bluuebunny/crossref_metadata_2025 huggingface dataset:
Pumilio Proteins Exert Distinct Biological Functions and Multiple Modes of Post-Transcriptional Regulation in Embryonic Stem Cell Pluripotency and Early Embryogenesis
Authors: Uyhazi Katherine E. , Yang Yiying , Liu Na , Qi Hongying , Huang Xiao A. , Mak Winifred , Weatherbee Scott D. , Song Xiaoling , Lin Haifan
Published: August 2019

Gene regulation in embryonic stem cells (ESCs) has been extensively studied at the epigenetic-transcriptional levels, but not at the post-transcriptional levels. Pumilio (Pum) proteins are among the few known translational regulators required for stem cell maintenance in invertebrates and plants. Here we report the essential function of two murine Pum proteins, Pum1 and Pum2, in ESCs and early embryogenesis. Pum1/2 double mutants are developmentally delayed at the morula stage and lethal by embryonic day 8.5 (e8.5). Correspondingly, Pum1/2 double mutant ESCs display severely reduced self-renewal and differentiation, revealing the combined function of Pum1 and Pum2 in ESC pluripotency. Remarkably, Pum1-deficient ESCs show increased expression of pluripotency genes but not differentiation genes, indicating that Pum1 mainly promote differentiation; whereas Pum2-deficient ESCs show decreased expression of pluripotency genes and accelerated differentiation, indicating that Pum2 promotes self-renewal. Thus, Pum1 and Pum2 each uniquely contributes to one of the two complementary aspects of pluripotency. Furthermore, we show that Pum1 and Pum2 achieve ESC functions by forming a negative auto- and inter-regulatory feedback loop that directly regulates at least 1,486 mRNAs. Pum1 and Pum2 regulate target mRNAs not only by repressing translation as expected but also by promoting translation and enhancing or reducing mRNA stability of different target mRNAs. Together, these findings reveal the distinct roles of individual mammalian Pum proteins in ESCs and their collectively essential functions in ESC pluripotency and embryogenesis. Moreover, they demonstrate three novel modes of regulation of Pum proteins towards target mRNAs.

SIGNIFICANCE STATEMENT

This report demonstrates the essential functions of mammalian Pumilio (Pum) proteins for embryonic stem cells (ESCs) pluripotency and embryogenesis. Moreover, it reveals the contrasting but complementary function of individual Pum proteins in regulating distinct aspects of ESC pluripotency, despite their largely overlapping expression and extremely high homology. Furthermore, it unravels a complex regulatory network in which Pum1 and Pum2 form a negative auto- and inter-regulatory feedback loop that regulates 1,486 mRNAs not only by translational repression as expected but also by promoting translation and enhancing or reducing stability of different target mRNAs, which reveals novel modes of post-transcriptional regulation mediated by Pum.
Why MontaneAnolisLizards are Moving Downhill While Puerto Rico Warms
Authors: Battey C. J. , Otero Luisa M. , Gorman George C. , Hertz Paul E. , Lister Bradford C. , García Andrés , Burrowes Patricia A. , Huey Raymond B.
Published: August 2019

1

Because Puerto Rico has warmed in recent decades, ectotherms there should have shifted their elevational ranges uphill. However, by comparing historical versus recent distributional records ofAnolislizards, we found that three “montane-forest” species have instead moved downhill in recent decades, almost to sea level. This downward shift appears related to the massive regeneration of Puerto Rican forests – especially in lowland areas – which started in the mid-20th century when the island’s economy began shifting from agriculture to manufacturing. The magnitude of local cooling caused by regenerated forests swamps recent climate warming, seemingly enabling cool-adapted “montane” lizards to track forests as they spread downhill from mountain refugia into abandoned plantations. Thus, contemporary distributional patterns are likely converging to those prior to the arrival of European settlers, who cleared most lowland forests for agriculture, thereby restricting forests and associated fauna to high-elevation remnants. In contrast with the montane species, three lowland species expanded their ranges to higher elevations in recent decades; but whether this movement reflects warming, land-use shifts, or hurricane-induced destruction of upland forests is unclear.
LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility
Authors: Moon Hyang Mi , Hippenmeyer Simon , Luo Liqun , Wynshaw-Boris Anthony
Published: August 2019

Heterozygous loss of human PAFAH1B1 (coding for LIS1) results in the disruption of neurogenesis and neuronal migration via dysregulation of microtubule (MT) stability and dynein motor function/localization that alters mitotic spindle orientation, chromosomal segregation, and nuclear migration. Recently, human induced pluripotent stem cell (iPSC) models revealed an important role for LIS1 in controlling the length of terminal cell divisions of outer radial glial (oRG) progenitors, suggesting cellular functions of LIS1 in regulating neural progenitor cell (NPC) daughter cell separation. Here we examined the late mitotic stages NPCs in vivo and mouse embryonic fibroblasts (MEFs) in vitro from Lis1-deficient mutants. Lis1-deficient neocortical NPCs and MEFs similarly exhibited cleavage plane displacement with mislocalization of furrow-associated markers, associated with actomyosin dysfunction and cell membrane hyper-contractility. Thus, it suggests LIS1 acts as a key molecular link connecting MTs/dynein and actomyosin, ensuring that cell membrane contractility is tightly controlled to execute proper daughter cell separation.
Speed and diffusion of kinesin-2 are competing limiting factors in flagellar length control model
Authors: M R , H NL , M WF , Q H
Published: August 2019

