluated a novel VLP platform based on duck HBV (known as Metavax) for malaria vaccine development. This platform can incorporate large and complex proteins into VLPs and is produced in a Hansenula cell line compatible with cGMP vaccine production. Here, we have established the expression of leading P. falciparum malaria vaccine candidates as VLPs. This includes Pfs230 and Pfs25, which are candidate transmission-blocking vaccine antigens. We demonstrated that the VLPs effectively induce antibodies to malaria vaccine candidates with minimal induction of antibodies to the duck-HBV scaffold antigen. Antibodies to Pfs230 also recognised native protein on the surface of gametocytes, and antibodies to both Pfs230 and Pfs25 demonstrated transmission-reducing activity in standard membrane feeding assays. These results establish the potential utility of this VLP platform for malaria vaccines, which may be suitable for the development of multi-component vaccines that achieve high vaccine efficacy and transmission-blocking immunity.
A simple and efficient CRISPR technique for protein tagging
Authors: Zeng Fanning , Beck Valerie , Schuierer Sven , Garnier Isabelle , Manneville Carole , Agarinis Claudia , Morelli Lapo , Quinn Lisa , Knehr Judith , Roma Guglielmo , Bassilana Frederic , Nash Mark
Published: April 2019

Genetic knock-in using homology directed repair is an inefficient process, requiring selection of few modified cells and hindering its application to primary cells. Here we describeHomologyindependent geneTagging (HiTag), a method to tag a protein of interest by CRISPR in up to 66% transfected cells with one single electroporation. The technique has proven effective in various cell types, can be used to knock in a fluorescent protein for live cell imaging, to modify the cellular location of a target protein and to monitor levels of a protein of interest by a luciferase assay in primary cells.
How the Avidity of Polymerase Binding to the -35/-10 Promoter Sites Affects Gene Expression
Authors: Einav Tal , Phillips Rob
Published: April 2019

Although the key promoter elements necessary to drive transcription inEscherichia colihave long been understood, we still cannot predict the behavior of arbitrary novel promoters, hampering our ability to characterize the myriad of sequenced regulatory architectures as well as to design novel synthetic circuits. This work builds on a beautiful recent experiment by Urtechoet al.who measured the gene expression of over 10,000 promoters spanning all possible combinations of a small set of regulatory elements. Using this data, we demonstrate that a central claim in energy matrix models of gene expression – that each promoter element contributes independently and additively to gene expression – contradicts experimental measurements. We propose that a key missing ingredient from such models is the avidity between the -35 and -10 RNA polymerase binding sites and develop what we call arefined energy matrixmodel that incorporates this effect. We show that this the refined energy matrix model can characterize the full suite of gene expression data and explore several applications of this framework, namely, how multivalent binding at the -35 and -10 sites can buffer RNAP kinetics against mutations and how promoters that bind overly tightly to RNA polymerase can inhibit gene expression. The success of our approach suggests that avidity represents a key physical principle governing the interaction of RNA polymerase to its promoter.

Significance Statement

Cellular behavior is ultimately governed by the genetic program encoded in its DNA and through the arsenal of molecular machines that actively transcribe its genes, yet we lack the ability to predict how an arbitrary DNA sequence will perform. To that end, we analyze the performance of over 10,000 regulatory sequences and develop a model that can predict the behavior of any sequence based on its composition. By considering promoters that only vary by one or two elements, we can characterize how different components interact, providing fundamental insights into the mechanisms of transcription.
Repeated phenotypic selection for cuticular blackness of armyworm larvae decreased stress resistance
Authors: Matsumura Takashi , Taya Hikaru , Matsumoto Hitoshi , Hayakawa Yoichi
Published: April 2019

ArmywormMythimna separatalarvae show changes in cuticle darkening depending on population densities and are roughly categorized into two phenotypes, a pale brown solitary type and black-colored gregarious type. Although the color difference in both larval types is apparent, it remains ambiguous whether any change in physiological traits accompanies the cuticle darkening. To answer this query, we repeated genetic selection of the blackness phenotype over one hundred generations in our laboratory colony and produced a black-colored (BL) strain. Comparison between non-selected control (CTL) and BL strains revealed an increased fecundity and adult life span in the BL strain compared with the CTL strain. In contrast, BL strain larvae were found to be significantly more sensitive to heat stress than CTL strain larvae. Hemolymph reactive oxygen species (ROS) levels were higher in the BL strain than in the CTL strain irrespective of stress. Antioxidant activities of the hemolymph were not significantly different between the two strains under non-stress condition, but the activities increased to higher levels in the CTL strain than those in the BL strain after heat stress. Activities and gene expression levels of antioxidant enzymes such as catalase and superoxide dismutase (SOD) in the fat body were significantly higher in CTL strain larvae than in BL strain larvae after heat treatment. Analysis of heat stress tolerance of F1 hybrids of CTL and BL strain adults showed that phenotype of stress tolerance was inherited maternally. These results indicate a trade-off between reproductive activity and stress resistance during repeated genetic selection.

