bluuebunny/crossref_metadata_2025 huggingface dataset:
Contribution of common and rare variants to bipolar disorder susceptibility in extended pedigrees from population isolates
Authors: Sul Jae Hoon , Service Susan K. , Huang Alden Y. , Ramensky Vasily , Hwang Sun-Goo , Teshiba Terri M. , Park YoungJun , Ori Anil P. S. , Zhang Zhongyang , Mullins Niamh , Loohuis Loes M. Olde , Fears Scott C. , Araya Carmen , Araya Xinia , Spesny Mitzi , Bejarano Julio , Ramirez Margarita , Castrillón Gabriel , Gomez-Makhinson Juliana , Lopez Maria C. , Montoya Gabriel , Montoya Claudia P. , Aldana Ileana , Escobar Javier I. , Ospina-Duque Jorge , Kremeyer Barbara , Bedoya Gabriel , Ruiz-Linares Andres , Cantor Rita M. , Molina Julio , Coppola Giovanni , Ophoff Roel A. , Macaya Gabriel , Lopez-Jaramillo Carlos , Reus Victor , Bearden Carrie E. , Sabatti Chiara , Freimer Nelson B.
Published: July 2018

Current evidence from case/control studies indicates that genetic risk for psychiatric disorders derives primarily from numerous common variants, each with a small phenotypic impact. The literature describing apparent segregation of bipolar disorder (BP) in numerous multigenerational pedigrees suggests that, in such families, large-effect inherited variants might play a greater role. To evaluate this hypothesis, we conducted genetic analyses in 26 Colombian (CO) and Costa Rican (CR) pedigrees ascertained for BP1, the most severe and heritable form of BP. In these pedigrees, we performed microarray SNP genotyping of 856 individuals and high-coverage whole-genome sequencing of 454 individuals. Compared to their unaffected relatives, BP1 individuals had higher polygenic risk scores estimated from SNPs associated with BP discovered in independent genome-wide association studies, and also displayed a higher burden of rare deleterious single nucleotide variants (SNVs) and rare copy number variants (CNVs) in genes likely to be relevant to BP1. Parametric and non-parametric linkage analyses identified 15 BP1 linkage peaks, encompassing about 100 genes, although we observed no significant segregation pattern for any particular rare SNVs and CNVs. These results suggest that even in extended pedigrees, genetic risk for BP appears to derive mainly from small to moderate effect rare and common variants.
Profiling of urine bacterial DNA to identify an “oncobiome” in a mouse model of bladder cancer
Authors: Forster Catherine S. , Cody James J. , Banskota Nirad , Stroud Crystal , Hsieh Yi-Ju , Farah Dannah , Lamanna Olivia , Hammam Olfat , Caldovic Ljubica , Hsieh Michael H.
Published: July 2018

Introduction

Recurrent urinary tract infections have been linked to increased risk of bladder cancer, suggesting a potential role of the urinary microbiome in bladder cancer pathogenesis.

Objective

Compare the urinary microbiomes in mice with and without bladder.

Methods

Longitudinal study of mice exposed to a dilute bladder-specific carcinogen (0.05% n-butyl-n-(4-hydroxybutyl) nitrosamine, BBN mice, n=10), and control mice (n=10). Urine was sampled monthly from individual mice for 4 months. Microbial DNA was extracted from the urine, and the V4 region of the 16S rRNA gene sequenced. Animals were sacrificed and their bladders harvested for histopathology. Bladder sections were graded by a blinded pathologist. The composition and diversity of the urinary microbiome were compared between the BBN and control mice. Metabolic pathway analysis was completed using PICRUST.

Results

Bladder histology in the BBN group showed normal tissue with inflammation (BBN-normal, n=5), precancerous pathologies, (BBN-precancerous, n=3), and invasive cancer (BBN-cancer, n=2). Alpha diversity did not differ between the mice exposed to BBN and the control mice at any timepoint. There were no differences in the urinary microbiomes between the BBN and control mice at baseline. At month 4, mice exposed to BBN had higher proportion of both Gardnerella and Bifidobacterium compared to control mice. There were no differences in proportions of specific bacteria between either the BBN-precancer or BBN-cancer and controls at month 4. However, the BBN-normal mice had higher proportions of Gardnerella, Haemophilus, Bifidobacterium, and Ureaplasma Actinobaculum, and lower proportions of Actinomyces, compared to control mice at month 4. Functional pathway analysis demonstrated increases in genes related to purine metabolism, phosphotransferase systems, peptidases, protein folding, and bacterial toxins in the BBN-mice compared to control mice at month 4.

