bluuebunny/crossref_metadata_2025 huggingface dataset:
The Use of Botulinum Toxin in Pain Management: Basic Science and Clinical Applications
Authors: Hehr Jason D. , Schoenbrunner Anna R. , Janis Jeffrey E
Published: February 2020

Pain is an unpleasant experience resulting from either tissue damage or insults to the somatosensory system. Approaches to pain management evolve as we better understand both pain pathways and the tools available to interrupt these. The interest surrounding botulinum neurotoxin as a chemodenervating agent has expanded to include its potential applications in painful pathologies, both within and beyond the confines of plastic surgery. In this article, the authors discuss botulinum neurotoxin’s mechanism of action as it pertains to both muscular paralysis and its interplay in the modulation of proinflammatory pain mediators. In addition, the authors review evidence supporting the use of botulinum neurotoxin in common painful conditions, in order to prepare the readership to aptly provide their patients with evidence-based recommendations. After reading this article, the participant should be able to discuss both mechanism of action and common applications of botulinum neurotoxin in painful conditions.
Mitigating Biases in a Cohort Study: A Critical Examination of the Silicone Arthroplasty in Rheumatoid Arthritis Study
Authors: Kim You J. , Chung Kevin C.
Published: February 2020

Research bias, or the systematic errors of a study, can arise before, during, or after a trial ends. These biases hinder the internal validity of the study, which is the accuracy of a study’s conclusions regarding the effects of an intervention on a given group of subjects. With the growing use of evidence-based medicine, there is a demand for high-quality evidence from the research community. Systematic reviews and meta-analyses of randomized controlled trials are considered the highest level of evidence, followed by individual randomized controlled trials. However, most surgical trials cannot be conducted as randomized controlled trials because of factors such as patient preferences and lack of equipoise among surgeons. Therefore, surgical trials may lack features that are held as important standards for high-quality evidence, such as randomization and blinding. To demonstrate the biases that surgical trials may encounter, the authors examined a prospective cohort study, the Silicone Arthroplasty in Rheumatoid Arthritis study. The authors focus on the challenges that arise during a surgical trial, including the design, implementation, and methods used to report the clinical evidence. By recognizing and addressing obstacles that exist in research, investigators will provide health care providers with high-quality evidence needed to make well-informed, evidence-based clinical decisions.
Polymorphisms of SOCS-1 Are Associated With a Rapid HIV Progression Rate
Authors: Hersberger Martin , Schlaepfer Erika , Buehler Marco , Bochud Pierre-Yves , Vernazza Pietro , Marti-Jaun Jacqueline , Nemeth Johannes , Zwahlen Marcel , Schmidlin Kurt , Speck Roberto F. ,   the Swiss HIV Cohort Study
Published: February 2020

Objectives:

Immune activation, among others driven by interferon (IFN)-α and IFN-γ activation, is a main feature of progressive HIV infection. Suppressor of cytokine signaling (SOCS) 1 and 3 are negative feedback regulators of the IFN-α and IFN-γ axis. Here, we analyzed the role of 9 single-nucleotide polymorphisms (SNPs) within SOCS-1 and SOCS-3 genes for their association with an HIV progression rate in a cohort of 318 rapid vs 376 slow progressors from the Swiss HIV Cohort Study.

Design and Methods:

We analyzed 9 SNPs, which we have identified in Swiss blood donors, in a cohort of HIV-infected patients (n = 1144), which have been categorized according to the decline in CD4+ T-cell counts. In all the conducted analyses, we focused on the comparison between rapid and slow progressors with regard to SNPs in SOCS-1 and SOCS-3 and with regard to haplotypes using multivariate logistic regression models.

Results:

Three SOCS-1 SNPs (rs193779, rs33989964, and rs4780355) are associated with a risk reduction for rapid progression. Two of these SNPs, rs33989964 and rs4780355, are in strong linkage disequilibrium, forming a frequent haplotype. Homozygous carriers of this haplotype are also associated with a risk reduction for rapid progression. By contrast, the minor TT genotype of rs33977706 is associated with twice the risk for rapid progression. No associations have been observed for the 4 SOCS-3 SNPs or the major SOCS-3 haplotypes.

Conclusions:

Our data suggest that SNPs in SOCS-1 are associated with HIV disease progression and speak in favor that immune activation is causal for the progressive immunodeficiency.
Outcomes of Three- Versus Six-Monthly Dispensing of Antiretroviral Treatment (ART) for Stable HIV Patients in Community ART Refill Groups: A Cluster-Randomized Trial in Zimbabwe
Authors: Fatti Geoffrey , Ngorima-Mabhena Nicoletta , Mothibi Eula , Muzenda Trish , Choto Regis , Kasu Tonderai , Tafuma Taurayi A. , Mahachi Nyika , Takarinda Kudakwashe C. , Apollo Tsitsi , Mugurungi Owen , Chasela Charles , Hoffman Risa M. , Grimwood Ashraf
Published: February 2020

Introduction:

Multimonth dispensing (MMD) of antiretroviral treatment (ART) aims to reduce patient-related barriers to access long-term treatment and improve health system efficiency. However, randomized evidence of its clinical effectiveness is lacking. We compared MMD within community ART refill groups (CARGs) vs. standard-of-care facility-based ART delivery in Zimbabwe.

