bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating β-lactam drug targets inMycobacterium tuberculosisusing chemical probes
Authors: Levine Samantha R. , Beatty Kimberly E. 
Published: December 2019

AbstractTuberculosis is a deadly disease that requires a flexible arsenal of drugs to treat it. Although β-lactam antibiotics are rarely used to treatMycobacterium tuberculosis(Mtb) infections today, the targets of these drugs are present in the bacterium. Moreover, the cell wall peptidoglycan ofMtbcontains an abundance of unusual (3→3) cross-links. These cross-links are formed by enzymes called L,D-transpeptidases, which are susceptible to inhibition by the carbapenem class of antibiotics. We developed new small molecule probes to investigate the L,D-transpeptidases and other β-lactam drug targets inMtb. We synthesized probes based on three classes of antibiotics, a monobactam, cephalosporin, and carbapenem. For the carbapenem, we synthesized a meropenem analogue conjugated to a far-red fluorophore. This probe was particularly useful in identifying active L,D-transpeptidases in protein gel-resolved lysates. Next we analyzed β-lactam targets in lysates from both hypoxic and actively-replicating cultures ofMtb. We identified numerous targets, including transpeptidases, carboxypeptidases, and the β-lactamase BlaC. Overall, we provide evidence thatMtbdynamically regulates the enzymes responsible for maintaining cell wall peptidoglycan and that meropenem is a good inhibitor of those enzymes.
Harnessing β-Lactam Antibiotics for Illumination of the Activity of Penicillin-Binding Proteins inBacillus subtilis
Authors: Sharifzadeh Shabnam , Dempwolff Felix , Kearns Daniel B. , Carlson Erin E. 
Published: December 2019

ABSTRACTSelective chemical probes enable individual investigation of penicillin-binding proteins (PBPs) and provide critical information about their enzymatic activity with spatial and temporal resolution. To identify scaffolds for novel probes to study peptidoglycan biosynthesis inBacillus subtilis, we evaluated the PBP inhibition profiles of 21 β-lactam antibiotics from different structural subclasses using a fluorescence-based assay. Most compounds readily labeled PBP1, PBP2a, PBP2b or PBP4. Almost all penicillin scaffolds were co-selective for all or combinations of PBP2a, 2b and 4. Cephalosporins, on the other hand, possessed the lowest IC50values for PBP1 alone or along with PBP4 (ceftriaxone, cefoxitin), 2b (cefotaxime) or 2a, 2b and 4 (cephalothin). Overall, five selective inhibitors for PBP1 (aztreonam, faropenem, piperacillin, cefuroxime and cefsulodin), one selective inhibitor for PBP5 (6-aminopenicillanic acid) and various co-selective inhibitors for other PBPs inB. subtiliswere discovered. Surprisingly, carbapenems strongly inhibited PBP3, formerly shown to have low affinity for β-lactams and speculated to be involved in resistance inB. subtilis. To investigate the specific roles of PBP3, we developed activity-based probes based on the meropenem core and utilized them to monitor the activity of PBP3 in living cells. We showed that PBP3 activity localizes as patches in single cells and concentrates as a ring at the septum and the division site during the cell growth cycle. Our activity-based approach enabled spatial resolution of the transpeptidation activity of individual PBPs in this model microorganism, which was not possible with previous chemical and biological approaches.
FluidFM as a Tool to Study Adhesion Forces of Bacteria - Optimization of Parameters and Comparison to Conventional Bacterial Probe Scanning Force Spectroscopy
Authors: Hofherr Linda , Müller-Renno Christine , Ziegler Christiane 
Published: December 2019

AbstractThe FluidFM enables the immobilization of single cells on a hollow cantilever using relative underpressure. In this study, we systematically optimize versatile measurement parameters to improve the quality of force-distance curves recorded with a FluidFM. Using single bacterial cells, we show that Single Cell Force Spectroscopy experiments with the FluidFM lead to comparable results to a conventional Single Cell Force Spectroscopy approach using polydopamine for chemical fixation of a bacterial cell.
Ser-653-Asn substitution in the acetohydroxyacid synthase gene confers resistance in weedy rice to imidazolinone herbicides imazapic and imazapyr in Malaysia
Authors: Ruzmi Rabiatuladawiyah , Ahmad-Hamdani M. S. , Mazlan Norida 
Published: December 2019