Conclusion

Mice exposed to 4 months of BBN, a bladder-specific carcinogen, have distinct urine microbial profiles compared to control mice.
Transgenic Zebrafish Models Reveal Distinct Molecular Mechanisms for Cataract-linked αA-Crystallin Mutants
Authors: Wu Shu-Yu , Zou Ping , Mishra Sanjay , Mchaourab Hassane S
Published: July 2018

Mutations in the small heat shock proteins α-crystallins have been linked to autosomal dominant cataracts in humans. Extensive studies in vitro have revealed a spectrum of alterations to the structure and function of these proteins including shifts in the size of the oligomer, modulation of subunit exchange and modification of their affinity to client proteins. Although mouse models of these mutants were instrumental in identifying changes in cellular proliferation and lens development, a direct comparative analysis of their effects on lens proteostasis has not been performed. Here, we have transgenically expressed cataract-linked mutants of αA- and αB-crystallin in the zebrafish lens to dissect the underlying molecular changes that contribute to the loss of lens optical properties. Zebrafish lines expressing these mutants displayed a range of morphological lens defects. Phenotype penetrance and severity were dependent on the mutation even in fish lines lacking endogenous α-crystallin. The mechanistic origins of these differences were investigated by the transgenic co-expression of a destabilized human γD-crystallin mutant. We found that the R49C but not the R116C mutant of αA-crystallin promoted aggregation of γD-crystallin, although both mutants have similar affinity to client proteins in vitro. Our working model attributes these differences to the propensity of R49C, located in the buried N-terminal domain of αA-crystallin, to disulfide crosslinking as previously demonstrated in vitro. Our findings complement and extend previous work in mouse models and emphasize the need of investigating chaperone/client protein interactions in appropriate cellular context.
Life history of the Rio Grande leopard frog (Lithobates berlandieri) in Texas
Authors: Hughes Daniel F. , Meshaka Walter E.
Published: July 2018

We ascertained various life-history traits from an examination of 310 museum specimens of the Rio Grande leopard frog (Lithobates berlandieriBaird, 1859) collected during 1907–2016 from Texas, USA.Lithobates berlandieriwas captured during every month of the year except November, and adults were most frequently encountered during January–September with a distinct peak in May. Mean body size of adult males (69.5 mm) was smaller than that of adult females (77.5 mm), and both sexes were larger in mean body sizes than those of New Mexico populations (M = 64.4 mm; F = 73.5 mm). Females were gravid during January–September, and most gravid females were captured from late-winter to early-summer. Gonadal enlargement in males was generally high throughout January–September with no detectable seasonal increase. Feeding became widespread in both sexes during May–June shortly after a spring breeding bout. Spent females were common in July and lipid deposition increased in June/July, signaling oogenesis for breeding in the fall. From 15 gravid females, we estimated a mean clutch size of 3,107 eggs which was correlated with female body size, yet egg diameter was not related to clutch or body size. Age to metamorphosis was likely 2 to 4 months depending upon whether eggs were laid in the winter/spring or late fall. If metamorphosis occurred in May/June, the minimum size at sexual maturity in adult males (50.1 mm) could have been reached in 3–4 months and in 6–7 months for adult females (57.2 mm). Mean adult body sizes, however, may have taken 12 to 17 months to reach. A synthesis across Texas populations suggests that the breeding season extends almost continuously from the fall through the winter and spring until mid-summer and is interrupted by winter and summer peaks in seasonal temperatures.
Dynamics of genomic change during evolutionary rescue in the seed beetleCallosobruchus maculatus
Authors: Rêgo Alexandre , Messina Frank J. , Gompert Zachariah
Published: July 2018

Rapid adaptation can prevent extinction when populations are exposed to extremely marginal or stressful environments. Factors that affect the likelihood of evolutionary rescue from extinction have been identified, but much less is known about the evolutionary dynamics (e.g., rates and patterns of allele frequency change) and genomic basis of successful rescue, particularly in multicellular organisms. We conducted an evolve-and-resequence experiment to investigate the dynamics of evolutionary rescue at the genetic level in the cowpea seed beetle,Callosobruchus maculatus, when it is experimentally shifted to a stressful host plant, lentil. Low survival (∼1%) at the onset of the experiment caused population decline. But adaptive evolution quickly rescued the population, with survival rates climbing to 69% by the F5 generation and 90% by the F10 generation. Population genomic data showed that rescue likely was caused by rapid evolutionary change at multiple loci, with many alleles fixing or nearly fixing within five generations of selection on lentil. Selection on these loci was only moderately consistent in time, but parallel evolutionary changes were evident in sublines formed after the lentil line had passed through a bottleneck. By comparing estimates of selection and genomic change on lentil across five independentC. maculatuslines (the new lentil-adapted line, three long-established lines, and one case of failed evolutionary rescue), we found that adaptation on lentil occurred via somewhat idiosyncratic evolutionary changes. Overall, our results suggest that evolutionary rescue in this system can be caused by very strong selection on multiple loci driving rapid and pronounced genomic change.
Predation risk and resource abundance mediate foraging behaviour and intraspecific resource partitioning among consumers in dominance hierarchies
Authors: Naman Sean M. , Ueda Rui , Sato Takuya
Published: July 2018

Dominance hierarchies and unequal resource partitioning among individuals are key mechanisms of population regulation. The strength of dominance hierarchies can be influenced by size dependent trade-offs between foraging and predator avoidance whereby competitively inferior subdominants can access a larger proportion of limiting resources by accepting higher predation risk. Foraging-predation risk trade-offs also depend on resource abundance. Yet, few studies have manipulated predation risk and resource abundance simultaneously; consequently, their joint effect on resource partitioning within dominance hierarchies are not well understood. We addressed this gap by measuring behavioural responses of masu salmon to experimental manipulations of predation risk and resource abundance in a natural temperate forest stream. Responses to predation risk depended on body size such that larger dominants exhibited more risk-averse behaviour (e.g., lower foraging and appearance rates) relative to smaller subdominants after exposure to a simulated predator. The magnitude of this effect was lower when resources were elevated, indicating that dominant fish accepted a higher predation risk to forage on abundant resources. However, the influence of resource abundance did not extend to the population level, where predation risk altered the distribution of foraging attempts (a proxy for energy intake) from being skewed towards large individuals to being skewed towards small individuals after predator exposure. Our results imply that size dependent foraging-predation risk trade-offs can mediate the strength of dominance hierarchies by allowing competitively inferior subdominants to access resources that would otherwise be monopolized.