Summary statement

Discrete cuticle color change from whitish to blackish, which was created by repeating the reciprocal crossing of selected dark-colored individuals, increased fecundity but lowered stress tolerance in the armyworm.
A meiosis-specific AAA+ assembly reveals repurposing of ORC during budding yeast gametogenesis
Authors: Villar-Fernández María Ascensión , da Silva Richard Cardoso , Pan Dongqing , Weir Elisabeth , Sarembe Annika , Raina Vivek B. , Weir John R. , Vader Gerben
Published: April 2019

ORC (Orc1-6) is an AAA+ complex that loads the AAA+ MCM helicase to replication origins. Orc1, a subunit of ORC, functionally interacts with budding yeast Pch2, a meiosis-specific AAA+ protein. Pch2 regulates several chromosomal events of gametogenesis, but mechanisms that dictate Pch2 function remain poorly understood. We demonstrate that ORC directly interacts with an AAA+ Pch2 hexamer. The ORC-Pch2 assembly is established without Cdc6, a factor crucial for ORC-MCM binding. Biochemical analysis suggests that Pch2 utilizes ORC’s Cdc6-binding interface and employs its non-enzymatic NH2-terminal domain and AAA+ core to engage ORC. In contrast to phenotypes observed upon Orc1 impairment, nuclear depletion of other subunits of ORC does not lead to Pch2-like phenotypes, indicating that ORC integrity per se is not required to support Pch2 function. We thus reveal functional interplay between Pch2 and ORC, and uncover the repurposing of ORC to establish a non-canonical and meiosis-specific AAA+ assembly.
Initial neural representation of individual rules after first-time instruction
Authors: Ruge Hannes , Schäfer Theo A. J. , Zwosta Katharina , Mohr Holger , Wolfensteller Uta
Published: April 2019

By following explicit instructions humans can instantaneously get the hang of tasks they have never performed before. Here, we used a specially calibrated multivariate analysis technique to uncover the elusive representational states following newly instructed arbitrary behavioural rules such as ‘for coffee, press red button’, while transitioning from ‘knowing what to do’ to ‘actually doing it’. Subtle variation in distributed neural activity patterns reflected rule-specific representations within the ventrolateral prefrontal cortex (VLPFC), confined to instructed stimulus-response learning in contrast to incidental learning involving the same stimuli and responses. VLPFC representations were established right after first-time instruction and remained stable across early implementation trials. More and more fluent application of novel rule representations was channelled through increasing cooperation between VLPFC and anterior striatum. These findings inform representational theories on how the prefrontal cortex supports behavioural flexibility by enabling ad-hoc coding of novel task rules without recourse to familiar sub-routines
Increased expression of schizophrenia-associated gene C4 leads to hypoconnectivity of prefrontal cortex and reduced social interaction
Authors: Comer Ashley L. , Jinadasa Tushare , Kretsge Lisa N. , Nguyen Thanh P.H. , Lee Jungjoon , Newmark Elena R. , Hausmann Frances S. , Rosenthal SaraAnn , Kot Kevin Liu , Yen William W. , Cruz-Martín Alberto
Published: April 2019

Schizophrenia is a severe mental disorder with an unclear pathophysiology. Increased expression of the immune gene C4 has been linked to a greater risk of developing schizophrenia; however, it is unknown whether C4 plays a causative role in this brain disorder. Using confocal imaging and whole-cell electrophysiology, we demonstrate that overexpression of C4 in mouse prefrontal cortex neurons leads to perturbations in dendritic spine development and hypoconnectivity, which mirror neuropathologies found in schizophrenia. We find evidence that microglia-neuron interactions and microglia-mediated synaptic engulfment are enhanced with increased expression of C4. We also show that C4-dependent circuit dysfunction in the frontal cortex leads to decreased social interactions in juvenile mice. These results demonstrate that increased expression of the schizophrenia-associated gene C4 causes aberrant circuit wiring in the developing prefrontal cortex and leads to deficits in early social behavior, suggesting that altered C4 expression contributes directly to schizophrenia pathogenesis.
Neuronal circuitry for stimulus selection in the visual system
Authors: Fernandes António M. , Larsch Johannes , Donovan Joseph C. , Helmbrecht Thomas O. , Mearns Duncan , Kölsch Yvonne , Dal Maschio Marco , Baier Herwig
Published: April 2019

