bluuebunny/crossref_metadata_2025 huggingface dataset:
A quantitative model for metabolic intervention using gut microbes
Authors: Mays Zachary JS , Nair Nikhil U
Published: April 2020

As medicine shifts toward precision-based and personalized therapeutics, utilizing more complex biomolecules to treat increasingly difficult and rare conditions, microorganisms provide an avenue for realizing the production and processing necessary for novel drug pipelines. More so, probiotic microbes can be co-opted to deliver therapeutics by oral administration as living drugs, able to survive and safely transit the digestive tract. As living therapeutics are in their nascency, traditional pharmacokinetic-pharmacodynamic (PK-PD) models for evaluating drug candidates are not appropriate for this novel platform. Using a living therapeutic in late-stage clinical development for phenylketonuria (PKU) as a case study, we adapt traditional oral drug delivery models to properly evaluate and inform the engineering of living therapeutics. We develop theadapted forlivingtherapeuticscompartmentalabsorption andtransit (ALT-CAT) model to provide metrics for drug efficacy across nine age groups of PKU patients and evaluate model parameters that are influenced by patient physiology, microbe selection and therapeutic production, and dosing formulations.

Importance

This work describes a kinetic model to study the behavior of orally delivered living therapeutics. Such therapeutics are becoming increasingly relevant and are an exciting mode of drug delivery that stems from the growing interest through the convergence of advances in synthetic biology of probiotics and gut microbes as well as microbiome science. In particular, this work describes the development of a mathematical framework (pharmacokinetic-pharmacodynamic, PK-PD) called ALT-CAT to model the behavior of orally delivered engineered bacteria that act as living therapeutics by adapting similar methods that have been developed and widely-used for small molecular drug delivery and absorption.
Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing
Authors: Kellman Benjamin P. , Baghdassarian Hratch M. , Pramparo Tiziano , Shamie Isaac , Gazestani Vahid , Begzati Arjana , Li Shengzhong , Nalabolu Srinivasa , Murray Sarah , Lopez Linda , Pierce Karen , Courchesne Eric , Lewis Nathan E.
Published: April 2020

RNA-Seq is ubiquitous, but depending on the study, sub-optimal sample handling may be required, resulting in repeated freeze-thaw cycles. However, little is known about how each cycle impacts downstream analyses, due to a lack of study and known limitations in common RNA quality metrics, e.g., RIN, at quantifying RNA degradation following repeated freeze-thaws. Here we quantify the impact of repeated freeze-thaw on the reliability of downstream RNA-Seq analysis. To do so, we developed a method to estimate the relative noise between technical replicates independently of RIN. Using this approach we inferred the effect of both RIN and the number of freeze-thaw cycles on sample noise. We find that RIN is unable to fully account for the change in sample noise due to freeze-thaw cycles. Additionally, freeze-thaw is detrimental to sample quality and differential expression (DE) reproducibility, approaching zero after three cycles for poly(A)-enriched samples, wherein the inherent 3’ bias in read coverage is more exacerbated by freeze-thaw cycles, while ribosome-depleted samples are less affected by freeze-thaws. The use of poly(A)-enrichment for RNA sequencing is pervasive in library preparation of frozen tissue, and thus, it is important during experimental design and data analysis to consider the impact of repeated freeze-thaw cycles on reproducibility.
Genome-wide association study in New YorkPhytophthora capsiciisolates reveals loci involved in mating type and mefenoxam sensitivity
Authors: Vogel Gregory , Gore Michael A. , Smart Christine D.
Published: April 2020

Phytophthora capsiciis a soilborne oomycete plant pathogen that causes severe vegetable crop losses in New York (NY) State and worldwide. This pathogen is difficult to manage, in part due to its production of long-lasting sexual spores and its tendency to quickly evolve fungicide resistance. We single-nucleotide polymorphism (SNP) genotyped 252P. capsiciisolates, predominantly from NY, in order to conduct a genome-wide association study for mating type and mefenoxam insensitivity. The population structure and extent of chromosomal copy number variation in this collection of isolates were also characterized. Population structure analyses showed isolates largely clustered by the field site where they were collected, with values of FSTbetween pairs of fields ranging from 0.10 to 0.31. Thirty-three isolates were putative aneuploids, demonstrating evidence for having up to four linkage groups present in more than two copies, and an additional two isolates appeared to be genome-wide triploids. Mating type was mapped to a region on scaffold 4, consistent with previous findings, and mefenoxam insensitivity was associated with several SNP markers at a novel locus on scaffold 62. We identified several candidate genes for mefenoxam sensitivity, including a homolog of yeast ribosome synthesis factor Rrp5, but failed to locate near the scaffold 62 locus any subunits of RNA Polymerase I, the enzyme that has been hypothesized to be the target site of phenylamide fungicides in oomycetes. This work expands our knowledge of the population biology ofP. capsiciand provides a foundation for functional validation of candidate genes associated with epidemiologically important phenotypes.
Admixture has obscured signals of historical hard sweeps in humans
Authors: Souilmi Yassine , Tobler Raymond , Johar Angad , Williams Matthew , Grey Shane T. , Schmidt Joshua , Teixeira João C. , Rohrlach Adam , Tuke Jonathan , Johnson Olivia , Gower Graham , Turney Chris , Cox Murray , Cooper Alan , Huber Christian D.
Published: April 2020