Flagellar length control in Chlamydomonas is a tractable model system for studying the general question of organelle size regulation. We have previously proposed that diffusive return of the kinesin motor that powers intraflagellar transport can play a key role in length regulation. Here we explore how the motor speed and diffusion coefficient for the return of kinesin-2 affect flagellar growth kinetics. We find that the system can exist in two distinct regimes, one dominated by motor speed and one by diffusion coefficient. Depending on length, a flagellum can switch between these regimes. Our results indicate that mutations can affect length in distinct ways. We discuss our theory’s implication for flagellar growth influenced by beating and provide possible explanations for the experimental observation that a beating flagellum is usually longer than its immotile mutant. These results demonstrate how our simple model can suggest explanations for mutant phenotypes.

Statement of Significance

The eukaryotic flagellum is an ideal case study in organelle size control because of its simple linear shape and well-understood building mechanism. In our previous work, we proved that flagellar length in the green algae Chlamydomonas can be controlled by the diffusive gradient of the kinesin-2 motors that deliver building blocks to the tip. In this study, we expand on the analytical formulation of the diffusion model to show how physical parameters affect final length and regeneration time, enhancing the model’s potential to explain length mutants and motivate future research with precise predictions.
Lipopolysaccharide Simulations are Sensitive to Phosphate Charge and Ion Parameterization
Authors: Rice Amy , Rooney Mary T. , Greenwood Alexander I. , Cotten Myriam L. , Wereszczynski Jeff
Published: August 2019

The high proportion of lipopolysaccharide (LPS) molecules in the outer membrane of Gram-negative bacteria make it a highly effective barrier to small molecules, antibiotic drugs, and other antimicrobial agents. Given this vital role in protecting bacteria from potentially hostile environments, simulations of LPS bilayers and outer membrane systems represent a critical tool for understanding the mechanisms of bacterial resistance and the development of new antibiotic compounds that circumvent these defenses. The basis of these simulations are parameterizations of LPS, which have been developed for all major molecular dynamics force fields. However, these parameterizations differ in both the protonation state of LPS as well as how LPS membranes behave in the presence of various ion species. To address these discrepancies and understand the effects of phosphate charge on bilayer properties, simulations were performed for multiple distinct LPS chemotypes with different ion parameterizations in both protonated or deprotonated lipid A states. These simulations show that bilayer properties, such as the area per lipid and inter-lipid hydrogen bonding, are highly influenced by the choice of phosphate group charges, cation type, and ion parameterization, with protonated LPS and monovalent cations with modified nonbonded parameters providing the best match to experiments. Additionally, alchemical free energy simulations were performed to determine theoretical pKa values for LPS, and subsequently validated by 31P solid-state NMR experiments. Results from these complementary computational and experimental studies demonstrate that the protonated state dominates at physiological pH, contrary to the deprotonated form modeled by many LPS force fields. In all, these results highlight the sensitivity of LPS simulations to phosphate charge and ion parameters, while offering recommendations for how existing models should be updated for consistency between force fields as well as to best match experiments.
Discovery of genes encoding a Streptolysin S-like toxin biosynthetic cluster in a select highly pathogenic methicillin resistantStaphylococcus aureusJKD6159 strain
Authors: Kane Trevor , Carothers Katelyn E. , Bao Yunjuan , Yeo Won-Sik , Bae Taeok , Park Claudia , Fields Francisco R. , Vu Henry M. , Hammers Daniel E. , Ross Jessica N. , Ploplis Victoria A. , Castellino Francis J. , Lee Shaun W.
Published: August 2019

Background

Staphylococcus aureus(S. aureus) is a major human pathogen owing to its arsenal of virulence factors, as well as its acquisition of multi-antibiotic resistance. Here we report the identification of a Streptolysin S (SLS) like biosynthetic gene cluster in a highly virulent community-acquired methicillin resistantS. aureus(MRSA) isolate, JKD6159. Examination of the SLS-like gene cluster in JKD6159 shows significant homology and gene organization to the SLS-associated biosynthetic gene (sag) cluster responsible for the production of the major hemolysin SLS in Group AStreptococcus.

Results

We took a comprehensive approach to elucidating the putative role of the sag gene cluster in JKD6159 by constructing a mutant in which one of the biosynthesis genes (sagB homologue) was deleted in the parent JKD6159 strain. Assays to evaluate bacterial gene regulation, biofilm formation, antimicrobial activity, as well as complete host cell response profile and comparativein vivoinfections in Balb/Cj mice were conducted.