Visual objects naturally compete for the brain’s attention, and selecting just one of them for a behavioural response is often crucial for the animal’s survival1. The neural correlate of such stimulus prioritisation might take the form of a saliency map by which responses to one target are enhanced relative to distractors in other parts of the visual field2. Single-cell responses consistent with this type of computation have been observed in the tectum of primates, birds, turtles and lamprey2–7. However, the exact circuit implementation has remained unclear. Here we investigated the underlying neuronal mechanism presenting larval zebrafish with two simultaneous looming stimuli, each of which was able to trigger directed escapes on their own. Behaviour tracking revealed that the fish respond to these competing stimuli predominantly with a winner-take-all strategy. Using brain-wide functional recordings, we discovered neurons in the tectum whose responses to the target stimulus were non-linearly modulated by the saliency of the distractor. When the two stimuli were presented monocularly in different positions of the visual field, stimulus selection was already apparent in the activity of retinal ganglion cell axons, a likely consequence of antagonistic mechanisms operating outside the classical receptive field8,9. When the two stimuli were presented binocularly, i.e., on opposite sides of the fish, our analysis indicates that a loop involving excitatory and inhibitory neurons in the nucleus isthmi (NI) and the tectum weighed stimulus saliencies across hemispheres. Consistent with focal enhancement and global suppression, glutamatergic NI cells branch locally in the tectum, whereas GABAergic NI cells project broadly across both tectal hemispheres. Moreover, holographic optogenetic stimulation confirmed that glutamatergic NI neurons can modulate visual responses in the tectum. Together, our study shows, for the first time, context-dependent contributions of retinotectal and isthmotectal circuits to the computation of the visual saliency map, a prerequisite for stimulus-driven, bottom-up attention.
Behavioural and neural interactions between objective and subjective performance in a Matching Pennies game
Authors: Dyson Benjamin James , Musgrave Cecile , Rowe Cameron , Sandhur Rayman
Published: April 2019

To examine the behavioural and neural interactions between objective and subjective performance during competitive decision-making, participants completed a Matching Pennies game where win-rates were fixed within three conditions (win > lose, win = lose, win < lose) and outcomes were predicted at each trial. Using random behaviour as the hallmark of optimal performance, we observed item (heads), contingency (win-stay, lose-shift) and combinatorial (HH, HT, TH, TT) biases across all conditions. Higher-quality behaviour represented by a reduction in combinatorial bias was observed during high win-rate exposure. In contrast, over-optimism biases were observed only in conditions where win rates were equal to, or less than, loss rates. At a group level, a neural measure of outcome evaluation (feedback-related negativity; FRN) indexed the binary distinction between positive and negative outcome. At an individual level, increased belief in successful performance accentuated FRN amplitude differences between wins and losses. Taken together, the data suggest that objective experiences of, or, subjective beliefs in, the predominance of positive outcomes are mutual attempts to self-regulate performance during competition. In this way, increased exposure to positive outcomes (real or imagined) help to weight the output of the more diligent and analytic System 2, relative to the impulsive and intuitive System 1.
Auditory and semantic cues facilitate decoding of visual object category in MEG
Authors: Brandman Talia , Avancini Chiara , Leticevscaia Olga , Peelen Marius V.
Published: April 2019

Sounds (e.g., barking) help us to visually identify objects (e.g., a dog) that are distant or ambiguous. While neuroimaging studies have revealed neuroanatomical sites of audiovisual interactions, little is known about the time-course by which sounds facilitate visual object processing. Here we used magnetoencephalography (MEG) to reveal the time-course of the facilitatory influence of natural sounds (e.g., barking) on visual object processing, and compared this to the facilitatory influence of spoken words (e.g., “dog”). Participants viewed images of blurred objects preceded by a task-irrelevant natural sound, a spoken word, or uninformative noise. A classifier was trained to discriminate multivariate sensor patterns evoked by animate and inanimate intact objects with no sounds, presented in a separate experiment, and tested on sensor patterns evoked by the blurred objects in the three auditory conditions. Results revealed that both sounds and words, relative to uninformative noise, significantly facilitated visual object category decoding between 300-500 ms after visual onset. We found no evidence for earlier facilitation by sounds than by words. These findings provide evidence for a semantic route of facilitation by both natural sounds and spoken words, whereby the auditory input first activates semantic object representations, which then modulate the visual processing of objects.
Pathological and non-pathological aging, SAMP8 and SAMR1. What do hippocampal neuronal populations tell us?
Authors: Lagartos-Donate MJ , Gonzáles-Fuentes J , Marcos-Rabal P , Insausti R , Arroyo-Jiménez MM
Published: April 2019