The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied upon genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has likely been underappreciated in the evolutionary history of humans and suggests that our current understanding of the tempo and mode of selection in natural populations may be quite inaccurate.
A high-throughput platform for feedback-controlled directed evolution
Authors: DeBenedictis Erika A. , Chory Emma J. , Gretton Dana , Wang Brian , Esvelt Kevin
Published: April 2020

Continuous directed evolution rapidly implements cycles of mutagenesis, selection, and replication to accelerate protein engineering. However, individual experiments are typically cumbersome, reagent-intensive, and require manual readjustment, limiting the number of evolutionary trajectories that can be explored. We report the design and validation of Phage-and-Robotics-Assisted Near-Continuous Evolution (PRANCE), an automation platform for the continuous directed evolution of biomolecules that enables real-time activitydependent reporter and absorbance monitoring of up to 96 parallel evolution experiments. We use this platform to characterize the evolutionary stochasticity of T7 RNA polymerase evolution, conserve precious reagents with miniaturized evolution volumes during evolution of aminoacyl-tRNA synthetases, and perform a massively parallel evolution of diverse candidate quadruplet tRNAs. Finally, we implement a feedback control system that autonomously modifies the selection strength in response to real-time fitness measurements. By addressing many of the limitations of previous methods within a single platform, PRANCE simultaneously enables multiplexed, miniaturized, and feedback-controlled continuous directed evolution.
Sufficiency of unidirectional allostery in KaiC in generating the cyanobacterial circadian rhythm
Authors: Koda Shin-ichi , Saito Shinji
Published: April 2020

The clock protein of cyanobacteria KaiC forms a homohexamer with two ring-shaped domains, C1 and C2. These domains undergo several domain-specific conformational transitions and allosterically communicate to generate a circadian rhythm. Interestingly, experiments show a possibility that C2 is independent of C1. However, detailed interplay among them remains elusive. Here we propose a mathematical model, which explicitly considers the interplay. The allostery in KaiC is here modeled to be unidirectional from C2 to C1. We demonstrate that the unidirectional allostery is sufficient for the circadian rhythm by showing the quantitative reproducibility of various experimental data, including temperature dependence of both phosphorylation oscillation and ATPase activity. Based on the present model, we further discuss possible functional roles of the unidirectional allostery particularly in the period robustness against both protein concentration and temperature.
Automatic identification of small molecules that promote cell conversion and reprogramming
Authors: Napolitano Francesco , Rapakoulia Trisevgeni , Annunziata Patrizia , Hasegawa Akira , Cardon Melissa , Napolitano Sara , Vaccaro Lorenzo , Iuliano Antonella , Wanderlingh Luca Giorgio , Kasukawa Takeya , Medina Diego L. , Cacchiarelli Davide , Gao Xin , di Bernardo Diego , Arner Erik
Published: April 2020

Controlling cell fate has great potential for regenerative medicine, drug discovery, and basic research. Although numerous transcription factors have been discovered that are able to promote cell reprogramming and trans-differentiation, methods based on their up-regulation tend to show low efficiency. The identification of small molecules that can facilitate conversion between cell types can ameliorate this problem working through safe, rapid, and reversible mechanisms. Here we present DECCODE, an unbiased computational method for the identification of such molecules solely based on transcriptional data. DECCODE matches the largest available collection of drug-induced profiles (the LINCS database) for drug treatments against the largest publicly available dataset of primary cell transcriptional profiles (FANTOM5), to identify drugs that either alone or in combination enhance cell reprogramming and cell conversion. Extensivein silicoandin vitrovalidation of DECCODE in the context of human induced pluripotent stem cells (hIPSCs) generation shows that the method is able to prioritize drugs enhancing cell reprogramming. We also generated predictions for cell conversion with single drugs and drug combinations for 145 different cell types and made them available for further studies.
Spatial variability in the risk of death from COVID-19 in 20 regions of Italy
Authors: Mizumoto Kenji , Dahal Sushma , Chowell Gerardo
Published: April 2020

Objectives

Italy has been disproportionately affected by the COVID-19 pandemic, becoming the nation with the third highest death toll in the world as of May 10th, 2020. We analyzed the severity of COVID-19 pandemic across 20 Italian regions.

Method

We manually retrieved the daily cumulative numbers of laboratory-confirmed cases and deaths attributed to COVID-19 across 20 Italian regions. For each region, we estimated the crude case fatality ratio and time-delay adjusted case fatality ratio (aCFR). We then assessed the association between aCFR and sociodemographic, health care and transmission factors using multivariate regression analysis.

Results

The overall aCFR in Italy was estimated at 17.4%. Lombardia exhibited the highest aCFR (24.7%) followed by Marche (19.3%), Emilia Romagna (17.7%) and Liguria (17.6%). Our aCFR estimate was greater than 10% for 12 regions. Our aCFR estimates were statistically associated with population density and cumulative morbidity rate in a multivariate analysis.