Conclusions

Although no significant phenotypic changes were observed in our assays, we postulate that the SLS-like toxin produced by this strain ofS. aureusmay be a highly specialized virulence factor utilized in specific environments for selective advantage; studies to better understand the role of this newly discovered virulence factor inS. aureuswarrant further investigation.
LINbase: A Web service for genome-based identification of microbes as members of crowdsourced taxa
Authors: Tian Long , Huang Chengjie , Heath Lenwood S. , Vinatzer Boris A.
Published: August 2019

The development of next generation and third generation DNA sequencing technologies in combination with new efficient algorithms allows scientists to economically, quickly, and precisely identify microbes at all taxonomic levels and even attribute pathogen isolates to specific disease outbreaks. However, current taxonomic practice has not kept up with the sequencing revolution and continues to rely on cumbersome journal publications to describe new species. Here we introduce a Web service that allows any user to genomically circumscribe any monophyletic group of bacteria as a taxon and associate with each taxon a name and short description. Any other user can immediately identify their unknown microbe as a member of any of these crowdsourced taxa using gene or genome sequences. The Web service is called LINbase. It leverages the previously described concept of Life Identification Numbers (LINs), which are codes assigned to individual organisms based on genome similarity. Most genomes currently in LINbase were imported from GenBank, but users have the option to upload their own genome sequences as well. Importantly, LINbase allows users to share the precise identity of their sequenced genomes without sharing the actual genome sequences, making not yet published or private genome sequences discoverable by the scientific community stimulating collaboration between academia and industry. LINbase is available at http://www.LINbase.org.
Sub-Nanometer Precision using Bayesian Grouping of Localizations
Authors: Fazel Mohamadreza , Wester Michael J. , Rieger Bernd , Jungmann Ralf , Lidke Keith A.
Published: August 2019

Single-molecule localization microscopy super-resolution methods such as DNA-PAINT and (d)STORM can generate multiple observed localizations over the time course of data acquisition from each dye or binding site that are not a priori assigned to those specific dyes or binding sites. We describe a Bayesian method of grouping and combining localizations from multiple blinking/binding events that can improve localization precision to better than one nanometer. The known statistical distribution of the number of binding/blinking events per dye/docking strand along with the precision of each localization event are used to estimate the true number and location of emitters in closely-spaced clusters.
Receptor-Like Kinase Phosphorylation of Arabidopsis Heterotrimeric G-Protein Gα - Subunit AtGPA1
Authors: Jia Haiyan , Song Gaoyuan , Werth Emily G. , Walley Justin W. , Hicks Leslie M. , Jones Alan M.
Published: August 2019

As molecular on-off switches, heterotrimeric G protein complexes, comprised of a Gα subunit and an obligate Gβγ dimer, transmit extracellular signals received by G protein– coupled receptors (GPCRs) to cytoplasmic targets that respond to biotic and abiotic stimuli. Signal transduction is modulated by phosphorylation of GPCRs and G protein complexes. In Arabidopsis thaliana, the Gα subunit AtGPA1 is phosphorylated by the receptor-like kinase (RLK) BRI1-ASSOCIATED Kinase 1 (BAK1), but the extent that other RLKs phosphorylates AtGPA1 is unknown. We mapped 22 trans-phosphorylation sites on AtGPA1 by 12 RLKs hypothesized to act in the Arabidopsis G protein signaling pathway. Cis-phosphorylation sites on these RLKs were also identified. BRI1, BAK1, and SERK1 have been reported as Ser/Thr and Tyr dual specificity kinases. We identified 4 more dual specificity kinases: IOS1, PSY1R, PEPR1, and AT2G37050. Multiple sites are present in the core AtGPA1 functional units, including pSer52 and pThr53 of the conserved P-loop that directly binds nucleotide/phosphate, pThr164 and pSer175 from αE helix in the intramolecular domain interface for nucleotide exchange and GTP hydrolysis, and pThr193 or pThr194 in Switch I (SwI) that coordinates nucleotide exchange and protein partner binding. Several AtGPA1 S/T phosphorylation sites are nucleotide-dependent phosphorylation patterns, such as S52/T53 in the P-loop and T193 and/or T194 in SwI.
Days Gained Response Discriminates Treatment Response in Patients with Recurrent Glioblastoma Receiving Bevacizumab-based Therapies
Authors: Singleton Kyle W. , Porter Alyx B. , Hu Leland S. , Johnston Sandra K , Bond Kamila M. , Rickertsen Cassandra R. , De Leon Gustavo , Whitmire Scott A. , Clark-Swanson Kamala R. , Mrugala Maciej M. , Swanson Kristin R.
Published: August 2019

Purpose

Accurate assessments of patient response to therapy are a critical component of personalized medicine. In glioblastoma multiforme (GBM), the most aggressive form of brain cancer, tumor growth dynamics are heterogenous across patients, complicating assessment of treatment response. This study aimed to analyze Days Gained (DG), a burgeoning model-based dynamic metric, for response assessment in patients with recurrent GBM who received bevacizumab-based therapies.

Experimental Design

Days Gained response scores were calculated using volumetric tumor segmentations for patients receiving bevacizumab with and without concurrent cytotoxic therapy (N=62). Kaplan-Meier and Cox proportional hazards analyses were implemented to examine DG prognostic relationship to overall (OS) and progression-free survival (PFS) from the onset of treatment for recurrent GBM.

