bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlated structure of neuronal firing in macaque visual cortex limits information for binocular depth discrimination
Authors: Smith Jackson E. T. , Parker Andrew J.
Published: November 2019

Variability in cortical neural activity potentially limits sensory discriminations. Theoretical work shows that information required to discriminate two similar stimuli is limited by the correlation structure of cortical variability. We investigated these information-limiting correlations by recording simultaneously from visual cortical areas V1 and V4 in macaque monkeys, performing a binocular, stereo-depth discrimination task. Within both areas, noise correlations on a rapid temporal scale (20-30ms) were stronger for neuron-pairs with similar selectivity for binocular depth, meaning that these correlations potentially limit information for making the discrimination. Between-area correlations (V1 to V4) were different, being weaker for neuron pairs with similar tuning, and having a slower temporal scale (100+ms). Fluctuations in these information-limiting correlations just prior to the detection event were associated with changes in behavioural accuracy. Although these correlations limit the recovery of information about sensory targets, their impact may be curtailed by integrative processing of signals across multiple brain areas.
Brief communication: Long-term absence of Langerhans cells alters the gene expression profile of keratinocytes and dendritic epidermal T cells
Authors: Su Qingtai , Bouteau Aurélie , Cardenas Jacob , Uthra Balaji , Wang Yuanyaun , Smitherman Cynthia , Gu Jinghua , Igyártó Botond Z.
Published: November 2019

Tissue-resident and infiltrating immune cells are continuously exposed to molecules derived from the niche cells that often come in form of secreted factors, such as cytokines. These factors are known to impact the immune cells’ biology. However, very little is known about whether the tissue resident immune cells in return also affect the local environment. In this study, with the help of RNA-sequencing, we show for the first time that long-term absence of epidermal resident Langerhans cells (LCs) led to significant gene expression changes in the local keratinocytes and resident dendritic epidermal T cells. Thus, immune cells might play an active role in maintaining tissue homeostasis, which should be taken in consideration at data interpretation.
De novo assembly and characterization of transcriptome towards understanding molecular mechanism associated with MYMIV-resistance in Vigna mungo - A computational study
Authors: Gupta Manoj Kumar , Donde Ravindra , Gouda Gayatri , Vadde Ramakrishna , Behera Lambodar
Published: November 2019

The fast climate change affects yield in Vigna mungo via enhancing both biotic and abiotic stresses. Out of all factors, the yellow mosaic disease has the most damaging effect. However, due to lack of reference genome of Vigna mungo, the complete mechanism associated with MYMIV (Mungbean Yellow Mosaic Indian Virus) resistance in Vigna mungo remain elusive to date. Considering this, the authors made an attempt to release new transcriptome and its annotation by employing computational approaches. Quality assessment of the generated transcriptomes reveals that it successfully aligned with 99.03% of the raw reads and hence can be employed for future research. Functional annotation of the transcriptome reveals that 31% and ∼14% of the total transcripts encode lncRNAs and protein-coding sequences, respectively. Further, analysis reveals that, out of total transcripts, only 4536 and 78808 are significantly down and up-regulated during MYMIV infection in Vigna mungo, respectively. These significant transcripts are mainly associated with ribosome, spliceosome, glycolysis /gluconeogenesis, RNA transport, oxidative phosphorylation, protein processing in the endoplasmic reticulum, MAPK signaling pathway - plant, methionine and cysteine metabolism, purine metabolism and RNA degradation. Unlike the previous study, this is for the first time, the present study identified these pathways may play key role in MYMIV resistance in Vigna mungo. Thus, information and transcriptomes data available in the present study make a significant contribution to understanding the genomic structure of Vigna mungo, enabling future analyses as well as downstream applications of gene expression, sequence evolution, and genome annotation.
Defined microbiota transplant restores Th17/RORγt+ regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas
Authors: Britton Graham J. , Contijoch Eduardo J. , Spindler Matthew P. , Aggarwala Varun , Bongers Gerold , Mateo Lani San , Baltus Andrew , Das Anuk , Gevers Dirk , Borody Thomas J. , Kaakoush Nadeem O. , Kamm Michael A. , Mitchell Hazel , Paramsothy Sudarshan , Clemente Jose C. , Colombel Jean-Frederic , Dubinsky Marla C. , Grinspan Ari , Faith Jeremiah J.
Published: November 2019

The building evidence for the contribution of microbiota to human disease has spurred an effort to develop therapies that target the gut microbiota. This is particularly evident in inflammatory bowel diseases, where clinical trials of fecal microbiota transplant have shown some efficacy. To aid the development of novel microbiota-targeted therapies and to better understand the biology underpinning such treatments, we have used gnotobiotic mice to model microbiota manipulations in the context of microbiotas from humans with inflammatory bowel disease. Mice colonized with IBD donor-derived microbiotas exhibit a stereotypical set of phenotypes, characterized by abundant mucosal Th17 cells and a deficit in the tolerogenic RORγt+ Treg cell subset. Transplanting healthy donor-derived microbiota into mice colonized with human IBD microbiotas lead to induction of RORγt+ Treg cells, which was associated with an increase in the density of the microbiotas following transplant. Microbiota transplant reduced gut Th17 cells in mice colonized with a microbiota from a donor with Crohn’s disease. By culturing strains from this microbiota and screening them in vivo, we identified a specific strain that potently induces Th17 cells. Microbiota transplants reduced the relative abundance of this strain in the gut microbiota, correlated with a reduction in Th17 cells.
The Rab5-Rab11 endosomal pathway is required for BDNF-induced CREB transcriptional regulation in neurons
Authors: González Andrés G. , Lazo Oscar M. , Bronfman Francisca C.
Published: November 2019

