bluuebunny/crossref_metadata_2025 huggingface dataset:
Dopamine Signaling in the Dorsomedial Striatum Promotes Compulsive Behavior
Authors: Seiler Jillian L. , Cosme Caitlin V. , Sherathiya Venus N. , Bianco Joseph M. , Bridgemohan Abigael S. , Lerner Talia N.
Published: April 2020

Compulsive behavior is a defining feature of disorders such as substance use disorder and obsessive-compulsive disorder. Current evidence suggests that corticostriatal circuits control the expression of established compulsions, but little is known about the mechanisms regulating the development of compulsions. We hypothesized that dopamine, a critical modulator of striatal synaptic plasticity, could control alterations in corticostriatal circuits leading to the development of compulsions (defined as continued reward-seeking in the face of punishment). We used dual-site fiber photometry to measure dopamine axon activity in the dorsomedial striatum (DMS) and the dorsolateral striatum (DLS) as compulsions emerged. Individual variability in the speed with which compulsions emerged was predicted by DMS dopamine axon activity. Amplifying this dopamine signal accelerated animals’ transitions to compulsion, whereas inhibition led to learning delays. In contrast, amplifying DLS dopamine signaling had no effect on the emergence of compulsions. These results establish DMS dopamine signaling as a key controller of the development of compulsive reward-seeking.
Long-Term Performance of Utah Slanted Electrode Arrays and Intramuscular Electromyographic Leads Implanted Chronically in Human Arm Nerves and Muscles
Authors: George Jacob A. , Page David M. , Davis Tyler S. , Duncan Christopher C. , Hutchinson Douglas T. , Rieth Loren W. , Clark Gregory A.
Published: April 2020

Objective

We explore the long-term performance and stability of seven percutanous Utah Slanted Electrode Arrays (USEAs) and intramuscular recording leads (iEMGs) implanted chronically in the residual arm nerves and muscles of three human amputees as a means to permanently restore sensorimotor function after upper-limb.

Approach

We quantify the number of functional recording and functional stimulating electrodes over time. We also calculate the signal-to-noise ratio of USEA and iEMG recordings and quantify the stimulation amplitude necessary to evoke detectable sensory percepts. Furthermore, we quantify the consistency of the sensory modality, receptive field location, and receptive field size of USEA-evoked percepts.

Main Results

In the most recent subject, involving USEAs with technical improvements, neural recordings persisted for 502 days (entire implant duration) and the number of functional recording electrodes for one USEA increased over time. However, for six out of seven USEAs the number of functional recording electrodes decreased within the first two months after implantation. The signal-to-noise ratio of neural recordings and electromyographic recordings stayed relatively consistent over time. Sensory percepts were consistently evoked over the span of 14 months, were not significantly different in size, and highlighted the nerves’ fascicular organization. The percentage of percepts with consistent modality or consistent receptive field location between sessions (~1 month apart) varied between 0–86.2% and 9.1–100%, respectively. Stimulation thresholds and electrode impedances increased initially but then remained relatively stable over time.

Significance

This work demonstrates improved performance of USEAs, and provides a basis for comparing the longevity and stability of USEAs to that of other neural interfaces. Although USEAs provide a rich repertoire of neural recordings and sensory percepts, performance still generally declines over time. Future work should leverage the results presented here to further improve USEA design or to develop adaptive algorithms that can maintain a high level of performance.
Female rats self-administer heroin by vapor inhalation
Authors: Gutierrez Arnold , Nguyen Jacques D. , Creehan Kevin M. , Taffe Michael A.
Published: April 2020