Results

In patients receiving concurrent bevacizumab and cytotoxic therapy, Kaplan-Meier analysis showed significant differences in OS and PFS at previously identified DG cutoffs consistent with previous DG analyses using gadolinium-enhanced T1 weighted MR imaging. DG scores for bevacizumab monotherapy only approached significance for PFS. Cox regression showed that increases of 25 DG were significantly associated with a 12.5% reduction in OS hazard for concurrent therapy patients and a 4.4% reduction in PFS hazard for bevacizumab monotherapy.

Conclusion

Days Gained has significant meaning in recurrent therapy as a metric of treatment response, even in the context of anti-angiogenic therapies. This provides further evidence supporting the use of DG as an adjunct response metric that quantitatively connects treatment response and clinical outcomes.
Moderate amounts of epistasis are not evolutionarily stable in small populations
Authors: Sydykova Dariya K. , LaBar Thomas , Adami Christoph , Wilke Claus O.
Published: August 2019

High mutation rates select for the evolution of mutational robustness where populations inhabit flat fitness peaks with little epistasis, protecting them from lethal mutagenesis. Recent evidence suggests that a different effect protects small populations from extinction via the accumulation of deleterious mutations. In drift robustness, populations tend to occupy peaks with steep flanks and positive epistasis between mutations. However, it is not known what happens when mutation rates are high and population sizes are small at the same time. Using a simple fitness model with variable epistasis, we show that the equilibrium fitness has a minimum as a function of the parameter that tunes epistasis, implying that this critical point is an unstable fixed point for evolutionary trajectories. In agent-based simulations of evolution at finite mutation rate, we demonstrate that when mutations can change epistasis, trajectories with a subcritical value of epistasis evolve to decrease epistasis, while those with supercritical initial points evolve towards higher epistasis. These two fixed points can be identified with mutational and drift robustness, respectively.
Single Cell RNA-sequencing reveals cellular heterogeneity, stage transition and antigenic variation during stress adaptation in synchronized Plasmodium falciparum
Authors: Rawat Mukul , Srivastava Ashish , Gupta Ishaan , Karmodiya Krishanpal
Published: August 2019

The malaria parasite has a complex life cycle exhibiting phenotypic and morphogenic variations in two different hosts. Phenotypic cell-to-cell variability can be an important determinant of cellular adaptation, stress tolerance and immune evasion in the host. To investigate cellular heterogeneity, we performed single cell RNA-sequencing (scRNA-seq) of 4949 and 6873 synchronized Plasmodium cells in control and under temperature stress condition (phenocopying the cyclic bouts of fever experienced during malarial infection). High-resolution clustering of scRNA-seq datasets and a combination of gene signatures allow identification of cellular heterogeneity and stage transition during stress adaptation. We identified a subset of parasites primed for gametogenesis and another subset primed for stress adaptation. Interestingly, temperature stress inducted the process of gametogenesis by upregulation of master regulator (AP2-G) of sexual conversion. Moreover, pseudotime analysis indicated bifurcation for cell-fate decision to gametogenesis at two different stages of intra-erythrocytic cycle. Furthermore, we identified a rare population of cells, which is only emerged during the stress condition, showing the reactive state of the pathogen against the temperature stress condition. Interestingly, genes associated with the gametogenesis, chaperon activity and maintenance of cellular homeostasis showed maximum variation under temperature stress condition. We also developed an online exploratory tool (website: http://bit.ly/plasmo_sync), which will provide new insights into gene function under normal and physiological stress condition. Thus, our study suggests that the variability and versatility of the maintenance of cellular homeostasis should enable cells to survive under different stress conditions, and may act as an important stimulator of development of drug-resistance in Plasmodium falciparum.
Variations of gut microbiome profile under different storage conditions and preservation periods: A multi-dimensional evaluation
Authors: Ma Junli , Sheng Lili , Xi Chuchu , Gu Yu , Hong Ying , Zheng Ningning , Chen Linlin , Wu Gaosong , Li Yue , Yan Juan , Han Ruiting , Li Bingbing , Qiu Huihui , Zhong Jing , Jia Wei , Li Houkai
Published: August 2019

Gut dysbiosis contributes to the development of various human diseases. There are thousands of publications per year for investigating the role of gut microbiota in development of various diseases. However, emerging evidence has indicated data inconsistency between different studies frequently, but gained very little attention by scientists. There are many factors that can cause data variation and inconsistency during the process of microbiota study, in particular, sample storage conditions and subsequent sequencing process. Here, we systemically evaluated the impacts of six fecal sample storage conditions (including −80 °C, −80 °C with 70% ethanol (ET_-80 °C), 4°C with 70% ethanol (ET_4°C), and three commercial storage reagents including OMNIgene•GUT OMR-200 (GT), MGIEasy (MGIE), and Longsee (LS)), storage periods (1, 2 weeks or 6 months), and sequencing platform on gut microbiome profile using 16S rRNA gene sequencing. Our results suggested that −80°C is acceptable for fecal sample storage, and the addition of 70% ethanol offers some benefits. Meanwhile, we found that samples in ET_4 °Cand GT reagents are comparable, both introduced multi-dimensional variations. The use of MGIE resulted in the least alteration, while the greatest changes were observed in samples stored in LS reagents during the whole experiment. Finally, we also confirmed that variations caused by storage condition were larger than that of storage time and sequencing platform.

