bluuebunny/crossref_metadata_2025 huggingface dataset:
SRPK3 regulates alternative pre-mRNA splicing required for B lymphocyte development and humoral responsiveness
Authors: Arends Tessa , Taliaferro J. Matthew , Peterman Eric , Knapp Jennifer R. , O’Connor Brian P. , Torres Raul M. , Hagman James R.
Published: September 2019

Alternative splicing (AS) of pre-mRNA is a critical component of transcriptional regulation that diversifies the cellular proteome. The Serine-Arginine Protein Kinases (SRPK) initiate early events in AS. Using conditional knockout mice (cKO), we demonstrated the importance of the X-linked geneSrpk3in B lymphocyte development and in response to immunization in vivo. Significantly decreased numbers of immature and mature B cells were observed inSrpk3-cKOBM relative to wild-type (WT). Immunization ofSrpk3-cKOmice with a T lymphocyte-independent type-2 antigen elicited greatly reduced amounts of specific IgG3.Srpk3deletion resulted in hundreds of differentially spliced mRNAs in B cells, including mRNAs encoding proteins associated with signaling pathways and mitochondrial function. Several alternative splicing outcomes inSrpk3-cKOcells are due to altered splicing regulation of SR proteins. We conclude thatSrpk3is an immunomodulatory kinase that controls humoral immunity via its regulation of pre-mRNA splicing, antibody production, and metabolism in B cells.

One Sentence Summary

SRPK3 regulates alternative splicing of pre-mRNA that is crucial for B cell development, activation and antibody responses.
Approximating complex musculoskeletal biomechanics using multidimensional autogenerating polynomials
Authors: Sobinov Anton , Boots Matthew , Gritsenko Valeriya , Fisher Lee E. , Gaunt Robert A. , Yakovenko Sergiy
Published: September 2019

Computational models of the musculoskeletal system are scientific tools used to study human movement, quantify the effects of injury and disease, and plan surgical interventions. Additionally, these models could also be used to intuitively link biological control signals and realistic high-dimensional articulated prosthetic limbs. However, implementing fast and accurate musculoskeletal computations that can be used to control a prosthetic limb in real-time is a challenging problem. As muscles typically span multiple joints, the wrapping over complex geometrical constraints changes their moment arms and length as a function of joint angle and, thus, their ability to generate joint torques. As a result of these biomechanical complexities, calculating these muscle state variables in real-time is a difficult simulation problem. Here, we report a method to accurately and efficiently calculate these variables for the forearm muscles that actuate the hand and wrist across multiple postures. The posture dependent muscle geometry, moment arms and lengths of modeled muscles, were captured using autogenerating polynomials that expanded their optimal selection of terms using information measurements. The iterative process approximated 33 musculotendon actuators, each spanning up to 6 DOFs in an 18 DOF model of the human arm and hand, defined over the full physiological range of motion. Using these polynomials, the entire forearm anatomy could be computed in <10 µs, which is far better than what is required for real-time performance, and with low errors in moment arms (below 5%) and lengths (below 0.4%). Moreover, we demonstrate that the number of elements in these autogenerating polynomials does not increase exponentially with the increase in complexity of muscles, increasing linearly instead. The similar structure and function of muscles are represented with specific invariant polynomial terms. Dimensionality reduction using the polynomial terms alone resulted in clusters comprised of muscles with similar functions, suggesting that the polynomials themselves captured biologically relevant features of muscle structure and function. We propose that this novel method of describing musculoskeletal biomechanics might further improve the applications of detailed and scalable models for the description of human movement.
PeSA: A Software Tool for Peptide Specificity Analysis
Authors: Topcu Emine , Biggar Kyle K.
Published: September 2019

The discovery of molecular interactions is crucial towards a better understanding of complex biological functions. Particularly protein-protein interactions (i.e., PPIs), which are responsible for a variety of cellular functions from epigenetic modifications to enzyme-substrate specificity, have been studied extensively over the past decades. Position-specific scoring matrices (PSSM) in particular are used extensively to help determine interaction specificity or candidate interaction motifs. However, not all studies successfully report their results as a candidate interaction motif. In many cases, this is the result of a lack of analysis tools for simple analysis and motif generation. Peptide Specificity Analyst (PeSA) is developed with the goal of filling this gap and providing an analysis software to aid peptide array analysis and subsequent motif generation. PeSA utilizes two models of motif creation: (1) frequency-based using a peptide list, and (2) weight-based using a quantified matrix. The ability to generate motifs effortlessly will make analyzing, interpreting and sharing peptide specificity study results in a simple and straightforward process.

GRAPHICAL ABSTRACT

HIGHLIGHTS

Biological motifs are widely used representations for peptide specificity analysis.

PeSA populates a list of peptides matching a set threshold from a quantified matrix.

Frequency-based motif using a peptide list to spot residue patterns.

