bluuebunny/crossref_metadata_2025 huggingface dataset:
Freezing and water availability structure the evolutionary diversity of trees across the Americas
Authors: Segovia R. A. , Pennington R. T. , Baker T. R. , de Souza F. Coelho , Neves D. M. , Davis C. C. , Armesto J. J. , Olivera-Filho A. T. , Dexter K. G.
Published: August 2019

The historical course of evolutionary diversification shapes the current distribution of biodiversity, but the main forces constraining diversification are unclear. We unveil the evolutionary structure of tree species diversity across the Americas to assess whether an inability to move (dispersal limitation) or to evolve (niche conservatism) is the predominant constraint in plant diversification and biogeography. We find a fundamental divide in tree lineage composition between tropical and extratropical environments, defined by the absence versus presence of freezing temperatures. Within the Neotropics, we uncover a further evolutionary split between moist and dry forests. Our results demonstrate that American tree lineages, though broadly distributed geographically, tend to retain their ancestral environmental relationships and that phylogenetic niche conservatism is the primary force structuring the distribution of tree biodiversity.
A low-cost, open-source evolutionary bioreactor and its educational use
Authors: Gopalakrishnan Vishhvaan , Crozier Dena , Card Kyle J. , Chick Lacy D. , Krishnan Nikhil P. , McClure Erin , Pelesko Julia , Williamson Drew F.K. , Nichol Daniel , Mandal Soumyajit , Bonomo Robert A. , Scott Jacob G.
Published: August 2019

The morbidostat automatically adjusts antibiotic concentration as a bacterial population evolves resistance. Although this device has advanced our understanding of the evolutionary and ecological processes that drive antibiotic resistance, no low-cost and open-source systems are available for educators. Here, we present the EVolutionary biorEactor (EVE), an accessible alternative to other morbidostats for use in low-resource classrooms that requires minimal engineering and programming experience. We first compare our system to others, emphasizing how it differs in design and cost. We then describe how we validated the EVE by evolving replicate Escherichia coli populations under chloramphenicol challenge and comparing our results to those in the published literature. Lastly, we detail how high school students used the EVE to learn about bacterial growth and antibiotic resistance.
Genomic profiling of PML bodies reveals transcriptional regulation by PML bodies through the DNMT3A exclusion
Authors: Kurihara Misuzu , Kato Kagayaki , Sanbo Chiaki , Shigenobu Shuji , Ohkawa Yasuyuki , Fuchigami Takeshi , Miyanari Yusuke
Published: August 2019

The promyelocytic leukaemia (PML) body is a phase-separated nuclear structure involved in various biological processes, including senescence, and tumour suppression1. PML bodies consist of various proteins, including PML proteins and several chromatin regulators2,3and physically associate with chromatin4,5, implying their crucial roles in particular genome functions. However, their roles in transcriptional regulation are largely unknown. Here, we developed APEX-mediated chromatin labelling and purification (ALaP), to identify the genomic regions associated with PML bodies. We find that PML bodies associate with active regulatory regions across the genome and prominently with a ∼300 kb of the short arm of the Y chromosome (YS300) in mouse embryonic stem cells (mESCs). The association with YS300 is essential for the transcriptional activities of neighbouring Y-linked cluster genes. Mechanistically, we show that PML bodies play a novel role in 3D nuclear organization by providing specific nuclear spaces that the de novo DNA methyltransferase DNMT3A cannot access, which results in the robust maintenance of the hypo-methylated states at the Y-linked gene promoters. Our study underscores a new mechanism for gene regulation in the 3D-nuclear space and provides insights into the functional properties of nuclear structures for genome functions.
Patterns of linkage disequilibrium reveal genome architecture in chum salmon
Authors: McKinney Garrett , McPhee Megan V. , Pascal Carita , Seeb James E. , Seeb Lisa W.
Published: August 2019

Many studies exclude loci exhibiting linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the signal of the sex-determining region was only obvious after restricting genetic analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. The results of this study highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of ignoring or excluding loci exhibiting LD.
Psychotic-like experiences, polygenic risk scores for schizophrenia and structural properties of the salience, default mode and central-executive networks in healthy participants from UK Biobank
Authors: Alloza C. , Blesa-Cábez M. , Bastin M.E. , Madole J.W. , Buchanan C.R. , Janssen J. , Gibson J. , Deary I.J. , Tucker-Drob E.M. , Whalley H.C. , Arango C. , McIntosh A.M , Cox S.R , Lawrie S.M
Published: August 2019