Methods:

A three-arm, cluster-randomized, pragmatic noninferiority trial was performed. Thirty health care facilities and associated CARGs were allocated to either ART collected three-monthly at facility (3MF, control); ART delivered three-monthly in CARGs (3MC); or ART delivered six-monthly in CARGs (6MC). Stable adults receiving ART ≥six months with baseline viral load (VL) <1000 copies/ml were eligible. Retention in ART care (primary outcome) and viral suppression (VS) 12 months after enrollment were compared, using regression models specified for clustering (ClinicalTrials.gov: NCT03238846).

Results:

4800 participants were recruited, 1919, 1335, and 1546 in arms 3MF, 3MC, and 6MC, respectively. For retention, the prespecified noninferiority limit (-3.25%, risk difference [RD]) was met for comparisons between all arms, 3MC (94.8%) vs. 3MF (93.0%), adjusted RD = 1.1% (95% CI: -0.5% to 2.8%); 6MC (95.5%) vs. 3MF: aRD = 1.2% (95% CI: -1.0% to 3.6%); and 6MC vs. 3MC: aRD = 0.1% (95% CI: -2.4% to 2.6%). VL completion at 12 months was 49%, 45%, and 8% in 3MF, 3MC, and 6MC, respectively. VS in 3MC (99.7%) was high and not different to 3MF (99.1%), relative risk = 1.0 (95% CI: 1.0-1.0). VS was marginally reduced in 6MC (92.9%) vs. 3MF, relative risk = 0.9 (95% CI: 0.9-1.0).

Conclusion:

Retention in CARGs receiving three- and six-monthly MMD was noninferior versus standard-of-care facility-based ART delivery. VS in 3MC was high. VS in six-monthly CARGs requires further evaluation.
Simultaneous Restoration of Swallowing and Voice Function With Ileocolon Free Flap
Authors: Lo Torto Federico , Ribuffo Diego , Manrique Oscar J. , Ciudad Pedro , Mouchammed Agko , Maruccia Michele , Nicoli Fabio , Turriziani Gianmarco , Chen Hung-Chi
Published: February 2020

Background:

Free ileocolon flap is a reliable technique allowing simultaneous restoration of swallowing and speech. The aim is to report our 6-year experience in a single center.

Methods:

Thirty-seven patients treated between 2010 and 2015 were included in the study. Swallowing and speech function were evaluated in 27 patients with a 7-point and 5-point Likert scale, respectively. Moreover, 12 of them consented to voice spectrum analysis (VSA).

Results:

Complications noted were: aspiration (3), esophagocutaneous fistula (2), and stricture (1). Seven patients experienced self-limited diarrhea. Regarding swallowing function, 77.8% scored ≥5 on Likert scale whereas speech Likert scale showed excellent results (score >12) in 74%. VSA demonstrated mean phonation time of 10.75 seconds, mean frequency of 131 Hz and mean dynamic range of 56 dB.

Conclusion:

In experienced hands, the ileocolon flap is safe and effective, particularly in patients with long-life expectancy, providing good swallowing and speech function without further procedures/prostheses.
Sleep Deprivation alters the influence of biological sex on active-phase sleep behavior
Authors: Nichols India , Vincent Scott , Hesse September , Ehlen J. Christopher , Brager Allison , Paul Ketema
Published: February 2020

Poor sleep is a hazard of daily life that oftentimes cannot be avoided. Gender differences in daily sleep and wake patterns are widely reported; however, it remains unclear how biological sex, which is comprised of genetic and endocrine components, directly influences sleep regulatory processes. In the majority of model systems studied thus far, sex differences in daily sleep amount are predominant during the active (wake) phase of the sleep-wake cycle. The pervasiveness of sex differences in sleep amount throughout phylogeny suggests a strong underlying genetic component. The goal of the current study is to determine if sex differences in active-phase sleep amount are dependent on sex chromosomes in mice.

Sleep was examined in the four-core genotype (FCG) mouse model, whose sex chromosome complement (XY, XX) is independent of sex phenotype (male or female). In this line, sex phenotype is determined by the presence or absence of theSrygene, which is dissociated from the Y chromosome. Polysomnographic sleep recordings were obtained from gonadectomized (GDX) FCG mice to examine spontaneous sleep states and the ability to recover from sleep loss. We report that during the active-phase, the presence of theSrygene accounts for most sex differences during spontaneous sleep; however, during recovery from sleep loss, sex differences in sleep amount are partially driven by sex chromosome complement. These results suggest that genetic factors on the sex chromosomes encode the homeostatic response to sleep loss.
Imaging cell lineage with a synthetic digital recording system
Authors: Chow Ke-Huan K. , Budde Mark W. , Granados Alejandro A. , Cabrera Maria , Yoon Shinae , Cho Soomin , Huang Ting-hao , Koulena Noushin , Frieda Kirsten L. , Cai Long , Lois Carlos , Elowitz Michael B.
Published: February 2020

Multicellular development depends on the differentiation of cells into specific fates with precise spatial organization. Lineage history plays a pivotal role in cell fate decisions, but is inaccessible in most contexts. Engineering cells to actively record lineage information in a format readablein situwould provide a spatially resolved view of lineage in diverse developmental processes. Here, we introduce a serine integrase-based recording system that allowsin situreadout, and demonstrate its ability to reconstruct lineage relationships in cultured stem cells and flies. The system, termed intMEMOIR, employs an array of independent three-state genetic memory elements that can recombine stochastically and irreversibly, allowing up to 59,049 distinct digital states. intMEMOIR accurately reconstructed lineage trees in stem cells and enabled simultaneous analysis of single cell clonal history, spatial position, and gene expression inDrosophilabrain sections. These results establish a foundation for microscopy-readable clonal analysis and recording in diverse systems.