Conclusion

Our aCFR estimates for overall Italy and for 7 out of 20 regions exceeded those reported for the most affected region in China. Our findings highlight the importance of social distancing to suppress incidence and reduce the death risk by preventing saturating the health care system.
The Ecology of Antihypertensives in the United States, 1997-2017
Authors: Johansen Michael E. , Niforatos Joshua D. , Sussman Jeremey B.
Published: April 2020

Background

Antihypertensives are the most used medication type in the United States, yet there remains uncertainty about the use of different antihypertensives. We sought to characterize use of antihypertensives by and within medication class(es) between 1997-2017.

Methods

A repeated cross-sectional study of 493,596 adult individuals using the 1997-2017 Medical Expenditure Panel Survey (MEPS). The Orange Book and published research were used for adjunctive information. The primary outcome was the estimated use by and within anti-hypertensive medication class(es).

Results

The proportion of individuals taking any antihypertensive during a year increased from 1997 to the early 2010’s and then remained stable. The proportion of the population taking 2 or more medications declined from 2015-2017. The proportion of adults using angiotensin II receptor-blockers (ARBs) and dihydropyridine calcium channel-blockers (CCBs) increased during the study period, while angiotensin-converting enzyme inhibitors (ACE-Is) increased until 2010 after which rates remained stable. Beta-blocker use was similar to ACE-Is with an earlier decline starting in 2012. Thiazide diuretic use increased from 1997-2007, leveled off until 2014, and declined from 2015-2017. Non-dihydropyridine CCBs use declined throughout the study. ACE-Is, ARBs, CCBs, thiazide diuretics, and loop diuretics all had one dominant in-class medication. There was a clear increase in the use of losartan within ARBs, lisinopril within ACE-Is, and amlodipine within CCBs following generic conversion. Furosemide and hydrochlorothiazide started with and maintained a dominant position in their classes. Metoprolol use increased throughout the study and became the dominant beta-blocker, while atenolol peaked around 2005 and then declined thereafter.

Conclusions

Antihypertensive classes appear to have a propensity to equilibrate to an individual medication, despite a lack of outcomes based research to compare medications within a class. Future research could focus on comparative effectiveness for within-class medications early in the life cycle of therapeutics that are probable to have wide spread use.
Using influenza surveillance networks to estimate state-specific case detection rates and forecast SARS-CoV-2 spread in the United States
Authors: Silverman Justin D. , Hupert Nathaniel , Washburne Alex D.
Published: April 2020

Detection of SARS-CoV-2 infections to date has relied on RT-PCR testing. However, a failure to identify early cases imported to a country, bottlenecks in RT-PCR testing, and the existence of infections which are asymptomatic, sub-clinical, or with an alternative presentation than the standard cough and fever have resulted in an under-counting of the true prevalence of SARS-CoV-2. Here, we show how publicly available CDC influenza-like illness (ILI) outpatient surveillance data can be repurposed to estimate the detection rate of symptomatic SARS-CoV-2 infections. We find a surge of non-influenza ILI above the seasonal average and show that this surge is correlated with COVID case counts across states. By quantifying the number of excess ILI patients in March relative to previous years and comparing excess ILI to confirmed COVID case counts, we estimate the syndromic case detection rate of SARS-CoV-2 in the US to be less than 13%. If only 1/3 of patients infected with SARS-CoV-2 sought care, the ILI surge would correspond to more than 8.7 million new SARS-CoV-2 infections across the US during the three week period from March 8 to March 28. Combining excess ILI counts with the date of onset of community transmission in the US, we also show that the early epidemic in the US was unlikely to be doubling slower than every 4 days. Together these results suggest a conceptual model for the COVID epidemic in the US in which rapid spread across the US are combined with a large population of infected patients with presumably mild-to-moderate clinical symptoms. We emphasize the importance of testing these findings with seroprevalence data, and discuss the broader potential to use syndromic time series for early detection and understanding of emerging infectious diseases.
The scar constituent Collagen I triggers coordinated collective migration and invasion in a 3D spheroid model of early endometriotic lesions
Authors: Stejskalova Anna , Fincke Victoria , Nowak Melissa , Schmidt Yvonne , von Wahlde Marie-Kristin , Schäfer Sebastian D. , Kiesel Ludwig , Greve Burkhard , Götte Martin
Published: April 2020

Endometriosis is a painful gynaecological condition characterized by ectopic growth of endometrial cells outside of the uterus. Little is known about the mechanisms by which endometrial fragments invade tissues. This is partially due to a lack of suitable experimental models. In this study, we show that a spheroid 3D model, but not single cells mimic the collective endometrial fragment-like invasion through the extracellular matrix. This model reveals that collagen I, the main constituent of surgical scars, significantly increases the rate of lesion formation by healthy endometrial stromal cells (St-T1b) in vitro compared to the basement membrane-like matrix Matrigel. Stromal cell invasion of collagen I requires MMPs, whereas collective migration of endometriotic epithelial 12Z cells involves Rac-signalling. We show that inhibiting ROCK signalling responsible for actomyosin contraction increases the lesion-size. Moreover, endometriotic epithelial 12Z cells, but not eutopic stromal cells St-T1b migrate on Matrigel. The rate of this migration is decreased by the microRNA miR-200b and increased by miR-145. Our 3D model offers a facile approach to dissect how endometrial fragments invade tissues and is an important step toward developing new personalized therapeutics for endometriosis. Moreover, our model is a suitable tool to screen small molecule drugs and microRNA-based therapeutics.
RANDOMIZE: A Web Server for Data Randomization
Authors: Wani Agaz H , Armstrong D , Dahrendorff Jan , Uddin Monica
Published: April 2020

DNA methylation microarray data may suffer from batch effects due to improper handling of the samples during the plating process. RANDOMIZE is a web-based application designed to perform randomization of relevant metadata to evenly distribute samples across the factors typically responsible for batch effects in DNA methylation microarrays, such as row, chips and plates. Randomization helps to reduce the likelihood of bias and impact of difference among groups.