Over the last two decades the United States has experienced a significant increase in the medical and non-medical use of opioid drugs, resulting in record numbers of opioid-related overdoses and deaths. There was an initial increase in non-medical use of prescription opioids around 2002, followed later by increased heroin use and then most recently fentanyl. Inhalation is a common route of administration for opioids, with a documented history spanning back to Mediterranean antiquity and up through modern use with e-cigarette devices. Unfortunately, preclinical studies using inhalation as the route of administration remain relatively few. This study was conducted to determine the efficacy of e-cigarette vapor inhalation of heroin in rats. Non-contingent exposure to heroin or methadone vapor produced anti-nociceptive efficacy in male and female rats. Female rats were trained to self-administer heroin vapor; the most-preferring half of the distribution obtained more vapor reinforcers when the concentration of heroin was reduced in the vapor vehicle and when pre-treated with the opioid receptor antagonist naloxone. The anti-nociceptive effect of heroin self-administered by vapor was identical in magnitude to that produced by intravenous self-administration. Finally, anxiety-like behavior increased 24-48 hours after last heroin vapor access, consistent with withdrawal signs observed after intravenous self-administration. In sum, these studies show that rewarding and anti-nociceptive effects of heroin are produced in rats by vapor inhalation using e-cigarette technology. Importantly, self-administration models by this route can be deployed to determine health effects of inhaled heroin or other opioids.
An engineered Abcb4 expressing model reveals the central role of NF-κB in the regulation of drug resistance in zebrafish
Authors: Sun Cong-Jie , Hu Rong-Yin , Li Zhi-Cao , Jin Lu , Ye Chuan , Lu He , Zhou Yan-Hua , Zhou Ting , He Zhi-Xu , Shu Li-Ping
Published: April 2020

Multidrug resistance (MDR) represents the major cause of unsatisfaction in the application of chemotherapy for cancer treatment. So far, anin vivorobust high-throughput screening system for anti-tumor drug MDR is still lacking and the molecular mechanisms for MDR still remain elusive. Given a myriad of merits of zebrafish relative to other animal models, we aimed to establish MDR system in zebrafish stably expressing ATP-binding cassette (ATP-cassette) superfamily transporters and study the potential regulatory mechanism. We first constructed aTg(abcb4:EGFP)transgenic zebrafish stably expressing both Abcb4 and EGFP using Tol2-mediated approach. The expression level of Abcb4 and EGFP was significantly induced whenTg(abcb4:EGFP)transgenic zebrafish embryos were exposed to doxorubicin (DOX) or vincristine (VCR), accompany with a marked decrease in rhodamine B (RhB) accumulation in embryos, which indicates a remarkable increase in drug efflux upon the exposure to DOX or VCR. Mechanistically, AKT and ERK signaling were activated when treated with DOX or VCR. With the application of AKT and ERK inhibitors, the drug resistance phenomena could be reversed with differential responsive effects. Of note, downstream NF-κB played a central role in the regulation of Abcb4-mediated drug resistance. Taken together, the engineeredTg(abcb4:EGFP)transgenic zebrafish model provides a new platform for drug resistance screeningin vivo, which could facilitate and accelerate the process of drug development.
Deletion of Murine Gammaherpesvirus GeneM2in AID-Expressing B Cells Impairs Host Colonization and Viral Reactivation
Authors: Owens Shana M. , Oldenburg Darby G. , White Douglas W. , Forrest J. Craig
Published: April 2020

Gammaherpesviruses (GHVs) are DNA tumor viruses that establish life-long, chronic infections in lymphocytes of humans and other mammals. GHV infections are associated with numerous cancers, especially in immune compromised hosts. While it is known that GHVs utilize host germinal center (GC) B cell responses during latency establishment, an understanding of how viral gene products function in specific B cell subsets to regulate this process is incomplete. Using murine gammaherpesvirus 68 (MHV68) as a small-animal model to define mechanisms of GHV pathogenesisin vivo, we generated a virus in which theM2gene was flanked byloxPsites (M2.loxP), enabling the use of Cre-lox technology to define M2 function in specific cell types in infection and disease. TheM2gene encodes a protein that is highly expressed in GC B cells that promotes plasma cell differentiation and viral reactivation.M2was efficiently deleted in Cre-expressing cells, and the presence ofloxPsites flankingM2did not alter viral replication or latency in mice that do not express Cre. In contrast, M2.loxP MHV68 exhibited a deficit in latency establishment and reactivation that resembled M2-null virus, following intranasal (IN) infection of mice that express Cre in all B cells (CD19-Cre). Nearly identical phenotypes were observed for M2.loxP MHV68 in mice that express Cre in germinal center (GC) B cells (AID-Cre). However, neither colonization of draining lymph nodes after IN infection nor the spleen after intraperitoneal (IP) infection required M2, although the reactivation defect was retained. Together, these data confirm that M2 function is B cell-specific and demonstrate that M2 primarily functions in AID-expressing cells to facilitate MHV68 dissemination to distal latency reservoirs within the host and reactivation from latency. Our study reveals that a viral latency gene functions within a distinct subset of cells to facilitate host colonization.