One sentence summary

A new genetic editing system termed intMEMOIR reveals the lineage histories of individual cells directly within their native tissue context.
Machine Learning Based Refined Differential Gene Expression Analysis of Pediatric Sepsis
Authors: Abbas Mostafa , EL-Manzalawy Yasser
Published: February 2020

Abstract

Background

Differential expression (DE) analysis of transcriptomic data enables genome-wide analysis of gene expression changes associated with biological conditions of interest. Such analysis often provide a wide list of genes that are differentially expressed between two or more groups. In general, identified differentially expressed genes (DEGs) can be subject to further downstream analysis for obtaining more biological insights such as determining enriched functional pathways or gene ontologies. Furthermore, DEGs are treated as candidate biomarkers and a small set of DEGs might be identified as biomarkers using either biological knowledge or data-driven approaches.

Methods

In this work, we present a novel approach for identifying biomarkers from a list of DEGs by re-ranking them according to the Minimum Redundancy Maximum Relevance (MRMR) criteria using repeated cross-validation feature selection procedure.

Results

Using gene expression profiles for 199 children with sepsis and septic shock, we identify 108 DEGs and propose a 10-gene signature for reliably predicting pediatric sepsis mortality with an estimated Area Under ROC (AUC) score of 0.89.

Conclusions

Machine learning based refinement of DE analysis is a promising tool for prioritizing DEGs and discovering biomarkers from gene expression profiles. Moreover, our reported 10-gene signature for pediatric sepsis mortality may facilitate the development of reliable diagnosis and prognosis biomarkers for sepsis.
Ketogenic Diet Prevents Heart Failure from Defective Mitochondrial Pyruvate Metabolism
Authors: McCommis Kyle S. , Kovacs Attila , Weinheimer Carla J. , Shew Trevor M. , Koves Timothy R. , Ilkayeva Olga R. , Kamm Dakota R. , Pyles Kelly D. , King M. Todd , Veech Richard L. , DeBosch Brian J. , Muoio Deborah M. , Gross Richard W. , Finck Brian N.
Published: February 2020

The myocardium is metabolically flexible and can use fatty acids, glucose, lactate/pyruvate, ketones, or amino acids to fuel mechanical work. However, impaired metabolic flexibility is associated with cardiac dysfunction in conditions including diabetes and heart failure. The mitochondrial pyruvate carrier (MPC) is required for pyruvate metabolism and is composed of a hetero-oligomer of two proteins known as MPC1 and MPC2. Interestingly, MPC1 and MPC2 expression is downregulated in failing human hearts and in a mouse model of heart failure. Mice with cardiac-specific deletion of MPC2 (CS-MPC2-/-) exhibited loss of both MPC2 and MPC1 proteins and reduced pyruvate-stimulated mitochondrial respiration. CS-MPC2-/- mice exhibited normal cardiac size and function at 6-weeks old, but progressively developed cardiac dilation and contractile dysfunction thereafter. Feeding CS-MPC2-/- mice a ketogenic diet (KD) completely prevented or reversed the cardiac remodeling and dysfunction. Other diets with higher fat content and enough carbohydrate to limit ketosis also improved heart failure in CS-MPC2-/- mice, but direct ketone body provisioning provided only minor improvements in cardiac remodeling. Finally, KD was also able to prevent further remodeling in an ischemic, pressure-overload mouse model of heart failure. In conclusion, loss of mitochondrial pyruvate utilization leads to dilated cardiomyopathy that can be corrected by a ketogenic diet.
Transcriptional control of parallel-acting pathways that remove discrete presynaptic proteins in remodeling neurons
Authors: Miller-Fleming Tyne W. , Cuentas-Condori Andrea , Manning Laura , Palumbos Sierra , Richmond Janet E. , Miller David M.
Published: February 2020

Synapses are actively dismantled to mediate circuit refinement, but the developmental pathways that regulate synaptic disassembly are largely unknown. We have previously shown that the epithelial sodium channel UNC-8 triggers an activity-dependent mechanism that drives the removal of presynaptic proteins liprin-α/SYD-2, Synaptobrevin/SNB-1, RAB-3 and Endophilin/UNC-57 in remodeling GABAergic neurons inC. elegans(Miller-Fleming et al., 2016). Here, we report that the transcription factor Iroquois/IRX-1 regulates UNC-8 expression as well as an additional pathway, independent of UNC-8, that functions in parallel to dismantle functional presynaptic terminals. We show that the additional IRX-1-regulated pathway is selectively required for the removal of the presynaptic proteins, Munc13/UNC-13 and ELKS, which normally mediate synaptic vesicle fusion and neurotransmitter release. Our findings are notable because they highlight the key role of transcriptional regulation in synapse elimination and reveal parallel-acting pathways that orchestrate synaptic disassembly by removing specific active zone proteins.
Clinical and genomic epidemiology of carbapenem-non-susceptibleCitrobacterspp. at a tertiary healthcare center over two decades
Authors: Babiker Ahmed , Evans Daniel R. , Griffith Marissa P. , McElheny Christi L. , Hassan Mohamed , Clarke Lloyd G. , Mettus Roberta T. , Harrison Lee H. , Doi Yohei , Shields Ryan K. , Van Tyne Daria
Published: February 2020