Brain-derived neurotrophic factor (BDNF) is a key regulator of the morphology and connectivity of central neurons. We have previously shown that BDNF/TrkB signaling regulates the activity and mobility of the GTPases Rab5 and Rab11, which in turn determine the post-endocytic sorting of signaling TrkB receptors. Moreover, altered Rab5 or Rab11 activity inhibits BDNF-induced dendritic branching. Whether Rab5 or Rab11 activity is important for local events only, or also for regulating nuclear signaling and gene expression, is unknown. Here, we investigated whether BDNF-induced signaling cascades were altered when early and recycling endosomes were disrupted by the expression of dominant negative mutants of Rab5 and Rab11. The activities of both Rab5 and Rab11 were required for sustained activity of Erk1/2 and nuclear CREB phosphorylation and for increased transcription of BDNF-dependent genes containing CRE-binding sites that include activity-regulated genes such as Arc, Dusp1, c-fos and Egr1 and growth and survival genes such as Atf3 and Nf1. Based on our results, we propose that the early and recycling endosomes provide a platform for the integration of neurotrophic signaling from the plasma membrane to the nucleus in neurons and that this mechanism likely regulates neuronal plasticity and neuronal survival.

Significance Statement

BDNF is a soluble neurotrophic factor that regulates plastic changes in the brain, including dendritic growth, by binding to its plasma membrane receptor TrkB. BDNF/TrkB activates signaling cascades leading to activation of CREB, a key transcription factor regulating circuit development and learning and memory. Our results uncover the cellular mechanisms that central neurons use to integrate the signaling of plasma membrane receptors with nuclear transcriptional responses. We found that the endosomal pathway is required for the signaling cascade initiated by BDNF and its receptors in the plasma membranes to modulate BDNF-dependent gene expression and neuronal dendritic growth mediated by the CREB transcription factor in the nucleus.
TheDrosophila melanogasterortholog of RFWD3 functions independently of RAD51 during DNA repair
Authors: Carvajal-Garcia Juan , Gales Evan R. , Ramsden Dale A. , Sekelsky Jeff
Published: November 2019

Repair of damaged DNA is required for the viability of all organisms. Studies inDrosophila melanogaster, driven by the power of genetic screens, pioneered the discovery and characterization of many genes and pathways involved in DNA repair in animals. However, fewer than half of the alleles identified in these screens have been mapped to a specific gene, leaving a potential for new discoveries in this field. Here we show that the previously uncharacterized mutagen sensitive genemus302codes for theDrosophila melanogasterortholog of the E3 ubiquitin ligase RING finger and WD domain protein 3 (RFWD3). In human cells, RFWD3 promotes ubiquitylation of RPA and RAD51 to facilitate repair of collapsed replication forks and double strand breaks through homologous recombination. Despite the high similarity in sequence to the human ortholog, our evidence fails to support a role for Mus302 in the repair of these types of damage. Last, we observe that the N-terminal third of RFWD3 is only present in mammals and absent in the rest of vertebrates and invertebrates. We propose that the additional N-terminal portion accounts for the acquisition of a new biological function in mammals that explains the functional differences between the human and the fly orthologs, and thatDrosophilaMus302 may retain the ancestral function of the protein.
The independent and combined influence of schizophrenia polygenic risk score and heavy cannabis use on risk for psychotic disorder: A case-control analysis from the EUGEI study.
Authors: Di Forti Marta , Wu-Choi Beatrice , Quattrone Diego , Richards Alexander L , Freeman Tom P , Tripoli Giada , Gayer-Anderson Charlotte , Rodriguez Victoria , Jongsma Hannah , Ferraro Laura , La Cascia Caterina , Tosato Sarah , Tarricone Ilaria , Berardi Domenico , Szoke Andrei , Arango Celso , Bobes Julio , Sanjuan Julio , Santos Jose Luis , Arrojo Manuel , Velthorst Eva , BERNARDO MIQUEL , Del Ben Cristina Marta , Selten Jean-Paul , Jones Peter B , Kirkbride James B , Rutten Bart NP , de Haan Lieuwe , van os Jim , Lynskey Michael , Morgan Craig , Vassos Evangelos , O'Donovan Michael , Lewis Cathryn , Sham Pak C , Murray Robin M ,   EU-GEI WP2 Group
Published: November 2019