Schizophrenia is a highly heritable disorder with considerable phenotypic heterogeneity. Hallmark psychotic symptoms can be considered as existing on a continuum from non-clinical to clinical populations. Assessing genetic risk and psychotic-like experiences (PLEs) in non-clinical populations and their associated neurobiological underpinnings can offer valuable insights into symptom-associated brain mechanisms without the potential confounds of the effects of schizophrenia and its treatment. We leveraged a large population-based cohort (UKBiobank) including information on PLEs, polygenic risk scores for schizophrenia (PRSSZ) and multi-modal brain imaging in combination with network neuroscience. Morphometric (cortical thickness, volume) and water diffusion (fractional anisotropy) properties of the regions and pathways belonging to the salience, default-mode and central-executive networks were computed. We hypothesized that these anatomical concomitants of functional dysconnectivity would be negatively associated with PRSSZand PLEs. PRSSZwas significantly associated with a latent measure of cortical thickness across the salience network (r = −0.069,p= 0.010) and PLEs showed a number of significant associations with properties of the salience and default mode networks (involving the insular cortex, supramarginal gyrus and pars orbitalis,pFDR< 0.050); with the cortical thickness of the insula largely mediating the relationship between PRSSZand auditory hallucinations. These results are consistent with the hypothesis that higher genetic liability for schizophrenia is related to subtle disruptions in brain structure and predisposes to PLEs even among healthy participants. In addition, our study suggests that networks engaged during auditory hallucinations show structural associations with PLEs in the general population.
Targeting EZH2 Increases Therapeutic Efficacy of Check-Point Blockade in Models of Prostate Cancer
Authors: Sheahan Anjali V. , Morel Katherine L. , Burkhart Deborah L. , Baca Sylvan C. , Labbé David P. , Roehle Kevin , Heckler Max , Calagua Carla , Ye Huihui , Galbo Phillip , Panja Sukanya , Mitrofanova Antonina , Hamid Anis A. , Kibel Adam S. , Choudhury Atish D. , Pomerantz Mark M. , Freedman Matthew L. , Sweeney Christopher J. , Dougan Stephanie K. , Sowalsky Adam G. , Loda Massimo , Olson Brian M. , Ellis Leigh
Published: August 2019

Prostate cancers are considered immunologically ‘cold’ tumors given the very few patients who respond to checkpoint inhibitor therapy (CPI). Recently, enrichment of interferon (IFN) response genes predicts a favorable response to CPI across various disease sites. The enhancer of zeste homolog-2 (EZH2) is over-expressed in prostate cancer and is known to negatively regulate IFN response genes. Here, we demonstrate that inhibition of EZH2 catalytic activity in prostate cancer models derepresses expression of double-strand RNA (dsRNA), associated with upregulation of genes involved in antigen presentation, Th-1 chemokine signaling, and interferon (IFN) response, including PD-L1. Similarly, application of a novel EZH2 derived gene signature to human prostate sample analysis indicated an inverse correlation between tumor EZH2 activity/expression with T-cell inflamed and IFN gene signatures and PD-L1 expression. EZH2 inhibition combined with PD-1 CPI significantly enhances antitumor response that is dependent on up-regulation of tumor PD-L1 expression. Further, combination therapy significantly increases intratumoral trafficking of activated CD8+ T-cells and M1 tumor associated macrophages (TAMs) with concurrent loss of M2 TAMs. Our study identifies EZH2 as a potent inhibitor of antitumor immunity and responsiveness to CPI. This data suggests EZH2 inhibition as a novel therapeutic direction to enhance prostate cancer response to PD-1 CPI.
Vitamins D3 and D2 have marked but different global effects on gene expression in a rat oligodendrocyte precursor cell line
Authors: Mengozzi Manuela , Hesketh Andrew , Bucca Giselda , Ghezzi Pietro , Smith Colin P.
Published: August 2019

Vitamin D deficiency increases the risk of developing multiple sclerosis (MS) but there is uncertainty about what dose and form of vitamin D could improve the clinical course of MS. The mechanisms underlying the effects of vitamin D in MS are not clear. Vitamin D3 increases the rate of differentiation of primary oligodendrocyte precursor cells (OPCs), suggesting that it might help remyelination in addition to modulating the immune response. Here we analyzed the transcriptome of differentiating rat CG4 OPCs treated with vitamin D2 or with D3 at 24 h and 72 h following onset of differentiation. Differentiation alone changed the expression of about 10% of the genes at 72 h compared to 24 h. Vitamin D2 and D3 exerted different effects on gene expression, with D3 influencing 1,272 genes and D2 574 at 24 h. The expression of the vast majority of these genes was either not changed in differentiating cells not exposed to vitamin D or followed the same trajectory as the latter. D3-repressed genes were enriched for gene ontology categories including transcription factors and the Notch pathway, while D3-induced genes were enriched for the Ras pathway. These findings should help to identify mechanisms mediating D3 action in MS.
Multivoxel codes for representing and integrating acoustic features in human cortex
Authors: Sohoglu Ediz , Kumar Sukhbinder , Chait Maria , Griffiths Timothy D.
Published: August 2019

Using fMRI and multivariate pattern analysis, we determined whether acoustic features are represented by independent or integrated neural codes in human cortex. Male and female listeners heard band-pass noise varying simultaneously in spectral (frequency) and temporal (amplitude-modulation [AM] rate) features. In the superior temporal plane, changes in multivoxel activity due to frequency were largely invariant with respect to AM rate (and vice versa), consistent with an independent representation. In contrast, in posterior parietal cortex, neural representation was exclusively integrated and tuned to specific conjunctions of frequency and AM features. Direct between-region comparisons show that whereas independent coding of frequency and AM weakened with increasing levels of the hierarchy, integrated coding strengthened at the transition between non-core and parietal cortex. Our findings support the notion that primary auditory cortex can represent component acoustic features in an independent fashion and suggest a role for parietal cortex in feature integration and the structuring of acoustic input.