Use of quantified matrices to create weight-based motifs using residue positions.
Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes
Authors: Treiber Michelle L. , Taft Diana H. , Korf Ian , Mills David A. , Lemay Danielle G.
Published: September 2019

Background

Shotgun metagenomes are often assembled prior to annotation of genes which biases the functional capacity of a community towards its most abundant members. For an unbiased assessment of community function, short reads need to be mapped directly to a gene or protein database. The ability to detect genes in short read sequences is dependent on pre- and post-sequencing decisions. The objective of the current study was to determine how library size selection, read length and format, protein database, e-value threshold, and sequencing depth impact gene-centric analysis of human fecal microbiomes when using DIAMOND, an alignment tool that is up to 20,000 times faster than BLASTX.

Results

Using metagenomes simulated from a database of experimentally verified protein sequences, we find that read length, e-value threshold, and the choice of protein database dramatically impact detection of a known target, with best performance achieved with longer reads, stricter e-value thresholds, and a custom database. Using publicly available metagenomes, we evaluated library size selection, paired end read strategy, and sequencing depth. Longer read lengths were acheivable by merging paired ends when the sequencing library was size-selected to enable overlaps. When paired ends could not be merged, a congruent strategy in which both ends are independently mapped was acceptable. Sequencing depths of 5 million merged reads minimized the error of abundance estimates of specific target genes, including an antimicrobial resistance gene.

Conclusions

Shotgun metagenomes of DNA extracted from human fecal samples sequenced using the Illumina platform should be size-selected to enable merging of paired end reads and should be sequenced in the PE150 format with a minimum sequencing depth of 5 million merge-able reads to enable detection of specific target genes. Expecting the merged reads to be 180-250bp in length, the appropriate e-value threshold for DIAMOND would then need to be more strict than the default. Accurate and interpretable results for specific hypotheses will be best obtained using small databases customized for the research question.
Acetylcholine modulates cerebellar granule cell spiking by regulating the balance of synaptic excitation and inhibition
Authors: Fore Taylor R. , Taylor Nathan , Brunel Nicolas , Hull Court
Published: September 2019

Sensorimotor integration in the cerebellum is essential for refining motor output, and the first stage of this processing occurs in the granule cell layer. Recent evidence suggests that granule cell layer synaptic integration can be contextually modified, though the circuit mechanisms that could mediate such modulation remain largely unknown. Here we investigate the role of Acetylcholine (ACh) in regulating granule cell layer synaptic integration. We find that Golgi cells, interneurons that provide the sole source of inhibition to the granule cell layer, express both nicotinic and muscarinic cholinergic receptors. While acute ACh application can modestly depolarize some Golgi cells, the net effect of longer, optogenetically induced ACh release is to strongly hyperpolarize Golgi cells. Golgi cell hyperpolarization by ACh leads to a significant reduction in both tonic and evoked granule cell synaptic inhibition. ACh also reduces glutamate release from mossy fibers by acting on presynaptic muscarinic receptors. Surprisingly, despite these consistent effects on Golgi cells and mossy fibers, ACh can either increase or decrease the spike probability of granule cells as measured by non-invasive cell attached recordings. By constructing an integrate and fire model of granule cell layer population activity, we find that the direction of spike rate modulation can be accounted for predominately by the initial balance of excitation and inhibition onto individual granule cells. Together, these experiments demonstrate that ACh can modulate population-level granule cell responses by altering the ratios of excitation and inhibition at the first stage of cerebellar processing.

Significance Statement

The cerebellum plays a key role in motor control and motor learning. While it is known that behavioral context can modify motor learning, the circuit basis of such modulation has remained unclear. Here we find that a key neuromodulator, Acetylcholine (ACh), can alter the balance of excitation and inhibition at the first stage of cerebellar processing. These results suggest that ACh could play a key role in altering cerebellar learning by modifying how sensorimotor input is represented at the input layer of the cerebellum.
Hybridizing salamanders experience accelerated diversification
Authors: Patton Austin H. , Margres Mark J. , Epstein Brendan , Eastman Jon , Harmon Luke J. , Storfer Andrew
Published: September 2019

Whether hybridization generates or erodes species diversity has long been debated, but to date most studies have been conducted at small taxonomic scales. Salamanders (order Caudata) represent a taxonomic order in which hybridization plays a prevalent ecological and evolutionary role. We employed a recently developed model of trait-dependent diversification to test the hypothesis that hybridization impacts the diversification dynamics of species that are currently hybridizing. We find strong evidence supporting this hypothesis, showing that hybridizing salamander lineages have significantly greater net-diversification rates than non-hybridizing lineages. This pattern is driven by concurrently increased speciation rates and decreased extinction rates in hybridizing lineages. Our results support the hypothesis that hybridization can act as a generative force in macroevolutionary diversification.
Admistration of Exogenous Melatonin Improves the Diurnal Rhythms of Gut Microbiota in High Fat Diet-Fed Mice
Authors: Yin Jie , Li Yuying , Han Hui , Liu Gang , Wu Xin , Huang Xingguo , Fang Rejun , Baba Kenkichi , Bin Peng , Zhu Guoqiang , Ren Wenkai , Tan Bie , Tosini Gianluca , He Xi , Li Tiejun , Yin Yulong
Published: September 2019