Author Contributions:

SN, TS, and RU designed the study and performed the fieldwork; SN analyzed the data and wrote the manuscript with input from all authors.
Intragenomic Conflict over Bet-Hedging
Authors: Wilkins Jon F , Bhattacharya Tanmoy
Published: July 2018

Genomic imprinting, where an allele’s expression pattern depends on its parental origin, is thought to result primarily from an intragenomic evolutionary conflict. Imprinted genes are widely expressed in the brain and have been linked to various phenotypes, including behaviors related to risk tolerance. In this paper, we analyze a model of evolutionary bet-hedging in a system with imprinted gene expression. Previous analyses of bet-hedging have shown that natural selection may favor alleles and traits that reduce reproductive variance, even at the expense of reducing mean reproductive success, with the trade-off between mean and variance depending on the population size. In species where the sexes have different reproductive variances, this bet-hedging trade-off differs between maternally and paternally inherited alleles. Where males have the higher reproductive variance, alleles are more strongly selected to reduce variance when paternally inherited than when maternally inherited. We connect this result to phenotypes connected with specific imprinted genes, including delay discounting and social dominance. The empirical patterns are consistent with paternally expressed imprinted genes promoting risk-averse behaviors that reduce reproductive variance. Conversely, maternally expressed imprinted genes promote risk-tolerant, variance-increasing behaviors. We indicate how future research might further test the hypotheses suggested by our analysis.
Curvature Dependent constraints drive remodeling of epithelia
Authors: Maechler Florian A. , Allier Cédric , Roux Aurélien , Tomba Caterina
Published: July 2018

Epithelial tissues are essential to keep a proper barrier for the organism. They usually have highly curved shapes, such as tubules or cysts. However, interplays between the environment and cell mechanical properties to set the shape are not known. In this study, we encapsulated two epithelial cell lineages, MDCK and J3B1A, into hollow alginate tubes and grew them under cylindrical confinement. Once formed, the epithelial MDCK layer detached from the alginate shell, while J3B1A layer remained adherent. Detachment resulted from contractile forces within cell layers that pulled cells away from the shell. We concluded that J3B1A cells have lower contractility than MDCK cells. As the pulling forces depend on the radius of the tube, we induced detachment of J3B1A cells by reducing the size of the hollow tube by two. Moreover, in bent tubes, detachment was more pronounced on the outer side of the turn, while extrusion occurred in the inner side, further highlighting the coupling between curvature and cell contractility.
Testing Causal Bidirectional Influences between Physical Activity and Depression using Mendelian Randomization
Authors: Choi Karmel W. , Chen Chia-Yen , Stein Murray B. , Klimentidis Yann C. , Wang Min-Jung ,   Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Koenen Karestan C. , Smoller Jordan W.
Published: July 2018

Background:

Burgeoning evidence from randomized controlled trials and prospective cohort studies suggests that physical activity protects against depression, pointing to a potential modifiable target for prevention. However, the direction of this inverse association is not clear: physical activity may reduce risk for depression, and/or depression may result in decreased physical activity. Here, we used bidirectional two-sample Mendelian randomization (MR) to test causal influences between physical activity and depression.

Methods:

For genetic instruments, we selected independent top SNPs associated with major depressive disorder (MDD, N = 143,265) and two physical activity phenotypes—self-reported (N = 377,234) and objective accelerometer-based (N = 91,084)—from the largest available, non-overlapping genome-wide association results. We used two sets of genetic instruments: (1) only SNPs previously reported as genome-wide significant, and (2) top SNPs meeting a more relaxed threshold (p < 1×10-7). For each direction of influence, we combined the MR effect estimates from each instrument SNP using inverse variance weighted (IVW) meta-analysis, along with other standard MR methods such as weighted median, MR-Egger, and MR-PRESSO.

Results:

We found evidence for protective influences of accelerometer-based activity on MDD (IVW odds ratio (OR) = 0.74 for MDD per 1 SD unit increase in average acceleration, 95% confidence interval (CI) = 0.59-0.92, p =.006) when using SNPs meeting the relaxed threshold (i.e., 10 versus only 2 genome-wide significant SNPs, which provided insufficient data for sensitivity analyses). In contrast, we found no evidence for negative influences of MDD on accelerometer-based activity (IVW b = 0.04 change in average acceleration for MDD versus control status, 95% CI = −0.43-0.51, p =.87). Furthermore, we did not see evidence for causal influences between self-reported activity and MDD, in either direction and regardless of instrument SNP criteria.