Alterations of cognitive processes and memory are one of the most important manifestations related to aging. However, not all memory types are affected in the same way. Learning and spatial memory are susceptible to these changes. The hippocampus represents the anatomical substrate of this type of memory, affected by structural and functional alterations along the normal aging and neurological diseases such as Alzheimer’s disease, Parkinson’s, schizophrenia and epilepsy. Some of the alterations related to aging are associated with alterations in the hippocampal interneuron populations and with an increase in excitability in the hippocampal circuit.

In order to understand better the underlying processes in normal and pathological aging mechanisms, a murine model (Senescence-Accelerated Mouse Prone, SAMP8) and its respective controls (Senescence-Accelerated Mouse Resistant, SAMR1) have been used. While SAMP8 is a naturally occurring mouse line that displays a phenotype of accelerated aging with learning and memory impairment and these changes of learning and memory might be linked to some alterations in neuronal populations of the hippocampus. Thus, we analyzed the distribution and density of PV, CR and STT interneurons in the hippocampus of young and old mice as well as possible morphological and cholinergic changes in hippocampal formation. Comparing SAMR1 and SAMP8 we did not find any neural population that was specifically affected by aging in both groups. Interestingly, CR immunoreactivity and STT immunoreactivity showed changes in SAMP8 mice when they were compared to their controls. In SAMP8 CR+ and STT+ neurons decreased significantly along aging which suggests that CR and STT interneurons play a more important role than PV neurons in the pathological aging of the brain. In the case of SAMP8 mice the neural changes might be related to changes of the cholinergic system that might be affecting the wiring into the hippocampus formation through the perforant pathway. Further studies of this local circuitry will help to comprehend better how different inputs into these neural populations of the hippocampus could be affecting the development of neurodegerative diseases.
Time resolved quantitative phosphoproteomics reveals distinct patterns of SHP2 dependence in EGFR signaling
Authors: Vemulapalli Vidyasiri , Chylek Lily , Erickson Alison , LaRochelle Jonathan , Subramanian Kartik , Mohseni Morvarid , LaMarche Matthew , Acker Michael G. , Sorger Peter K. , Gygi Steven P. , Blacklow Stephen C.
Published: April 2019

SHP2 is a protein tyrosine phosphatase that normally potentiates intracellular signaling by growth factors, antigen receptors, and some cytokines; it is frequently mutated in childhood leukemias and other cancers. Here, we examine the role of SHP2 in the responses of breast cancer cells to EGF by monitoring phosphoproteome dynamics when SHP2 is allosterically inhibited by the small molecule SHP099. Data on phosphotyrosine abundance at more than 400 tyrosine residues reveals six distinct response signatures following SHP099 treatment and washout. These include putative substrate sites with increased phosphotyrosine abundance at early or late timepoints, and another class of sites that shows reduced phosphotyrosine abundance when SHP099 is present. Sites of decreased phospho-abundance are enriched on proteins with two nearby phosphotyrosine residues, which can be directly protected from dephosphorylation by the paired SH2 domains of SHP2 itself. These findings highlight how analysis of phosphoproteomic dynamics can provide insight into transmembrane signaling responses.
Disease-related single-point mutations alter the global dynamics of a tetratricopeptide (TPR) a-solenoid domain
Authors: Llabrés Salomé , Zachariae Ulrich
Published: April 2019