Carbapenem-non-susceptibleCitrobacterspp. (CNSC) are increasingly recognized as healthcare-associated pathogens. Information regarding their clinical epidemiology, genetic diversity, and mechanisms of carbapenem resistance is lacking. We examined microbiology records of adult patients at the University of Pittsburgh Medical Center (UMPC) Presbyterian Hospital (PUH) from 2000-2018 for CNSC, as defined by ertapenem non-susceptibility. Over this timeframe, the proportion of CNSC increased from 4% to 10% (P=0.03), as did carbapenem daily defined doses/1000 patient days (6.52 to 34.5, R2=0.831,P<0.001), which correlated with the observed increase in CNSC (lag=0 years, R2=0.660). Twenty CNSC isolates from 19 patients at PUH and other UPMC hospitals were available for further analysis, including whole-genome short-read sequencing and additional antimicrobial susceptibility testing. Of the 19 patients, nearly all acquired CNSC in the healthcare setting and over half had polymicrobial cultures containing at least one other organism. Among the 20 CNSC isolates,C. freundiiwas the predominant species identified (60%). CNSC genomes were compared with genomes of carbapenem-susceptibleCitrobacterspp. from UPMC, and with other publicly available CNSC genomes. Isolates encoding carbapenemases (blaKPC-2,blaKPC-3, andblaNDM-1) were also long-read sequenced, and their carbapenemase-encoding plasmid sequences were compared with one another and with publicly available sequences. Phylogenetic analysis of 102 UPMCCitrobacterspp. genomes showed that CNSC from our setting did not cluster together. Similarly, a global phylogeny of 64 CNSC genomes showed a diverse population structure. Our findings suggest that both local and global CNSC populations are genetically diverse, and that CNSC harbor carbapenemase-encoding plasmids found in otherEnterobacterales.
“Polar mutagenesis of bacterial transcriptional units using Cas12a”
Authors: Graffeuil Antoine , Uhlin Bernt Eric , Cisneros David A.
Published: February 2020

Bacterial genes are often organized in functionally related transcriptional units or operons. One such example is thefimAICDFGHoperon, which codes for type I fimbriae inEscherichia coli. We tested the hypothesis that markerless polar mutations could be efficiently engineered using CRISPR/Cas12a in thefimoperon. Cas12a-mediated engineering of a terminator sequence inside thefimAgene occurred with efficiencies between 10 and 30%, whilst other types of mutations, such as a 97 bp deletion, occurred with 100% efficiency. Our results showed that some of the obtained mutants, including one with a single base substitution at thefimlocus, had decreased mRNA levels offimA, suggesting that the regulation of thefimoperon was disrupted. We corroborated the polar effect of these mutants by phenotypic assays and quantitative PCR, showing up to a 43 fold decrease in expression of genes downstreamfimA. We believe this strategy could be useful in engineering the transcriptional shut-down of multiple genes in one single step. For bio-production inE. coli, this opens the possibility of inhibiting competing metabolic routes.
A CURE for physiological characterization of bacterioplankton in liquid culture
Authors: Lanclos V. Celeste , Coelho Jordan T. , Hyer Alex J. , Brooks Mindy M. , Savoie Emily R. , Kosiba Scott , Thrash J. Cameron
Published: February 2020

Bacterial characterization is an important aspect of microbiology that includes experimentally determining growth rates, environmental conditions conducive to growth, and the types of energy sources microorganisms can use. Researchers use this information to help understand and predict an organism’s ecological distribution and environmental functions. Microbiology students generally conduct bacterial characterization experiments in their coursework; however they are frequently restricted to model organisms without ecological relevance and for which the results have been known for decades. We present a course-based undergraduate research experience (CURE) curriculum to involve students in characterization of previously untested, ecologically relevant bacterioplankton cultures to identify the carbon substrates used for growth, as well as the temperature and salinity ranges conducive to growth. Students use these results to connect their organism’s physiology to the isolation environment. This curriculum also exposes students to advanced microbiology methods such as flow cytometry for measuring cell concentrations, teaches them to use the programming language R for data plotting, and emphasizes scientific communication through writing, speaking, poster creation/presentation, and social media. This CURE is an attractive introduction to scientific research and was successfully tested with 147 students during the fall semester of 2018.
AmpliCI: A High-resolution Model-Based Approach for Denoising Illumina Amplicon Data
Authors: Peng Xiyu , Dorman Karin
Published: February 2020

Motivation

Next-generation amplicon sequencing is a powerful tool for investigating microbial communities. One main challenge is to distinguish true biological variants from errors caused by PCR and sequencing. In the traditional analysis pipeline, such errors are eliminated by clustering reads within a sequence similarity threshold, usually 97%, and constructing operational taxonomic units, but the arbitrary threshold leads to low resolution and high false positive rates. Recently developed “denoising” methods have proven able to resolve single-nucleotide amplicon variants, but they still miss low frequency sequences, especially those near abundant variants, because they ignore the sequencing quality information.

Results

We introduce AmpliCI, a reference-free, model-based method for rapidly resolving the number, abundance and identity of error-free sequences in massive Illumina amplicon datasets. AmpliCI takes into account quality information and allows the data, not an arbitrary threshold or an external database, to drive conclusions. AmpliCI estimates a finite mixture model, using a greedy strategy to gradually select error-free sequences and approximately maximize the likelihood. We show that AmpliCI is superior to three popular denoising methods, with acceptable computation time and memory usage.