AbstractThe IMI-herbicides rice package has been recognized by all means among the most efficient chemical approaches for weedy rice control nowadays. Inevitably, the continuous and sole dependence, as well as ignorance on the appropriate use of imidazolinone herbicides in the IMI-herbicides rice package by rice growers has caused the development of herbicide resistance in weedy rice populations across many IMI-herbicides rice package adopted countries, inclusive of Malaysia. Hence, a comprehensive study was conducted to elucidate the occurrence, level, and mechanisms endowing resistance to IMI-herbicides on field-reported resistant (R) weedy rice populations collected from IMI-rice fields in Kampung Simpang Sanglang, Perlis (A), Kampung Behor Mentalon, Perlis (B), and Kampung Sungai Kering, Kedah (C). The collected weedy rice populations were compared with a susceptible weedy rice population (S), an imidazolinone-resistant rice cultivar (IMI-rice), and a susceptible local rice cultivar (MR219). Dose-response experiments were carried out using commercial IMI-herbicides (premix of imazapic and imazapyr) available in the IMI-herbicides rice package, in the seed bioassay and whole-plant dose-response. Based on the Resistance Index (RI) quantification in both experiments, the cross-resistance pattern of weedy rice populations and rice varieties to imazapic and imazapyr was determined. Molecular investigation was carried out by comparing acetohydroxyacid synthase (AHAS) gene sequences between resistant (R) weedy rice populations (A, B, and C), S population, IMI-rice, and MR219. Evidently, the AHAS gene sequences of R weedy rice were identical to the IMI-rice, revealing that amino acid substitution of Ser-653-Asn occurs in both R populations and IMI-rice, but neither in MR219 nor S plants.In vitroassays were conducted using analytical grade imidazolinone herbicides of imazapic (99.3%) and imazapyr (99.6%) with seven concentrations. The results demonstrated that the AHAS enzyme extracted from R populations and IMI-rice were less sensitive to IMI-herbicides in comparison to S and MR219, further supporting the IMI-herbicides resistance was conferred by target site mutation. In conclusion, the basis of imidazolinone resistance in selected populations of Malaysia weedy rice was due to a Ser-653-Asn mutation that reduced sensitivity of the target site to IMI-herbicides. The current study presents the first report of resistance mechanism in weedy rice in Malaysian rice fields.
A novel IKK- and proteasome-independent mechanism of RelA activation triggers senescence associated secretome via transcriptional repression of NFKBIA
Authors: Kolesnichenko Marina , Mikuda Nadine , Höpken Uta E. , Milanovic Maja , Tufan A. Bugra , Uyar Bora , Sun Wei , Schleich Kolja , von Hoff Linda , Willenbrock Michael , Krahn Inge , Jungmann Sabine , Hinz Michael , Akalin Altuna , Lee Soyoung , Schmidt-Ullrich Ruth , Schmitt Clemens A. , Scheidereit Claus 
Published: December 2019

ABSTRACTThe IκB kinase (IKK) - NF-κB pathway is activated as part of the DNA damage response and controls both resistance to apoptosis and inflammation. How these different functions are achieved remained unknown. We demonstrate here that DNA double strand breaks elicit two subsequent phases of NF-κB activationin vivoandin vitro, which are mechanistically and functionally distinct. RNA-sequencing reveals that the first phase controls anti-apoptotic gene expression, while the second drives expression of senescence-associated secretory phenotype (SASP) genes. The first, rapidly activated phase is driven by the ATM-PARP1-TRAF6-IKK cascade, which triggers proteasomal destruction of IκBα and is terminated through IκBα (NFKBIA) re-expression. The second phase is activated days later in senescent cells but is independent of IKK and the proteasome. An altered phosphorylation status of p65, in part driven by GSK3β, results in transcriptional silencing ofNFKBIAand IKK-independent, constitutive activation of NF-κB in senescence. Collectively, our study reveals a novel physiological mechanism of NF-κB activation with important implications for genotoxic cancer treatment.
Loss of the Reissner Fiber and increased URP neuropeptide signaling underlie scoliosis in a zebrafish ciliopathy mutant
Authors: Vesque Christine , Anselme Isabelle , Pezeron Guillaume , Cantaut-Belarif Yasmine , Eschstruth Alexis , Djebar Morgane , Santos Diego López , Ribeuz Hélène Le , Jenett Arnim , Khoury Hanane , Véziers Joëlle , Parmentier Caroline , Schneider-Maunoury Sylvie 
Published: December 2019