Significance statement

A major goal for neuroscience is discovering the sensory features to which the brain is tuned and how those features are integrated into cohesive perception. We used whole-brain human fMRI and a statistical modeling approach to quantify the extent to which sound features are represented separately or in an integrated fashion in cortical activity patterns. We show that frequency and AM rate, two acoustic features that are fundamental to characterizing biological important sounds such as speech, are represented separately in primary auditory cortex but in an integrated fashion in parietal cortex. These findings suggest that representations in primary auditory cortex can be simpler than previously thought and also implicate a role for parietal cortex in integrating features for coherent perception.
Glucagon-like peptide-1 receptor agonist, exendin-4, reduces reinstatement of heroin seeking behavior in rats
Authors: Douton Joaquin E. , Augusto Corinne , Stultzfus Brooke A , Carkaci-Salli Nurgul , Vrana Kent E. , Grigson Patricia S.
Published: August 2019

Background

Studies have shown that ‘satiety’ agents such as exendin-4 (a glucagon-like peptide-1 analog) reduce responding for addictive drugs (e.g., cocaine, nicotine, alcohol). In this study we tested the effect of exendin-4 on cue-induced and drug-induced reinstatement of heroin seeking behavior in rats.

Methods

This study consisted of three phases: In Phase 1, 55 male Sprague-Dawley rats had 15 daily pairings of saccharin with heroin self-administration. In Phase 2, rats experienced a 16-day home cage abstinence period and daily treatment with vehicle or exendin-4. On day 17, an extinction/reinstatement test was performed to assess drug seeking. In Phase 3, rats experienced 9 days of extinction followed by a reinstatement only test. Finally, expression of mRNA for various receptors in the nucleus accumbens shell (NAcS) was measured using RTqPCR.

Results

In Phase 1, rats that avoided intake of the heroin-paired saccharin cue exhibited shorter latency to obtain the first infusion. In Phase 2, treatment with exendin-4 decreased cue-induced, but not drug-induced heroin seeking. In Phase 3, saccharin avoiders previously treated with exendin-4 increased acceptance of saccharin, and 1-hour pretreatment with Exendin-4 abolished drug-induced heroin seeking. Finally, exendin-4 treatment increased expression of mRNA for the Orexin 1 receptor (OX1) in the NAcS, but did not affect expression of dopamine D2 receptors, GLP-1 receptors, or leptin receptors in this same structure.

Conclusion

Exendin-4 reduced cue- and drug-induced heroin seeking and increased acceptance of the drug-associated saccharin cue. These changes in behavior were accompanied by an increase in the expression of the OX1 receptor in the NAcS.
Multiplexed, bioorthogonal labeling of multicomponent, biomolecular complexes using genomically encoded, non-canonical amino acids
Authors: Desai Bijoy J. , Gonzalez Ruben L.
Published: August 2019

Stunning advances in the structural biology of multicomponent biomolecular complexes (MBCs) have ushered in an era of intense, structure-guided mechanistic and functional studies of these complexes. Nonetheless, existing methods to site-specifically conjugate MBCs with biochemical and biophysical labels are notoriously impracticable and/or significantly perturb MBC assembly and function. To overcome these limitations, we have developed a general, multiplexed method in which we genomically encode non-canonical amino acids (ncAAs) into multiple, structure-informed, individual sites within a target MBC; select for ncAA-containing MBC variants that assemble and function like the wildtype MBC; and site-specifically conjugate biochemical or biophysical labels to these ncAAs. As a proof-of-principle, we have used this method to generate unique single-molecule fluorescence resonance energy transfer (smFRET) signals reporting on ribosome structural dynamics that have thus far remained inaccessible to smFRET studies of translation.
Non-Homology-Based Prediction of Gene Functions
Authors: Dai Xiuru , Xu Zheng , Liang Zhikai , Tu Xiaoyu , Zhong Silin , Schnable James C. , Li Pinghua
Published: August 2019

Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging. Genes descended from a common ancestral sequence are likely to have common functions. As a result homology is widely used for gene function prediction. This means functional annotation errors also propagate from one species to another. Several approaches based on machine learning classification algorithms were evaluated for their ability to accurately predict gene function from non-homology gene features. Among the eight supervised classification algorithms evaluated, random forest-based prediction consistently provided the most accurate gene function prediction. Non-homology-based functional annotation provides complementary strengths to homology-based annotation, with higher average performance in Biological Process GO terms, the domain where homology-based functional annotation performs the worst, and weaker performance in Molecular Function GO terms, the domain where the accuracy of homology-based functional annotation is highest. Non-homology-based functional annotation based on machine learning may ultimately prove useful both as a method to assign predicted functions to orphan genes which lack functionally characterized homologs, and to identify and correct functional annotation errors which were propagated through homology-based functional annotations.
U1 snRNP regulates cancer cell migration and invasion
Authors: Oh Jung-Min , Venters Christopher C. , Di Chao , Pinto Anna Maria , Wan Lili , Younis Ihab , Cai Zhiqiang , Arai Chie , So Byung Ran , Dreyfuss Gideon
Published: August 2019

Stimulated cells and cancer cells have widespread shortening of mRNA 3’-utranslated regions (3’UTRs) and switches to shorter mRNA isoforms due to usage of more proximal polyadenylation signals (PASs) in the last exon and in introns. U1 snRNA (U1), vertebrates’ most abundant non-coding (spliceosomal) small nuclear RNA, silences proximal PASs and its inhibition with antisense morpholino oligonucleotides (U1 AMO) triggers widespread mRNA shortening. Here we show that U1 AMO also modulates cancer cells’ phenotype, dose-dependently increasing migration and invasion in vitro by up to 500%, whereas U1 over-expression has the opposite effect. In addition to 3’UTR length, numerous transcriptome changes that could contribute to this phenotype are observed, including alternative splicing, and mRNA expression levels of proto-oncogenes and tumor suppressors. These findings reveal an unexpected link between U1 regulation and oncogenic and activated cell states, and suggest U1 as a potential target for their modulation.
Structure-function analysis reveals a DNA polymerization-independent role for mitochondrial DNA polymerase IC in African trypanosomes
Authors: Miller Jonathan C , Delzell Stephanie B , Concepción-Acevedo Jeniffer , Boucher Michael J , Klingbeil Michele M
Published: August 2019

The mitochondrial DNA ofTrypanosoma bruceiand related parasites is a catenated network containing thousands of minicircles and tens of maxicircles called kinetoplast DNA (kDNA). Replication of the single nucleoid requires at least three DNA polymerases (POLIB, POLIC, and POLID) each having discrete localization near the kDNA during S phase. POLIB and POLID have roles in minicircle replication while the specific role of POLIC in kDNA maintenance is less clear. Here, we use an RNAi-complementation system to dissect the functions of the distinct POLIC domains: the conserved family A DNA polymerase domain (POLA) and the uncharacterized N-terminal region (UCR). While RNAi complementation with wild-type POLIC restored kDNA content and cell cycle localization, active site point mutations in the POLA domain impaired minicircle replication similarly to POLIB and POLID depletions. Complementation with the POLA domain alone abolished POLIC foci formation and partially rescued the RNAi phenotype. Furthermore, we provide evidence of a crucial role for the UCR in cell cycle localization and segregation of kDNA daughter networks. This is the first report of a DNA polymerase that impacts DNA segregation.

Summary statement

Mitochondrial DNA segregation in African trypanosomes is supported by a dual-functioning DNA polymerase.
Principles for engineering microbial composition and ecosystem functioning
Authors: Albright Michaeline B.N. , Sevanto Sanna , Gallegos-Graves La Verne , Dunbar John
Published: August 2019

Microbial probiotics are designed to improve functions in diverse ecosystems, yet probiotics often fail to have the desired beneficial effects. The introduction of probiotics to an environment with a preexisting microbiome is analogous to an invasion event, but is rarely considered in this light. Here, we tested the relative importance of propagule pressure (inoculation dose and frequency) compared to biotic interactions (composition of introduced and resident communities) in driving microbial composition and functional outcomes following microbial community invasions in experimental microcosms. Ecosystem functioning was assessed through measurements of CO2production and DOC (dissolved organic carbon) accumulation, an activity and an environmental modification metric, respectively. Further, to test the dependence of propagule pressures versus biotic interactions was dependent on environmental context, experiments were performed on two different substrates, R2A agar and plant litter. In both environments, we found that biotic interactions were more important than propagule pressure in driving microbial composition. Moreover, bacteria were more successful invaders than fungi. While successful invasion is a first step, ultimately the success of microbial invasions in microbiome engineering applications is measured by the impact on ecosystem functioning. As with shaping the microbiome composition, biotic interactions were key to functional outcomes, but the magnitude of the functional impact varied by environment. Identifying general principles that determine the community composition and functioning following microbial invasions is key to efficient community engineering.