Availability

Source code available athttps://github.com/DormanLab/AmpliCI
Cryo-EM structures of HKU2 and SADS-CoV spike glycoproteins and insights into coronavirus evolution
Authors: Yu Jinfang , Qiao Shuyuan , Guo Runyu , Wang Xinquan
Published: February 2020

A new porcine coronavirus SADS-CoV was recently identified from suckling piglets with severe diarrhea in southern China and its genome sequence is most identical (~95% identity) to that of bat α-coronavirus HKU2. It again indicates bats are the natural reservoir of many coronaviruses that have great potential for cross-species transmission to animals and humans by recombination and/or mutation. Here we report the cryo-EM structures of HKU2 and SADS-CoV spike glycoprotein trimers at 2.38 Å and 2.83 Å resolution, respectively. HKU2 and SADS-CoV spikes exhibit very high structural similarity, with subtle differences mainly distributed in the NTD and CTD of the S1 subunit responsible for cell attachment and receptor binding. We systematically analyzed and compared the NTD, CTD, SD1 and SD2 domains of the S1 subunit and the S2 subunit of HKU2 spike with those of α-, β-, γ-, and δ-coronavirus spikes. The results show that the NTD and CTD of HKU2/SADS-CoV are probably the most ancestral in the evolution of spike. Although the S2 subunit mediating membrane fusion is highly conserved, the connecting region after fusion peptide in HKU2/SADS-CoV S2 subunit also adopts a conformation distinct from other coronaviruses. These results structurally demonstrate a close evolutionary relationship between HKU2 /SADS-CoV and β-coronavirus spikes and provide new insights into the evolution and cross-species transmission of coronaviruses.
Prebiotically-relevant low polyion multivalency can improve functionality of membraneless compartments
Authors: Cakmak Fatma Pir , Choi Saehyun , Meyer McCauley O. , Bevilacqua Philip C. , Keating Christine D.
Published: February 2020

Multivalent polyions can undergo complex coacervation, producing membraneless compartments that accumulate ribozymes and enhance catalysis, and offering a mechanism for functional prebiotic compartmentalization in the origins of life. Here, we evaluated the impact of low, prebiotically-relevant polyion multivalency in coacervate performance as functional compartments. As model polyions, we used positively and negatively charged homopeptides with one to 100 residues, and adenosine mono-, di-, and triphosphate nucleotides. Polycation/polyanion pairs were tested for coacervation, and resulting membraneless compartments were analyzed for salt resistance, ability to provide a distinct internal microenvironment (apparent local pH, RNA partitioning), and effect on RNA structure formation. We find that coacervates formed by phase separation of the relatively shorter polyions more effectively generated distinct pH microenvironments, accumulated RNA, and preserved duplexes. Hence, reduced multivalency polyions are not only viable as functional compartments for prebiotic chemistries, but they can offer advantages over higher molecular weight analogues.
Barriers to coexistence limit the poleward range of a globally-distributed plant
Authors: Armitage David W. , Jones Stuart E.
Published: February 2020

Species’ poleward ranges are thought to be primarily limited by climatic constraints rather than biotic interactions such as competition. However, theory suggests that a species’ tolerance to competition is reduced in harsh environments, such as at the extremes of its climatic niche. This implies that under certain conditions, interspecific competition near species’ range margins can prevent the establishment of populations into otherwise tolerable environments and results in geographic distributions being shaped by the interaction of climate and competition. We test this prediction by challenging an experimentally-parameterized mechanistic competition model to predict the poleward range boundaries of two widely co-occurring and ecologically-similar aquatic duckweed plants. We show that simple, mechanistic ecological niche models which include competition and thermal response terms best predict the northern range limits of our study species, outperforming competition-free mechanistic models and matching the predictive ability of popular statistical niche models fit to occurrence records. Next, using the theoretical framework of modern coexistence theory, we show that relative nonlinearity in competitors’ responses to temperature fluctuations maintains coexistence at the subordinate competitor’s poleward range boundary, highlighting the importance of this underappreciated fluctuation-dependent coexistence mechanism. Our results demonstrate the predictive utility of mechanistic niche models and support a more nuanced, interactive role of climate and species interactions in determining range boundaries, which may help explain the conflicting results from previous tests of classic range limit theory and contribute to a more mechanistic understanding of range dynamics under global change.
The Drosophila HP1 family is associated with active gene expression across chromatin contexts
Authors: Schoelz John M. , Feng Justina X. , Riddle Nicole C.
Published: February 2020