Discussion:

We apply MR for the first time to examine causal influences between physical activity and MDD. We discover that objectively measured—but not self-reported—physical activity is inversely associated with MDD. Of note, prior work has shown that accelerometer-based physical activity is more heritable than self-reported activity, in addition to being more representative of actual movement. Our findings validate physical activity as a protective factor for MDD and point to the importance of objective measurement of physical activity in epidemiological studies in relation to mental health. Overall, this study supports the hypothesis that enhancing physical activity is an effective prevention strategy for depression.
Parkinson-associatedSNCAenhancer variants revealed by open chromatin in mouse dopamine neurons
Authors: McClymont Sarah A. , Hook Paul W. , Soto Alexandra I. , Reed Xylena , Law William D. , Kerans Samuel J. , Waite Eric L. , Briceno Nicole J. , Thole Joey F. , Heckman Michael G. , Diehl Nancy N. , Wszolek Zbigniew K. , Moore Cedric D. , Zhu Heng , Akiyama Jennifer A. , Dickel Diane E. , Visel Axel , Pennacchio Len A. , Ross Owen A. , Beer Michael A. , McCallion Andrew S.
Published: July 2018

The progressive loss of midbrain (MB) dopaminergic (DA) neurons defines the motor features of Parkinson disease (PD) and modulation of risk by common variation in PD has been well established through GWAS. Anticipating that a fraction of PD-associated genetic variation mediates their effects within this neuronal population, we acquired open chromatin signatures of purified embryonic mouse MB DA neurons. Correlation with >2,300 putative enhancers assayed in mice reveals enrichment for MB cis-regulatory elements (CRE), data reinforced by transgenic analyses of six additional sequences in zebrafish and mice. One CRE, within intron 4 of the familial PD geneSNCA, directs reporter expression in catecholaminergic neurons of transgenic mice and zebrafish. Sequencing of this CRE in 986 PD patients and 992 controls reveals two common variants associated with elevated PD risk. To assess potential mechanisms of action, we screened >20,000 DNA interacting proteins and identify a subset whose binding is impacted by these enhancer variants. Additional genotyping across theSNCAlocus identifies a single PD-associated haplotype, containing the minor alleles of both of the aforementioned PD-risk variants. Our work posits a model for how common variation atSNCAmay modulate PD risk and highlights the value of cell context-dependent guided searches for functional non-coding variation.
Synchronised brood transport by ants occurs without communication
Authors: Mersch Danielle P. , Eckmann Jean-Pierre , Crespi Alessandro , Keller Laurent
Published: July 2018

Collective behaviours in societies such as those formed by ants are thought to be the result of distributed mechanisms of information processing and direct decision-making by well-informed individuals, but their relative importance remains unclear. Here we tracked all ants and brood movements to investigate the decision strategy underlying brood transport in nests of the antCamponotus fellah. Changes in environmental conditions induced workers to quickly transport the brood to a preferred location. Only a minority of the workers, mainly nurses, participated in this task. Using a large number of statistical tests we could further show that these transporters omitted to recruit help, and relied only on private information rather than information obtained from other workers. This reveals that synchronised group behaviour, often suggestive of coordinated actions among workers, can also occur in the complete absence of communication.
Fast and interpretable alternative splicing and differential gene-level expression analysis using transcriptome segmentation with Yanagi
Authors: Gunady Mohamed K , Mount Stephen M , Bravo Héctor Corrada
Published: July 2018

Introduction:

Analysis of differential alternative splicing from RNA-seq data is complicated by the fact that many RNA-seq reads map to multiple transcripts, besides, the annotated transcripts are often a small subset of the possible transcripts of a gene. Here we describe Yanagi, a tool for segmenting transcriptome to create a library of maximal L-disjoint segments from a complete transcriptome annotation. That segment library preserves all transcriptome substrings of length L and transcripts structural relationships while eliminating unnecessary sequence duplications.

Contributions:

In this paper, we formalize the concept of transcriptome segmentation and propose an efficient algorithm for generating segment libraries based on a length parameter dependent on specific RNA-Seq library construction. The resulting segment sequences can be used with pseudo-alignment tools to quantify expression at the segment level. We characterize the segment libraries for the reference transcriptomes of Drosophila melanogaster and Homo sapiens and provide gene-level visualization of the segments for better interpretability. Then we demonstrate the use of segments-level quantification into gene expression and alternative splicing analysis. The notion of transcript segmentation as introduced here and implemented in Yanagi opens the door for the application of lightweight, ultra-fast pseudo-alignment algorithms in a wide variety of RNA-seq analyses.

Conclusion:

Using segment library rather than the standard transcriptome succeeds in significantly reducing ambigious alignments where reads are multimapped to several sequences in the reference. That allowed avoiding the quantification step required by standard kmer-based pipelines for gene expression analysis. Moreover, using segment counts as statistics for alternative splicing analysis enables achieving comparable performance to counting-based approaches (e.g. rMATS) while rather using fast and lighthweight pseudo alignment.
SosA inhibits cell division inStaphylococcus aureusin response to DNA damage
Authors: Bojer Martin S. , Wacnik Katarzyna , Kjelgaard Peter , Gallay Clement , Bottomley Amy L. , Cohn Marianne T. , Lindahl Gunnar , Frees Dorte , Veening Jan-Willem , Foster Simon J. , Ingmer Hanne
Published: July 2018