IMPORTANCE

Gammaherpesviruses establish life-long chronic infections in cells of the immune system that can lead to lymphomas and other diseases. To facilitate colonization of a host, gammaherpesviruses encode gene products that manipulate processes involved in cellular proliferation and differentiation. Whether and how these viral gene products function in specific cells of the immune system is poorly defined. We report here the use of a viral genetic system that allows for deletion of specific viral genes in discrete populations of cells. We employ this system in anin vivomodel to demonstrate cell-type-specific requirements for a particular viral gene. Our findings reveal that a viral gene product can function in distinct cellular subsets to direct gammaherpesvirus pathogenesis.
A mechanical cusp catastrophe imposes a universal developmental constraint on the shapes of tip-growing cells
Authors: Dumais Jacques , Rojas Enrique R.
Published: April 2020

Understanding the mechanistic basis for cell morphology is a central problem in biology. Evolution has converged on tip growth many times, yielding filamentous cells, yet tip-growing cells display a range of apical morphologies. To understand this variability, we measured the spatial profiles of cell-wall expansion for three species that spanned the phylogeny and morphology of tip-growth. Profiles were consistent with a mechanical model whereby the wall was stratified and stretched by turgor pressure during cell growth. We calculated the spatial profiles of wall mechanical properties, which could be accurately fit with an empirical two-parameter function. Combined with the mechanical model, this function yielded a “morphospace” that accounted for the shapes of diverse tip-growing species. However, natural shapes were bounded by a cusp bifurcation in the morphospace that separated thin, fast-growing cells from (nonexistent) wide, slow-growing cells. This constraint has important implications for our understanding of the evolution of tip-growing cells.
Analysis of insertion mutants in distal α9 portion of C-terminal heptad repeat (CHR) of HIV-1 gp41 subunit
Authors: Wang Hongyun , Song Jiping , Kawaguchi Yasushi , Inoue Jun-ichiro , Matsuda Zene
Published: April 2020

We have made insertion mutants in α9 of HXB2 gp41 and observed similar phenotypes like recent JRFL mutants: insertion of alanine (653+A), but not glutamine (653+Q), severely attenuated membrane fusion. To understand the underlying mechanism, we performed the fusion inhibition assay by corresponding mutant C34 peptides. Both mutant C34 peptides added at the beginning of the coculture of the effector and target cells showed less efficient inhibition of membrane fusion, which was similar to wildtype C34 added after 30 min of coculture, indicating slow association of mutant C34 peptides with the N-terminal heptad region of gp41. Due to uninterpretable CD profiles of C34 and N36, we tested the longer peptide pairs (N46 and C42) and observed CD profiles indicative of weak α-helix formation. The melting temperatures for N46-C42 pairs of 653+A, 653+Q, and wild type were 56.8 °C, 59.8°C, and 96°C, respectively. Taken together, our data suggested that the phenotypic difference in membrane fusion between 653+A and 653+Q (or wild type) was not based on the stability of the six-helix bundle (6HB), but due to differences in the kinetics of 6HB formation. Further, we examined additional insertions (E, R, I, and L) at position 653, for which only I and L showed fusion recovery similar to Q, suggesting that the polar nature of glutamine was not a phenotypic determinant.
Fragmentation of Small-cell Lung Cancer Regulatory States in Heterotypic Microenvironments
Authors: Schaff Dylan L. , Singh Shambhavi , Kim Kee-Beom , Sutcliffe Matthew D. , Park Kwon-Sik , Janes Kevin A.
Published: April 2020