Drosophila Heterochromatin Protein 1a (HP1a) is essential for heterochromatin formation and is involved in transcriptional silencing. However, certain loci require HP1a to be transcribed properly. One model posits that HP1a acts as a transcriptional silencer within euchromatin while acting as an activator within heterochromatin. However, HP1a has been observed as an activator of a set of euchromatic genes. Therefore, it is not clear whether, or how, chromatin context informs the function of HP1 proteins. To understand the role of HP1 proteins in transcription, we examined the genome-wide binding profile of HP1a as well as two other Drosophila HP1 family members, HP1B and HP1C, to determine whether coordinated binding of these proteins is associated with specific transcriptional outcomes. We found that HP1 proteins share a majority of their endogenous binding targets. These genes are marked by active histone modifications and are expressed at higher levels than non-target genes in both heterochromatin and euchromatin. In addition, HP1 binding targets displayed increased RNA polymerase pausing compared to non-target genes. Specifically, co-localization of HP1B and HP1C was associated with the highest levels of polymerase pausing and gene expression. Analysis of HP1 null mutants suggests these proteins coordinate activity at transcription start sites (TSSs) to regulate transcription. Depletion of HP1B or HP1C alters expression of protein-coding genes bound by HP1 family members. Our data broadens understanding of the mechanism of transcriptional activation by HP1a and highlights the need to consider particular protein-protein interactions, rather than broader chromatin context, to predict impacts of HP1 at TSSs.
Convergent Evolution of Conserved Mitochondrial Pathways Underlies Repeated Adaptation to Extreme Environments
Authors: Greenway Ryan , Barts Nick , Henpita Chathurika , Brown Anthony P. , Rodriguez Lenin Arias , Rodríguez Peña Carlos M. , Arndt Sabine , Lau Gigi Y. , Murphy Michael P. , Wu Lei , Lin Dingbo , Shaw Jennifer H. , Kelley Joanna L. , Tobler Michael
Published: February 2020

Extreme environments test the limits of life; yet, some organisms thrive in harsh conditions. Extremophile lineages inspire questions about how organisms can tolerate physiochemical stressors and whether the repeated colonization of extreme environments is facilitated by predictable and repeatable evolutionary innovations. We identified the mechanistic basis underlying convergent evolution of tolerance to hydrogen sulfide (H2S)—a toxicant that impairs mitochondrial function—across evolutionarily independent lineages of a fish (Poecilia mexicana, Poeciliidae) from H2S-rich springs. Using comparative biochemical and physiological analyses, we found that mitochondrial function is maintained in the presence of H2S in sulfide springP. mexicana, but not ancestral lineages from nonsulfidic habitats, due to convergent adaptations in the primary toxicity target and a major detoxification enzyme. Genome-wide local ancestry analyses indicated that convergent evolution of increased H2S tolerance in different populations is likely caused by a combination of selection on standing genetic variation andde novomutations. At a macroevolutionary scale, H2S tolerance in 10 independent lineages of sulfide spring fishes across multiple genera of Poeciliidae is correlated with the convergent modification and expression changes of genes associated with H2S toxicity and detoxification. Our results demonstrate that the modification of highly conserved physiological pathways associated with essential mitochondrial processes mediates tolerance to physiochemical stress. In addition, the same pathways, genes, and—in some instances—codons are implicated in H2S adaptation in lineages that span 40 million years of evolution.

Significance Statement

Some organisms can tolerate environments lethal for most others, but we often do not know what adaptations allow them to persist and whether the same mechanisms underly adaptation in different lineages exposed to the same stressors. Investigating fish inhabiting springs rich in toxic hydrogen sulfide (H2S), we show that tolerance is mediated by the modification of pathways that are inhibited by H2S and those that can detoxify it. Sulfide spring fishes across multiple genera have evolved similar modifications of toxicity targets and detoxification pathways, despite abundant lineage-specific variation. Our study highlights how constraints associated with the physiological consequences of a stressor limit the number of adaptive solutions and lead to repeatable evolutionary outcomes across organizational and evolutionary scales.
Dpp and Hedgehog promote the Glial response to neuronal damage in the developing Drosophila Visual system
Authors: Velarde Sergio B. , Quevedo Alvaro , Estella Carlos , Baonza Antonio
Published: February 2020

Damage in the nervous system induces a stereotypical response that is mediated by glial cells. Here, we use the eye disc to explore the mechanisms involved in promoting glial cell response after neural injuries. We demonstrate that eye glia cells rapidly respond to neuronal injury by increasing in number and undergoing morphological changes, which grant them phagocytic abilities. We found that this glial response is controlled by the activity of the long-range signalling pathways,decapentaplegic(dpp) andhedgehog(hh). These pathways are activated in the damaged region and their functions are necessary for inducing glial cell proliferation and migration to the eye discs. The latter of these two processes depends on the function of the JNK pathway, which is cooperatively activated bydppandhhsignalling.
Basal leakage in oscillation: coupled transcriptional and translational control using feed-forward loops
Authors: Joanito Ignasius , Yan Ching-Cher Sanders , Chu Jhih-Wei , Wu Shu-Hsing , Hsu Chao-Ping
Published: February 2020

The circadian clock is a complex system that plays many important roles in most organisms. Previously, many mathematical models have been used to sharpen our understanding of theArabidopsisclock. However, these models are mostly dependent on transcriptional regulation, and the importance of post-translational regulation is still rarely discussed from theoretical aspects. In this study, we built a series of simplified oscillators with different regulations to study the importance of post-translational regulation (specifically, 26S proteasome degradation) in the clock system. We found that a simple transcriptional-based oscillator can already generate sustained oscillation, but the oscillation can be easily destroyed in the presence of transcriptional leakage. Coupling post-translational control with transcriptional-based oscillator in a feed-forward loop will greatly improve the robustness of the oscillator in the presence of basal leakage. Using these general models, we were able to replicate the increased variability observed in the E3 ligase mutant for both plant and mammalian clocks. With this insight, we also predict a plausible regulator of several E3 ligase genes in the plant’s clock. Thus, our results provide insights into and the plausible importance in coupling transcription and post-translation controls in the clock system.