Melatonin, a circadian hormone, has been reported to improve host lipid metabolism by reprogramming gut microbiota, which also exhibits rhythmicity in a light/dark cycle. However, the effect of admistartion of exogenous melatonin on the diurnal variation in gut microbiota in high fat diet (HFD)-fed mice is obscure. Here, we further confirmed the anti-obesogenic effect of melatonin on in mice feed with HFD for two weeks. Samples were collected every 4 h within a 24-h period and diurnal rhythms of clock genes expression (Clock, Cry1, Cry2, Per1, and Per2) and serum lipid indexes varied with diurnal time. Notably, Clock and triglycerides (TG) showed a marked rhythm only in the control and melatonin treated mice, but not in the HFD-fed mice. Rhythmicity of these parameters were similar between control and melatonin treated HFD mice compared with the HFD group, indicating an improvement of melatonin in the diurnal clock of host metabolism in HFD-fed mice. 16S rDNA sequencing showed that most microbiota exhibited a daily rhythmicity and the trends differentiated at different groups and different time points. We also identified several specific microbiota correlating with the circadian clock genes and serum lipid indexes, which might contribute the potential mechanism of melatonin in HFD-fed mice. Interestingly, administration of exogenous melatonin only at daytime exhibited higher resistance to HFD-induced lipid dysmetabolism than nighttime treatment companying with altered gut microbiota (Lactobacillus, Intestinimonas, and Oscillibacter). Importantly, the responses of microbiota transplanted mice to HFD feeding also varied at different transplanting times (8:00 and 16:00) and different microbiota donors. In summary, daily oscillations in the expression of circadian clock genes, serum lipid indexes, and gut microbiota, appears to be driven by a short-time feeding of an HFD. Administration of exogenous melatonin improved the compositions and diurnal rhythmicity of gut microbiota, which might be linked to host diurnal rhythm and metabolism.

Importance

Previous studies show that a circadian hormone, melatonin, involves in host lipid metabolism by reprogramming gut microbiota, which also exhibits rhythmicity in a light/dark cycle. However, the effect of melatonin drinking on the diurnal variation in gut microbiota in high fat diet-fed mice is obscure. Here, we found that 24-h oscillations were widely occurred in circadian clock genes, serum lipid indexes, and gut microbiota. Melatonin drinking improved the compositions and circadian rhythmicity of gut microbiota, which might be linked to host circadian rhythm and metabolism.
α-synuclein in the retina leads to degeneration of dopamine amacrine cells impairing vision
Authors: Elena Marrocco , Federica Esposito , Valeria Tarallo , Anna Carboncino , Grazia Alvino Filomena , Sandro De Falco , Brunella Franco , Maria De Risi , Indrieri Alessia , Maria Surace Enrico , Elvira De Leonibus
Published: September 2019

Introduction

α-synuclein aggregates have been identified in the retina of Parkinson’s disease patients associated to vision impairment. In this study, we sought to determine the effects of α-synuclein overexpression on the survival and function of dopaminergic (DA) amacrine cells in the retina.

Methods

Adult mice were intravitreally injected with an adeno-associated viral (AAV) vector to overexpress human wild-type α-synuclein in the inner retina. Following systemic injections of levodopa (L-DOPA), retinal responses and visual acuity driven behavior were measured by electroretinography (ERG) and water maze task, respectively. Amacrine cells and ganglion cells were counted at 1, 2 and 3 months post-injection.

Results

α-synuclein led to an early loss of DA cells, which was associated with the decrease of light-adapted ERG responses and visual acuity. Systemic injections of L-DOPA rescued these retinal and visual abnormalities.

Conclusions

The data show that α-synuclein affects dopamine neurons in the retina. The approach provides a novel accessible mode of modeling the underlying mechanisms implicated in synucleinophaties pathogenesis and for testing novel treatments.
Degradation of recalcitrant polyurethane and xenobiotic additives by a selected landfill microbial community and its biodegradative potential revealed by proximity ligation-based metagenomic analysis
Authors: Gaytán Itzel , Sánchez-Reyes Ayixon , Burelo Manuel , Vargas-Suárez Martín , Liachko Ivan , Press Maximilian , Sullivan Shawn , Javier Cruz-Gómez M. , Loza-Tavera Herminia
Published: September 2019