Small-cell lung cancers derive from pulmonary neuroendocrine cells, which have stemlike properties to reprogram into other cell types upon lung injury. It is difficult to uncouple transcriptional plasticity of these transformed cells from genetic changes that evolve in primary tumors or secondary metastases. Profiling of single cells also problematic if the required sample dissociation activates injury-like signaling and reprogramming. Here, we defined cell-state heterogeneities in situ through laser capture microdissection-based 10-cell transcriptomics coupled with stochastic-profiling fluctuation analysis. Using labeled cells from a small-cell lung cancer mouse model initiated by neuroendocrine deletion ofRb1–Trp53, we profiled variations in transcript abundance to identify cell-to-cell differences in regulatory state in vitro and in vivo. Fluctuating transcripts in spheroid culture were partly shared amongRb1–Trp53-null models, and heterogeneities increased considerably when cells were delivered intravenously to colonize the liver. Colonization of immunocompromised animals drove fractional appearance of alveolar type II-like markers and poised cells for paracrine stimulation from immune cells and hepatocytes. Immunocompetency further exaggerated the fragmentation of tumor states in the liver, yielding mixed stromal signatures evident in bulk sequencing from autochthonous tumors and metastases. Dozens of transcript heterogeneities recur irrespective of biological context; their mapped orthologs brought together observations of murine and human small-cell lung cancer. Candidate heterogeneities recurrent in the liver also stratified primary human tumors into discrete groups not readily explained by molecular subtype but with prognostic relevance. We conclude that heterotypic interactions in the liver and lung are an accelerant for intratumor heterogeneity in small-cell lung cancer.

Statement of significance

The single-cell regulatory heterogeneity of small-cell lung cancer becomes increasingly elaborate in the liver, a common metastatic site for the disease.
Lipoprotein(a) and cardiovascular disease: prediction, attributable risk fraction and estimating benefits from novel interventions
Authors: Welsh Paul , Welsh Claire , Celis-Morales Carlos A , Brown Rosemary , Ferguson Lyn D , Mark Patrick B , Lewsey James , Gray Stuart R , Lyall Donald M , Gill Jason MR , Pell Jill P , de Lemos James A , Willeit Peter , Sattar Naveed
Published: April 2020

Background

Lipoprotein (a) (Lp(a)) is a CVD risk factor amenable to intervention and might help guide risk prediction.

Objectives

To investigate the population attributable fraction due to elevated Lp(a) and its utility in risk prediction.

Methods

Using a prospective cohort study, 413,724 participants from UK Biobank, associations of serum Lp(a) with composite fatal/nonfatal CVD (n=10,065 events), fatal CVD (n=3247), coronary heart disease (n=16,649), ischaemic stroke (n=3191), and peripheral vascular disease (n=2716) were compared using Cox models. Predictive utility was determined by C-index changes. The population attributable fraction was estimated.

Results

Median Lp(a) was 19.7nmol/L (interquartile interval 7.6-75.3nmol/L). 20.8% had Lp(a) values >100nmol/L; 9.2% had values >175nmol/L. After adjustment for classical risk factors, in participants with no baseline CVD and not taking a statin, 1 standard deviation increment in log Lp(a) was associated with a HR for fatal/nonfatal CVD of 1.09 (95%CI 1.07-1.11). Associations were similar for fatal CVD, coronary heart disease, and peripheral vascular disease. Adding Lp(a) to a prediction model containing traditional CVD risk factors improved the C-index by +0.0017 (95% CI 0.0009, 0.0026). We estimated that having Lp(a) values >100nmol/L accounts for 5.7% of CVD events in the whole cohort. We modelled that an ongoing trial to lower Lp(a) in patients with CVD and Lp(a) above ∼175nmol/L may reduce CVD risk by 20.3%, assuming causality, and an achieved Lp(a) reduction of 80%.