Tetratricopeptide repeat (TPR) proteins belong to the class of α-solenoid proteins, in which repetitive units of α-helical hairpin motifs stack to form superhelical, often highly flexible structures. TPR domains occur in a wide variety of proteins, and perform key functional roles including protein folding, protein trafficking, cell cycle control and post-translational modification. Here, we look at the TPR domain of the enzyme O-linked GlcNAc-transferase (OGT), which catalyses O-GlcNAcylation of a broad range of substrate proteins. A number of single-point mutations in the TPR domain of human OGT have been associated with the disease Intellectual Disability (ID). By extended steered and equilibrium atomistic simulations, we show that the OGT-TPR domain acts as a reversibly elastic nanospring, and that each of the ID-related local mutations substantially affect the global dynamics of the TPR domain. Since the nanospring character of the OGT-TPR domain is key to its function in binding and releasing OGT substrates, these changes of its biomechanics likely lead to defective substrate interaction. Our findings may not only help to explain the ID phenotype of the mutants, but also aid the design of TPR proteins with tailored biomechanical properties.
Geosmin attractsAedes aegyptimosquitoes to oviposition sites
Authors: Melo Nadia , Wolff Gabriella H. , Costa-da-Silva Andre Luis , Arribas Robert , Triana Merybeth Fernandez , Gugger Muriel , Riffell Jeffrey A. , DeGennaro Matthew , Stensmyr Marcus C.
Published: April 2019

Geosmin is one of the most recognizable and common microbial smells on the planet. Some insects, like mosquitoes, require microbial-rich environments for their progeny, whereas for other insects such microbes may prove dangerous. In the vinegar flyDrosophila melanogaster, geosmin is decoded in a remarkably precise fashion and induces aversion, presumably signaling the presence of harmful microbes. We have here investigated the effect of geosmin on the behavior of the yellow fever mosquitoAedes aegypti. In contrast to flies, geosmin is not aversive in mosquitoes but stimulates egg-laying site selection. Female mosquitoes could associate geosmin with microbes, including cyanobacteria consumed by larvae, who also find geosmin – as well as geosmin producing cyanobacteria – attractive. Usingin vivomultiphoton imaging from mosquitoes with pan-neural expression of the calcium reporter GCaMP6s, we show thatAe. aegypticode geosmin in a similar fashion to flies, i.e. with extreme sensitivity and with a high degree of selectivity. We further demonstrate that geosmin can be used as bait under field conditions, and finally we show that geosmin, which is both expensive and difficult to obtain, can be substituted by beetroot peel extract, providing a cheap and viable mean of mosquito control and surveillance in developing countries.
Complementing 16S rRNA gene amplicon sequencing with estimates of total bacterial load to infer absolute species concentrations in the vaginal microbiome
Authors: Boshier Florencia Tettamanti , Srinivasan Sujatha , Lopez Anthony , Hoffman Noah G. , Proll Sean , Fredricks David N. , Schiffer Joshua T.
Published: April 2019

Whereas 16S rRNA gene amplicon sequencing quantifies relative abundances of bacterial taxa, variation in total bacterial load between samples restricts its ability to reflect absolute concentration of individual species. Quantitative PCR (qPCR) can quantify individual species, but it is not practical to develop a suite of qPCR assays for every bacterium present in a diverse sample. We analyzed 1320 samples from 20 women with a history of frequent bacterial vaginosis, who self-collected vaginal swabs daily over 60 days. We inferred bacterial concentrations by taking the product of species relative abundance (assessed by 16S rRNA gene amplicon sequencing) and total bacterial load (measured by broad-range 16S rRNA gene qPCR). Log10-converted inferred concentrations correlated with targeted qPCR (r = 0. 935, p<2.2e-16) for seven key bacterial species. The mean inferred concentration error varied across bacteria, with rarer bacterial vaginosis-associated bacteria associated with larger errors. 92% of errors >0.5 log10 occurred when relative abundance was <10%. Many errors occurred during early bacterial expansion or late contraction. When relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR. However, targeted qPCR is required to capture bacteria at low relative abundance, particularly with BV-associated bacteria during the early onset of bacterial vaginosis.
Scopolamine and medial frontal stimulus-processing during interval timing
Authors: Zhang Qiang , Jung Dennis , Larson Travis , Kim Youngcho , Narayanan Nandakumar S.
Published: April 2019

Neurodegenerative diseases such as Parkinson’s disease (PD), dementia with Lewy Bodies (DLB), and Alzheimer’s disease (AD) involve loss of cholinergic neurons in the basal forebrain. Here, we investigate how cholinergic dysfunction impacts the frontal cortex during interval timing, a process that can be impaired in PD and AD patients. Interval timing requires participants to estimate an interval of several seconds by making a motor response, and depends on the medial frontal cortex (MFC), which is richly innervated by basal forebrain cholinergic projections. Past work has shown that scopolamine, a muscarinic cholinergic receptor antagonist, reliably impairs interval timing. We tested the hypothesis that scopolamine would attenuate time-related ramping, a key form of temporal processing in the MFC. We recorded neuronal ensembles from 8 mice during performance of a 12-s fixed-interval timing task, which was impaired by the administration of scopolamine. Consistent with past work, scopolamine impaired timing. To our surprise, we found that time-related ramping was unchanged, but stimulus-related activity was enhanced in the MFC. Principal component analyses revealed no consistent changes in time-related ramping components, but did reveal changes in higher components. Taken together, these data indicate that scopolamine changes stimulus-processing rather than temporal processing in the MFC. These data could help understand how cholinergic dysfunction affects cortical circuits in diseases such as PD, DLB, and AD.