Polyurethanes (PU) are the sixth more produced plastics with around 19-million tons/year, but since they are not recyclable they are burned or landfilled, generating ecological damage. To elucidate the mechanisms that landfill microbial communities perform to attack recalcitrant PU plastic, we studied the BP8 community selected by its capability to grow in a water PU dispersion (WPUD) that contains a polyether-polyurethane-acrylate (PE-PU-A) copolymer and xenobiotic additives (N-methyl 2-pyrrolidone, isopropanol and glycol ethers), and performed a proximity ligation-based metagenomic analysis for revealing the community structure and potential biodegradative capacity. Additives were consumed early whereas the copolymer was cleaved throughout the 25-days incubation. BP8 metagenomic deconvolution reconstructed five genomes, three of them from novel species. Genes encoding enzymes for additives biodegradation were predicted. The chemical and physical analysis of the biodegradation process, and the identified biodegradation products show that BP8 cleaves esters, aromatic urethanes, C-C and ether groups by hydrolytic and oxidative mechanisms. The metagenomic analysis allowed to predicting comprehensive metabolic pathways and enzymes that explain the observed PU biodegradation. This is the first study revealing the metabolic potential of a landfill microbial community that thrives within a WPUD system and shows potential for bioremediation of polyurethane- and xenobiotic additives-contaminated sites.
The circadian clock gene circuit controls protein and phosphoprotein rhythms inArabidopsis thaliana
Authors: Krahmer Johanna , Hindle Matthew , Perby Laura K , Nielsen Tom H , Halliday Karen J , van Ooijen Gerben , Le Bihan Thierry , Millar Andrew J
Published: September 2019

24-hour, circadian rhythms control many eukaryotic mRNA levels, whereas the levels of their more stable proteins are not expected to reflect the RNA rhythms, emphasizing the need to test the circadian regulation of protein abundance and modification. Here we present circadian proteomic and phosphoproteomic time-series fromArabidopsis thalianaplants under constant light conditions, estimating that just 0.4% of quantified proteins but a much larger proportion of quantified phospho-sites were rhythmic. Approximately half of the rhythmic phospho-sites were most phosphorylated at subjective dawn, a pattern we term the ‘phospho-dawn’. Members of the SnRK/CDPK family of protein kinases are candidate regulators. ACCA1-over-expressing line that disables the clock gene circuit lacked most circadian protein phosphorylation. However, the few phospho-sites that fluctuated despiteCCA1-over-expression still tended to peak in abundance close to subjective dawn, suggesting that the canonical clock mechanism is necessary for most but perhaps not all protein phosphorylation rhythms. To test the potential functional relevance of our datasets, we conducted phosphomimetic experiments using the bifunctional enzyme fructose-6-phosphate-2-kinase / phosphatase (F2KP), as an example. The rhythmic phosphorylation of diverse protein targets is controlled by the clock gene circuit, implicating post-translational mechanisms in the transmission of circadian timing information in plants.
A nonhomologous end-joining mutant forNeurospora sitophilaresearch
Authors: Rhoades Nicholas A. , Webber Elise K. , Hammond Thomas M.
Published: September 2019

Disruption of the nonhomologous end-joining (NHEJ) pathway has been shown to increase the efficiency of transgene integration into targeted genomic locations ofNeurospora crassaand other fungi. Here, we report that a similar phenomenon occurs in a second Neurospora species:N. sitophila. Specifically, we show that deletion ofN. sitophila mus-51increases the efficiency of targeted-transgene integration, presumably by disrupting NHEJ. Researchers interested in obtaining theN. sitophila mus-51Δstrains described in this study can obtain them from the Fungal Genetics Stock Center (FGSC).
A missing link in mutualistic networks: symbiotic fungi in plant-animal interactions
Authors: Chaverri Priscila , Chaverri Gloriana
Published: September 2019

We explored the hypothesis of an indirect mutualistic relationship (i.e., when the association between two species is modified by a third one) within a plant-animal seed dispersal network. Bats are important long-distance dispersers of many tropical plants, yet, by consuming fruits they may disperse not only the plant’s seeds, but also the endosymbiotic fungi within those fruits. We characterized fungal communities in fruits ofFicus colubrinaeand in feces ofEctophylla albato determine if passage through the digestive tract of the bats affected the total mycobiome. Results show a significant reduction, after passage through the gut, of fungi known to be plant pathogenic, while abundance of species known to have beneficial properties significantly increased. These findings suggest that the role of frugivores in plant-animal mutualistic networks may extend beyond seed dispersal: they also promote the dispersal of potentially beneficial microbial symbionts while hindering those that can cause plant disease.
Evolution of generalists by phenotypic plasticity
Authors: Fraebel David T. , Gowda Karna , Mani Madhav , Kuehn Seppe
Published: September 2019

Adapting organisms face a tension between specializing their phenotypes for certain ecological tasks or developing generalist strategies which permit persistence in multiple environmental conditions. Understanding when and how generalists or specialists evolve is therefore an important question in evolutionary dynamics. Here we study the evolution of bacterial range expansions by selectingEscherichia colifor faster migration through porous media containing one of four different sugars supporting growth and chemotaxis. We find that selection in any one sugar drives the evolution of faster migration in all sugars relative to the ancestral strain. Measurements of growth and motility of all evolved lineages in all nutrient conditions reveal that the ubiquitous evolution of fast migration arises via phenotypic plasticity. Phenotypic plasticity permits evolved strains to exploit distinct phenotypic strategies to achieve fast migration in each environment irrespective of the environment in which they were evolved. Our work suggests that plasticity plays an important role in the evolution of generalist phenotypes.
Collective behaviour is not robust to disturbance, yet parent and offspring colonies resemble each other in social spiders
Authors: Fisher David N. , Lichtenstein James L.L. , Costa-Pereira Raul , Yeager Justin , Pruitt Jonathan N.
Published: September 2019