IMPORTANCE

In the current study, we performed a multi-dimensional evaluation on the variations introduced by types of storage conditions, preservation period and sequencing platform on the basis of data acquired from 16S rRNA gene sequencing. The efficacy of preservation methods was comprehensively evaluated by DNA yield and quality, α and β diversity, relative abundance of the dominant bacteria and functional bacteria associated with SCFAs producing and BAs metabolism. Our results confirmed that variations introduced by storage condition were larger than that of storage periods and sequencing platform. Collectively, our study provided a comprehensive view to the impacts of storage conditions, storage times, and sequencing platform on gut microbial profile.
Vibrio choleraeOmpR represses the ToxR regulon in response to membrane intercalating agents that are prevalent in the human gastrointestinal tract
Authors: Kunkle DE , Bina TF , Bina XR , Bina JE
Published: August 2019

Multidrug efflux systems belonging Resistance-Nodulation-Division (RND) superfamily are ubiquitous in Gram-negative bacteria. RND efflux systems are often associated with multiple antimicrobial resistance but also contribute to the expression of diverse bacterial phenotypes including virulence, as documented in the intestinal pathogenVibrio cholerae, the causative agent of the severe diarrheal disease cholera. Transcriptomic studies with RND efflux-negativeV. choleraesuggested that RND-mediated efflux was required for homeostasis, as loss of RND efflux resulted in the activation of transcriptional regulators, including multiple environmental sensing systems. In this report we investigated six RND efflux responsive regulatory genes for contributions toV. choleraevirulence factor production. Our data showed thatV. choleraegene VC2714, encoding a homologue ofEscherichia coliOmpR, was a virulence repressor. The expression ofompRwas elevated in an RND-null mutant andompRdeletion partially restored virulence factor production in the RND-negative background. Virulence inhibitory activity in the RND-negative background resulted from OmpR repression of the key ToxR regulon virulence activatoraphB, andompRoverexpression in WT cells also repressed virulence throughaphB.We further show thatompRexpression was not altered by changes in osmolarity, but instead was induced by membrane intercalating agents that are prevalent in the host gastrointestinal tract, and which are substrates of theV. choleraeRND efflux systems. Our collective results indicate thatV. cholerae ompRis anaphBrepressor and regulates the expression of the ToxR virulence regulon in response to novel environmental cues.
Loss of BubR1 Acetylation instigates Replication Stress leading to Complex Chromosomal Rearrangement in tumors
Authors: Park Jiho , Yeu Song-Yion , Paik Sangjin , Lee Junyeob , Jang Jinho , Lee Semin , Koh Young-Il , Lee Hyunsook
Published: August 2019

Chromosome number and structure instability is the hallmark of cancer. Equal chromosome segregation is guaranteed by the spindle assembly checkpoint (SAC), thus defective SAC leads to chromosome instability. However, aneuploidy alone is not oncogenic, and whether compromised SAC is associated with structure instability remains elusive. BubR1 is a core component of SAC, which is acetylated at lysine 250 in mitosis. Previously, we showed that deficiency of BubR1 acetylation in mice (K243R/+) leads to spontaneous tumorigenesis via chromosome mis-segregation. Here, we asked whether loss of BubR1 acetylation is associated with chromosome structure instability by examiningK243R/+mice intercrossed top53-deficient mice. Genome-wide sequencing and spectral karyotyping of the double mutant mouse tumors revealed that BubR1 acetylation deficiency leads to complex chromosome rearrangements, including Robertsonian-like whole-arm translocations and premature sister-chromatid separations (PMSCS). In primary MEFs, replication stress was markedly increased in telomeres and centromeres, suggesting that the replication stress underlies the significant increase of DNA damage and subsequent chromosome rearrangements. Furthermore, defects in BubR1 acetylation at K250 were detected in human cancers as well. Collectively, we propose that chromosome mis-segregation by the loss of BubR1 acetylation causes chromosome structure instability, leading to massive chromosome rearrangements through the induction of replication stress.
Selective Sweep at a QTL in a Randomly Fluctuating Environment
Authors: Chevin Luis-Miguel
Published: August 2019

Adaptation is mediated by phenotypic traits that are often near continuous, and undergo selective pressures that may change with the environment. The dynamics of allelic frequencies at underlying quantitative trait loci (QTL) depend on their own phenotypic effects, but also possibly on other polymorphic loci affecting the same trait, and on environmental change driving phenotypic selection. Most environments include a substantial component of random noise, characterized by both its magnitude and its temporal autocorrelation, which sets the timescale of environmental predictability. I investigate the dynamics of a mutation affecting a quantitative trait in an autocorrelated stochastic environment that causes random fluctuations of an optimum phenotype. The trait under selection may also exhibit background polygenic variance caused by many polymorphic loci of small effects elsewhere in the genome. In addition, the mutation at the QTL may affect phenotypic plasticity, the phenotypic response of given genotype to its environment of development or expression. Stochastic environmental fluctuations increases the variance of the evolutionary process, with consequences for the probability of a complete sweep at the QTL. Background polygenic variation critically alters this process, by setting an upper limit to stochastic variance of population genetics at the QTL. For a plasticity QTL, stochastic fluctuations also influences the expected selection coefficient, and alleles with the same expected trajectory can have very different stochastic variances. Finally, a mutation may be favored through its effect on plasticity despite causing a systematic mismatch with optimum, which is compensated by evolution of the mean background phenotype.
Single-cell RNA sequencing reveals functional heterogeneity and sex differences of glioma-associated brain macrophages
Authors: Ochocka Natalia , Segit Pawel , Walentynowicz Kacper Adam , Wojnicki Kamil , Cyranowski Salwador , Swatler Julian , Mieczkowski Jakub , Kaminska Bozena
Published: August 2019