Significance

With increasing frequency humans are introducing new microbes into pre-existing microbiomes to alter functioning. Examples include, modification of microflora in human guts for better health, and soil for food security and/or climate management. Probiotic applications are often approached as trial-and-error endeavors and have mixed outcomes. We propose that increased success in microbiome engineering may be achieved by better understanding of microbial invasions. We conducted a microbial community invasion experiment, to test the relative importance of propagule pressure and biotic interactions in driving microbial community composition and ecosystem functioning in microcosms. We found that biotic interactions were more important than propagule pressure in determining the impact of microbial invasions. Furthermore, the principles for community engineering vary among organismal groups (bacteria versus fungi).
STAT3 and GR cooperate to drive basal-like triple negative breast cancer gene expression and proliferation
Authors: Conway Megan E. , McDaniel Joy M. , Graham James M. , Guillen Katrin P. , Oliver Patsy G. , Parker Stephanie L. , Yue Peibin , Turkson James , Buchsbaum Donald J. , Welm Bryan E. , Myers Richard M. , Varley Katherine E.
Published: August 2019

Breast cancers can be divided into subtypes with different prognoses and treatment responses based on global gene expression differences. Luminal breast cancer gene expression and proliferation are driven by the transcription factors Estrogen Receptor α (ER), FOXA1 and GATA3. Targeting ER is the most effective therapy for treating luminal breast cancer because ER is the master regulator of the luminal gene expression program. In contrast, it is unclear which transcription factors are responsible for driving the gene expression signature that defines basal-like triple negative breast cancer, and there are no targeted therapies approved to treat this aggressive subtype of the disease. This study utilized integrated analysis of DNA methylation, chromatin accessibility, transcription factor binding, and gene expression in large collections of breast cancer cell lines and patient tumors to identify transcription factors responsible for the basal-like gene expression program. The results of this study indicate that glucocorticoid receptor (GR) and signal transducer and activator of transcription 3 (STAT3) bind to the same genomic regulatory regions that are specifically open and unmethylated in basal-like breast cancer. These transcription factors cooperate to regulate expression of hundreds of genes in the basal-like gene expression signature and these downstream genes are associated with poor prognosis in patients. Furthermore, combination treatment with small molecule drugs that inhibit both transcription factors leads to synergistic decreases in cell proliferation in cell lines and patient-derived organoid models. This study demonstrates that GR and STAT3 cooperate to regulate the basal-like breast cancer gene expression program and provides the basis for improved therapy for basal-like triple negative breast cancer through rational combination of STAT3 and GR inhibitors.
Endosomal explosion induced by hypertonicity
Authors: Wang Shupeng , Wu Song
Published: August 2019

Transferring DNA into cells to regulate cell function is a novel research field in recent decades.
Chitosan is a gene vector with the properties of low-cost and safe, but high efficient delivery has remained challenging. We developed a strategy termed EEIH for endosomal explosion induced by hypertonicity, in which short-time exposure to hypertonic solutions triggers endosomes destabilization like explosions. EEIH can force chitosan/DNA polyplexes to break through the endosomal barriers to approach the nucleus, which results in boosting the transfection efficiency of chitosan in several cell lines. We demonstrate that EEIH is a significant and practical strategy in chitosan transfection system without sophisticated modification of chitosan.
Rapid Sensorimotor Reinforcement in the Olfactory Striatum
Authors: Millman Daniel J. , Murthy Venkatesh N.
Published: August 2019

Rodents can successfully learn multiple, novel stimulus-response associations after only a few repetitions when the contingencies predict reward. The circuits modified during such reinforcement learning to support decision making are not known, but the olfactory tubercle (OT) and posterior piriform cortex (pPC) are candidates for decoding reward category from olfactory sensory input and relaying this information to cognitive and motor areas. Here, we show that an explicit representation for reward category emerges in the OT within minutes of learning a novel odor-reward association, whereas the pPC lacks an explicit representation even after weeks of overtraining. The explicit reward category representation in OT is visible in the first sniff (50-100ms) of an odor on each trial, and precedes the motor action. Together, these results suggest that coding of stimulus information required for reward prediction does not occur within olfactory cortex, but rather in circuits involving the olfactory striatum.
Tradeoffs in optimal control capture patterns of human sensorimotor control and adaptation
Authors: Cluff Tyler , Crevecoeur Frederic , Scott Stephen H.
Published: August 2019

Modern control theory highlights strategies that consider a range of factors, such as errors caused by environmental disturbances or inaccurate estimates of body or environmental dynamics. Here we reveal similar diversity in how humans naturally adapt and control their arm movements. We divided participants into groups based on how well they adapted to interaction loads during a single session of reaching movements. This classification revealed differences in how participants controlled their movements and responded to mechanical perturbations. Interestingly, variation in behaviour across good and partial adapters resembled simulations from stochastic and robust optimal feedback control, respectively, where the latter minimizes the effect of disturbances, including those introduced by inaccurate internal models of movement dynamics. In a second experiment, we varied the interaction loads over short time periods making it difficult to adapt. Under these conditions, participants who otherwise adapted well altered their behaviour and more closely resembled those using a robust control strategy. Taken together, the results suggest the diversity of how humans control and adapt their arm movements may reflect the accuracy of (or confidence in) their internal models. Our findings may open novel perspectives for interpreting motor behaviour in uncertain environments, or when neurologic dysfunction compromises motor adaptation.
Characterization of neurogenic niches in the telencephalon of juvenile and adult sharks
Authors: Docampo-Seara A , Pereira-Guldrís S , Sánchez-Farías N , Mazan S , Rodríguez MA , Candal E
Published: August 2019