Inhibition of cell division is critical for cell viability under DNA damaging conditions. In bacterial cells, DNA damage induces the SOS response, a process that inhibits cell division while repairs are being made. In coccoid bacteria, such as the human pathogenStaphylococcus aureus, the process remains poorly understood. Here we have characterized an SOS-induced cell-division inhibitor, SosA, inS. aureus. We find that in contrast to the wildtype,sosAmutant cells continue division under DNA damaging conditions with decreased viability as a consequence. Conversely, overproduction of SosA leads to cell division inhibition and reduced growth. The SosA protein is localized in the bacterial membrane and mutation of an extracellular amino acid, conserved between homologs of other staphylococcal species, abolished the inhibitory activity as did truncation of the C-terminal 30 amino acids. In contrast, C-terminal truncation of 10 amino acids lead to SosA accumulation and a strong cell division inhibitory activity. A similar phenotype was observed upon expression of wildtype SosA in a mutant lacking the membrane protease, CtpA. Thus, the extracellular C-terminus of SosA is required both for cell-division inhibition and for turnover of the protein. Functional studies showed that SosA is likely to interact with one or more divisome components and, without interfering with early cell-division events, halts cell division at a point where septum formation is initiated yet being unable to progress to septum closure. Our findings provide important insights into cell-division regulation in staphylococci that may foster development of new classes of antibiotics targeting this essential process.

Importance

Staphylococcus aureusis a serious human pathogen and a model organism for cell-division studies in spherical bacteria. We show that SosA is the DNA-damage-inducible cell-division inhibitor inS. aureusthat upon expression causes cell swelling and cessation of the cell cycle at a characteristic stage post septum initiation but prior to division plate completion. SosA appears to function via an extracellular activity and is likely to do so by interfering with the essential membrane-associated division proteins, while at the same time being negatively regulated by the membrane protease CtpA. This report represents the first description of the process behind cell-division inhibition in coccoid bacteria. As several pathogens are included in this category, uncovering the molecular details of SosA activity and control can lead to identification of new targets for development of valuable anti-bacterial drugs.
Resource limitation modulates the fate of dissimilated nitrogen in a dual-pathway Actinobacterium
Authors: Vuono David C. , Read Robert W. , Hemp James , Sullivan Benjamin W. , Arnone John A. , Neveux Iva , Blank Bob , Staub Carl , Loney Evan , Miceli David , Winkler Mari , Chakraborty Romy , Stahl David A. , Grzymski Joseph J.
Published: July 2018

Respiratory ammonification and denitrification are two evolutionarily unrelated dissimilatory nitrogen (N) processes central to the global N cycle, the activity of which is thought to be controlled by carbon (C) to nitrate (NO3-) ratio. Here we find thatIntrasporangium calvumC5, a novel menaquinone-based dual-pathway denitrifier/respiratory ammonifier, disproportionately utilizes ammonification rather than denitrification when grown under carbon or nitrate limitation, not C:NO3-ratio. Instead, C:NO3-ratio is a confounding variable for resource limitation. We find that the protein atomic composition for denitrification modules (NirK) are significantly cost minimized for C and N compared to ammonification modules (NrfA), indicating that resource limitation is a major selective pressure imprinted in the architecture of these proteins. The evolutionary precedent for these findings suggests ecological and biogeochemical importance as evidenced by higher growth rates whenI. calvumgrows predominantly using its ammonification pathway and by assimilating its end-product (ammonium) for growth under ammonium-deplete conditions. Genomic analysis ofI. calvumfurther reveals a versatile ecophysiology to cope with nutrient stress and redox conditions. Metabolite and transcriptional profiles during growth indicate that transcript abundances encoding for its nitrite reducing enzyme modules, NrfAH and NirK, significantly increase in response to nitrite production. Mechanistically, our results suggest that pathway selection is driven by intracellular redox potential (redox poise), which may be lowered during resource limitation, thereby decreasing catalytic activity of upstream electron transport steps needed for denitrification enzymes. Our work advances our understanding of the biogeochemical flexibility of N-cycling organisms, pathway evolution, and ecological food-webs.
Macrophage-Dependent Trafficking and Remodeling of the Basement Membrane-Interstitial Matrix Interface
Authors: Bahr Julian C. , Weiss Stephen J.
Published: July 2018

Macrophages infiltrate and remodel extracellular matrix barriers during development and disease. Bahr and Weiss demonstrate that human macrophages remodel native basement membrane barriers in an MT1-MMP-dependent fashion while retaining the ability to traverse tissue barriers by actomyosin-dependent forces alone.

