bluuebunny/crossref_metadata_2025_split huggingface dataset:
High throughput screen identifies IFN-γ-dependent inhibitors of Toxoplasma gondii growth
Authors: Radke Joshua B. , Carey Kimberly L. , Shaw Subrata , Metkar Shailesh R. , Mulrooney Carol , Gale Jennifer P. , Bittker Joshua A. , Hilgraf Robert , Comer Eamon , Schreiber Stuart L. , Virgin Herbert W. , Perez Jose R. , Sibley L. David 
Published: June 2018

AbstractToxoplasma gondii is an obligate intracellular parasite capable of causing severe disease due to congenital infection and in patients with compromised immune systems. Control of infection is dependent on a robust Th1 type immune response including production of interferon gamma (IFN-γ), which is essential for control. IFN-γ activates a variety of anti-microbial mechanisms in host cells, which are then able to control intracellular parasites such as T. gondii. Despite the effectiveness of these pathways in controlling acute infection, the immune system is unable to eradicate chronic infections that can persist for life. Similarly, while antibiotic treatment can control acute infection, it is unable to eliminate chronic infection. To identify compounds that would act synergistically with IFN-γ, we performed a high-throughput screen of diverse small molecule libraries to identify inhibitors of T. gondii. We identified a number of compounds that inhibited parasite growth in vitro at low μM concentrations and that demonstrated enhanced potency in the presence of low level of IFN-γ. A subset of these compounds act by enhancing the recruitment of LC3 to the parasite-containing vacuole, suggesting they work by an autophagy-related process, while others were independent of this pathway. The pattern of IFN-γ-dependence was shared among the majority of analogs from 6 priority scaffolds and analysis of structure activity relationships for one such class revealed specific stereochemistry associated with this feature. Identification of these IFN-γ-dependent leads may lead to development of improved therapeutics due to their synergistic interactions with immune responses.
Proteomic Analysis of Urine from California Sea Lions (Zalophus californianus): a Resource for Urinary Biomarker Discovery
Authors: Neely Benjamin A. , Prager Katherine C. , Bland Alison M. , Fontaine Christine , Gulland Frances M. , Janech Michael G. 
Published: June 2018

AbstractUrinary markers for the assessment of kidney diseases in wild animals are limited, in part, due to the lack of urinary proteome data, especially for marine mammals. One of the most prevalent kidney diseases in marine mammals is caused byLeptospira interrogans, which is the second most common etiology linked to stranding of California sea lions (Zalophus californianus). Urine proteins from eleven sea lions with leptospirosis kidney disease and eight sea lions without leptospirosis or kidney disease were analyzed using shotgun proteomics. In total, 2694 protein groups were identified and 316 were differentially abundant between groups. Major urine proteins in sea lions were similar to major urine proteins in dogs and humans except for the preponderance of resistin, lysozyme C, and PDZ domain containing 1, which appear to be over-represented. Previously reported urine protein markers of kidney injury in humans and animals were also identified. Notably, neutrophil gelatinase-associated lipocalin, osteopontin, and epidermal fatty acid binding protein were elevated over 20-fold in the leptospirosis-infected sea lions. Consistent with leptospirosis infection in rodents, urinary proteins associated with the renin-angiotensin system were depressed, including neprilysin. This study represents a foundation from which to explore the clinical use of urinary protein markers in California sea lions.AbbreviationsRASrenin-angiotensin systemleptoleptospirosisSCrserum creatinineBUNblood urea nitrogen
Toward machine-guided design of proteins
Authors: Biswas Surojit , Kuznetsov Gleb , Ogden Pierce J. , Conway Nicholas J. , Adams Ryan P. , Church George M. 
Published: June 2018