Neurogenesis is a multistep process by which progenitor cells become terminally differentiated neurons. Adult neurogenesis has gathered increasing interest with the aim of developing new cell-based treatments for neurodegenerative diseases in humans. Active sites of adult neurogenesis exist from fish to mammals, although in the adult mammalian brain the number and extension of neurogenic areas is considerably reduced in comparison to non-mammalian vertebrates, and they become mostly reduced to the telencephalon. Much of our understanding in this field is based in studies on mammals and zebrafish, a modern bony fish. The use of the cartilaginous fish Scyliorhinus canicula (representative of basal gnathostomes) as a model expands the comparative framework to a species that shows highly neurogenic activity in the adult brain. In this work, we studied the proliferation pattern in the telencephalon of juvenile and adult specimens of S. canicula by using antibodies against the proliferation marker PCNA. We have characterized proliferating niches by using stem cell markers (Sox2), glial markers (GFAP, BLBP and GS), intermediate progenitor cell markers (Dlx2 and Tbr2) and markers for migrating neuroblasts (DCX). Based in the expression pattern of these markers, we demonstrate the existence of different cell subtypes within the PCNA immunoreactive zones including non-glial stem cells, glial progenitors, intermediate progenitor-like cells and migratory neuroblasts, which were widely distributed in the ventricular zone of the pallium, suggesting that the main progenitor types that constitute the neurogenic niche in mammals are already present in cartilaginous fishes.
Chagas disease serological test performance in United States blood donor specimens
Authors: Whitman Jeffrey D. , Bulman Christina A. , Gunderson Emma L. , Irish Amanda M. , Townsend Rebecca L. , Stramer Susan L. , Sakanari Judy A. , Bern Caryn
Published: August 2019

Background

Chagas disease affects an estimated 300,000 individuals in the US. Diagnosis in the chronic phase requires positive results by two different IgG serological tests. Three ELISAs (Hemagen, Ortho, Wiener) and one rapid test (InBios) are FDA-cleared, but comparative data in US populations are sparse.

Methods

We evaluated 500 seropositive and 300 seronegative blood donor plasma samples. Country of birth was known for 255 seropositive specimens and grouped into regions: Mexico (n=94), Central America (n=88) and South America (n=73). Specimens were tested by the four FDA-cleared IgG serological assays. Test performance was evaluated by two comparators and latent class analysis.

Results

InBios had the highest sensitivity (97.4-99.3%), but lowest specificity (87.5-92.3%). Hemagen had the lowest sensitivity (88.0-92.0%), but high specificity (99.0-100.0%). Sensitivity was intermediate for Ortho (92.4-96.5%) and Wiener (94.0-97.1%); both had high specificity (98.8-100.0% and 96.7-99.3%, respectively). Antibody reactivity and clinical sensitivity was lowest in donors from Mexico, intermediate in those from Central America and highest in those from South America.

Conclusions

Our findings provide an initial evidence base to improve laboratory diagnosis of Chagas disease in the US. The best current testing algorithm would employ a high sensitivity screening test followed by a high specificity confirmatory test.
Efficient CRISPR/Cas9 gene ablation in uncultured naïve mouse T cells for in vivo studies
Authors: Nüssing Simone , House Imran G. , Kearney Conor J. , Vervoort Stephin J. , Beavis Paul A. , Oliaro Jane , Johnstone Ricky W. , Trapani Joseph A. , Parish Ian A.
Published: August 2019

CRISPR/Cas9 technologies have revolutionised our understanding of gene function in complex biological settings, including T cell immunology. Current CRISPR-mediated gene deletion strategies in T cells require in vitro stimulation or culture that can both preclude studies of gene function within unmanipulated naïve T cells and can alter subsequent differentiation. Here we demonstrate highly efficient gene deletion within uncultured primary naïve murine CD8+ T cells by electroporation of recombinant Cas9/sgRNA ribonucleoprotein immediately prior to in vivo adoptive transfer. Using this approach, we generated single and double gene knock-out cells within multiple mouse infection models. Strikingly, gene deletion occurred even when the transferred cells were left in a naïve state, suggesting that gene deletion occurs independent of T cell activation. This protocol thus expands CRISPR-based probing of gene function beyond models of robust T cell activation, to encompass both naïve T cell homeostasis and models of weak activation, such as tolerance and tumour models.
Conidial melanin of the human pathogenic fungusAspergillus fumigatusdisrupts cell autonomous defenses in amoebae
Authors: Ferling Iuliia , Dunn Joe Dan , Ferling Alexander , Soldati Thierry , Hillmann Falk
Published: August 2019