Groups of animals possess phenotypes such as collective behaviour, which may determine the fitness of group members. However, the stability and robustness to perturbations of collective phenotypes in natural conditions is not established. Furthermore, whether group phenotypes are transmitted from parent to offspring groups is required for understanding how selection on group phenotypes contributes to evolution, but parent-offspring resemblance at the group level is rarely estimated. We evaluated robustness to perturbation and parent-offspring resemblance of collective foraging aggressiveness in colonies of the social spiderAnelosimus eximius. Among-colony differences in foraging aggressiveness were consistent over time but changed if the colony was perturbed through the removal of individuals, or via their removal and subsequent return. Offspring and parent colony behaviour were correlated, but only once the offspring colony had settled after being translocated. The parent-offspring resemblance was not driven by a shared elevation but could be due to other environmental factors. Laboratory collective behaviour was not correlated with behaviour in the field. Colony aggression seems sensitive to initial conditions and easily perturbed between behavioural states. Despite this sensitivity, offspring colonies have collective behaviour that resembles that of their parent colony, provided they are given enough time to settle into the environment.
A dual function of the IDA peptide in regulating cell separation and modulating plant immunity at the molecular level
Authors: Lalun Vilde Olsson , Breiden Maike , Galindo-Trigo Sergio , Smakowska-Luzan Elwira , Simon Rüdiger , Butenko Melinka A.
Published: September 2019

The abscission of floral organs and emergence of lateral roots in Arabidopsis is regulated by the peptide ligand INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) and the receptor protein kinases HAESA (HAE) and HAESA-LIKE 2 (HSL2). During these cell separation processes, the plant induces defense-associated genes to protect against pathogen invasion. However, the molecular coordination between abscission and immunity has not been thoroughly explored. Here we show that IDA induces a release of cytosolic calcium ions (Ca2+) and apoplastic production of reactive oxygen species, which are signatures of early defense responses. In addition, we find that IDA promotes late defense responses by the transcriptional upregulation of genes known to be involved in immunity. When comparing the IDA induced early immune responses to known immune responses, such as those elicited by flagellin22 treatment, we observe both similarities and differences. We propose a molecular mechanism by which IDA promotes signatures of an immune response in cells destined for separation to guard them from pathogen attack.
Locally acting transcription factors are required for p53-dependent cis-regulatory element activity
Authors: Catizone Allison N. , Uzunbas Gizem Karsli , Celadova Petra , Kuang Sylvia , Bose Daniel , Sammons Morgan A.
Published: September 2019

The master tumor suppressor p53 controls transcription of a wide-ranging gene network involved in apoptosis, cell cycle arrest, DNA damage repair, and senescence. Recent studies revealed pervasive binding of p53 to cis-regulatory elements (CRE), which are non-coding segments of DNA that spatially and temporally control transcription through the combinatorial binding of local transcription factors (TFs). Although the role of p53 as a strong trans-activator of gene expression is well known, the co-regulatory factors and local sequences acting at p53-bound CREs are comparatively understudied. We designed and executed a massively parallel reporter assay (MPRA) to investigate the effect of transcription factor binding motifs and local sequence context on p53-bound CRE activity. Our data indicate that p53-bound CREs are both positively and negatively affected by alterations in local sequence context and changes to co-regulatory TF motifs. We identified a SP1/KLF family motif located in an intronic p53 CRE that is required for the endogenous expression of the p53-dependent gene CCNG1. We also identified ATF3 as a factor that co-regulates the expression of the p53-dependent gene GDF15 through binding with p53 in an upstream CRE. Loss of either p53 or ATF3 severely reduces CRE activity and alters endogenous GDF15 mRNA levels in the cell. Our data suggests that p53 has the flexibility to cooperate with a variety of transcription factors in order to regulate CRE activity. By utilizing different sets of co-factors across CREs, we hypothesize that p53 activity is guarded against loss of any one regulatory partner allowing for dynamic and redundant control of p53-mediated transcription.
JAM-A functions as a female microglial tumor suppressor in glioblastoma
Authors: Turaga Soumya M. , Silver Daniel J. , Bayik Defne , Paouri Evi , Peng Sen , Borjini Nozha , Stanko Sarah , Naik Ulhas , Keri Ruth A. , Connor James R. , Barnholtz-Sloan Jill S. , Rubin Joshua B. , Berens Michael , Davalos Dimitrios , Lathia Justin D.
Published: September 2019

Glioblastoma (GBM) remains refractory to treatment. In addition to its cellular and molecular heterogeneity, epidemiological studies indicate the presence of additional complexity associated with biological sex. GBM is more prevalent and aggressive in male compared to female patients, suggesting the existence of sex-specific growth, invasion, and therapeutic resistance mechanisms. While sex-specific molecular mechanisms have been reported at a tumor cell-intrinsic level, sex-specific differences in the tumor microenvironment have not been investigated. Using transgenic mouse models, we demonstrate that deficiency of junctional adhesion molecule-A (JAM-A) in female mice enhances microglia activation, GBM cell proliferation, and tumor growth. Mechanistically, JAM-A suppresses anti-inflammatory/pro-tumorigenic gene activation via interferon-activated gene 202b (Ifi202b) and found in inflammatory zone (Fizz1) in female microglia. Our findings suggest that cell adhesion mechanisms function to suppress pathogenic microglial activation in the female tumor microenvironment, which highlights an emerging role for sex differences in the GBM microenvironment and suggests that sex differences extend beyond previously reported tumor cell intrinsic differences.