Macrophages dominate inflammatory environments where they modify the extracellular matrix by mobilizing complex repertoires of proteolytic enzymes. Nevertheless, the dominant proteinases used by macrophage as they confront physiologic tissue barriers remain undefined. Herein, we have characterized the molecular mechanisms that define human macrophage-extracellular matrix interactions ex vivo. Resting and immune-polarized macrophages are shown to proteolytically remodel basement membranes while infiltrating the underlying interstitial matrix. In an unbiased screen to identify key proteases, we find that the macrophage metalloproteinase, MT1-MMP, is the dominant effector of basement membrane degradation and invasion. Unexpectedly, macrophages can alternatively use actomyosin-dependent forces to transmigrate native basement membrane pores that provide cells with proteinase-independent access to the interstitial matrix. These studies not only identify MT1-MMP as a key proteolytic effector of extracellular matrix remodeling by human macrophages, but also define the invasive strategies used by macrophages to traverse physiologic tissue barriers.
Reconciling disparate estimates of viral genetic diversity during human influenza infections
Authors: Xue Katherine S. , Bloom Jesse D.
Published: July 2018

Deep sequencing can measure viral genetic diversity within human influenza infections, but published studies disagree in their estimates of how much genetic diversity is typically present. One large-scale deep-sequencing study of human influenza reported high levels of shared viral genetic diversity among infected individuals in Hong Kong, but subsequent studies of other cohorts have reported little shared viral diversity. We re-analyze sequencing data from four studies of within-host genetic diversity encompassing more than 500 acute human influenza infections. We identify an anomaly in the Hong Kong data that provides a technical explanation for these discrepancies: read pairs from this study are often split between different biological samples, indicating that some reads are incorrectly assigned. These technical abnormalities explain the high levels of within-host variation and loose transmission bottlenecks reported by this study. Studies without these anomalies consistently report low levels of genetic diversity in acute human influenza infections.
Considerations in using recurrent neural networks to probe neural dynamics
Authors: Kao Jonathan C
Published: July 2018

Recurrent neural networks (RNNs) are increasingly being used to model complex cognitive and motor tasks performed by behaving animals. Here, RNNs are trained to reproduce animal behavior while also recapitulating key statistics of empirically recorded neural activity. In this manner, the RNN can be viewed as an in silico circuit whose computational elements share similar motifs with the cortical area it is modeling. Further, as the RNN’s governing equations and parameters are fully known, they can be analyzed to propose hypotheses for how neural populations compute. In this context, we present important considerations when using RNNs to model motor behavior in a delayed reach task. First, by varying the network’s nonlinear activation and rate regularization, we show that RNNs reproducing single neuron firing rate motifs may not adequately capture important population motifs. Second, by visualizing the RNN’s dynamics in low-dimensional projections, we demonstrate that even when RNNs recapitulate key neurophysiological features on both the single neuron and population levels, it can do so through distinctly different dynamical mechanisms. To militate between these mechanisms, we show that an RNN consistent with a previously proposed dynamical mechanism is more robust to noise. Finally, we show that these dynamics are sufficient for the RNN to generalize to a target switch task it was not trained on. Together, these results emphasize important considerations when using RNN models to probe neural dynamics.
Structural and Functional Consequences of Age-Related Isomerization in α-Crystallins
Authors: Lyon Yana A. , Riggs Dylan L. , Collier Miranda P. , Degiacomi Matteo T. , Benesch Justin L.P. , Julian Ryan R.
Published: July 2018

Long-lived proteins are subject to spontaneous degradation and may accumulate a range of modifications over time, including subtle alterations such as isomerization. Recently, tandem-mass spectrometry approaches have enabled the identification and detailed characterization of such peptide isomers, including those differing only in chirality. However, the structural and functional consequences of these perturbations remain largely unexplored. Here we examine the site-specific impact of isomerization of aspartic acid and epimerization of serine in human αA- and αB-crystallin. From a total of 81 sites of modification identified in aged eye lenses, four (αBSer59,αASer162,αBAsp62,αBAsp109) map to crucial oligomeric interfaces. To characterize the effect of isomerization on quaternary assembly, molecular dynamics calculations and native mass spectrometry experiments were performed on recombinant forms of αA- and αB-crystallin that incorporate, or mimic, isomerized residues. In all cases, oligomerization is significantly affected, with epimerization of a single serine residue (αASer162) sufficing to weaken inter-subunit binding dramatically. Furthermore, phosphorylation ofαBSer59, known to play an important regulatory role in oligomerization, is severely inhibited by serine epimerization and altered by isomerization of nearbyαBAsp62. Similarly, isomerization ofαBAsp109 disrupts a vital salt-bridge withαBArg120, a loss previously shown to yield aberrant oligomerization and aggregation in several disease variants. Our results illustrate how isomerization of amino-acid residues, which may seem like a minor structural perturbation, can have profound consequences on protein assembly and activity by disrupting specific hydrogen bonds and salt bridges.

Significance Statement

Proteins play numerous critical roles in our bodies but suffer damage with increasing age. For example, isomerization is a spontaneous post-translational modification that alters the three-dimensional connectivity of an amino acid, yet remains invisible to traditional proteomic experiments. Herein, radical-based fragmentation was used for isomer identification while molecular dynamics and native mass spectrometry were utilized to assess structural consequences. The results demonstrate that isomerization disrupts both oligomeric assembly and phosphorylation in the α-crystallins, which are long-lived proteins in the lens of the eye. The loss of function associated with these modifications is likely connected to age-related diseases such as cataract and neurodegenerative disorders, while the methodologies we present represent a framework for structure-function studies on other isomerized proteins.
Adaptive strategies of the candidate probioticE. coliNissle in the mammalian gut
Authors: Crook Nathan , Ferreiro Aura , Gasparrini Andrew J. , Pesesky Mitchell , Gibson Molly K. , Wang Bin , Sun Xiaoqing , Condiotte Zevin , Dobrowolski Stephen , Peterson Daniel , Dantas Gautam
Published: July 2018