Author summary

For circadian clocks, several current models had successfully captured the essential dynamic behavior of the clock system mainly with transcriptional regulation. Previous studies have shown that the 26s (1, 2) proteasome degradation controls are important in maintaining the stability of circadian rhythms. However, how the loss-of-function or over-expression mutant of this targeted degradations lead to unstable oscillation is still unclear. In this work, we investigate the importance of coupled transcriptional and post-translational feedback loop in the circadian oscillator. With general models our study indicate that the unstable behavior of degradation mutants could be caused by the increase in the basal level of the clock genes. We found that coupling a non-linear degradation control into this transcriptional based oscillator using feed-forward loop improves the robustness of the oscillator. Using this finding, we further predict some plausible regulators of Arabidopsis’s E3 ligase protein such as COP1 and SINAT5. Hence, our results provide insights on the importance of coupling transcription and post-translation controls in the clock system.
A pan-cancer analysis of the frequency of DNA alterations across cell cycle activity levels
Authors: Lundberg Arian , Lindström Linda S. , Parker Joel S. , Löverli Elinor , Perou Charles M. , Bergh Jonas , Tobin Nicholas P.
Published: February 2020

Background

Pan-cancer genomic analyses based on the magnitude of pathway activity are currently lacking. Focusing on the cell cycle, we examined the DNA mutations and chromosome arm-level aneuploidy within tumours with low, intermediate and high cell cycle activity.

Patients and methods

Matching mRNA, gene mutational status, chromosomal arm-level aberrations and clinico-pathological data was assembled from pan-cancer studies of 9,515 patients with 32 different cancers. Cell cycle activity was estimated from mRNA data using the cell cycle score (CCS) signature. Barplots were used to visualise mutation and chromosomal aberration frequency within CCS subgroups. Kaplan-Meier and multivariable Cox-regression analyses were used to determine survival differences between CCS subgroups.

Results

Cell cycle activity varied broadly across and within all cancers.TP53andPIK3CAmutations were common in all CCS subgroups but with increasing frequency as cell cycle activity levels increased (P< 0.001). Mutations inBRAFand gains in 16p were less frequent CCS high tumours (P< 0.001). In Kaplan-Meier analysis, patients whose tumours were CCS Low had a longer PFI relative to intermediate or high (P< 0.001) and this significance remained in multivariable analysis (CCS intermediate: HR = 1.37; 95% CI 1.17 – 1.60, CCS high: 1.54; 1.29 – 1.84, CCS Low = Ref).

Conclusions

Cell cycle activity varies across and within cancers and whilst similar DNA alterations can be found at all activity levels, some notable exceptions exist. These data also demonstrate that independent prognostic information can be derived on a pan-cancer level from a simple measure of cell cycle activity.
Polycystin-2 (TRPP2) Regulates Primary Cilium Length in LLC-PK1 Renal Epithelial Cells
Authors: Perez Paula L. , Scarinci Noelia , Cantiello Horacio F. , del Rocío Cantero María
Published: February 2020

Polycystin-2 (PC2, TRPP2) is a Ca2+permeable non-selective cation channel whose dysfunction generates autosomal dominant polycystic kidney disease (ADPKD). PC2 is present in different cell locations, including the primary cilium of renal epithelial cells. Little is known, however, as to whether PC2 contributes to the structure of the primary cilium. Here, we explored the effect(s) of external Ca2+, PC2 channel blockers, andPKD2gene silencing on the length of primary cilia in wild type LLC-PK1 renal epithelial cells. To identify primary cilia and measure their length, confluent cell monolayers were fixed and immuno-labeled with an anti-acetylated α-tubulin antibody. Although primary cilia length measurements did not follow a Normal distribution, data were normalized by Box-Cox transformation rendering statistical difference under all experimental conditions. Cells exposed to high external Ca2+(6.2 mM) decreased a 13.5% (p < 0.001) primary cilia length as compared to controls (1.2 mM Ca2+). In contrast, the PC2 inhibitors amiloride (200 μM) and LiCl (10 mM), both increased primary ciliary length by 33.2% (p < 0.001), and 17.4% (p < 0.001), respectively.PKD2gene silencing by siRNA also elicited a statistically significant, 10.3% (p < 0.001) increase in primary cilia length, as compared to their respective scrambled RNA transfected cells. The data indicate that maneuvers that either regulate PC2 function or gene expression, modify the length of primary cilia in renal epithelial cells. Proper regulation of PC2 function in the primary cilium may be essential in the onset of mechanisms that trigger cyst formation in ADPKD.

Significance Statement

Polycystin-2 (PC2, TRPP2) is a Ca2+permeable non-selective cation channel causing the autosomal dominant polycystic kidney disease (ADPKD). The importance of intact cilia and of fully functional polycystins in the onset of ADPKD cyst formation, point to yet unknown signaling mechanisms occurring within this organelle. We determined that the extracellular Ca2+concentration, PC2 channel blockers, andPKD2gene silencing, all contribute to the length of primary cilia in wild type LLC-PK1 renal epithelial cells. The data indicate that proper regulation of PC2 function in the primary cilium may be essential in the onset of mechanisms that trigger cyst formation in ADPKD.
Infra-slow modulation of fast beta/gamma oscillations in the mouse visual system
Authors: Orlowska-Feuer Patrycja , Allen Annette Elisabeth , Brown Timothy Matthew , Szkudlarek Hanna Jowita , Lucas Robert James , Storchi Riccardo
Published: February 2020