Turaga et al. demonstrate that female microglia drive a more aggressive glioblastoma phenotype in the context of JAM-A deficiency. These findings highlight a sex-specific role for JAM-A and represent the first evidence of sexual dimorphism in the glioblastoma microenvironment.
Mother knows best: maternal egg-clutch size predicts larval group size in pine sawflies (genusNeodiprion)
Authors: Terbot John W. , Linnen Catherine R.
Published: September 2019

Evolutionary conflicts are pervasive in nature and have the potential to drive antagonistic coevolution of conflict-related traits. However, when such conflicts are weak or idiosyncratic, phenotypic signatures of coevolutionary arms races may be absent. Here, we ask whether variation in group-living traits among pine-sawfly species in the genusNeodiprionis consistent with a history of parent-offspring conflict. To address this question, we compile data on adult female clutch size, larval aggregation behavior, and larval group size for a monophyletic group of 19 eastern North AmericanNeodiprionspecies from field observations, laboratory assays, and published descriptions. We then evaluate the extent to which each trait exhibits phylogenetic signal and, based on these results, examine correlations between group-size traits both with and without phylogenetic correction. Although female oviposition behavior and larval grouping behavior varies among species and variation in these traits is decoupled from phylogeny, we find no evidence of antagonistic coevolution between these traits. Furthermore, while larvae are physically capable of dispersal, female clutch size is a strong predictor of larval colony size, indicating that larvae do not substantially alter initial group size after hatching. Thus, although theoretical work demonstrates the potential for parent-offspring conflict over group size in animals that lack parental care, our data suggest that this type of conflict is not likely to be a long-term driver of phenotypic evolution.
Deamidation in Moxetumomab Pasudotox Leading to Conformational Change and Immunotoxin Activity Loss
Authors: Lu X. , Lin S. , De Mel N. , Parupudi A. , Pandey M. , Delmar J. , Wang X. , Wang J.
Published: September 2019

Asparagine deamidation is a common posttranslational modification in which asparagine is converted to aspartic acid or isoaspartic acid. By introducing a negative charge, deamidation could potentially impact the binding interface and biological activities of protein therapeutics. We identified a deamidation variant in moxetumomab pasudotox, an immunotoxin Fv fusion protein drug derived from a 38-kilodalton (kDa) truncated Pseudomonas exotoxin A (PE38) for the treatment of hairy-cell leukemia. Although the deamidation site, Asn-358, was outside of the binding interface, the modification had a significant impact on the biological activity of moxetumomab pasudotox. Surprisingly, the variant eluted earlier than its unmodified form on anion exchange chromatography, which suggests a higher positive charge. Here we describe the characterization of the deamidation variant with differential scanning calorimetry and hydrogen-deuterium exchange mass spectrometry, which revealed that the Asn-358 deamidation caused the conformational changes in the catalytic domain of the PE38 region. These results provide a possible explanation for why the deamidation affected the biological activity of moxetumomab pasudotox and suggest an approach that can be used for process control to ensure product quality and process consistency.

Statement of Significance

Asparagine deamidation can have a potentially significant impact on protein therapeutics. Previous studies have revealed that deamidation at a single site significantly reduces the biological activity of moxetumomab pasudotox, a recombinant anti-CD22 immunotoxin developed for the treatment of B-cell malignancies. Surprisingly, despite the fact that deamidation introduced a negative charge, the deamidated variant eluted earlier than its unmodified form on anion exchange chromatography. In order to understand these observations, we isolated the deamidated variant using an anion exchange column and characterized it by differential scanning calorimetry and hydrogen-deuterium exchange mass spectrometry. The results revealed the conformational change caused by the deamidation, which explains the diminished biological activity of the variant and its early elution time on anion exchange chromatography.
Mental geometry of 3D size and shape perception
Authors: Maruya Akihito , Zaidi Qasim
Published: September 2019

Judging poses, sizes and shapes of objects accurately is necessary for organisms and machines to operate successfully in the world. Retinal images of 3D objects are mapped by the rules of projective geometry, and preserve the invariants of that geometry. Since Plato, it has been debated whether geometry is innate to the human brain, and Poincare and Einstein thought it worth examining whether formal geometry arises from experience with the world. We examine if humans have learned to exploit projective geometry to estimate sizes and shapes of objects in 3D scenes.