AbstractProteins—molecular machines that underpin all biological life—are of significant therapeutic and industrial value. Directed evolution is a high-throughput experimental approach for improving protein function, but has difficulty escaping local maxima in the fitness landscape. Here, we investigate how supervised learning in a closed loop with DNA synthesis and high-throughput screening can be used to improve protein design. Using the green fluorescent protein (GFP) as an illustrative example, we demonstrate the opportunities and challenges of generating training datasets conducive to selecting strongly generalizing models. With prospectively designed wet lab experiments, we then validate that these models can generalize to unseen regions of the fitness landscape, even when constrained to explore combinations of non-trivial mutations. Taken together, this suggests a hybrid optimization strategy for protein design in which a predictive model is used to explore difficult-to-access but promising regions of the fitness landscape that directed evolution can then exploit at scale.
Closed-loop coupling of a muscle to a robotic device for dynamic assessment of muscle function
Authors: Sundar Kartik , Ting Lena H. , DeWeerth Stephen P. 
Published: June 2018

AbstractThe contributions of individual muscles to the performance of functional tasks are difficult to evaluate using traditional isolated muscle protocols. During movements, skeletal muscles work against a variety of environmental loads that influence their energetics and function. In turn, these changes in muscle length and muscle velocity alter the forces that the muscle can generate. Classic single-muscle experiments clamp at least one muscle state (length, velocity, force) such that it is independent of the other states, interrupting the dynamic interactions between the muscle and its environment. The purpose of this study was to design and build a real-time feedback system to virtually couple an isolated muscle to a robotic device. Using this approach, the muscle length is not prescribed, but results from the dynamic interactions between the muscle and a physical environment. Therefore our device facilitates the study of how physical interactions between a muscle, limb, and environments alter the force and motion produced by the muscle during controlled muscle activation. To demonstrate the utility of our system, we replicated some salient features of frog swimming, we coupled a frog plantaris longus muscle to a one-degree of freedom “limb” that drove a frog foot through water. We demonstrate that under identical muscle stimulation parameters, changes to muscle moment arm, environmental viscosity, and muscle fatigue can significantly alter the resulting muscle force, length, and work.
Genetic diversity and distribution of indigenous soybean-nodulating bradyrhizobia in the Philippines
Authors: Tabing Mason Maria Luisa , Cortez Tabing Baby Lyn , Yamamoto Akihiro , Saeki Yuichi 
Published: June 2018

ABSTRACTThe diversity of indigenous bradyrhizobia from soils collected at 11 locations in the Philippines was investigated using PSB-SY2 local soybean cultivar as the host plant. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) treatment for 16S rRNA, 16S-23S rRNA internal transcribed spacer (ITS) region and rpoB housekeeping gene was performed primarily to detect the genetic variation among the 424 isolates collected. Then, sequence analysis of 16S rRNA, ITS region and rpoB gene was performed for the representative isolates. Majority of the isolates were classified under Bradyrhizobium elkanii, B. diazoefficiens, B. japonicum, Bradyrhizobium sp., and few isolates were related to B. yuanmingense. Genetic variations observed through PCR-RFLP and sequence analyses of the ITS region and rpoB gene generally occurred in B. elkanii, suggesting an occurrence of gene transfer. Shannon’s diversity index showed varied results with a lowest score of 0.00 and highest at 0.98 indicating a very diverse population of bradyrhizobia across the country. Among all the factors considered in this work, soil management such as period of flooding and some soil properties provided major influence on the distribution and diversity of soybean bradyrhizobia in the country. Thus, it is proposed that the major micro-symbiont of soybean in the Philippines are B. elkanii for non-flooded soils, then B. diazoefficiens and B. japonicum for flooded soils.ImportanceAgriculture production in the Philippines has been and is currently heavily dependent on chemical inputs with mainly rice or corn mono-cropping that it rendered the soil acidic and unproductive. Legume research in the country are mainly focused on plant varietal improvements and very few are aimed at understanding the ecological niche of rhizobia present in the soil. Since soybean has mutual relationship with rhizobia, this legume is a good fallow crop or a rotation crop after rice and corn to help build up the nitrogen stock in the soil. The significance of this research is the better understanding of the ecological niche of indigenous soybean bradyrhizobia, particularly in a tropical archipelago like the Philippines. This work was conceptualized with the utmost goal to increase soybean yield by harnessing and evaluating the indigenous rhizobia in the soil to make production more sustainable and human-friendly.
Synergistic Activity of Silver Nanoparticles and Vancomycin Against a Spectrum ofStaphylococcus aureusBiofilm Types
Authors: Hair Bryan B. , Conley Matthew E. , Wienclaw Trevor M. , Conley Mark J. , Berges Bradford K. 
Published: June 2018