The human pathogenic fungusAspergillus fumigatusis a ubiquitous saprophyte that causes fatal infections in immunocompromised individuals. Following inhalation, conidia are ingested by innate immune cells and can arrest phagolysosome maturation. How such general virulence traits could have been selected for in natural environments is unknown. Here, we used the model amoebaDictyostelium discoideumto follow the antagonistic interaction ofA. fumigatusconidia with environmental phagocytes in real time. We found that conidia covered with the green pigment 1,8-dihydroxynaphthalene-(DHN)-melanin were internalized at far lower rates when compared to those lacking the pigment, despite high rates of initial attachment. Immediately after uptake of the fungal conidia, nascent phagosomes were formed through sequential membrane fusion and fission events. Using single-cell assays supported by a computational model integrating the differential dynamics of internalization and phagolysosome maturation, we could show that acidification of phagolysosomes was transient and was followed by neutralization and, finally, exocytosis of the conidium. For unpigmented conidia, the cycle was completed in less than 1 h, while the process was delayed for conidia covered with DHN-melanin. At later stages of infection, damage to infected phagocytes triggered the ESCRT membrane repair machinery, whose recruitment was also attenuated by DHN-melanin, favoring prolonged persistence and the establishment of an intracellular germination niche in this environmental phagocyte. Increased exposure of DHN-melanin on the conidial surface also improved fungal survival when confronted with the fungivorous predatorProtostelium aurantium, demonstrating its universal antiphagocytic properties.
Population genomics of the widespread African savannah treesAfzelia africanaandAfzelia quanzensis(Caesalpinioideae, Fabaceae) reveals no significant past fragmentation of their distribution ranges
Authors: Donkpegan Armel S.L. , Piñeiro Rosalía , Heuertz Myriam , Duminil Jérôme , Daïnou Kasso , Doucet Jean-Louis , Hardy Olivier J.
Published: August 2019

Few studies have addressed the evolutionary history of tree species from African savannahs at large geographic scales, particularly in the southern hemisphere (Zambezian region).Afzelia(Fabaceae: Caesalpinioideae) contains economically important timber species, including two species widely distributed in African savannahs:A. africanain the Sudanian region andA. quanzensisin the Zambezian region. To characterize the population genetic diversity and structure of these two species across their distribution ranges, we used nuclear microsatellites (simple sequence repeats, SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241A. africanaand 113A. quanzensisindividuals, while 2,800 and 3,841 high-quality single nucleotide polymorphisms (SNPs) were identified in 30A. africanaand 12A. quanzensisindividuals, respectively. Both species appeared to be outcrossing (selfing rate ~ 0%). The spatial genetic structure was consistent with isolation-by-distance expectations based on both SSR and SNP data, suggesting that gene dispersal is spatially restricted in both species (bLd (SSR)= −0.005and −0.007andbLd (SNP)= −0.008and −0.006 forA. africanaandA. quanzensis, respectively). Bayesian clustering of SSR genotypes failed to identify genetic structure within species. In contrast, SNP data resolved intraspecific genetic clusters in both species, illustrating the higher resolving power of GBS at shallow levels of divergence. However, the clusters identified by SNPs revealed low levels of differentiation and no clear geographical entities. These results suggest that, although gene flow has been restricted over short distances in both species, populations have remained connected throughout the large, continuous Savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during past climate changes, in contrast to patterns commonly found in African rainforest trees.
Natural genetic variation underlying tiller development in barley (Hordeum vulgareL)
Authors: Haaning Allison M. , Smith Kevin P. , Brown-Guedira Gina L. , Chao Shiaoman , Tyagi Priyanka , Muehlbauer Gary J.
Published: August 2019

In barley (Hordeum vulgareL.), lateral branches called tillers contribute to grain yield and define shoot architecture, but genetic control of tiller number and developmental rate are not well characterized. The primary objectives of this work were to examine relationships between tiller number and other agronomic and morphological traits and identify natural genetic variation associated with tiller number and rate, and related traits. We grew 768 lines from the USDA National Small Grain Core Collection in the field and collected data over two years for tiller number and rate, and agronomic and morphological traits. Our results confirmed that spike row-type and days to heading are correlated with tiller number, and as much as 28% of tiller number variance is attributed to these traits. In addition, negative correlations between tiller number and leaf width and stem diameter were observed, indicating trade-offs between tiller development and other vegetative growth. Thirty-three quantitative trait loci (QTL) were associated with tiller number or rate. Of these, 40% overlapped QTL associated with days to heading and 22% overlapped QTL associated with spike row-type, further supporting that tiller development is influenced by these traits. Despite this, some QTL associated with tiller number or rate, including the major QTL on chromosome 3H, were not associated with any other traits, suggesting that tiller number can be modified independently of other important agronomic traits. These results enhance our knowledge of the genetic control of tiller development in barley, which is important for optimizing tiller number and rate for yield improvement.
A mechanical memory of pancreatic cancer cells
Authors: Carnevale Ilaria , Capula Mjriam , Giovannetti Elisa , Schmidt Thomas , Coppola Stefano
Published: August 2019