SUMMARYCilia-driven movements of the cerebrospinal fluid (CSF) are involved in zebrafish axis straightness, both in embryos and juveniles [1, 2]. In embryos, axis straightness requires cilia-dependent assembly of the Reissner fiber (RF), a SCO-spondin polymer running down the brain and spinal cord CSF-filled cavities [3]. Reduced expression levels of theurp1andurp2genes encoding neuropeptides of the Urotensin II family in CSF-contacting neurons (CSF-cNs) also underlie embryonic ventral curvature of several cilia motility mutants [4]. Moreover, mutants forscospondinanduts2r3(a Urotensin II peptide family receptor gene) develop scoliosis at juvenile stages [3, 4]. However, whether RF maintenance and URP signaling are perturbed in juvenile scoliotic ciliary mutants and how these perturbations are linked to scoliosis is unknown. Here we produced mutants in the zebrafish ortholog of the humanRPGRIP1Lciliopathy gene encoding a transition zone protein [5–7].rpgrip1l-/-zebrafish had normal embryogenesis and developed 3D spine torsions in juveniles. Cilia lining the CNS cavities were normal inrpgrip1l-/-embryos but sparse and malformed in juveniles and adults. Hindbrain ventricle dilations were present at scoliosis onset, suggesting defects in CSF flow. Immunostaining showed a secondary loss of RF correlating with juvenile scoliosis. Surprisingly, transcriptome analysis ofrgprip1lmutants at scoliosis onset uncovered increased levels ofurp1andurp2expression. Overexpressingurp2infoxj1-expressing cells triggered scoliosis inrpgrip1lheterozygotes. Thus, our results demonstrate that increased URP signaling drives scoliosis onset in a ciliopathy mutant. We propose that imbalanced levels of URP neuropeptides in CSF-cNs may be an initial trigger of scoliosis.
Local sleep-like cortical reactivity in the awake brain after focal injury
Authors: Sarasso Simone , D’Ambrosio Sasha , Fecchio Matteo , Casarotto Silvia , Viganò Alessandro , Landi Cristina , Mattavelli Giulia , Gosseries Olivia , Quarenghi Matteo , Laureys Steven , Devalle Guya , Rosanova Mario , Massimini Marcello 
Published: December 2019

AbstractThe functional consequences of brain injury are known to depend on neuronal alterations extending beyond the area of structural damage. Although a lateralized EEG slowing over the injured hemisphere was known since the early days of clinical neurophysiology, its electrophysiological mechanisms were not systematically investigated. In parallel, basic sleep research has thoroughly characterized the neuronal events underlying EEG slow waves in physiological conditions. These EEG events reflect brief interruptions of neuronal firing (OFF-periods) that can occur locally and have prominent consequences on network and behavioral functions. Notably, the EEG slow waves observed following focal brain injury have been never explicitly connected to local sleep-like neuronal events. In previous works, probing cortical circuits with transcranial magnetic stimulation coupled with EEG (TMS/EEG) proved as an effective way to reveal the tendency of cortical circuits to transiently plunge into silent OFF-periods. Here, using this approach, we show that the intact cortex surrounding focal brain injuries engages locally in pathological sleep-like dynamics. Specifically, we employed TMS/EEG in a cohort of thirty conscious awake patients with chronic focal and multifocal brain injuries of various etiologies. TMS systematically evoked prominent slow waves associated with sleep-like OFF-periods in the area surrounding focal cortico-subcortical lesions. These events were associated with a local disruption of signal complexity and were absent when stimulating the contralateral hemisphere. Perilesional sleep-like OFF-periods may represent a valid read-out of the electrophysiological state of discrete cortical circuits following brain injury as well as a potential target of interventions aimed at fostering functional recovery.One Sentence SummaryFocal cortical injuries are associated with local intrusion of sleep-like dynamics over the perilesional areas which disrupt local signal complexity and coexist with typical wakefulness cortical reactivity patterns within the same brain.
A dual mechanism underlying retroactive shifts of auditory spatial attention: dissociating target- and distractor-related modulations of alpha lateralization
Authors: Klatt Laura-Isabelle , Getzmann Stephan , Begau Alexandra , Schneider Daniel 
Published: December 2019