Highlights

The cholinergic muscarinic inhibitor scopolamine impairs interval timing behavior.

Scopolamine does not change time-related ramping activity in the medial frontal cortex.

Medial prefrontal stimulus-related modulation increased
Restoration of susceptibility to amikacin by 8-hydroxyquinoline analogs complexed to zinc
Authors: Magallón Jesus , Chiem Kevin , Tran Tung , Ramirez María S. , Jimenez Verónica , Tolmasky Marcelo E.
Published: April 2019

Gram-negative pathogens resistant to amikacin and other aminoglycosides of clinical relevance usually harbor the 6’-N-acetyltransferase type Ib [AAC(6’)-Ib], an enzyme that catalyzes inactivation of the antibiotic by acetylation using acetyl-CoA as donor substrate. Inhibition of the acetylating reaction could be a way to induce phenotypic conversion to susceptibility in these bacteria. We have previously observed that Zn+2 acts as an inhibitor of the enzymatic acetylation of aminoglycosides by AAC(6’)-Ib, and in complex with ionophores it effectively reduced the levels of resistance in cellulo. We compared the activity of 8-hydroxyquinoline, three halogenated derivatives, and 5-[N-Methyl-N-Propargylaminomethyl]-8-Hydroxyquinoline in complex with Zn+2 to inhibit growth of amikacin-resistant Acinetobacter baumannii in the presence of the antibiotic. Two of the compounds, clioquinol (5-chloro-7-iodo-8-hydroxyquinoline) and 5,7-diiodo-8-hydroxyquinoline, showed robust inhibition of growth of the two A. baumannii clinical isolates that produce AAC(6’)-Ib. However, none of the combinations had any activity on another amikacin-resistant A. baumannii strain that possesses a different, still unknown mechanism of resistance. Time-kill assays showed that the combination of clioquinol or 5,7-diiodo-8-hydroxyquinoline with Zn+2 and amikacin was bactericidal. Addition of 8-hydroxyquinoline, clioquinol, or 5,7-diiodo-8-hydroxyquinoline, alone or in combination with Zn+2, and amikacin to HEK293 cells did not result in significant toxicity. These results indicate that ionophores in complex with Zn+2 could be developed into potent adjuvants to be used in combination with aminoglycosides to treat Gram-negative pathogens in which resistance is mediated by AAC(6’)-Ib and most probably other related aminoglycoside modifying enzymes.
Elevated prevalence of azole resistant Aspergillus fumigatus in urban versus rural environments in the United Kingdom
Authors: Sewell Thomas R , Zhang Yuyi , Brackin Amelie P , Shelton Jennifer MG , Rhodes Johanna , Fisher Matthew C
Published: April 2019

Azole resistance in the opportunistic pathogen Aspergillus fumigatus is increasing, dominated primarily by two environmentally-associated resistance alleles: TR34/L98H and TR46/Y121F/T289A. Using an environmental sampling strategy across the South of England we assess the prevalence of azole resistant A. fumigatus (ARAf) in soil samples collected in both urban and rural locations. We characterise the susceptibility profiles of the resistant isolates to three medical azoles, identify the underlying genetic basis of resistance and investigate their genetic relationships. ARAf was detected in 6.7% of the soil samples, with a higher prevalence in urban (13.8%) compared to rural (1.1%) locations. Nineteen isolates were confirmed to exhibit clinical breakpoints for resistance to at least one of three medical azoles, with 18 isolates exhibiting resistance to itraconazole, four to voriconazole, with two also showing additional elevated minimum inhibitory concentration to posaconazole. Thirteen of the resistant isolates harboured the TR34/L98H resistance allele and six isolates carried TR46/Y121F/T289A allele. The 19 azole-resistant isolates were spread across five csp1 genetic subtypes, t01, t02, t04B, t09 and t18 with t02 the predominant subtype. Our study demonstrates that ARAf can be easily isolated in the South of England, especially in urban city centres, which appear to play an important role in the epidemiology of environmentally-linked drug resistant A. fumigatus.
Within-finger maps of tactile and nociceptive input in the human parietal cortex
Authors: Mancini Flavia , Sereno Martin I. , Lee Min-Ho , Iannetti Giandomenico D , Tracey Irene
Published: April 2019