Background: Some recent studies have challenged the direction of causality for the association between cannabis use and psychotic disorder, suggesting that cannabis use initiation is explained by common genetic variants associated with risk of schizophrenia. We used data from the European Union Gene-Environment Interaction consortium (EUGEI) case-control study to test for the independent and combined effect of heavy cannabis use, and of Schizophrenia Polygenic risk score (SZ PRS), on risk for psychotic disorder. Methods: Genome-wide data were obtained from 492 first episode psychosis patients (FEPp) and from 787 controls of European Ancestry, and used to generate SZ PRS from the summary results of an independent meta-analysis. Information on pattern of cannabis use was used to build a 7-level frequency-type composite cannabis use measure that we previously found was a strong predictor of psychotic disorder. Results: SZ PRS did not predict cannabis initiation (b=0.027; p=0.51) or how frequently controls (b=0.027; p=0.06) or FEPp (b=0.006; p=0.91) used it, or the type of cannabis they used (Controls: b = 0.032; p=0.31); FEPp: b= 0.005; p=0.89). The frequency-type composite cannabis use measure (OR=1.32; 95% CI 1.22-1.44) and SZ PRS (OR=2.29; 95%CI 1.71-3.05) showed independent effects from each other on the OR for psychotic disorder. Conclusion: SZ PRS does not predict an individual s propensity to try cannabis, frequency of use, or the potency of the cannabis used. Our findings provide the first evidence that SZ PRS and heavy cannabis use exert effects independent from each other on the risk for psychotic disorder.
Nuclear GAPDH cascade mediates pathological cardiac hypertrophy
Authors: Zhang Manling , Kariya Taro , Numata Genri , Sasaki Hideyuki , Sasaki Masayuki , Ramos Adriana , Nakamura Shun , Iwakiri Masaki , Koitabashi Norimichi , Zhu Guangshuo , Tsujimura Tsuyoshi , Lee Dong-ik , Tristan Carlos , Shahani Neelam , Tsuchiya Yukihiro , Jaaro-Peled Hanna , Sasano Tetsuo , Slusher Barbara , Kass David A. , Saitoh Toshiaki , Ishizuka Koko , Sawa Akira , Takimoto Eiki
Published: November 2019

Pathological stressors disrupt cellular homeostasis, causing various diseases. We report a non-glycolytic role for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in the pathological growth response of the heart. In cellular and animal models for cardiac hypertrophy, nuclear translocation of GAPDH was elicited in cardiac myocytes, followed by activation of p300 histone acetyl-transferase (HAT), an inducer of heart hypertrophy gene programs. The hypertrophy was inhibited by a compound antagonizing the nuclear GAPDH cascade. In mice with selective deletion of GAPDH’s nuclear function in cardiac myocytes, the stress-induced cardiac hypertrophy and functional deficits were normalized. Nuclear GAPDH cascade plays a pivotal role in stress response/homeostatic control in the heart. GAPDH may act as a key homeostatic mediator in living organisms through its stress-responsive nuclear translation.

One-sentence summary

Non-glycolytic function of GAPDH critically regulates heart homeostasis and mediates cardiac pathological hypertrophy
A comparison of humans and baboons suggests germline mutation rates do not track cell divisions
Authors: Wu Felix L. , Strand Alva , Ober Carole , Wall Jeffrey D. , Moorjani Priya , Przeworski Molly
Published: November 2019

In humans, most germline mutations are inherited from the father. This observation is widely interpreted as resulting from the replication errors that accrue during spermatogenesis. If so, the male bias in mutation should be substantially lower in a closely related species with similar rates of spermatogonial stem cell divisions but a shorter mean age of reproduction. To test this hypothesis, we resequenced two 3–4 generation nuclear families (totaling 29 individuals) of olive baboons (Papio anubis), who reproduce at ~10 years of age on average. We inferred sex-specific mutation rates by analyzing the data in parallel with three three-generation human pedigrees (26 individuals). The mutation rate per generation in baboons is 0.55×10−8 per base pair, approximately half that of humans. Strikingly, however, the degree of male mutation bias is approximately 3:1, similar to that of humans; in fact, a similar male bias is seen across mammals that reproduce months, years or decades after birth. These results echo findings in humans that the male bias is stable with parental ages and cast further doubt on the assumption that germline mutations track cell divisions. Our mutation rate estimates for baboons raise a further puzzle in suggesting a divergence time between apes and Old World Monkeys of 67 My, too old to be consistent with the fossil record; reconciling them now requires not only a slowdown of the mutation rate per generation in humans but also in baboons.
Transversal otolithic membrane deflections evoked by the linear accelerations
Authors: Goussev V.
Published: November 2019

Considered is the model of the transversal utricle membrane deflections evoked by the linear accelerations. The real 3D utricle membrane structure was simplified by considering its middle section and evaluating its elastic properties in 2D space. The steady state transversal deflections along the membrane are analytically evaluated and numerically simulated using the 2D elasticity theory. The transversal deflections are found to be more expressive and stronger as compared to the conventional longitudinal deformations. The revealed properties could be used for explanation of the transduction processes in the otholith organ. Based on the implemented modeling approach the new otolithic membrane mechanical properties are discussed and new explanations for the available experimental data are given.
Predictive regression modeling with MEG/EEG: from source power to signals and cognitive states
Authors: Sabbagh David , Ablin Pierre , Varoquaux Gaël , Gramfort Alexandre , Engemann Denis A.
Published: November 2019