Availability

The tool is freely available online athttps://coph-usf.shinyapps.io/RANDOMIZE/and can be accessed using any web browser. Sample data and tutorial is also available with the tool.

Contact

ahwani@usf.edu
Three-dimensional mapping identifies distinct vascular niches for myelopoiesis
Authors: Zhang Jizhou , Wu Qingqing , Johnson Courtney B. , Olsson Andre , Slaughter Anastasiya , May Margot , Weinhaus Benjamin , D’Alessandro Angelo , Engel James Douglas , Jiang Jean X. , Koffron J. Matthew , Huang L. Frank , Salomonis Nathan , Grimes H. Leighton , Lucas Daniel
Published: April 2020

In contrast to virtually all other tissues in the body the anatomy of differentiation in the bone marrow remains unknown. This is due to the lack of strategies to examine blood cell production in situ, which are required to better understand differentiation, lineage commitment decisions, and to define how spatial organizing cues inform tissue function. Here we developed imaging approaches to map all myeloid cells in whole bones and generated 3D atlases of granulocyte and monocyte/dendritic cell differentiation during homeostasis. We found that myeloid progenitors leave the hematopoietic stem cell niche during differentiation. Granulocyte and monocyte dendritic cell progenitors (MDP) do not interact, instead they localize to different sinusoids where they give rise to clusters of immature cells. MDP cluster with Ly6Clomonocytes and conventional dendritic cells; these localize to a unique subset of colony stimulating factor 1 (CSF1, the major regulator of monopoiesis1) -expressing sinusoids. Csf1 deletion in the vasculature disrupted the MDP clusters and their interaction with sinusoids, leading to reduced MDP numbers and differentiation ability, with subsequent loss of peripheral Ly6Clomonocytes and dendritic cells. These data indicate that there is a specific spatial organization of definitive hematopoiesis and that local cues produced by distinct blood vessels are responsible for this organization. These maps provide a blueprint for in situ analyses of hematopoiesis in blood disorders.
Invasion of epithelial cells are correlated with secretion of Biosurfactant via the type 3 secretion system (SST3) ofShigella flexneri
Authors: Kinavouidi Duchel Jeanedvi Kinouani , Kayath Christian Aimé , NGuimbi Etienne
Published: April 2020

Biosurfactants are amphipathic molecules produced by many microorganisms, usually bacteria, fungi and yeasts. They possess the property of reducing the tension of the membrane interfaces. No studies have been conducted onShigellaspecies showing their involvement of biosurfactant like molecules (BLM) in pathogenicity. This study aims to show that environmental and clinical strains ofShigellaare able to produce BLM by emulsifying gasoline and diesel fuels. Our study has shown that BLM are secreted in the extracellular medium with EI24 ranging from 80 to 100%. The secretion is depending on the type III secretion system (T3SS). We did show thatS. flexneri,S. boydiiandS. sonneiare able to interact with hydrophobic areas with respectively 17.64%, 21.42% and 22.22% of hydrophobicity. 100 mM Benzoic and 1.5mg/mL Salycilic acids have been inhibited T3SS and this totally stops the BLM secretion.Pseudomonas aeruginosawhich has T3SS is able to produce 100% of BLM in the presence or in the absence of both T3SS inhibitors. The secreted BLM is extractable with an organic solvent such as chloroform and could entirely be considered like lipopeptide or polypeptidic compound. By secreting BLM,Shigellais able to perform multicellular phenomena like “swarming” allowing to invade and disseminate inside epithelial cells.
Geometric differences between nuclear envelopes of Wild-type and Chlamydia trachomatis-infected HeLa cells
Authors: Karabağ Cefa , Jones Martin L. , Peddie Christopher J. , Weston Anne E. , Collinson Lucy M. , Reyes-Aldasoro Constantino Carlos
Published: April 2020

In this work, the geometrical characteristics of two different types of cells observed with Electron Microscopy were analysed. The nuclear envelope of Wild-type HeLa cells and Chlamydia trachomatis-infected HeLa cells were automatically segmented and then modelled against a spheroid and converted to a two-dimensional surface. Geometric measurements from this surface and the volumetric nuclear envelope were extracted to compare the two types of cells. The measurements included the nuclear volume, the sphericity of the nucleus, its flatness or spikiness. In total 13 different cells were segmented: 7 Wild-type and 6 Chlamydia trachomatis-infected. The cells were statistically different in the following measurements. Wild-type HeLa cells have greater volumes than that of Chlamydia trachomatis-infected HeLa cells and they are more spherical as Jaccard index suggests. Standard deviation (σ), and range of values for the nuclear envelope, which shows the distance of the highest peaks and deepest valleys from the spheroid, were also extracted from the modelling against a spheroid and these metrics were used to compare two different data sets in order to draw conclusions.
Linking Activity in Human Superior Temporal Cortex to Perception of Noisy Audiovisual Speech
Authors: Rennig Johannes , Beauchamp Michael S
Published: April 2020