Probiotics are living microorganisms that are increasingly used as gastrointestinal therapeutics by virtue of their innate or engineered genetic function. Unlike abiotic therapeutics, probiotics can replicate in their intended site, subjecting their genomes and therapeutic properties to natural selection. By exposing the candidate probioticE. coliNissle (EcN) to the mouse gastrointestinal tract over several weeks, we uncovered the consequences of gut transit, inter-species competition, antibiotic pressure, and engineered genetic function on the processes under selective pressure during both within-genome and horizontal evolutionary modes. We then show the utility of EcN as a chassis for engineered function by achieving the highest reported reduction in serum phenylalanine levels in a mouse model of phenylketonuria using an engineered probiotic. Collectively, we demonstrate a generalizable pipeline which can be applied to other probiotic strains to better understand their safety and engineering potential.
A conserved genetic interaction between Spt6 and Set2 regulates H3K36 methylation
Authors: Gopalakrishnan Rajaraman , Winston Fred
Published: July 2018

The transcription elongation factor Spt6 and the H3K36 methyltransferase Set2 are both required for H3K36 methylation and transcriptional fidelity in Saccharomyces cerevisiae. By selecting for suppressors of a transcriptional defect in an spt6 mutant, we have isolated dominant SET2 mutations (SET2sup mutations) in a region encoding a proposed autoinhibitory domain. The SET2sup mutations suppress the H3K36 methylation defect in the spt6 mutant, as well as in other mutants that impair H3K36 methylation. ChIP-seq studies demonstrate that the H3K36 methylation defect in the spt6 mutant, as well as its suppression by a SET2sup mutation, occur at a step following the recruitment of Set2 to chromatin. Other experiments show that a similar genetic relationship between Spt6 and Set2 exists in Schizosaccharomyces pombe. Taken together, our results suggest a conserved mechanism by which the Set2 autoinhibitory domain requires multiple interactions to ensure that H3K36 methylation occurs specifically on actively transcribed chromatin.
Host Enzymes Heparanase and Cathepsin L Promote Herpes Simplex Virus-2 Release from Cells
Authors: Hopkins James , Yadavalli Tejabhiram , Agelidis Alex , Shukla Deepak
Published: July 2018

Herpes simplex virus-2 (HSV-2) can productively infect many different cell types of human and non-human origin. Here we demonstrate interconnected roles for two host enzymes, heparanase (HPSE) and cathepsin L in HSV-2 release from cells. In vaginal epithelial cells and other cell lines tested, HSV-2 causes heparan sulfate shedding and upregulation in HPSE levels during the productive phase of infection. We also noted increased levels of cathepsin L and show that regulation of HPSE by cathepsin L via cleavage of HPSE proenzyme is important for infection. Furthermore, inhibition of HPSE by a specific inhibitor, OGT 2115, dramatically reduces HSV-2 release from vaginal epithelial cells. Likewise, we show evidence that the inhibition of cathepsin L is detrimental to the infection. The HPSE increase after infection is mediated by an increased NF-kB nuclear localization and a resultant activation of HPSE transcription. Together these mechanisms contribute to the removal of heparan sulfate from the cell surface, and thus facilitate virus release from cells.
A Multiplex Droplet Digital PCR Assay for Quantification of HTLV-1c DNA Proviral Load and T-Cells from Blood and Respiratory Exudates Sampled in a Remote Setting
Authors: Yurick David , Khoury Georges , Clemens Bridie , Loh Liyen , Pham Hai , Kedzierska Katherine , Einsiedel Lloyd , Purcell Damian
Published: July 2018

During human T-cell leukemia virus type-1 (HTLV-1) infection the frequency of cells harboring an integrated copy of viral cDNA, the proviral load (PVL), is the main risk factor for progression of HTLV-1-associated diseases. Accurate quantification of provirus by droplet digital PCR (ddPCR) is a powerful diagnostic tool with emerging uses for monitoring viral expression. Current ddPCR techniques quantify HTLV-1 PVL in terms of whole genomic cellular material, while the main target of HTLV-1 infection is the CD4+and CD8+T-cell. Our understanding of HTLV-1 proliferation and the amount of viral burden present in different compartments is limited. Recently a sensitive ddPCR assay was applied to quantifying T-cells by measuring loss of germline T-cell receptor genes as method of distinguishing non-T-cell from recombined T-cell DNA. In this study, we demonstrated and validated novel applications of the duplex ddPCR assay to quantify T-cells from various sources of human gDNA extracted from frozen material (PBMCs, bronchoalveolar lavage, and induced sputum) from a cohort of remote Indigenous Australians and then compared the T-cell measurements by ddPCR to the prevailing standard method of flow cytometry. The HTLV-1c PVL was then calculated in terms of extracted T-cell gDNA from various compartments. Because HTLV-1c preferentially infects CD4+T-cells, and the amount of viral burden correlates with HTLV-1c disease pathogenesis, application of this ddPCR assay to accurately measure HTLV-1c-infected T-cells can be of greater importance for clinical diagnostics, prognostics as well as monitoring therapeutic applications.
Genome-wide characterization of the Fur regulatory network reveals a link between catechol degradation and bacillibactin metabolism in Bacillus subtilis
Authors: Pi Hualiang , Helmann John D.
Published: July 2018