The spatial representation of nociceptive input in the human parietal cortex is not fully understood. For instance, it is known that the primary somatosensory cortex (S1) contains a representation of nociceptive-selective input to different fingers, but it is unclear whether S1 subdivisions contain finer-grained, within-finger maps of nociceptive input. It is also unknown whether within-finger maps of somatosensory input exist in intraparietal regions. Therefore, we used high-field 7T functional MRI to reveal within-finger maps of nociceptive and tactile inputs in the human parietal cortex. Although we replicated the previous findings of between-finger maps of nociceptive input spanning S1 subdivisions, we found weak and inconsistent evidence for within-finger maps of nociceptive input in S1 subdivisions. In the same subjects, we found mirrored, within-finger maps of tactile input in areas 3a, 3b, and 1. Importantly, we discovered a within-finger map of nociceptive input, but not of tactile input, in the human intraparietal area 1 (hIP1). In conclusion, our study indicates that the spatial representation of nociceptive input in the parietal cortex partly differs from that of tactile input and reports the discovery of a within-finger map of nociceptive input in hIP1.

New & Noteworthy

We report the discovery of a fine-grained map of nociceptive input to finger segments in the human intraparietal area 1.
Disentangling a Complex Response in Cell Reprogramming and Probing the Waddington Landscape by Automatic Construction of Petri Nets
Authors: Rätzel Viktoria , Werthmann Britta , Haas Markus , Strube Jan , Marwan Wolfgang
Published: April 2019

We analyzed the developmental switch to sporulation of a multinucleatePhysarum polycephalumplasmodial cell, a complex response to phytochrome photoreceptor activation. Automatic construction of Petri nets from trajectories of differential gene expression in single cells revealed alternative, genotype-dependent interconnected developmental routes and identified metastable states, commitment points, and subsequent irreversible steps together with molecular signatures associated with cell fate decision and differentiation. Formation of transition-invariants in mutants that are locked in a proliferative state is remarkable considering the view that oncogenic alterations may cause the formation of cancer attractors. We conclude that the Petri net approach is useful to probe the Waddington landscape of cellular reprogramming, to disentangle developmental routes for the reconstruction of the gene regulatory network, and to understand how genetic alterations or physiological conditions reshape the landscape eventually creating new basins of attraction. Unraveling the complexity of pathogenesis, disease progression, and drug response or the analysis of attractor landscapes in other complex systems of uncertain structure might be additional fields of application.
Basal ganglia contributions during the learning of a visuomotor rotation: effect of dopamine, deep brain stimulation and reinforcement
Authors: Singh Puneet , Lenka Abhishek , Stezin Albert , Jhunjhunwala Ketan , Pal Pramod Kumar , Ghosal Ashitava , Murthy Aditya
Published: April 2019

It is commonly thought that visuomotor adaptation is mediated by the cerebellum while reinforcement learning is mediated by the basal ganglia. In contrast to this strict dichotomy, we demonstrate a role for the basal ganglia in visuomotor adaptation (error-based motor learning) in patients with Parkinson’s disease (PD) by comparing the degree of motor learning in the presence and absence of dopamine medication. We further show similar modulation of learning rates in the presence and absence of subthalamic deep brain stimulation. We also report that reinforcement is an essential component of visuomotor adaptation by demonstrating the lack of motor learning in patients with PD during the ON-dopamine state relative to the OFF-dopamine state in the absence of a reinforcement signal. Taken together, these results suggest that the basal ganglia modulate the gain of visuomotor adaptation based on the reinforcement received at the end of the trial.
Diminution of feeding response in Helicoverpa armigera by inhibition or silencing of sugar gustatory receptor
Authors: Agnihotri Aniruddha R. , Zunjarrao Sanyami S. , Nagare Mukta , Joshi Rakesh S.
Published: April 2019