Regions of the human posterior superior temporal gyrus and sulcus (pSTG/S) respond to the visual mouth movements that constitute visual speech and the auditory vocalizations that constitute auditory speech. We hypothesized that these multisensory responses in pSTG/S underlie the observation that comprehension of noisy auditory speech is improved when it is accompanied by visual speech. To test this idea, we presented audiovisual sentences that contained either a clear auditory component or a noisy auditory component while measuring brain activity using BOLD fMRI. Participants reported the intelligibility of the speech on each trial with a button press. Perceptually, adding visual speech to noisy auditory sentences rendered them much more intelligible. Post-hoc trial sorting was used to examine brain activations during noisy sentences that were more or less intelligible, focusing on multisensory speech regions in the pSTG/S identified with an independent visual speech localizer. Univariate analysis showed that less intelligible noisy audiovisual sentences evoked a weaker BOLD response, while more intelligible sentences evoked a stronger BOLD response that was indistinguishable from clear sentences. To better understand these differences, we conducted a multivariate representational similarity analysis. The pattern of response for intelligible noisy audiovisual sentences was more similar to the pattern for clear sentences, while the response pattern for unintelligible noisy sentences was less similar. These results show that for both univariate and multivariate analyses, successful integration of visual and noisy auditory speech normalizes responses in pSTG/S, providing evidence that multisensory subregions of pSTG/S are responsible for the perceptual benefit of visual speech.

Significance Statement

Enabling social interactions, including the production and perception of speech, is a key function of the human brain. Speech perception is a complex computational problem that the brain solves using both visual information from the talker’s facial movements and auditory information from the talker’s voice. Visual speech information is particularly important under noisy listening conditions when auditory speech is difficult or impossible to understand alone Regions of the human cortex in posterior superior temporal lobe respond to the visual mouth movements that constitute visual speech and the auditory vocalizations that constitute auditory speech. We show that the pattern of activity in cortex reflects the successful multisensory integration of auditory and visual speech information in the service of perception.
Messenger RNA levels of enzymes involved in glycerolipid synthesis in the brain of the mouse and its alterations inAgpat2-/-and db/db mice
Authors: González-Hódar Lila , Agarwal Anil K. , Cortés Víctor
Published: April 2020

Aims

Expression of genes encoding enzymes involved in glycerolipid and monoacylglycerol pathways in specific brain regions is poorly known and its impact in insulin resistance (IR) and type 2 diabetes (T2D) in the brain remains unreported. We determined mRNA levels of enzymes involved in glycerolipid synthesis in different regions of the mouse brain and evaluated their changes in two models of IR and T2D, theAgpat2-/-andLeprdb/dbmice.

Methods

Cerebral cortex, hypothalamus, hippocampus and cerebellum were dissected from adultAgpat2-/-mice,Leprdb/dbmice and their respective wild type littermates. Total RNA was isolated and mRNA abundance was measured by RT-qPCR.

Key findings

GPAT1, AGPAT1-4, LIPIN1/2, DGAT1/2 and MOGAT1 mRNAs were detected in all studied brain regions, whereas GPAT2, LIPIN3 and MOGAT2 were undetectable. Abundance of AGPATs, LIPIN1 and DGAT1, was higher in cerebellum and hypothalamus. LIPIN2 and MOGAT1 levels were higher in hypothalamus, and DGAT2 was higher in cortex and hypothalamus. InAgpat2-/-mice, LIPIN1 levels were increased in all the brain regions. By contrast, GPAT1 in cortex and hypothalamus, AGPAT3 in hippocampus and hypothalamus, AGPAT4 in hypothalamus, and MOGAT1 in cortex, hypothalamus and cerebellum were lower inAgpat2-/-mice.Leprdb/dbmice showed fewer and milder changes, with increased levels of GPAT1 and LIPIN1 in cerebellum, and AGPAT3 in hypothalamus.

Conclusions and Significance

Enzymes of glycerolipids synthesis are differentially expressed across regions of the mouse brain. Two mouse models of IR and T2D have altered gene expression of glycerolipid enzymes in the brain.
DNA replication and chromosome positioning throughout the interphase in three dimensional space of plant nuclei
Authors: Alžběta Němečková , Koláčková Veronika , Jan Vrána , Jaroslav Doležel , Eva Hřibová
Published: April 2020

Despite the recent progress, our understanding of the principles of plant genome organization and its dynamics in three-dimensional space of interphase nuclei remains limited. In this study, DNA replication timing and interphase chromosome positioning was analyzed in sevenPoaceaespecies differing in genome size. A multidisciplinary approach combining newly replicated DNA labelling by EdU, nuclei sorting by flow cytometry, three-dimensional immuno-FISH, and confocal microscopy revealed similar replication timing order for telomeres and centromeres as well as for euchromatin and heterochromatin in all seven species. The Rabl configuration of chromosomes that lay parallel to each other and their centromeres and telomeres are localized at opposite nuclear poles, was observed in wheat, oat, rye and barley with large genomes, as well as inBrachypodiumwith a small genome. On the other hand, chromosomes of rice with a small genome and maize with relatively large genome did not assume proper Rabl configuration. In all species, the interphase chromosome positioning inferred from the location of centromeres and telomeres was stable throughout the interphase. These observations extend earlier studies indicating a more complex relation between genome size and interphase chromosome positioning, which is controlled by factors currently not known.