Predicting biomedical outcomes from Magnetoencephalography and Electroencephalography (M/EEG) is central to applications like decoding, brain-computer-interfaces (BCI) or biomarker development and is facilitated by supervised machine learning. Yet most of the literature is concerned with classification of outcomes defined at the event-level. Here, we focus on predicting continuous outcomes from M/EEG signal defined at the subject-level, and analyze about 600 MEG recordings from Cam-CAN dataset and about 1000 EEG recordings from TUH dataset. Considering different generative mechanisms for M/EEG signals and the biomedical outcome, we propose statistically-consistent predictive models that avoid source-reconstruction based on the covariance as representation. Our mathematical analysis and ground truth simulations demonstrated that consistent function approximation can be obtained with supervised spatial filtering or by embedding with Riemannian geometry. Additional simulations revealed that Riemannian methods were more robust to model violations, in particular geometric distortions induced by individual anatomy. To estimate the relative contribution of brain dynamics and anatomy to prediction performance, we propose a novel model inspection procedure based on biophysical forward modeling. Applied to prediction of outcomes at the subject-level, the analysis revealed that the Riemannian model better exploited anatomical information while sensitivity to brain dynamics was similar across methods. We then probed the robustness of the models across different data cleaning options. Environmental denoising was globally important but Riemannian models were strikingly robust and continued performing well even without preprocessing. Our results suggest each method has its niche: supervised spatial filtering is practical for event-level prediction while the Riemannian model may enable simple end-to-end learning.
ATAC-seq identifies thousands of extrachromosomal circular DNA in cancers and cell lines
Authors: Kumar Pankaj , Kiran Shashi , Saha Shekhar , Su Zhangli , Paulsen Teressa , Chatrath Ajay , Dutta Anindya
Published: November 2019

Extrachromosomal circular DNAs (eccDNAs) lack centromeres and are not passed equally into daughter cells and thus provide a source of cell-cell heterogeneity in normal and tumor cells. Previously we and other groups purified circular DNA and linearized them by rolling circle amplification for paired end high throughput sequencing to identify eccDNA in cells and tissues. We hypothesized that many eccDNA will have more open chromatin and so will be susceptible to linearization and sequencing by tagmentation. Indeed, we find that ATAC-seq on cell lines and cancers, without any enrichment of circular DNA, identifies thousands of eccDNAs. The identified eccDNAs in cell lines were validated by inverse PCR on DNA that survives exonuclease digestion of linear DNA and by metaphase FISH. We demonstrate that ATAC-seq data generated in Lower Grade Gliomas (LGG) and Glioblastomas (GBM) identify eccDNAs, including one containing the well-known EGFR gene amplicon from chr7. Many of the eccDNAs are identified even before amplification of the locus is detected by genotyping arrays. Thus, standard ATAC-seq is a sensitive method to detect segments of DNA that are present as eccDNA in a subset of the tumor cells, ready to be further amplified under appropriate selection, as during therapy.
Spreading of a mycobacterial cell surface lipid into host epithelial membranes promotes infectivity
Authors: Cambier C.J. , Banik Steven M. , Buonomo Joseph A. , Bertozzi Carolyn R.
Published: November 2019

Several virulence lipids populate the outer cell wall of pathogenic mycobacteria (Jackson, 2014). Phthiocerol dimycocerosate (PDIM), one of the most abundant outer membrane lipids (Anderson, 1929), plays important roles in both defending against host antimicrobial programs (Camacho et al., 2001; Cox et al., 1999; Murry et al., 2009) and in evading these programs altogether (Cambier et al., 2014a; Rousseau et al., 2004). Immediately following infection, mycobacteria rely on PDIM to evade toll-like receptor (TLR)-dependent recruitment of bactericidal monocytes which can clear infection (Cambier et al., 2014b). To circumvent the limitations in using genetics to understand virulence lipid function, we developed a chemical approach to introduce a clickable, semi-synthetic PDIM onto the cell wall of Mycobacterium marinum. Upon infection of zebrafish, we found that PDIM rapidly spreads into host epithelial membranes, and that this spreading inhibits TLR activation. PDIM’s ability to spread into epithelial membranes correlated with its enhanced fluidity afforded by its methyl-branched mycocerosic acids. Additionally, PDIM’s affinity for cholesterol promoted its occupation of epithelial membranes; treatment of zebrafish with statins, cholesterol synthesis inhibitors, decreased spreading and provided protection from infection. This work establishes that interactions between host and pathogen lipids influence mycobacterial infectivity and suggests the use of statins as tuberculosis preventive therapy by inhibiting PDIM spread.
Structure based analysis of protein cluster size for super-resolution microscopy in the nervous system
Authors: Wong Chia-En , Lee Cheng-Che , Tsai Kuen-Jer
Published: November 2019

To overcome the diffraction limit and resolve target structures in greater detail, far-field super-resolution techniques such as stochastic optical reconstruction microscopy (STORM) have been developed, and different STORM algorithms have been developed to deal with the various problems that arise. In particular, the effect of local structure is an important issue. For objects with closely correlated distributions, simple Gaussian-based localization algorithms often used in STORM imaging misinterpret overlapping point spread functions (PSFs) as one and this limits the ability of super-resolution imaging to resolve nanoscale local structures and leading to inaccurate length measurements. In the present study, we proposed a novel, structure-based, super-resolution image analysis method: structure-based analysis (SBA), which combines a structural function and a super-resolution localization algorithm. Using SBA, we estimated the size of fluorescent beads, inclusion proteins, and subtle synaptic structures in both wide-field and STORM images. The results showed that SBA has comparable and often superior performance to commonly used full-width-at-half-maximum parameters. We also demonstrated that SBA provides size estimations that corroborate previously published electron microscopy data.
Kinetic Proofreading and the Limits of Thermodynamic Uncertainty
Authors: Piñeros William D. , Tlusty Tsvi
Published: November 2019