Conclusions

Population screening for elevated Lp(a) may help to predict CVD and target Lp(a) lowering drugs, if such drugs prove efficacious, to those with markedly elevated levels.
Optimal timing for social distancing during an epidemic
Authors: Patterson-Lomba Oscar
Published: April 2020

Social distancing is an effective way to contain the spread of a contagious disease, particularly when facing a novel pathogen and no pharmacological interventions are available. In such cases, conventional wisdom suggests that social distancing measures should be introduced as soon as possible after the beginning of an outbreak to more effectively mitigate the spread of the disease. Using a simple epidemiological model we show that, however, there is in fact an optimal time to initiate a temporal social distancing intervention if the goal is to reduce the final epidemic size or “flatten” the epidemic curve. The optimal timing depends strongly on the effective reproduction number (R0) of the disease, such that as the R0 increases, the optimal time decreases non-linearly. Additionally, if pharmacological interventions (e.g., a vaccine) become available at some point during the epidemic, the sooner these interventions become available the sooner social distancing should be initiated to maximize its effectiveness. Although based on a simple model, we hope that these insights inspire further investigations within the context of more complex and data-driven epidemiological models, and can ultimately help decision makers to improve temporal social distancing policies to mitigate the spread of epidemics.
Electronic Health Record Documentation of Psychiatric Assessments in Massachusetts Emergency Department and Outpatient Settings During the COVID-19 Pandemic
Authors: Castro Victor M. , Perlis Roy H.
Published: April 2020

Key Points

Question

How did documentation of psychiatric symptoms in outpatient and emergency room settings change with onset of COVID-19 infection in Eastern Massachusetts?

Findings

In this cohort study spanning 2 academic medical centers and 3 community hospitals, prevalence of narrative notes referencing depression or anxiety decreased 75-81% in outpatient settings following onset of coronavirus in March 2019, and by 44–45% in emergency departments.

Meaning

The observation that documentation of psychiatric symptoms declined sharply with increasing coronavirus infection in Massachusetts, even as prevalence of such symptoms is anticipated to increase, suggests additional efforts may be required to address these symptoms in the context of COVID-19.
Estimating the risk of COVID-19 death during the course of the outbreak in Korea, February- May, 2020
Authors: Shim Eunha , Mizumoto Kenji , Choi Wongyeong , Chowell Gerardo
Published: April 2020

Background: In Korea, a total of 10,840 confirmed cases of COVID-19 including 256 deaths have been recorded as of May 9, 2020. The time-delay adjusted case fatality risk (CFR) of COVID-19 in Korea is yet to be estimated. Methods: We obtained the daily series of confirmed cases and deaths in Korea reported prior to May 9, 2020. Using statistical methods, we estimated the time-delay adjusted risk for death from COVID-19 in Daegu, Gyeongsangbuk-do, other regions in Korea, as well as the entire country. Results: Our model-based crude CFR fitted the observed data well throughout the course of the epidemic except for the very early stage in Gyeongsangbuk-do; this was partially due to the reporting delay. Our estimates of the risk of death in Gyeongsangbuk-do reached 25.9% (95% CrI: 19.6%-33.6%), 20.8% (95% CrI: 18.1%-24.0%) in Daegu and 1.7% (95% CrI: 1.1%-2.5%) in other regions, whereas the national estimate was 10.2% (95% CrI: 9.0%-11.5%). Conclusions: The latest estimates of CFR of COVID-19 in Korea are considerably high, even with the early implementation of public health interventions including widespread testing, social distancing, and delayed school openings. Geographic differences in the CFR are likely influenced by clusters tied to hospitals and nursing homes.
Whole-chromosome fusions in the karyotype evolution ofSceloporus(Iguania, Reptilia) are more intense in sex chromosomes than autosomes
Authors: Lisachov Artem P. , Tishakova Katerina V. , Romanenko Svetlana A. , Molodtseva Anna S. , Prokopov Dmitry Yu. , Pereira Jorge C. , Ferguson-Smith Malcolm A. , Borodin Pavel M. , Trifonov Vladimir A.
Published: April 2020