Microglia are resident myeloid cells in the central nervous system (CNS) that control homeostasis and protect CNS from damage and infections. Microglia and peripheral myeloid cells accumulate and adapt tumor supporting roles in human glioblastomas that show prevalence in men. Cell heterogeneity and functional phenotypes of myeloid subpopulations in gliomas remain elusive. Single-cell RNA sequencing (scRNA-seq) of CD11b+myeloid cells in naïve and GL261 glioma-bearing mice revealed distinct profiles of microglia, infiltrating monocytes/macrophages and CNS border-associated macrophages. We demonstrated an unforeseen molecular heterogeneity among myeloid cells in naïve and glioma-bearing brains, validated selected marker proteins and showed distinct spatial distribution of identified subsets in experimental gliomas. We found higher expression of MHCII encoding genes in glioma-activated male microglia, which was corroborated in bulk and scRNA-seq data from human diffuse gliomas. Sex-specific gene expression in glioma-activated microglia may be relevant to sex differences in incidence and outcomes of glioma patients.
Lack of regularity between letters impacts word recognition performance
Authors: Beier Sofie , Bernard Jean-Baptiste
Published: August 2019

Physical inter-letter dissimilarity has been suggested as a solution to increase perceptual differences between letter shapes and hence a solution to improve reading performance. However, the deleterious effects of font tuning suggest that low inter-letter regularity (due to the enhancement of specific letter features to make them more differentiable) may impair word recognition performance. The aim of the present investigation was 1) to validate our hypothesis that reducing inter-letter regularity impairs reading performance, as suggested by font tuning, and 2) to test whether some forms of non-regularities could impair visual word recognition more. To do so, we designed four new fonts. For each font we induced one type of increased perceptual difference: for the first font, the letters have longer extender length; for the second font, the letters have different slants; and for the third font, the letters have different font cases. We also designed a fourth font where letters differ on all three aspects (worst regularity across letters). Word recognition performance was measured for each of the four fonts in comparison to a traditional sans serif font (best regularity across letters) through a lexical decision task. Results showed a significant decrease in word recognition performance only for the fonts with mixed-case letters, suggesting that fonts with low regularity, such as mixed-case letters, should be avoided in the definition of new “optimal” fonts. Letter recognition performance measured for the five different fonts through a trigram recognition task showed that this effect is not consistently due to poor letter identification.
Health care service providers’ experiences, understanding and conceptions of voluntary medical male circumcision in KwaZulu-Natal, South Africa
Authors: Nxumalo Celenkosini Thembelenkosini , Mchunu Gugu Gladness
Published: August 2019

Background

There is compelling evidence that voluntary medical male circumcision reduces the chances of heterosexual transmission of HIV infection. Health care workers are among the key influencers in terms of scale up of VMMC as they are often involved in mobilization for uptake. Adequate knowledge and competence are essential to ensuring that the delivery of VMMC services is line with the recommended comprehensive package of HIV prevention services.

Aim

The aim of this study was to analyse health care service providers’ conceptions, experiences and understanding of VMMC in KwaZulu-Natal, South Africa.

Methods

The study employed a qualitative approach using a phenomenographic design. Ethical clearance to conduct the study was obtained from the University of KwaZulu-Natal’s Biomedical Research Ethics Committee (BE627/18).Data were collected from a purposive sample of 15 health care worker who were doctors, nurses and clinical associates working in six different rural clinics in KwaZulu-Natal, South Africa. Individual in-depth interviews were used collect data guided by a semi-structured interview schedule. An audiotape was used to record the interviews, which were then transcribed verbatim, and analysed thematically.

Results

Categories of description in healthcare providers’ experiences, conceptions and understanding of voluntary medical male circumcision emerged. The findings of this study revealed that health care workers conceptions, experiences and understanding of VMMC were influenced by stereotypical cultural, religious and traditional beliefs. The challenges of implementing VMMC were shortage of staff and poor training of health care workers on VMMC.