To mitigate errors induced by the cell’s heterogeneous noisy environment, its main information channels and production networks utilize the kinetic proofreading (KPR) mechanism. Here, we examine two extensively-studied KPR circuits, DNA replication by the T7 DNA polymerase and translation by the E. coli ribosome. Using experimental data, we analyze the performance of these two vital systems in light of the fundamental bounds set by the recently-discovered thermodynamic uncertainty relation (TUR), which places an inherent trade-off between the precision of a desirable output and the amount of energy dissipation required. We show that the DNA polymerase operates close to the TUR lower bound, while the ribosome operates ~ 5 times farther from this bound. This difference originates from the enhanced binding discrimination of the polymerase which allows it to operate effectively as a reduced reaction cycle prioritizing correct product formation. We show that approaching this limit also decouples the thermodynamic uncertainty factor from speed and error, thereby relaxing the accuracy-speed trade-off of the system. Altogether, our results show that operating near this reduced cycle limit not only minimizes thermodynamic uncertainty, but also results in global performance enhancement of KPR circuits.
Optimizing the Timing and Composition of Therapeutic Phage Cocktails: A Control-theoretic Approach
Authors: Li Guanlin , Leung Chung Yin , Wardi Yorai , Debarbieux Laurent , Weitz Joshua S.
Published: November 2019

Viruses that infect bacteria, i.e., bacteriophage or ‘phage’, are increasingly considered as treatment options for the control and clearance of bacterial infections, particularly as compassionate use therapy for multi-drug resistant infections. In practice, clinical use of phage often involves the application of multiple therapeutic phage, either together or sequentially. However, the selection and timing of therapeutic phage delivery remains largely ad hoc. In this study, we evaluate principles underlying why careful application of multiple phage (i.e., a ‘cocktail’) might lead to therapeutic success in contrast to the failure of single-strain phage therapy to control an infection. First, we use a nonlinear dynamics model of within-host interactions to show that a combination of fast intra-host phage decay, evolution of phage resistance amongst bacteria, and/or compromised immune response might limit the effectiveness of single-strain phage therapy. To resolve these problems, we combine dynamical modeling of phage, bacteria, and host immune cell populations with control-theoretic principles (via optimal control theory) to devise evolutionarily robust phage cocktails and delivery schedules to control the bacterial populations. Our numerical results suggest that optimal administration of single-strain phage therapy may be sufficient for curative outcomes in immunocompetent patients, but may fail in immunodeficient hosts due to phage resistance. We show that optimized treatment with a two-phage cocktail that includes a counter-resistant phage can restore therapeutic efficacy in immunodeficient hosts.
Entropy-Based Analysis of Vertebrate Sperm Protamine Sequences: Evidence of Dityrosine and Cysteine-Tyrosine Cross-Linking in Sperm Protamines
Authors: Powell Christian D. , Kirchhoff Daniel C. , DeRouchey Jason E. , Moseley Hunter N.B.
Published: November 2019

Background

Spermatogenesis is the process by which germ cells develop into spermatozoa in the testis. Sperm protamines are small, arginine-rich nuclear proteins which replace somatic histones during spermatogenesis, allowing a hypercondensed DNA state that leads to a smaller nucleus and facilitating sperm head formation. In eutherian mammals, the protamine-DNA complex is achieved through a combination of intra- and intermolecular cysteine cross-linking and possibly histidine-cysteine zinc ion binding. Most metatherian sperm protamines lack cysteine but perform the same function. This lack of dicysteine cross-linking has made the mechanism behind metatherian protamines folding unclear.

Results

Protamine sequences from UniProt’s databases were pulled down and sorted into homologous groups. Multiple sequence alignments were then generated and a gap weighted relative entropy score calculated for each position. For the eutherian alignments, the cysteine containing positions were the most highly conserved. For the metatherian alignment, the tyrosine containing positions were the most highly conserved and corresponded to the cysteine positions in the eutherian alignment.

Conclusions

High conservation indicates likely functionally/structurally important residues at these positions in the metatherian protamines and the correspondence with cysteine positions within the eutherian alignment implies a similarity in function. One explanation is that the metatherian protamine structure relies upon dityrosine cross-linking between these highly conserved tyrosines. Also, the human protamine P1 sequence has a tyrosine substitution in a position expecting eutherian dicysteine cross-linking. Similarly, some members of the metatherian Planigales genus contain cysteine substitutions in positions expecting plausible metatherian dityrosine cross-linking. Rare cysteine-tyrosine cross-linking could explain both observations.
An Autonomous Molecular Bioluminescent Reporter (AMBER) for voltage imaging in freely moving animals
Authors: Srinivasan Prasanna , Griffin Nicole M , Joshi Pradeep , Thakur Dhananjay , Nguyen-Le Alex , McCotter Sean , Jain Akshar , Saeidi Mitra , Kulkarni Prajakta , Eisdorfer Jaclyn T. , Rothman Joel , Montell Craig , Theogarajan Luke
Published: November 2019

1.