Gustatory receptor (GR) is one of the essential chemosensory molecules in Lepidopteran pests. GR is involved in sensing several canonical tastes which in turn regulate the diverse behavioral and physiological responses of these insects. In this article, we have evaluated the alteration in feeding response of Helicoverpa armigera by blocking and silencing of sugar-sensing gustatory receptor 9 (HarmGr9). Sf9 cells based assay showed that glucose analogue, Miglitol, can bind to the expressed HarmGr9. This binding might lead to an inhibition of receptor activation and downstream signaling, indicated by reduced intracellular Ca2+ fluorescence. Further, the in-vivo study illustrated the feeding rate reduced on a diet containing miglitol as compared to the larvae fed on the artificial diet. Reduction in feeding rate was prolonged in insects fed on the miglitol containing diet even after switching to the control glucose diet. Competitive cell-based assay and feeding assay, using equimolar glucose and miglitol, also showed an inhibitory effect on HarmGr-9 activation and insect feeding rate. We have observed similar feeding rate reduction in HarmGr9 knockdown in H. armigera larvae. We believe this unique approach of H. armigera feeding response inhibition by blocking the sugar receptor can be further used to develop a novel strategy for agricultural pest management.
A passive, camera-based head-tracking system for real-time, 3D estimate of head position and orientation in rodents
Authors: Vanzella Walter , Grion Natalia , Bertolini Daniele , Perissinotto Andrea , Zoccolan Davide
Published: April 2019

Tracking head’s position and orientation of small mammals is crucial in many behavioral neurophysiology studies. Yet, full reconstruction of the head’s pose in 3D is a challenging problem that typically requires implanting custom headsets made of multiple LEDs or inertial units. These assemblies need to be powered in order to operate, thus preventing wireless experiments, and, while suitable to study navigation in large arenas, their application is unpractical in the narrow operant boxes employed in perceptual studies. Here we propose an alternative approach, based on passively imaging a 3D-printed structure, painted with a pattern of black dots over a white background. We show that this method is highly precise and accurate and we demonstrate that, given its minimal weight and encumbrance, it can be used to study how rodents sample sensory stimuli during a perceptual discrimination task and how hippocampal place cells represent head position over extremely small spatial scales.
RNAi screen reveals a role for PACSIN2 and caveolins during bacterial cell-to-cell spread
Authors: Sanderlin Allen G. , Vondrak Cassandra , Scricco Arianna J. , Fedrigo Indro , Ahyong Vida , Lamason Rebecca L.
Published: April 2019

Listeria monocytogenes is a human bacterial pathogen that disseminates through host tissues using a process called cell-to-cell spread. This critical yet understudied virulence strategy resembles a vesicular form of intercellular trafficking that allows L. monocytogenes to move between host cells without escaping the cell. Interestingly, eukaryotic cells can also directly exchange cellular components via intercellular communication pathways (e.g. trans-endocytosis) using cell-cell adhesion, membrane trafficking, and membrane remodeling proteins. Therefore, we hypothesized that L. monocytogenes would hijack these types of host proteins during spread. Using a focused RNAi screen, we identified 22 host genes that are important for L. monocytogenes spread. We then found that caveolins (CAV1 and CAV2) and the membrane sculpting F-BAR protein PACSIN2 promote L. monocytogenes protrusion engulfment during spread, and that PACSIN2 specifically localized to protrusions. Overall, our study demonstrates that host intercellular communication pathways may be co-opted during bacterial spread and that specific trafficking and membrane remodeling proteins promote bacterial protrusion resolution.

The human bacterial pathogen Listeria monocytogenes disseminates through host tissues using a process called cell-to-cell spread. In this study, Sanderlin et al., discover that host proteins that normally regulate membrane trafficking and membrane remodeling in uninfected settings are also co-opted by Listeria to promote spread.
Negative Binomial Additive Model for RNA-Seq Data Analysis
Authors: Ren Xu , Kuan Pei Fen
Published: April 2019

High-throughput sequencing experiments followed by differential expression analysis is a widely used approach for detecting genomic biomarkers. A fundamental step in differential expression analysis is to model the association between gene counts and co-variates of interest. Existing models assume linear effect of covariates, which is restrictive and may not be sufficient for some phenotypes. In this paper, we introduce NBAMSeq, a flexible statistical model based on the generalized additive model and allows for information sharing across genes in variance estimation. Specifically, we model the logarithm of mean gene counts as sums of smooth functions with the smoothing parameters and coefficients estimated simultaneously within a nested iterative method. The variance is estimated by the Bayesian shrinkage approach to fully exploit the information across all genes. Based on extensive simulation and case studies of RNA-Seq data, we show that NBAMSeq offers improved performance in detecting nonlinear effect and maintains equivalent performance in detecting linear effect compared to existing methods. Our proposed NBAMSeq is available for download athttps://github.com/reese3928/NBAMSeqand in submission to Bioconductor repository.