Highlight

Telomere and centromere replication timing and interphase chromosome positioning in seven grass species differing in genome size indicates a more complex relation between genome size and the chromosome positioning.
Testing and Correcting for Weak and Pleiotropic Instruments in Two-Sample Multivariable Mendelian Randomisation
Authors: Sanderson Eleanor , Spiller Wes , Bowden Jack
Published: April 2020

Multivariable Mendelian Randomisation (MVMR) is a form of instrumental variable analysis which estimates the direct effect of multiple exposures on an outcome using genetic variants as instruments. Mendelian Randomisation and MVMR are frequently conducted using two-sample summary data where the association of the genetic variants with the exposures and outcome are obtained from separate samples. If the genetic variants are only weakly associated with the exposures either individually or conditionally, given the other exposures in the model, then standard inverse variance weighting will yield biased estimates for the effect of each exposure. Here we develop a two-sample conditional F-statistic to test whether the genetic variants strongly predict each exposure conditional on the other exposures included in a MVMR model. We show formally that this test is equivalent to the individual level data conditional F-statistic, indicating that conventional rule-of-thumb critical values of F > 10, can be used to test for weak instruments. We then demonstrate how reliable estimates of the causal effect of each exposure on the outcome can be obtained in the presence of weak instruments and pleiotropy, by re-purpousing a commonly used heterogeneity Q-statistic as an estimating equation. Furthermore, the minimised value of this Q-statistic yields an exact test for heterogeneity due to pleiotropy. We illustrate our methods with an application to estimate the causal effect of blood lipid fractions on age related macular degeneration.
TheArabidopsisNOT4A E3 ligase coordinates PGR3 expression to regulate chloroplast protein translation
Authors: Bailey Mark , Ivanauskaite Aiste , Grimmer Julia , Akintewe Oluwatunmise , Payne Adrienne C. , Etherington Ross , Labandera Anne-Marie , Osborne Rory , Rantala Marjaana , Baginsky Sacha , Mulo Paula , Gibbs Daniel J.
Published: April 2020

Chloroplast function requires the coordinated action of nuclear- and chloroplast-derived proteins, including several hundred nuclear-encoded pentatricopeptide repeat (PPR) proteins that regulate plastid mRNA metabolism. Despite their large number and importance, regulatory mechanisms controlling PPR expression are poorly understood. Here we show that the Arabidopsis NOT4A ubiquitin-ligase positively regulates PROTON GRADIENT 3 (PGR3), a PPR protein required for translating 30S ribosome subunits and several thylakoid-localised photosynthetic components within chloroplasts. Loss of NOT4A function leads to a strong depletion of plastid ribosomes, which reduces mRNA translation and negatively impacts photosynthetic capacity, causing pale-yellow and slow-growth phenotypes. Quantitative transcriptome and proteome analyses reveal that these defects are due to a lack of PGR3 expression innot4a, and we show that normal plastid function is restored through transgenic PGR3 expression. Our work identifies NOT4A as crucial for ensuring robust photosynthetic function during development and stress-response, through modulating PGR3 levels to coordinate chloroplast protein synthesis.
Activation of silent secondary metabolite gene clusters by nucleosome map-guided positioning of the synthetic transcription factor VPR-dCas9
Authors: Schüller Andreas , Wolansky Lisa , Berger Harald , Studt Lena , Gacek-Matthews Agnieszka , Sulyok Michael , Strauss Joseph
Published: April 2020

Current methods for forced expression of selected target genes are based on promoter exchange or on overexpressing native or hybrid transcriptional activators in which gene-specific DNA binding domains are coupled to strong activation domains. While these approaches are very useful for promoters with known or synthetically introduced transcription factor binding sites, they are not suitable to turn on genes in biosynthetic gene clusters which often lack pathway-specific activators. To expand the discovery toolbox, we designed a Cas9-based RNA guided synthetic transcription activation system forAspergillus nidulansbased on enzymatically disabled dCas9 fused to three consecutive activation domains (VPR-dCas9). Targeting two biosynthetic gene clusters involved in the production of secondary metabolites, we demonstrate the utility of the system. Especially in silent regions facultative heterochromatin and strictly positioned nucleosomes can constitute a relevant obstacle to the transcriptional machinery. To avoid this negative impact and to facilitate optimal positioning of RNA-guided VPR-dCas9 to our targeted promoters we have created a genome-wide nucleosome map to identify the cognate nucleosome-free-regions (NFRs). Based on these maps, different single-guide RNAs (sgRNA) were designed and tested for their targeting and activation potential. Our results demonstrate that the system can be used to activate silent BGCs inA. nidulans, partially to very high expression levels and also open the opportunity to stepwise turn on individual genes within a BGC that allows to decipher the correlated biosynthetic pathway.
Immunity to infections in arboviral vectors by integrated viral sequences: an evolutionary perspective
Authors: Crava Cristina , Varghese Finny S. , Pischedda Elisa , Halbach Rebecca , Palatini Umberto , Marconcini Michele , Mattia Annamaria , Redmond Seth , Afrane Yaw , Ayala Diego , Paupy Christophe , Carballar-Lejarazu Rebeca , Miesen Pascal , van Rij Ronald P. , Bonizzoni Mariangela
Published: April 2020