Genetically encoded reporters have greatly increased our understanding of biology, especially in neuroscience. While fluorescent reporters have been widely used, photostability and phototoxicity have hindered their use in long-term experiments. Bioluminescence overcomes some of these challenges but requires the addition of an exogenous luciferin limiting its use. Using a modular approach we have engineered Autonomous Molecular BioluminEscent Reporter (AMBER), an indicator of membrane potential. Unlike other luciferase-luciferin bioluminescent systems, AMBER encodes the genes to express both the luciferase and luciferin. AMBER is a voltage-gated luciferase coupling the functionalities of theCionavoltage-sensing domain (VSD) and bacterial luciferase, luxAB. When AMBER is co-expressed with the luciferin producing genes it reversibly switches the bioluminescent intensity as a function of membrane potential. Using biophysical and biochemical methods we show that AMBER modulates its enzymatic activity as a function of the membrane potential. AMBER shows several-fold increase in the luminescent (ΔL/L) signal upon switching from the off to on state when the cell is depolarized.In vivoexpression of AMBER inC. elegansallowed detecting pharyngeal pumping action and mechanosensory neural activity from multiple worms simultaneously. AMBER reports neural activity of multiple animals at the same time and can be used in social behavior assays to elucidate the role of membrane potential underlying behavior.

2.

Significance Statement

There have been many exciting advances in the development of genetically encoded voltage indicators to monitor intracelluar voltage changes. Most sensors employ fluorescence, which requires external light, potentially causing photobleaching or overheating. Consequently, there has been interest in developing luminescence reporters. However, they require addition of an exogenous substrate to produce light intracellularly. Here, we engineered a genetically encoded bioluminescent voltage indicator, AMBER, which unlike other bioluminescent activity indicators, does not require addition of an exogenous substrate. AMBER allows a large differential signal, a high signal-to-noise ratio, and causes minimal metabolic demand on cells. We used AMBER to record voltage activity in freely-moving C.elegans, demonstrating that AMBER is a important new tool for monitoring neuronal activity during social behavior.
Biodiversity-based innovations fortify agricultural growth in Asia-Pacific economies
Authors: Wyckhuys K.A.G. , Lu Y.H. , Zhou W.W. , Cock M.J.W. , Furlong M.J.
Published: November 2019

The Green Revolution (GR) is widely credited with alleviating famine, mitigating poverty and driving aggregate economic growth over the past 6 decades. In Asia, GR technologies secured a tripling of rice output, with one-off germplasm improvements providing benefits beyond US$ 4.3 billion/year. Here, we unveil the magnitude and macro-economic relevance of parallel biodiversity-induced productivity growth in non-rice crops from 1918 to 2018. We empirically demonstrate how biological control (BC) defused invasive pest threats in multiple agricultural commodities, ensuring annually-accruing (on-farm) benefits of US$ 22.6 billion/year. Scientifically-guided BC permitted 73-100% yield-loss recovery in critical food, feed and fiber crops including cassava, banana, breadfruit and coconut. As such, BC promoted rural growth and prosperity even in marginal, poorly-endowed, non-rice environments. By placing agro-ecological innovations on equal footing with input-intensive measures, our work provides lessons for future efforts to mitigate invasive species, restore ecological resilience and sustainably raise output of global agri-food systems.
Biological and statistical interpretation of size-at-age, mixed-effects models of growth
Authors: Vincenzi Simone , Jesensek Dusan , Crivelli Alain J
Published: November 2019

The differences in life-history traits and processes between organisms living in the same or different populations contribute to determine their ecological and evolutionary dynamics. Recent advances in statistical and computational methods make it easier to investigate individual and group variation in life-history traits.

We developed mixed-effect model formulations of the popular size-at-age von Bertalanffy and Gompertz growth functions to estimate individual and group variation in body growth, using as a model system four freshwater fish populations living in Slovenian streams, where tagged individuals were sampled for more than 10 years. We used the software Template Model Builder to estimate the parameters of the mixed-effect growth models.

Estimates of asymptotic size from the Gompertz and von Bertalanffy models were not significantly correlated, but their predictions of size-at-age of individuals were strongly correlated (r> 0.99). Tests on data that were not used to estimate model parameters showed that predictions of individual growth trajectories using the random-effects model were accurately predicted (R2> 0.80 for the best models over more than 500 predictions) starting from one single observation of body size early in life. Model results pointed to size ranks that are largely maintained throughout the lifetime of individuals in all populations.
Nova proteins direct synaptic integration of somatostatin interneurons through activity-dependent alternative splicing
Authors: Ibrahim Leena A. , Wamsley Brie , Al-Ghamdi Norah , Yusuf Nusrath , Sevier Elaine , Hairston Ariel , Sherer Mia , Jaglin Xavier Hubert , Xu Qing , Guo Lihua , Khodadadi-Jamayran Alireza , Favuzzi Emilia , Yuan Yuan , Dimidschstein Jordane , Darnell Robert , Fishell Gord
Published: November 2019

Somatostatin interneurons are the earliest born population of cortical inhibitory cells. They are crucial to support normal brain development and function; however, the mechanisms underlying their integration into nascent cortical circuitry are not well understood. In this study, we begin by demonstrating that the maturation of somatostatin interneurons is activity dependent. We then investigated the relationship between activity, alternative splicing and synapse formation within this population. Specifically, we discovered that the Nova family of RNA-binding proteins are activity-dependent and are essential for the maturation of somatostatin interneurons, as well as their afferent and efferent connectivity. Within this population, Nova2 preferentially mediates the alternative splicing of genes required for axonal formation and synaptic function independently from its effect on gene expression. Hence, our work demonstrates that the Nova family of proteins through alternative splicing are centrally involved in coupling developmental neuronal activity to cortical circuit formation.
Metabolic switching ofMycobacterium tuberculosisduring hypoxia is controlled by the virulence regulator PhoP
Authors: Singh Prabhat Ranjan , Anil Kumar Vijjamarri , Sarkar Dibyendu
Published: November 2019