AbstractStaphylococcus aureus(SA) is an important human pathogen, causing potentially lethal infections of the blood, skin, and lungs. SA is becoming increasingly difficult to treat due to high levels of antibiotic resistance, and new treatments are needed. SA is able to evade antibiotics and immune surveillance through biofilm development. Biofilms are communities of microorganisms that are able to prevent the entry of antimicrobials and immune cells. Biofilms are also involved in SA transmission because biofilms can form on medical devices. In this study, we tested silver nanoparticles and vancomycin for their anti-biofilm effects on SA. We used 10 different SA isolates, representing a spectrum of biofilm-forming ability, and a crystal violet assay to measure biofilm mass. 2μg/mL vancomycin treatment resulted in a significant reduction in established SA biofilms in 7/10 isolates, including 4/5 methicillin susceptible SA (MSSA) and 3/5 methicillin-resistant (MRSA) isolates (mean reduction in crystal violet stain of 13.0%; high of 26.5% and low of 0%). Silver nanoparticle treatment of SA biofilms resulted in a significant reduction in 6/10 isolates, including 4/5 MSSA and 2/5 MRSA (mean reduction of 8.7%; high of 21.2% and low of 0%). A combinatorial treatment with silver nanoparticles and vancomycin resulted in significant reductions in 9/10 isolates (mean reduction of 20.8%; high of 39.3% and low of 0%). We conclude that both vancomycin and silver nanoparticle treatment of established tissue culture-based SA biofilms result in significant reductions in biofilm mass, with a combinatorial treatment even more effective than either treatment alone.
In vivovirulence characterization of pregnancy-associatedListeria monocytogenesinfections
Authors: Morrison Holly A. , Lowe David , Robbins Jennifer R. , Bakardjiev Anna I. 
Published: June 2018

AbstractListeria monocytogenesis a foodborne pathogen that infects the placenta and can cause pregnancy complications. Listeriosis infections usually occur as sporadic infections, but large outbreaks are also reported. Virulence from clinical isolates is rarely analyzed due to the large number of animals required, but this knowledge could help guide the response to an outbreak. We implemented a DNA barcode system using signature tags that allowed us to efficiently assay variations in virulence across a large number of isolates. We tested 77 signature-tagged clones of clinicalL. monocytogenesstrains from 72 infected human placentas and five immunocompromised patients, all isolated since 2000. These strains were tested for virulence in a modified competition assay in comparison to the laboratory strain 10403S. We used twoin vivomodels of listeriosis: the non-pregnant mouse and the pregnant guinea pig. Strains that were frequently found at high abundance within infected organs were considered “hypervirulent,” while strains frequently found at low abundance were considered “hypovirulent.” Virulence split relatively evenly among hypovirulent, hypervirulent, and strains equally virulent to 10403S. The laboratory strain was found to have an intermediate virulence phenotype, supporting its suitability for pathogenesis studies. Further, we found that splenic and placental virulence are closely linked in both guinea pig and mouse models. This suggests that outbreak and sporadic pregnancy-associatedL. monocytogenesare not generally more virulent than lab reference strains. However, some strains did show consistent and reproducible virulence differences, suggesting that their further study may reveal deeper insights into the biological underpinnings of listeriosis.
Specialized mechanoreceptor systems in rodent glabrous skin
Authors: Walcher Jan , Ojeda-Alonso Julia , Haseleu Julia , Oosthuizen Maria K. , Rowe Ashlee H. , Bennett Nigel C. , Lewin Gary R. 
Published: June 2018