In the model organismDrosophila melanogaster, the PIWI-interacing RNA pathway contributes in silencing transposable elements (TEs) through smallRNAs (piRNAs), which arise from genomic loci (piRNA clusters) that contain sequences of previously-acquired TEs. As such, they are a functionally-immune archive of previous TE invasions that is passed to the offspring. In the arboviral vectorAedes aegypti, piRNA clusters contain TEs and endogenous viral elements from nonretroviral RNA viruses (nrEVEs) which produce piRNAs, supporting the hypothesis that nrEVEs are heritable immunity effectors. However, direct evidence that nrEVEs mediate adaptive immunity is lacking. Here, by using an analytic approach intersecting population genomics with molecular biology we demonstrate that the composition of piRNA clusters is modular through acquisition and absence of nrEVEs. We show that the genomes of wild-caught mosquitoes have a different set of nrEVEs than those annotated in the reference genome, including population-specific integrations. nrEVEs are not distributed in mosquito genomes only by genetic drift, but some show signs of positive selection. Moreover, by comparing natural mosquito populations expressing or lacking two newly characterised nrEVEs with high sequence complementarity to cell fusing agent virus, we show that nrEVEs confer antiviral immunity in ovaries against the cognate virus. Our results confirm that some nrEVEs have been co-opted for adaptive immunity to viral infections.
Pangaea: A modular and extensible collection of tools for mining context dependent gene relationships from the biomedical literature
Authors: Pirvan Liviu , Samarajiwa Shamith A.
Published: April 2020

Motivation

Pangaea is a scalable and extensible command line interface (CLI) software that integrates gene-relationship detection features to extract context-dependent structured gene-gene and gene-term relationships from the biomedical literature. It provides computational methods to identify biological relationships between a collection of genes and can be used to search and extract different types of contextual relationships amongst genes.

Results

We implemented a CLI-based software for downloading PubMed articles and extracting gene relationships from abstracts using natural language processing methods. In terms of scalability, the software was designed to support the retrieval and processing of millions of articles whilst minimising memory requirements and optimising for parallel processing on multiple CPU cores. To allow extensibility, the tool permits the use of contextual custom-made models for the text processing parts, and the output is serialised as JSON objects to allow flexible post-processing workflows.

Availability

The software is available online at:https://github.com/ss-lab-cancerunit/pangaea
Multivoxel Neural Reinforcement Changes Resting-State Functional Connectivity Within the Threat Regulation Network
Authors: Taschereau-Dumouchel Vincent , Chiba Toshinori , Koizumi Ai , Kawato Mitsuo , Lau Hakwan
Published: April 2020

Using neural reinforcement, participants can be trained to pair a reward with the activation of specific multivoxel patterns in their brains. In a double-blind placebo-controlled experiment, we previously showed that this intervention can decrease the physiological reactivity associated with naturally feared animals. However, the mechanisms behind the effect remain incompletely understood and its usefulness for treatment remains unclear. If the intervention fundamentally changed the brain responses, we might expect to observe relatively stable changes in the functional connectivity within the threat regulation network. To evaluate this possibility, we conducted functional magnetic resonance imaging (fMRI) sessions while subjects were at rest, before and after neural reinforcement, and quantified the changes in resting-state functional connectivity accordingly. Our results indicate that neural reinforcement increased the connectivity of prefrontal regulatory regions with the amygdala and the ventral temporal cortex (where the visual representations of phobic targets are). Surprisingly, we found no evidence of Hebbian-like learning during neural reinforcement, contrary to what one may expect based on previous neurofeedback studies. These results suggest that multivoxel neural reinforcement, also known as decoded neurofeedback (DecNef), may operate via unique mechanisms, distinct from those involved in conventional neurofeedback.
Positive autofeedback regulation of Ptf1a transcription generates the levels of PTF1A required to generate itch circuit neurons
Authors: Mona Bishakha , Villarreal Juan , Savage Trisha K. , Kollipara Rahul K. , Boisvert Brooke E. , Johnson Jane E.
Published: April 2020