AbstractAttention can be allocated to mental representations to select information from working memory. To date, it remains ambiguous whether such retroactive shifts of attention involve the inhibition of irrelevant information or the prioritization of relevant information. Investigating asymmetries in posterior alpha-band oscillations during an auditory retroactive cueing task, we aimed at differentiating those mechanisms. Participants were cued to attend two out of three sounds in an upcoming sound array. Importantly, the resulting working memory representation contained one laterally and one centrally presented item. A centrally presented retro-cue then indicated the lateral, the central, or both items as further relevant for the task (comparing the cued item(s) to a memory probe). Time-frequency analysis revealed opposing patterns of alpha lateralization depending on target eccentricity: A contralateral decrease in alpha power intarget lateraltrials indicated the involvement of target prioritization. A contralateral increase in alpha power when the central item remained relevant (distractor lateraltrials) suggested the de-prioritization of irrelevant information. No lateralization was observed when both items remained relevant, supporting the notion that auditory alpha lateralization is restricted to situations in which spatial information is task-relevant. Altogether, the data demonstrate that retroactive attentional deployment involves excitatory and inhibitory control mechanisms.
Druggability Assessment in TRAPP using Machine Learning Approaches
Authors: Yuan Jui-Hung , Han Sungho Bosco , Richter Stefan , Wade Rebecca C. , Kokh Daria B. 
Published: December 2019

AbstractAccurate protein druggability predictions are important for the selection of drug targets in the early stages of drug discovery. Due to the flexible nature of proteins, the druggability of a binding pocket may vary due to conformational changes. We have therefore developed two statistical models, a logistic regression model (TRAPP-LR) and a convolutional neural network model (TRAPP-CNN), for predicting druggability and how it varies with changes in the spatial and physicochemical properties of a binding pocket. These models are integrated into TRAPP (TRAnsient Pockets in Proteins), a tool for the analysis of binding pocket variations along a protein motion trajectory. The models, which were trained on publicly available and self-augmented data sets, show equivalent or superior performance to existing methods on test sets of protein crystal structures, and have sufficient sensitivity to identify potentially druggable protein conformations in trajectories from molecular dynamics simulations. Visualization of the evidence for the decisions of the models in TRAPP facilitates identification of the factors affecting the druggability of protein binding pockets.
Microclimate buffering and thermal tolerance across elevations in a tropical butterfly
Authors: Montejo-Kovacevich Gabriela , Martin Simon H. , Meier Joana I. , Bacquet Caroline N. , Monllor Monica , Jiggins Chris D. , Nadeau Nicola J. 
Published: December 2019

AbstractMicroclimatic variability in tropical forests plays a key role in shaping species distributions and their ability to cope with environmental change, especially for ectotherms. Yet, currently available climatic datasets lack data from the forest interior and our knowledge of thermal tolerance among tropical ectotherms is limited. To tackle this, we studied natural variation in the microclimate experienced by a tropical genus of butterflies (Heliconius sp.) along their Andean range across a single year. We found that the forest strongly buffers temperature and humidity in the understory, especially in the lowlands where temperatures are more extreme. There were systematic differences between our yearly records and macroclimate databases (WorldClim2), with lower interpolated minimum temperatures and maximum temperatures higher than expected. We then assessed thermal tolerance of ten Heliconius butterfly species in the wild and showed that populations at high elevations had significantly lower heat tolerance than those at lower elevations. However, when we reared populations of the widespread H. erato from high and low elevations in a common-garden environment, the difference in heat tolerance across elevations was reduced, indicating plasticity in this trait. Microclimate buffering is not currently captured in publicly available datasets but could be crucial for enabling upland shifting of species sensitive to heat such as highland Heliconius. Plasticity in thermal tolerance may alleviate the effects of global warming on some widespread ectotherm species, but more research is needed to understand the long-term consequences of plasticity on populations and species.Summary statementTropical forests along the Andes were found to greatly buffer climate. The butterflies inhabiting high elevations were less thermally tolerant but not when reared in common-garden conditions, indicating plasticity.
Neural correlates of conscious tactile perception: An analysis of BOLD activation patterns and graph metrics
Authors: Grund Martin , Forschack Norman , Nierhaus Till , Villringer Arno 
Published: December 2019