AbstractRodents use their forepaws to actively interact with their tactile environment. Studies on the physiology and anatomy of glabrous skin that makes up the majority of the forepaw are almost non-existent in the mouse. Here we developed a preparation to record from single sensory fibers of the forepaw and compared anatomical and physiological receptor properties to those of the hind paw glabrous and hairy skin. We found that the mouse forepaw skin is equipped with a very high density of mechanoreceptors; >3 fold more than hind paw glabrous skin. In addition, rapidly adapting mechanoreceptors that innervate Meissner’s corpuscles of the forepaw were several-fold more sensitive to slowly moving mechanical stimuli compared to their counterparts in the hind paw glabrous skin. All other mechanoreceptors types as well as myelinated nociceptors had physiological properties that were invariant regardless of which skin area they occupied. We discovered a novel D-hair receptor innervating a small group of hairs in the middle of the hind paw glabrous skin in mice. Glabrous D-hair receptors were direction sensitive albeit with an orientation sensitivity opposite to that described for hairy skin D-hair receptors. Glabrous D-hair receptors do not occur in all rodents, but are present in North American and African rodent species that diverged more than 65 million years ago. The function of these specialized hairs is unknown, but they are nevertheless evolutionarily very ancient. Our study reveals novel physiological specializations of mechanoreceptors in the glabrous skin that likely evolved to facilitate tactile exploration.
The genetic basis of mutation rate variation in yeast
Authors: Gou Liangke , Bloom Joshua S. , Kruglyak Leonid 
Published: June 2018

AbstractMutations are the root source of genetic variation and underlie the process of evolution. Although the rates at which mutations occur vary considerably between species, little is known about differences within species, or the genetic and molecular basis of these differences. Here we leveraged the power of the yeastSaccharomyces cerevisiaeas a model system to uncover natural genetic variants that underlie variation in mutation rate. We developed a high-throughput fluctuation assay and used it to quantify mutation rates in natural yeast isolates and in 1040 segregant progeny from a cross between BY, a lab strain, and RM, a wine strain. We observed that mutation rate varies among yeast strains and is highly heritable (H2=0.46). We performed linkage mapping in the segregants and identified four quantitative trait loci (QTLs) underlying mutation rate variation in the cross. We fine-mapped two QTLs to the underlying causal genes,RAD5andMKT1, that contribute to mutation rate variation. These genes also underlie sensitivity to the DNA damaging agents 4NQO and MMS, suggesting a connection between spontaneous mutation rate and mutagen sensitivity.
Genome-scale oscillations in DNA methylation during exit from pluripotency
Authors: Rulands Steffen , Lee Heather J , Clark Stephen J , Angermueller Christof , Smallwood Sébastien A , Krueger Felix , Mohammed Hisham , Dean Wendy , Nichols Jennifer , Rugg-Gunn Peter , Kelsey Gavin , Stegle Oliver , Simons Benjamin D , Reik Wolf 
Published: June 2018

SummaryPluripotency is accompanied by the erasure of parental epigenetic memory with naïve pluripotent cells exhibiting global DNA hypomethylation bothin vitroandin vivo. Exit from pluripotency and priming for differentiation into somatic lineages is associated with genome-widede novoDNA methylation. We show that during this phase, coexpression of enzymes required for DNA methylation turnover, DNMT3s and TETs, promotes cell-to-cell variability in this epigenetic mark. Using a combination of single-cell sequencing and quantitative biophysical modelling, we show that this variability is associated with coherent, genome-scale, oscillations in DNA methylation with an amplitude dependent on CpG density. Analysis of parallel single-cell transcriptional and epigenetic profiling provides evidence for oscillatory dynamics bothin vitroandin vivo. These observations provide fresh insights into the emergence of epigenetic heterogeneity during early embryo development, indicating that dynamic changes in DNA methylation might influence early cell fate decisions.HighlightsCo-expression of DNMT3s and TETs drive genome-scale oscillations of DNA methylationOscillation amplitude is greatest at a CpG density characteristic of enhancersCell synchronisation reveals oscillation period and link with primary transcriptsMultiomic single-cell profiling provides evidence for oscillatory dynamicsin vivo
Stiffness as a control factor for object manipulation
Authors: Kennedy Scott D. , Schwartz Andrew B. 
Published: June 2018