Cells sense and respond to mechanical stimuli in healthy and pathological conditions. Although the major mechanisms un-derlying cellular mechanotransduction have been described, it remains largely unclear how cells store information on past mechanical cues over time. Such mechanical memory is extremely relevant in the onset of metastasis in which cancer cells migrate through tissues of different stiffness, e.g. from a stiffer tumor microenvironment to softer metastatic sites as commonly occurs for pancreatic cancer. Here, we used micropillar-based traction force microscopy to show that Suit-2.28 pancreatic cancer cells mechanically primed on a stiff matrix exerted higher traction forces even when transferred to a soft secondary matrix, as compared to soft-primed cells. This mechanical memory effect was mediated by the Yes-associated protein (YAP) and the microRNA-21 (miR-21) that are two mechanosensors initially identified as long-term memory keepers in mesenchymal stem cells. Soft-primed cells showed (i) a lower YAP nuclear translocation when transferred to a stiff secondary matrix and (ii) a loss of rigidity sensing through YAP, as compared to stiff-primed cells. The mechanical adaptation resulted in a differential expression of miR-21, inversely proportional to the priming rigidity. The long-term mechanical memory retained by miR-21 unveiled a previously unidentified mechanical modulation of drug resistance by past matrix stiffness. The higher expression of miR-21 in soft-primed cells correlated with the increased resistance to gemcitabine, as compared to stiff-primed and non-primed pancreatic cancer cells.
Inferring reaction network structure from single-cell, multiplex data, using toric systems theory
Authors: Wang Shu , Lin Jia-Ren , Sontag Eduardo D. , Sorger Peter K.
Published: August 2019

The goal of many single-cell studies on eukaryotic cells is to gain insight into the biochemical reactions that control cell fate and state. In this paper we introduce the concept of effective stoichiometric space (ESS) to guide the reconstruction of biochemical networks from multiplexed, fixed time-point, single-cell data. In contrast to methods based solely on statistical models of data, the ESS method leverages the power of the geometric theory of toric varieties to begin unraveling the structure of chemical reaction networks (CRN). This application of toric theory enables a data-driven mapping of covariance relationships in single cell measurements into stoichiometric information, one in which each cell subpopulation has its associated ESS interpreted in terms of CRN theory. In the development of ESS we reframe certain aspects of the theory of CRN to better match data analysis. As an application of our approach we process cytomery- and image-based single-cell datasets and identify differences in cells treated with kinase inhibitors. Our approach is directly applicable to data acquired using readily accessible experimental methods such as Fluorescence Activated Cell Sorting (FACS) and multiplex immunofluorescence.

Author summary

We introduce a new notion, which we call the effective stoichiometric space (ESS), that elucidates network structure from the covariances of single-cell multiplexed data. The ESS approach differs from methods that are based on purely statistical models of data: it allows a completely new and data-driven translation of the theory of toric varieties in geometry and specifically their role in chemical reaction networks (CRN). In the process, we reframe certain aspects of the theory of CRN. As illustrations of our approach, we find stoichiometry in different single-cell datasets, and pinpoint dose-dependence of network perturbations in drug-treated cells.
Immunomodulatory activity of Momordica charantia L. (Cucurbitaceae) leaf diethyl ether and methanol extracts on Salmonella typhi infected mice and LPS-induced phagocytic activities of macrophages and neutrophils
Authors: Mahamat Oumar , Flora Hakoueu N. , Christopher Tume , Albert Kamanyi
Published: August 2019

Infections due to salmonella strains constitute one of the major health problems in humans, particularly in Africa. Use of traditional herbs has proven effective in reducing the incidence of infection in some high-risk groups. To assess the effects of Momordica charantia leaf extracts that influence blood infestation, in vitro study of the effect on macrophages and neutrophils, and treatment of mouse model of S. typhi infection was done. Methanol and diethyl ether extracts were concerned by this study. In vitro study was to assess the effects of extracts on phagocytosis and related intracellular killing mechanisms of macrophages were examined. Later, mobilization of leukocytes and production of antibodies against S. typhi were measured followed by quantitating cultures evaluation of the blood infestation of orally inoculated mice with S. thyphi. Ingestion or attachment of carbon particles, production of superoxide anion, nitric oxide and that of lysosomal acid phosphatase by macrophages and neutrophils were significantly increased by methanol and diethyl extracts at concentrations ranging from 40 μg/ml to 640 μg/ml. Antibody titer and mobilization of leukocytes, particularly lymphocytes against S. typhi were highly increased by both methanol and diethyl extracts at concentrations of 500 and 1000 mg/kg. In the same the extracts have reduced the rate of blood infestation in mice inoculated with 108 CFU of S. typhi for 28 days. Reduction in blood infestation rates was similar for levamisole mice group. Results of this study should prove useful of leave of Momordica charantia for treatment of infections by salmonella strains and for assessment of drugs for therapeutic intervention.