Numerous studies have examined size invariance as a function of physical distance, which changes scale on the retina, but surprisingly, possible constancy or inconstancy of relative size seems not to have been investigated for object pose, which changes retinal image size differently along different axes. We show systematic underestimation of length for extents pointing towards or away from the observer, both for static objects and dynamically rotating objects. Observers do correct for projected shortening according to the optimal back-transform, obtained by inverting the projection function, but the correction is inadequate by a multiplicative factor. The clue is provided by the greater underestimation for longer objects, and the observation that they appear more slanted towards the observer. Adding a multiplicative factor for perceived slant in the back-transform model provides good fits to the corrections used by observers. We quantify the slant illusion with relative slant measurements, and use a dynamic demonstration to show the power of the slant illusion.

In biological and mechanical objects, distortions of shape are manifold, and changes in aspect ratio and relative limb sizes are functionally important. Our model shows that observers try to retain invariance of these aspects of shape to 3D rotation by correcting retinal image distortions due to perspective projection, but the corrections can fall short. We discuss how these results imply that humans have internalized particular aspects of projective geometry through evolution or learning, and how assuming that images are preserving the continuity, collinearity, and convergence invariances of projective geometry, supplements the Generic Viewpoint assumption, and simply explains other illusions, such as Ames’ Chair.
Individual Learning Phenotypes Drive Collective Cognition
Authors: Cook Chelsea N. , Lemanski Natalie J. , Mosqueiro Thiago , Ozturk Cahit , Gadau Jürgen , Pinter-Wollman Noa , Smith Brian H.
Published: September 2019

Variation in cognition can influence how individuals respond to and communicate about their environment, which may scale to shape how a collective solves a cognitive task. However, few empirical examples of variation in collective cognition emerges from variation in individual cognition exist. Here, we show that interactions among individuals that differ in the performance of a cognitive task drives collective foraging behavior in honey bee colonies by utilizing a naturally variable and heritable learning behavior called latent inhibition (LI). We artificially selected two distinct phenotypes: high LI bees that are better at ignoring previously unrewarding familiar stimuli, and low LI bees that can learn previously unrewarding and novel stimuli equally well. We then provided colonies composed of these distinct phenotypes with a choice between a familiar feeder or a novel feeder. Colonies of high LI individuals preferred to visit familiar food locations, while low LI colonies visited novel and familiar food locations equally. However, in colonies of mixed learning phenotypes, the low LI bees showed a preference to visiting familiar feeders, which contrasts with their behavior when in a uniform low LI group. We show that the shift in feeder preference of low LI bees is driven by foragers of the high LI phenotype dancing more intensely and attracting more followers. Our results reveal that cognitive abilities of individuals and their interactions drive emergent collective outcomes.

Significance Statement

Variation in individual cognition affects how animals perceive their environment and which information they share with others. Here we provide empirical evidence that how individual honey bees learn contributes to collective cognition of a colony. By creating colonies of distinct learning phenotypes, we evaluated how bees make foraging choices in the field. Colonies containing individuals that learn to ignore unimportant information preferred familiar food locations, however colonies of individuals that are unable to ignore familiar information visit novel and familiar feeders equally. A 50/50 mix of these phenotypes prefer familiar food locations, because individuals who learn the familiar location recruit nestmates by dancing more intensely. Our results reveal that variation in individual cognition scales non-linearly to shape collective outcomes.
Genetic Portrait of North-West Indian Population based on X ChromosomeAluInsertion Markers
Authors: Singh Gagandeep , Srinivas Yellapu
Published: September 2019

Aluinsertion elements represent the largest family of Short Interspersed Nuclear Elements (SINEs) in the human genome. PolymorphicAluelements are stable and conservative markers that can potentially be applied in studying human origin and relationships as they are identical by descent and known for lack of insertion in ancestral state. In this study, 10Aluinsertions of X chromosome were utilized to tabulate allele frequency distributions and compute parameters of forensic relevance in the 379 unrelated healthy individuals belonging to four different ethnic groups (Brahmin, Khatri, Jat Sikh and Scheduled Caste) of North-West India. Furthermore, theDAandFSTvalues of pairwise interpopulation differentiations, multidimensional scaling and Bayesian structure clustering analysis were also computed to probe the genetic relationships between present studied populations and with other 21 reference populations. Six X-Aluinsertions were observed to be polymorphic in all the populations, whereas the others appeared as monomorphic in at least one studied population. The insertion allele frequencies were in the range of 0.15 at Ya5DP3 to 0.9888 at Ya5DP77. Most polymorphicAluelements showed moderate to low genetic diversity. The maximum value of power of exclusion (PE) was 0.1645 at Ya5NBC37 marker, whereas the minimum was 0.0001 at Ya5DP4 locus, implying the significance of X chromosomeAluelements in forensic genetic investigations. Genetic relationships agree with a geographical pattern of differentiation among populations. The results of present study establish that X chromosomeAluelements comprise a reliable set of genetic markers useful to describe human population relationships and structure.
Urban birdsongs: higher minimum song frequency of an urban colonist persists in a common garden experiment
Authors: Reichard Dustin G. , Atwell Jonathan W. , Pandit Meelyn M. , Cardoso Gonçalo C. , Price Trevor D. , Ketterson Ellen D.
Published: September 2019