Mycobacterium tuberculosis(Mtb) retains the unique ability to establish an asymptomatic latent infection. A fundamental question in mycobacterial physiology is to understand the mechanisms involved in hypoxic stress, a critical player in persistence. Here, we show that the virulence regulator PhoP responds to hypoxia, the dormancy signal and effectively integrates hypoxia with nitrogen metabolism. We also provide evidence to demonstrate that both under nitrogen limiting conditions and during hypoxia,phoPlocus controls key genes involved in nitrogen metabolism. Consistently, under hypoxiaΔphoPshows growth attenuation even with surplus nitrogen, the alternate electron acceptor, and complementation of the mutant restores bacterial growth. Together, our observations provide new biological insights into the role of PhoP in integrating nitrogen metabolism with hypoxia by the assistance of the hypoxia regulator DosR. The results have significant implications on the mechanism of intracellular survival and growth of the tubercle bacilli under a hypoxic environment within the phagosome.

Importance

Mtb retains the unique ability to establish an asymptomatic latent infection. To understand the mechanisms involved in hypoxic stress which plays a critical role in persistence, we show that the virulence regulator PhoP responds to hypoxia, the dormancy signal. In keeping with this,phoPwas shown to play a major role in Mtb growth under hypoxia even in presence of surplus nitrogen, the alternate electron acceptor. Our results showing regulation of hypoxia-responsive genes provide new biological insights into role of the virulence regulator in metabolic switching by sensing hypoxia and integrating nitrogen metabolism with hypoxia by the assistance of the hypoxia regulator DosR.
Pseudorabies Virus Infection Accelerates Degradation of the Kinesin-3 Motor KIF1A
Authors: Huang Hao , Koyuncu Orkide O. , Enquist Lynn W.
Published: November 2019

Alphaherpesviruses, including pseudorabies virus (PRV), are neuroinvasive pathogens that establish life-long latency in peripheral ganglia following the initial infection at mucosal surfaces. The establishment of latent infection and the subsequent reactivations during which newly-assembled virions are sorted into and transported anterogradely inside axons to the initial mucosal site of infection, rely on axonal bidirectional transport mediated by microtubule-based motors. Previous studies using cultured peripheral nervous system (PNS) neurons have demonstrated that KIF1A, a kinesin-3 motor, mediates the efficient axonal sorting and transport of newly-assembled PRV virions. In this study, we report that KIF1A, unlike other axonal kinesins, is an intrinsically unstable protein prone to proteasomal degradation. Interestingly, PRV infection of neuronal cells leads not only to a non-specific depletion of KIF1A mRNA, but also to an accelerated proteasomal degradation of KIF1A proteins, leading to a near depletion of KIF1A protein late in infection. Using a series of PRV mutants deficient in axonal sorting and anterograde spread, we identified the PRV US9/gE/gI protein complex as a viral factor facilitating the proteasomal degradation of KIF1A proteins. Moreover, by using compartmented neuronal cultures that fluidically and physically separate axons from cell bodies, we found that the proteasomal degradation of KIF1A occurs in axons during infection. We propose that PRV anterograde sorting complex, gE/gI/US9, recruits KIF1A to viral transport vesicles for axonal sorting and transport, and eventually accelerates the proteasomal degradation of KIF1A in axons.

Importance

Pseudorabies virus (PRV) is an alphaherpesvirus related to human pathogens herpes simplex virus −1, −2 and varicella zoster virus. Alphaherpesviruses are neuroinvasive pathogens that establish life-long latent infections in the host peripheral nervous system (PNS). Following reactivation from latency, infection spreads from the PNS back via axons to the peripheral mucosal tissues, a process mediated by kinesin motors. Here, we unveil and characterize the underlying mechanisms for a PRV-induced, accelerated degradation of KIF1A, a kinesin-3 motor promoting the sorting and transport of PRV virions in axons. We show that PRV infection disrupts the synthesis of KIF1A, and simultaneously promotes the degradation of intrinsically unstable KIF1A proteins by proteasomes in axons. Our work implies that the timing of motor reduction after reactivation would be critical because progeny particles would have a limited time window for sorting into and transport in axons for further host-to-host spread.
CosR is a repressor of compatible solute biosynthesis and transporter systems
Authors: Gregory Gwendolyn J. , Morreale Daniel P. , Boyd E. Fidelma
Published: November 2019

Bacteria accumulate small, organic compounds, called compatible solutes, via uptake from the environment or biosynthesis from available precursors to maintain the turgor pressure of the cell in response to osmotic stress.Vibrio parahaemolyticushas biosynthesis pathways for the compatible solutes ectoine (ectABCasp_ect)and glycine betaine (betIBAproXWV), four betaine-carnitine-choline transporters (bcct1-bcct4) and a second ProU transporter (proVWX).Most of these systems are induced in high salt. CosR, a MarR-type regulator, which is divergently transcribed frombcct3, was previously shown to be a direct repressor ofectABCasp_ectinVibriospecies. In this study, we investigated the role of CosR in glycine betaine biosynthesis and compatible solute transporter gene regulation. Expression analyses demonstrated thatbetIBAproXWV,bcct1,bcct3, andproVWXare repressed in low salinity. Examination of an in-framecosRdeletion mutant shows induced expression of these systems in the mutant at low salinity compared to wild-type. DNA binding assays demonstrate that purified CosR binds directly to the regulatory region of each system. InEscherichia coliGFP reporter assays, we demonstrate that CosR directly represses transcription ofbetIBAproXWV,bcct3, andproVWX. Similar toV. harveyi, we showbetIBAproXWVis positively regulated by the LuxR homolog OpaR. Bioinformatics analysis demonstrates that CosR is widespread within the genus, present in over 50 species. In several species, thecosRhomolog was clustered with thebetIBAproXWVoperon, which again suggests the importance of this regulator in glycine betaine biosynthesis. Incidentally, in fourAliivibriospecies that contain ectoine biosynthesis genes, we identified another MarR-type regulator,ectR, clustered with these genes, which suggests the presence of a novel ectoine regulator. Homologs of EctR in this genomic context were present inA. fischeri, A. finisterrensis, A. sifiaeandA. wodanis.