Conclusion

Tailored messaging targeting health care workers misconceptions and poor understanding of VMMC in necessary. In addition, resource allocation for training and infrastructure could significantly improve the quality of VMMC services and uptake thereof.
Inverse correlation between heme synthesis and the Warburg effect in cancer cells
Authors: Sugiyama Yuta , Takahashi Erika , Takahashi Kiwamu , Nakajima Motowo , Tanaka Tohru , Ogura Shun-ichiro
Published: August 2019

Abstracts

Cancer cells show a bias toward the glycolytic system over the conventional mitochondrial electron transfer system for obtaining energy. This biased metabolic adaptation is called the Warburg effect. Cancer cells also exhibit a characteristic metabolism, a decreased heme synthesizing ability. Here we show that heme synthesis and the Warburg effect are inversely correlated. We used human gastric cancer cell lines to investigate glycolytic metabolism and electron transfer system toward promotion/inhibition of heme synthesis. Under hypoxic conditions, heme synthesis was suppressed and the glycolytic system was enhanced. Addition of a heme precursor for the promotion of heme synthesis led to an enhanced electron transfer system and inhibited the glycolytic system and vice versa. Enhanced heme synthesis leads to suppression of cancer cell proliferation by increasing intracellular reactive oxygen species levels. Collectively, the promotion of heme synthesis in cancer cells eliminated the Warburg effect by shifting energy metabolism from glycolysis to oxidative phosphorylation.
A comparative genomic analysis of the barley pathogen Pyrenophora teres f. teres identifies sub-telomeric regions as drivers of virulence
Authors: Wyatt Nathan A. , Richards Jonathan K. , Brueggeman Robert S. , Friesen Timothy L.
Published: August 2019

Pyrenophora teres f. teres causes net form net blotch of barley and is an economically important pathogen throughout the world. However, P. teres f. teres is lacking in the genomic resources necessary to characterize the mechanisms of virulence. Recently a high quality reference genome was generated for P. teres f. teres isolate 0-1. Here, we present the reference quality sequence and annotation of four new isolates and we use the five available P. teres f. teres genomes for an in-depth comparison resulting in the generation of hypotheses pertaining to the potential mechanisms and evolution of virulence. Comparative analyses were performed between all five P. teres f. teres genomes examining genomic organization, structural variations, and core and accessory genomic content, specifically focusing on the genomic characterization of known virulence loci and the localization of genes predicted to encode secreted and effector proteins. We showed that 14 of 15 currently published virulence quantitative trait loci (QTL) span accessory genomic regions consistent with these accessory regions being important drivers of host adaptation. Additionally, these accessory genomic regions were frequently found in sub-telomeric regions of chromosomes with 10 of the 14 accessory region QTL localizing to sub-telomeric regions. Comparative analysis of the sub-telomeric regions of P. teres f. teres chromosomes revealed translocation events where homology was detected between non-homologous chromosomes at a significantly higher rate than the rest of the genome. These results indicate that the sub-telomeric accessory genomic compartments not only harbor most of the known virulence loci, but also that these regions have the capacity to rapidly evolve.
Nanoscale distribution of nuclear sites analyzed by superresolution STED-ICCS
Authors: Oneto M. , Scipioni L. , Sarmento M.J. , Cainero I. , Pelicci S. , Furia L. , Pelicci P.G. , Dellino G.I. , Bianchini P. , Faretta M. , Gratton E. , Diaspro A. , Lanzanò L.
Published: August 2019

Deciphering the spatiotemporal coordination between nuclear functions is important to understand its role in the maintenance of human genome. In this context, superresolution microscopy has gained considerable interest as it can be used to probe the spatial organization of functional sites in intact single cell nuclei in the 20-250 nm range. Among the methods that quantify colocalization from multicolor images, image cross-correlation spectroscopy (ICCS) offers several advantages, namely it does not require a pre-segmentation of the image into objects and can be used to detect dynamic interactions. However, the combination of ICCS with super-resolution microscopy has not been explored yet.

Here we combine dual color stimulated emission depletion (STED) nanoscopy with ICCS (STED-ICCS) to quantify the nanoscale distribution of functional nuclear sites. We show that STED-ICCS provides not only a value of colocalized fraction but also the characteristic distances associated to correlated nuclear sites. As a validation, we quantify the nanoscale spatial distribution of three different pairs of functional nuclear sites in MCF10A cells. As expected, transcription foci and a transcriptionally repressive histone marker (H3K9me3) are not correlated. Conversely, nascent DNA replication foci and the Proliferating cell nuclear antigen (PCNA) protein have a high level of proximity and are correlated at a nanometer distance which is close to the limit of our experimental approach. Finally, transcription foci are found at a distance of 130 nm from replication foci, indicating a spatial segregation at the nanoscale. Overall, our data demonstrate that STED-ICCS can be a powerful tool for the analysis of nanoscale distribution of functional sites in the nucleus.

Statement of significance

Several methods are available to quantify the proximity of two labeled molecules from dual color images. Among them, image cross-correlation spectroscopy (ICCS) is attractive as it does not require a pre-segmentation of the image into objects and can be used to detect dynamic interactions. Here, we combine for the first time ICCS with superresolution stimulated emission depletion (STED) microscopy (STED-ICCS) to quantify the spatial distribution of functional sites in the nucleus. Our results show that STED-ICCS, in addition to quantifying the colocalized fraction, detects characteristic nanometer distances associated to correlated nuclear sites. This work shows that STED-ICCS can be a powerful tool to quantify the nanoscale distribution of functional sites in the nucleus.
The Cannabis Multi-Omics Draft Map Project
Authors: Jenkins Conor , Orsburn Ben
Published: August 2019

Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these plants. We report herein our progress on constructing a comprehensive draft map of the Cannabis proteome. To date we have identified over 17,000 potential protein sequences. Unfortunately, no annotated genome of Cannabis plants currently exists. We present a method by which “next generation” DNA sequencing output and shotgun proteomics data can be combined to produce annotated FASTA files, bypassing the need for annotated genetic information altogether in traditional proteomics workflows. The resulting material represents the first comprehensive annotated FASTA for any Cannabis plant. Using this annotated database as reference we can refine our protein identifications, resulting in the confident identification of 13,000 proteins with putative function. Furthermore, we demonstrate that post-translational modifications play an important role in the proteomes of Cannabis flower, particularly lysine acetylation and protein glycosylation. To facilitate the evolution of analytical investigations into these plant materials, we have created a portal to host resources we have developed from proteomic and metabolomic analysis of Cannabis plant material as well as our results integrating these resources. All data for this project is available to view or download at www.CannabisDraftMap.Org
Winter is coming: pathogen emergence in seasonal environments
Authors: Carmona Philippe , Gandon Sylvain
Published: August 2019

Many infectious diseases exhibit seasonal dynamics driven by periodic fluctuations of the environment. Predicting the risk of pathogen emergence at different points in time is key for the development of effective public health strategies. Here we study the impact of seasonality on the probability of emergence of directly transmitted pathogens under different epidemiological scenarios. We show that when the period of the fluctuation is large relative to the duration of the infection, the probability of emergence varies dramatically with the time at which the pathogen is introduced in the host population. In particular, we identify a new effect of seasonality (the winter is coming effect) where the probability of emergence is vanishingly small even though pathogen transmission is high. We use this theoretical framework to compare the impact of different control strategies on the average probability of emergence. We show that, when pathogen eradication is not attainable, the optimal strategy is to act intensively in a narrow time interval. Interestingly, the optimal control strategy is not always the strategy minimizing R0, the basic reproduction ratio of the pathogen. This theoretical framework is extended to study the probability of emergence of vector borne diseases in seasonal environments and we show how it can be used to improve risk maps of Zika virus emergence.
Paucity of adaptive selection in PmrAB two-component system may resist emergence of colistin resistance in Acinetobacter baumannii
Authors: Pagal Sudhakar , Saranathan Rajagopalan , Rani Anshu , Tomar Archana , Arunkumar K. P. , Prashanth K.
Published: August 2019

Investigations on the selection pressure acting on point mutations in PmrAB two-component system may provide insights into the future of colistin therapy in Acinetobacter baumannii, since mutations in pmrAB are implicated in colistin resistance. We performed adaptive selection analysis of pmrAB and compared with the available data on colistin resistant strains. We analysed PmrAB sequences in 3113 draft genomes of A. baumannii obtained from RefSeq database. Adaptive selection analysis was performed by two widely used programs namely, HyPhy and PAML. In addition, to examine the reliability of the approach, the same analysis was performed on gyrA of Escherichia coli and Salmonella enterica, since adaptive mutations on gyrA confer quinolone resistance. Mutations that had caused colistin resistance were found to be neither adaptive nor polymorphic, rather they occur at sites that are either under neutral or purifying selection. Strong negative evolutionary selection pressure is also observed at sites throughout both PmrA and PmrB. Sites with high levels of polymorphisms in PmrAB were found to be under neutral selection. Notably, there was no sign of positive selection. Some of them are rather deleterious. These conditions might be maintaining the incidence of colistin resistance in A. baumannii under check. Therefore, in the context of colistin resistance, natural selection plays only a minor role and we assert that in future, A. baumannii may not be able to sustain and successfully disseminate colistin resistance. Therefore, at present the concerns raised about continuing the usage of colistin for the treatment against A. baumannii infections appears to be unnecessary.
A winner in the Anthropocene: changing host plant distribution explains geographic range expansion in the gulf fritillary butterfly
Authors: Halsch Christopher A. , Shapiro Arthur M. , Thorne James H. , Waetjen David P. , Forister Matthew L.
Published: August 2019

The changing climate is altering the geographic distributions of species around the world with consequences for population dynamics, resulting in winners and losers in the Anthropocene.

Agraulis vanillae, the gulf fritillary butterfly, has expanded its range in the past one hundred years in the western United States. We combine time series analysis with species distribution modeling to investigate factors limiting the distribution ofA. vanillaeand to predict future shifts under warming scenarios.

In the western US, where we have time series and geographic data, urban development has a positive influence (the host plant is an ornamental in gardens), being associated with year of colonization. Colonization was also associated to a lesser extent with winter maximum temperatures, while a negative impact of minimum temperatures and precipitation was apparent on population growth rates.

Across the country, the butterfly is primarily limited by host availability and positively affected by human presence. Perhaps counter-intuitively for a largely tropical ectotherm, current effects of a warming climate (in the years post-colonization) are either negative (on population growth rate) or indirect, likely mediated through availability of areas that can support the host.

Under future climate scenarios, conditions are predicted to become more suitable forPassiflorain many urban areas, which would likely result in further expansion ofA. vanillaeduring the dispersive season. These results illustrate the value of combining time series with spatial modeling to understand and predict shifting geographic ranges in the Anthropocene.