AbstractTheories of human consciousness substantially vary in the proposed spatial extent of brain activity associated with conscious perception as well as in the assumed functional alterations within the involved brain regions. Here, we investigate which local and global changes in brain activity accompany conscious somatosensory perception following electrical finger nerve stimulation, and whether there are whole-brain functional network alterations by means of graph metrics. Thirty-eight healthy participants performed a somatosensory detection task and reported their decision confidence during fMRI. For conscious tactile perception in contrast to undetected near-threshold trials (misses), we observed increased BOLD activity in the precuneus, the intraparietal sulcus, the insula, the nucleus accumbens, the inferior frontal gyrus and the contralateral secondary somatosensory cortex. For misses compared to correct rejections, bilateral secondary somatosensory cortices, supplementary motor cortex and insula showed greater activations. The analysis of whole-brain functional network topology for hits, misses and correct rejections, did not result in any significant differences in modularity, participation, clustering or path length, which was supported by Bayes factor statistics. In conclusion, for conscious somatosensory perception, our results are consistent with an involvement of (probably) domain-general brain areas (precuneus, insula, inferior frontal gyrus) in addition to somatosensory regions; our data do not support the notion of specific changes in graph metrics associated with conscious experience. For the employed somatosensory submodality of fine electrical current stimulation, this speaks for a global broadcasting of sensory content across the brain without substantial reconfiguration of the whole-brain functional network resulting in an integrative conscious experience.
Role of adenosine in functional recovery following anoxic coma inLocusta migratoria
Authors: Van Dusen Rachel A. , Lanz Christopher , Robertson R. Meldrum 
Published: December 2019

AbstractWhen exposed to prolonged anoxia insects enter a reversible coma during which neural and muscular systems temporarily shut down. Nervous system shut down is a result of spreading depolarization throughout neurons and glial cells. Upon return to normoxia, recovery occurs following the restoration of ion gradients. However, there is a delay in the functional recovery of synaptic transmission following membrane repolarization. In mammals, the build-up of extracellular adenosine following spreading depolarization contributes to this delay. Adenosine accumulation is a marker of metabolic stress and it has many downstream effects through the activation of adenosine receptors. Here we demonstrate that adenosine lengthens the time to functional recovery following anoxic coma in locusts. Caffeine, used as an adenosine receptor antagonist, decreased the time to recovery in intact animals and lengthened the time to recovery in semi-intact animals. Our results show that the rate of recovery in insect systems is affected by the presence of adenosine.
A machine learning approach to define antimalarial drug action from heterogeneous cell-based screens
Authors: Ashdown George W. , Dimon Michelle , Fan Minjie , Terán Fernando Sánchez-Román , Witmer Katrin , Gaboriau David C. A. , Armstrong Zan , Hazard Jon , Ando D. Michael , Baum Jake 
Published: December 2019

AbstractDrug resistance threatens the effective prevention and treatment of an ever-increasing range of human infections. This highlights an urgent need for new and improved drugs with novel mechanisms of action to avoid cross-resistance. Current cell-based drug screens are, however, restricted to binary live/dead readouts with no provision for mechanism of action prediction. Machine learning methods are increasingly being used to improve information extraction from imaging data. Such methods, however, work poorly with heterogeneous cellular phenotypes and generally require time-consuming human-led training. We have developed a semi-supervised machine learning approach, combining human- and machine-labelled training data from mixed human malaria parasite cultures. Designed for high-throughput and high-resolution screening, our semi-supervised approach is robust to natural parasite morphological heterogeneity and correctly orders parasite developmental stages. Our approach also reproducibly detects and clusters drug-induced morphological outliers by mechanism of action, demonstrating the potential power of machine learning for accelerating cell-based drug discovery.One Sentence SummaryA machine learning approach to classifying normal and aberrant cell morphology from plate-based imaging of mixed malaria parasite cultures, facilitating clustering of drugs by mechanism of action.