Infra-slow (<0.02 Hz) and fast beta/gamma (20 – 100 Hz) oscillations in neurophysiological activity have been widely found in the subcortical visual system. While it is well established that fast beta/gamma oscillations are involved in visual processing, the role (if any) of infra-slow oscillations is currently unknown. One possibility is that infra-slow oscillations exert influence by modulating the amplitude of fast oscillations, yet the extent to which these different oscillations arise independently and interact remains unknown. We addressed these questions by recordingin vivospontaneous activity from subcortical visual system of visually intact mice, and animals whose retinal network was disrupted by advanced rod/cone degeneration (rd/rd cl) or melanopsin loss(Opn4-/-We found many neurons expressing only one type of oscillation, and indeed fast oscillations were absent inrd/rd cl.Conversely, neurons co-expressing the two oscillations were also common, and were encountered more often than expected by chance in visually intact but notOpn4-/-mice. Finally, where they co-occurred we found that beta/gamma amplitude was modulated by the infra-slow rhythm. Our data thus reveal that: 1.) infra-slow and beta-gamma oscillations are separable phenomena; and 2.) that they actively co-occur in a subset of neurones in which the phase of infra-slow oscillations define beta-gamma oscillation amplitude. These findings suggest that infra-slow oscillations could influence vision by modulating beta-gamma oscillations, and raise the possibility that disruptions in these oscillatory behaviours contribute to vision dysfunction in retinal dystrophy.

KEY POINTS SUMMARY

Neurophysiological activity in the subcortical visual system fluctuates in both infra-slow and fast oscillatory ranges, however the level of co-occurrence and potential functional interaction of these rhythms is unknown.

Analyzing dark-adapted spontaneous activity in the mouse subcortical visual system, we find that these two types of oscillation interact uniquely through a population of neurons expressing both rhythms.

Genetic ablation of rod/cone signaling potentiates infra-slow and abolishes fast beta/gamma oscillations while genetic ablation of melanopsin substantially diminishes the interaction between these two rhythms.

Our results indicate that in an intact visual system the phase of infra-slow modulates fast beta/gamma oscillations.

Thus one possible impact of infra-slow oscillations in vision is to guide visual processing by interacting with fast narrowband oscillations.
Copper nanoparticle application enhances plant growth and grain yield in maize under drought stress conditions
Authors: Nguyen Dong Van , Nguyen Huong Mai , Le Nga Thanh , Nguyen Kien Huu , Le Huong Mai , Nguyen Anh Trung , Dinh Ngan Thi Thu , Hoang Son Anh , Ha Chien Van
Published: February 2020

Abiotic stresses, including drought, detrimentally affect the growth and productivity of many economically important crop plants, leading to significant yield losses, which can result in food shortages and threaten the sustainability of agriculture. Balancing between plant growth and stress responses is one of the most important characters for agricultural application to maximize plant production. In this study, we initially report that copper nanoparticle priming positively regulates drought stress responses in maize. The copper nanoparticle priming plants displayed enhanced drought tolerance indicated by their higher leaf water content and plant biomass under drought as compared with water-treated plants. Moreover, our data showed that the treatment of copper nanoparticle on plants increased anthocyanin, chlorophyll and carotenoid contents compared to water-treated plants under drought stress conditions. Additionally, histochemical analyses with nitro blue tetrazolium and 3,3’-diaminobenzidine revealed that reactive oxygen species accumulation of priming plants was decreased as a result of enhancement of reactive oxygen species scavenging enzyme activities under drought. Furthermore, our comparative yield analysis data indicated applying copper nanoparticle to plant increased total seed number and grain yield under drought stress conditions. Our data provided the evidences that copper nanoparticle regulates plant protective mechanisms associated with drought tolerance, which is a promising approach for the production of drought tolerant crop plants.
A self-initiated cue-reward learning procedure for neural recording in rodents
Authors: Reverte Ingrid , Volz Stephen , Alhazmi Fahd H. , Kang Mihwa , Kaufman Keith , Chan Sue , Jou Claudia , Iordanova Mihaela D. , Esber Guillem R.
Published: February 2020

Background

Single-unit recording in Pavlovian conditioning tasks requires the use of within-subject designs as well as sampling a considerable number of trials per trial type and session, which increases the total trial count. Pavlovian conditioning, on the other hand, requires a long average intertrial interval (ITI) relative to cue duration for cue-specific learning to occur. These requirements combined can make the session duration unfeasibly long.

New Method

To circumvent this issue, we developed a self-initiated variant of the Pavlovian magazine-approach procedure in rodents. Unlike the standard procedure, where the animals passively receive the trials, the self-initiated procedure grants animals agency to self-administer and self-pace trials from a predetermined, pseudorandomized list. Critically, whereas in the standard procedure the typical ITI is in the order of minutes, our procedure uses a much shorter ITI (10 s).

Results

Despite such a short ITI, discrimination learning in the self-initiated procedure is comparable to that observed in the standard procedure with a typical ITI, and superior to that observed in the standard procedure with an equally short ITI.

Comparison with Existing Method(s)

The self-initiated procedure permits delivering 100 trials in a ∼1-h session, almost doubling the number of trials safely attainable over that period with the standard procedure.

Conclusions

The self-initiated procedure enhances the collection of neural correlates of cue-reward learning while producing good discrimination performance. Other advantages for neural recording studies include ensuring that at the start of each trial the animal is engaged, attentive and in the same location within the conditioning chamber.