Environmental changes caused by urbanization and noise pollution can have profound effects on acoustic communication. Many organisms use higher sound frequencies in urban environments with low-frequency noise, but the developmental and evolutionary mechanisms underlying these shifts are less clear. We used a common garden experiment to ask whether changes in minimum song frequency observed 30 years after a songbird colonized an urban environment are a consequence of behavioral flexibility or canalized changes that occur early in development. We captured male juvenile dark-eyed juncos (Junco hyemalis thurberi) from two recently diverged populations (urban and mountain) soon after they reached independence (aged 25-40 days), raised them in identical indoor aviaries, and studied their songs at an age of three years. We found that the large population difference in minimum frequency observed in the field persisted undiminished in the common garden despite the absence of noise. We also found some song sharing between the common garden and natal field populations, indicating that early song memorization before capture could contribute to the persistent song differences in adulthood. These results are the first to show that frequency shifts in urban birdsong are maintained in the absence of noise by genetic evolution and/or early life experiences.
Endogenous esterases of Clostridium thermocellum are identified and disrupted for enhanced isobutyl acetate production from cellulose
Authors: Seo Hyeongmin , Nicely Preston N. , Trinh Cong T.
Published: September 2019

Medium chain esters are potential drop-in biofuels and versatile chemicals. Currently, these esters are largely produced by the conventional chemical process that uses harsh operating conditions and requires high energy input. Alternatively, the microbial conversion route has recently emerged as a promising platform for sustainable and renewable ester production. The ester biosynthesis pathways can utilize either esterases/lipases or alcohol acyltransferase (AAT), but the AAT-dependent pathway is more thermodynamically favorable in aqueous fermentation environment. Even though cellulolytic thermophiles such as Clostridium thermocellum harboring the engineered AAT-dependent pathway can directly convert lignocellulosic biomass into esters, the production is currently not efficient and requires optimization. One potential bottleneck is the ester degradation caused by the endogenous carbohydrate esterases (CEs) whose functional roles are poorly understood. In this study, we developed a simple, high-throughput colorimetric assay to screen the endogenous esterases of C. thermocellum responsible for ester hydrolysis. We identified, characterized, and disrupted two critical endogenous esterases that significantly contributes to isobutyl acetate degradation in C. thermocellum. We demonstrated that not only did the engineered esterase-deficient strain alleviate ester hydrolysis but also helped improve isobutyl acetate production while not affecting its robust metabolism for effective cellulose assimilation.

IMPORTANCE

Carbohydrate esterases (CEs) are important enzymes in the deconstruction of lignocellulosic biomass by the cellulolytic thermophile C. thermocellum, yet some are potential ester degraders in a microbial ester production system. Currently, the functional roles of CEs for hydrolyzing medium chain esters and negatively affecting the ester microbial biosynthesis are not well understood. This study discovered novel CEs responsible for isobutyl acetate degradation in C. thermocellum and hence identified one of the critical bottlenecks for direct conversion of lignocellulosic biomass into esters.
An exploration of ambigrammatic sequences in narnaviruses
Authors: DeRisi Joseph L. , Huber Greg , Kistler Amy , Retallack Hanna , Wilkinson Michael , Yllanes David
Published: September 2019

Narnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ∼ 3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ‘ambigrammatic’ and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The > 3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.
Evolutionary route of resistant genes in Staphylococcus aureus
Authors: John Jiffy , George Sinumol , Nori Sai Ravi Chandra , Nelson-Sathi Shijulal
Published: September 2019

Multi-drug resistant S. aureus is a leading concern worldwide. Coagulase-Negative Staphylococci (CoNS) are claimed to be the reservoir and source of important resistant elements in S. aureus. However, the origin and evolutionary route of resistant genes in S. aureus are still remaining unknown. Here, we performed a detailed phylogenomic analysis of 152 completely sequenced S. aureus strains in comparison with 7,529 non-S. aureus reference bacterial genomes. Our results reveals that S. aureus has a large open pan-genome where 97 (55%) of its known resistant related genes belonging to its accessory genome. Among these genes, 47 (27%) were located within the Staphylococcal Cassette Chromosome (SCCmec), a transposable element responsible for resistance against major classes of antibiotics including beta-lactams, macrolides and aminoglycosides. However, the physically linked mec-box genes (MecA-MecR-MecI) that are responsible for the maintenance of SCCmec elements is not unique to S. aureus, instead it is widely distributed within Staphylococcaceae family. The phyletic patterns of SCCmec encoded resistant genes in Staphylococcus species are significantly different from that of its core genes indicating frequent exchange of these genes between Staphylococcus species. Our in-depth analysis of SCCmec resistant gene phylogenies reveals that genes such as blaZ, ble, kmA and tetK that are responsible for beta-lactam, bleomycin, kanamycin and tetracycline resistance in S. aureus were laterally transferred from non-Staphylococcus sources. In addition, at least 11 non-SCCmec encoded resistant genes in S. aureus, mostly present in plasmid are laterally acquired from distantly related species. Our study evidently shows that gene transfers played a crucial role in shaping the evolution of antibiotic resistance in S. aureus.