AbstractWe act on the world by producing forces that move objects. During manipulation, force is exerted with the expectation that an object will move in an intended manner. This prediction is a learned coordination between force and displacement. Mechanically, impedance is a way to describe this coordination. As an efficient control strategy, object interaction could be anticipated by setting impedance before the hand moves the object. We examined this possibility with a paradigm in which subjects moved a handle to a specific target position along a track. The handle was locked in place until the subject exerted enough force to cross a specific threshold; then the handle was abruptly released and could move along the track. We hypothesized that this ballistic-release task would encourage subjects to modify their arm impedance in anticipation of the upcoming movement. If we consider the handle as an object, this paradigm loosely approximates the uncertainty encountered at the end of a reach when contacting a fixed object. We found that one component of arm impedance, stiffness, varied in a way that matched the behavioral demands of the task and we were able to dissociate stiffness from changes in force and displacement. We also found separate components of muscle activity that corresponded to stiffness and to changes in force. Our results show that subjects used a robust and efficient strategy to coordinate force and displacement by modulating muscle activity in a way that was behaviorally relevant in the task.New & NoteworthyThe arm can behave like a spring, suggesting the concept of exerting force to move an object by selecting a spring of a certain length and stiffness that, respectively, depend on the movement and force requirements of the task. We show that these spring-like characteristics describe the strategy used to arrest a pre-loaded handle. These results extend our understanding of the arm’s spring-like behavior to include force and movement constraints, important factors for object interaction.
Yeast PAF1 complex restricts the accumulation of RNA polymerase III and counters the replication stress on the transcribed genes
Authors: Bhalla Pratibha , Vernekar Dipti , Shukla Ashutosh , Gilquin Benoit , Couté Yohann , Bhargava Purnima 
Published: June 2018

AbstractMany regulatory proteins and complexes influence transcription by RNA polymerase (pol) II. In comparison, only a few regulatory proteins are known for pol III, which transcribes mostly house-keeping and non-coding genes. Yet, pol III transcription is precisely regulated under various stress conditions like starvation. We used pol III transcription complex components TFIIIC (Tfc6), pol III (Rpc128) and TFIIIB (Brf1) as baits to identify potential interactors through mass spectrometry-based proteomics. A large interactome constituting known chromatin modifiers, factors and regulators of transcription by pol I and pol II revealed the possibility of a large number of signaling cues for pol III transcription against adverse conditions. We found one of the pol II-associated factors, Paf1 complex (PAF1C) interacts with the three baits. Its occupancy on the pol III-transcribed genes is low and not correlated with pol III occupancy. Paf1 deletion leads to higher occupancy of pol III, γ-H2A and DNA pol2 but no change in nucleosome positions. Genotoxins exposure causes pol III but not Paf1 loss from the genes. PAF1C promotes the pol III pausing and restricts its accumulation on the genes, which reduces the replication stress caused by the pol III barrier and transcription-replication conflict on these highly transcribed genes.
Critical role of post-transcriptional regulation for IFN-γ in tumor-infiltrating T cells
Authors: Salerno Fiamma , Guislain Aurelie , Freen-van Heeren Julian J. , Nicolet Benoit P. , Young Howard A. , Wolkers Monika C. 
Published: June 2018

AbstractProtective T cell responses against tumors require the production of Interferon gamma (IFN-γ). However, tumor-infiltrating T cells (TILs) gradually lose their capacity to produce IFN-γ and therefore fail to clear malignant cells. Dissecting the underlying mechanisms that block cytokine production is thus key for improving T cell products. Here we show that although TILs express substantial levels of Ifng mRNA, post-transcriptional mechanisms impede the production of IFN-γ protein due to loss of mRNA stability. CD28 triggering, but not PD1 blocking antibodies, effectively restores the stability of Ifng mRNA. Intriguingly, TILs devoid of AU-rich elements within the 3’untranslated region maintain stabilized Ifng mRNA and produce more IFN-γ protein than wild-type TILs. This sustained IFN-γ production translates into effective suppression of tumor outgrowth, which is almost exclusively mediated by direct effects on the tumor cells. We therefore conclude that post-transcriptional mechanisms could be modulated to potentiate effective T cell therapies in cancer.