The ferric uptake regulator (Fur) is the global iron biosensor in many bacteria. Fur functions as an iron-activated transcriptional repressor for most of its regulated genes. There are a few examples where holo-Fur activates transcription, either directly or indirectly. Recent studies suggest that apo-Fur might also act as a positive regulator and, besides iron metabolism, the Fur regulon might encompass other biological processes such as DNA synthesis, energy metabolism, and biofilm formation. Here, we obtained a genomic view of the Fur regulatory network in Bacillus subtilis using ChIP-seq. Besides the known Fur target sites, 70 putative DNA binding sites were identified, and the vast majority had higher occupancy under iron sufficient conditions. Among the new sites detected, a Fur binding site in the promoter region of the catDE operon is of particular interest. This operon, encoding catechol 2,3-dioxygenase, is critical for catechol degradation and is under negative regulation by CatR and YodB. These three repressors function cooperatively to regulate the transcription of catDE, with Fur functioning as a sensor of iron-limitation and CatR as the major sensor of catechol stress. Genetic analysis suggests that CatDE is involved in metabolism of the catecholate siderophore bacillibactin, particularly when bacillibactin is constitutively produced and accumulates intracellularly, potentially generating endogenous toxic catechol derivatives. This study documents a role for catechol degradation in bacillibactin metabolism, and provides evidence that catechol 2,3-dioxygenase can detoxify endogenously produced catechol substrates in addition to its more widely studied role in biodegradation of environmental aromatic compounds and pollutants.

Importance

Many bacteria synthesize high affinity iron chelators (siderophores). Siderophore-mediated iron acquisition is an efficient and widely utilized strategy for bacteria to meet their cellur iron requirements. One prominent class of siderophores uses catecholate groups to chelate iron. B. subtilis bacillibactin, structurally similar to enterobactin (made by enteric bacteria), is a triscatecholate siderophore that is hydrolyzed to monomeric units after import to release iron. However, the ultimate fate of these catechol compounds and their potential toxicity have not been defined previously. Here, we performed genome-wide identification of Fur binding sites in vivo and uncovered a connection between catechol degradation and bacillibactin metabolism in B. subtilis. Beside its role in detoxification of environmental catechols, the catechol 2,3-dioxygenase encoded by catDE also protects cells from intoxication by endogeous bacillibactin-derived catechol metabolites under iron-limited conditions. These findings shed light on the degradation pathway and precursor recycling of the catecholate siderophores.
Internal noise in contrast discrimination propagates forwards from early visual cortex
Authors: Vilidaite Greta , Marsh Emma , Baker Daniel H.
Published: July 2018

Human contrast discrimination performance is limited by transduction nonlinearities and variability of the neural representation (noise). Whereas the nonlinearities have been well-characterised, there is less agreement about the specifics of internal noise. Psychophysical models assume that it impacts late in sensory processing, whereas neuroimaging and intracranial electrophysiology studies suggest that the noise is much earlier. We investigated whether perceptually-relevant internal noise arises in early visual areas or later decision making areas. We recorded EEG and MEG during a two-interval-forced-choice contrast discrimination task and used multivariate pattern analysis to decode target/non-target and selected/non-selected intervals from evoked responses. We found that perceptual decisions could be decoded from both EEG and MEG signals, even when the stimuli in both intervals were physically identical. Above-chance decision classification started <100ms after stimulus onset, suggesting that neural noise affects sensory signals early in the visual pathway. Classification accuracy increased over time, peaking at >500ms. Applying multivariate analysis to separate anatomically-defined brain regions in MEG source space, we found that occipital regions were informative early on but then information spreads forwards across parietal and frontal regions. This is consistent with neural noise affecting sensory processing at multiple stages of perceptual decision making. We suggest how early sensory noise might be resolved with Birdsall’s linearisation, in which a dominant noise source obscures subsequent nonlinearities, to allow the visual system to preserve the wide dynamic range of early areas whilst still benefitting from contrast-invariance at later stages. A preprint of this work is available at:http://dx.doi.org/10.1101/364612
Ad-Seq, a genome-wide DNA-adduct profiling assay
Authors: Harismendy Olivier , Howell Stephen B.
Published: July 2018

Carcinogens form adducts with the DNA which, when not properly repaired, can lead to mutations and drive oncogenesis. The identity, sequence specificity and mutagenicity of most DNA-adducts is however poorly understood and current molecular assays are limited in their scope and scalability. We present a novel genome-wide DNA adduct sequencing (Ad-Seq) assay to map the location of DNA-adducts at single-nucleotide resolution. Ad-Seq enriches for DNA fragments containing nuclease digestion resistant DNA-adducts. The genomic location of the resulting reads is aggregated in a quantitative profile showing the DNA-adduct sequence context. Ad-Seq is quantitative and confirms known specificity of damages from Ultra-Violet light (di-pyrimidine) and cisplatin (AG and GG di-purines). Furthermore, in cells, Ad-Seq profile can be compared to chromatin segments to show that cisplatin associated adducts are depleted in open and active chromatin regions. The Ad-Seq assay can therefore generate a broad DNA signature of DNA damage and, by comparing to mutagen exposure or downstream mutational profile and signatures, be used to improve our understanding of cancer molecular etiology.