Peripheral somatosensory input is modulated in the dorsal spinal cord by a network of excitatory and inhibitory interneurons. PTF1A is a transcription factor essential in dorsal neural tube progenitors for specification of these inhibitory neurons. Thus, mechanisms regulating Ptf1a expression are key for generating neuronal circuits underlying somatosensory behaviors. Mutations targeted to distinct cis-regulatory elements for Ptf1a in mice, tested the in vivo contribution of each element individually and in combination. Mutations in an autoregulatory enhancer resulted in reduced levels of PTF1A, and reduced numbers of specific dorsal spinal cord inhibitory neurons, particularly those expressing Pdyn and Gal. Although these mutants survive postnatally, at ∼3–5 wk they elicit a severe scratching phenotype. Behaviorally, the mutants have increased sensitivity to itch, but acute sensitivity to other sensory stimuli such as mechanical or thermal pain is unaffected. We demonstrate a requirement for positive transcriptional autoregulatory feedback to attain the level of the neuronal specification factor PTF1A necessary for generating correctly balanced neuronal circuits.
Rapid evolution of piRNA-mediated silencing of an invading transposable element was driven by abundant de novo mutations
Authors: Zhang Shuo , Pointer Beverly , Kelleher Erin S.
Published: April 2020

The regulation of transposable element (TE) activity by small RNAs is a ubiquitous feature of germlines. However, despite the obvious benefits to the host in terms of ensuring the production of viable gametes and maintaining the integrity of the genomes they carry, it remains controversial whether TE regulation evolves adaptively. We examined the emergence and evolutionary dynamics of repressor alleles after P-elements invaded the Drosophila melanogaster genome in the mid-twentieth century. In many animals including Drosophila, repressor alleles are produced by transpositional insertions into piRNA clusters, genomic regions encoding the Piwi-interacting RNAs (piRNAs) that regulate TEs. We discovered that ∼94% of recently collected isofemale lines in the Drosophila melanogaster Genetic Reference Panel (DGRP) contain at least one P-element insertion in a piRNA cluster, indicating that repressor alleles are produced by de novo insertion at an exceptional rate. Furthermore, in our sample of approximately 200 genomes, we uncovered no fewer than 80 unique P-element insertion alleles in at least 15 different piRNA clusters. Finally, we observe no footprint of positive selection on P-element insertions in piRNA clusters, suggesting that the rapid evolution of piRNA-mediated repression in D. melanogaster was driven primarily by mutation. Our results reveal for the first time how the unique genetic architecture of piRNA production, in which numerous piRNA clusters can encode regulatory small RNAs upon transpositional insertion, facilitates the nonadaptive rapid evolution of repression.
Groupoid description of modular structures
Authors: Nespolo Massimo , Souvignier Bernd , Stöger Berthold
Published: April 2020

Modular structures are crystal structures built by subperiodic (zero-, mono- or diperiodic) substructures, called modules. The whole set of partial operations relating substructures in a modular structure build up a groupoid; modular structures composed of identical substructures are described by connected groupoids, or groupoids in the sense of Brandt. A general approach is presented to describe modular structures by Brandt's groupoids and how to obtain the corresponding space groups, in which only the partial operations that have an extension to the whole crystal space appear.
An efficient method for indexing grazing-incidence X-ray diffraction data of epitaxially grown thin films
Authors: Simbrunner Josef , Schrode Benedikt , Domke Jari , Fritz Torsten , Salzmann Ingo , Resel Roland
Published: April 2020

Crystal structure identification of thin organic films entails a number of technical and methodological challenges. In particular, if molecular crystals are epitaxially grown on single-crystalline substrates a complex scenario of multiple preferred orientations of the adsorbate, several symmetry-related in-plane alignments and the occurrence of unknown polymorphs is frequently observed. In theory, the parameters of the reduced unit cell and its orientation can simply be obtained from the matrix of three linearly independent reciprocal-space vectors. However, if the sample exhibits unit cells in various orientations and/or with different lattice parameters, it is necessary to assign all experimentally obtained reflections to their associated individual origin. In the present work, an effective algorithm is described to accomplish this task in order to determine the unit-cell parameters of complex systems comprising different orientations and polymorphs. This method is applied to a polycrystalline thin film of the conjugated organic material 6,13-pentacenequinone (PQ) epitaxially grown on an Ag(111) surface. All reciprocal vectors can be allocated to unit cells of the same lattice constants but grown in various orientations [sixfold rotational symmetry for the contact planes (102) and (102)]. The as-determined unit cell is identical to that reported in a previous study determined for a fibre-textured PQ film. Preliminary results further indicate that the algorithm is especially effective in analysing epitaxially grown crystallites not only for various orientations, but also if different polymorphs are present in the film.
SPIND-TC: an indexing method for two-color X-ray diffraction data
Authors: Li Xuanxuan , Li Chufeng , Liu Haiguang
Published: April 2020

Recent developments of two-color operation modes at X-ray free-electron laser facilities provide new research opportunities, such as X-ray pump/X-ray probe experiments and multiple-wavelength anomalous dispersion phasing methods. However, most existing indexing methods were developed for indexing diffraction data from monochromatic X-ray beams. Here, a new algorithm is presented for indexing two-color diffraction data, as an extension of the sparse-pattern indexing algorithm SPIND, which has been demonstrated to be capable of indexing diffraction patterns with as few as five peaks. The principle and implementation of the two-color indexing method, SPIND-TC, are reported in this paper. The algorithm was tested on both simulated and experimental data of protein crystals. The results show that the diffraction data can be accurately indexed in both cases. Source codes are publicly available at https://github.com/lixx11/SPIND-TC.