Importance

Vibrio parahaemolyticuscan accumulate compatible solutes via biosynthesis and transport, which allow the cell to survive in high salinity conditions. There is little need for compatible solutes under low salinity conditions, and biosynthesis and transporter systems are repressed. However, the mechanism of this repression is not fully elucidated. CosR plays a major role in the repression of multiple compatible solute systems inV. parahaemolyticusas a direct negative regulator of ectoine and glycine betaine biosynthesis systems and four transporters. Homology analysis suggests that CosR functions in this manner in many otherVibriospecies. InAliivibriospecies, we identified a new MarR family regulator EctR that clusters with the ectoine biosynthesis genes.
Spectrum of protein localization in proteomes captures evolutionary relation between species
Authors: Marot-Lassauzaie Valérie , Goldberg Tatyana , Rost Burkhard
Published: November 2019

The native subcellular localization or cellular compartment of a protein is the one in which it acts most often; it is one aspect of protein function. Do ten eukaryotic model organisms differ in theirlocation spectrum, i.e. the fraction of its proteome in each of its seven major compartments? As experimental annotations of locations remain biased and incomplete, we need prediction methods to answer this question. To gauge the bias of prediction methods, we merged all available experimental annotations for the human proteome. In doing so, we found important values in both Swiss-Prot and the Human Protein Atlas (HPA). After systematic bias corrections, the complete but faulty prediction methods appeared to be more appropriate to compare location spectra between species than the incomplete more accurate experimental data. This work compared the location spectra for ten eukaryotes:Homo sapiens, Gorilla gorilla, Pan troglodytes, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Anopheles gambiae, Caenorhabitis elegans, Saccharomyces cerevisiaeandSchizosaccharomyces pombe. Overall, the predicted location spectra were similar. However, the detailed differences were significant enough to plot trees and 2D (PCA) maps relating the ten organisms using a simple Euclidean distance in seven states, corresponding to the seven studied localization classes. The relations based on the simple predicted location spectra captured aspects of cross-species comparisons usually revealed only by much more detailed evolutionary comparisons.
Biophysical characterization of DNA origami nanostructures reveals inaccessibility to intercalation binding sites
Authors: Miller Helen L. , Contera Sonia , Wollman Adam J.M. , Hirst Adam , Dunn Katherine E. , Schröter Sandra , O’Connell Deborah , Leake Mark C.
Published: November 2019

Intercalation of drug molecules into synthetic DNA nanostructures formed through self-assembled origami has been postulated as a valuable future method for targeted drug delivery. This is due to the excellent biocompatibility of synthetic DNA nanostructures, and high potential for flexible programmability including facile drug release into or near to target cells. Such favourable properties may enable high initial loading and efficient release for a predictable number of drug molecules per nanostructure carrier, important for efficient delivery of safe and effective drug doses to minimise non-specific release away from target cells. However, basic questions remain as to how intercalation-mediated loading depends on the DNA carrier structure. Here we use the interaction of dyes YOYO-1 and acridine orange with a tightly-packed 2D DNA origami tile as a simple model system to investigate intercalation-mediated loading. We employed multiple biophysical techniques including single-molecule fluorescence microscopy, atomic force microscopy, gel electrophoresis and controllable damage using low temperature plasma on synthetic DNA origami samples. Our results indicate that not all potential DNA binding sites are accessible for dye intercalation, which has implications for future DNA nanostructures designed for targeted drug delivery.
Optogeneticlacoperon to control chemical and protein production inEscherichia coliwith light
Authors: Lalwani Makoto A. , Ip Samantha S. , Carrasco-Lopez Cesar , Zhao Evan M. , Kawabe Hinako , Avalos José L.
Published: November 2019

Control of thelacoperon with IPTG has been used for decades to regulate gene expression inE. colifor countless applications, including metabolic engineering and recombinant protein production. However, optogenetics offers unique capabilities such as easy tunability, reversibility, dynamic induction strength, and spatial control that are difficult to obtain with chemical inducers. We developed an optogeneticlacoperon in a series of circuits we call OptoLAC. With these circuits, we control gene expression from various IPTG-inducible promoters using only blue light. Applying them to metabolic engineering improves mevalonate and isobutanol production by 24% and 27% respectively, compared to IPTG induction, in light-controlled fermentations scalable to at least 2L bioreactors. Furthermore, OptoLAC circuits enable light control of recombinant protein production, reaching yields comparable to IPTG induction, but with enhanced tunability of expression and spatial control. OptoLAC circuits are potentially useful to confer light controls over other cell functions originally engineered to be IPTG-inducible.