There is a growing body of evidence that the common ancestor of vertebrates had a bimodal karyotype, i.e. consisting of large macrochromosomes and small microchromosomes. This type of karyotype organization is preserved in most reptiles. However, certain species independently experience microchromosome fusions. The evolutionary forces behind this are unclear. We investigated the karyotype of the green spiny lizard,Sceloporus malachiticus,an iguana species which has 2n=22, whereas the ancestral karyotype of iguanas had 2n=36. We obtained and sequenced flow-sorted chromosome-specific DNA samples and found that most of the microchromosome fusions in this species involved sex chromosomes. We found that certain ancestral squamate chromosomes, such as the homologue of theAnolis carolinensischromosome 11, are repeatedly involved in sex chromosome formation in different species. To test the hypothesis that the karyotypic shift could be associated with changes in recombination patterns, and to study sex chromosome synapsis and recombination in meiosis, we performed synaptonemal complex analysis in this species and inS. variabilis,a related species with 2n=34. We found that in the species studied the recombination patterns correlate more with phylogeny than with the structure of the karyotype. The sex chromosomes had two distal pseudoautosomal regions and a medial differentiated region.
Algal Neurotoxin Biosynthesis Repurposes the Terpene Cyclase Structural Fold Into anN-prenyltransferase
Authors: Chekan Jonathan R. , McKinnie Shaun M. K. , Noel Joseph P. , Moore Bradley S.
Published: April 2020

Prenylation is a common biological reaction in all domains of life whereupon prenyl diphosphate donors transfer prenyl groups onto small molecules as well as large proteins. The enzymes that catalyze these biotransformations are structurally distinct from ubiquitous terpene cyclases that instead assemble terpene molecules via intramolecular rearrangements. Herein we report the structure and molecular details of a new family of prenyltransferases from marine algae that repurposes the terpene cyclase structural fold for theN-prenylation of glutamic acid during the biosynthesis of the potent neurochemicals domoic acid and kainic acid. We solved the X-ray crystal structure of the prenyltransferase found in domoic acid biosynthesis, DabA, and show distinct active site binding modifications that remodel the canonical Mg2+-binding motif. We then applied our structural knowledge of DabA and a homologous enzyme from the kainic acid biosynthetic pathway, KabA, to alter their isoprene donor specificities (geranyl versus dimethylallyl diphosphate) by a single amino acid switch. While the diatom DabA and seaweed KabA enzymes share a common evolutionary lineage, they are distinct from all other terpene cyclases, suggesting a very distant ancestor.

Significance

Domoic acid is a neurotoxin produced by marine algae that readily bioaccumulates in shellfish and significantly impacts both human and animal life. The first committed step of the biosynthesis of domoic acid is theN-prenylation of L-glutamic acid by the enzyme DabA. By solving the crystal structure of DabA, we demonstrate that this enzyme has repurposed the common terpene cyclase fold to catalyze an extremely unusual reaction,N-prenylation of an unactivated primary amine. Application of these structural insights enabled rational engineering of twoN-prenyltransferase enzymes to accept alternative prenyl donors. Ultimately, these results not only expand the scope of reactions catalyzed by a terpene cyclase family member, but will help inform future domoic acid environmental monitoring efforts.
Exogenous and endogenous HDAC inhibitor effects in Rubinstein-Taybi syndrome models
Authors: Di Fede Elisabetta , Ottaviano Emerenziana , Grazioli Paolo , Ceccarani Camilla , Parodi Chiara , Colombo Elisa Adele , Bassanini Giulia , Severgnini Marco , Milani Donatella , Verduci Elvira , Vaccari Thomas , Massa Valentina , Borghi Elisa , Gervasini Cristina
Published: April 2020

Rubinstein-Taybi syndrome (RSTS) is an autosomal dominant disorder with specific clinical signs and neurodevelopmental impairment. The two known proteins altered in the majority of RSTS patients are the histone acetylation regulators CBP and p300. For assessing possible ameliorative effects of exogenous and endogenous HDAC inhibitors (HDACi), we exploitedin vivoandin vitroRSTS models. First, HDACi effects were tested onDrosophila melanogaster, showing molecular rescue. In the same model, we observed a shift in gut microbiota composition. We then studied HDACi effects in RSTS cell lines compared to healthy donor cells. We observed patients-specific molecular rescue of acetylation defects at subtoxic concentrations. Finally, we assessed commensal gut microbiota composition in a cohort of RSTS patients compared to healthy siblings. Intriguingly, we observed a significant depletion in butyrate-producing bacteria in RSTS patients. In conclusion, this study reports the possibility of modulating acetylation equilibrium by HDACi treatments and the importance of microbiota composition in a chromatinopathy.
Phylogenetic, geographic and habitat distribution of the green-brown polymorphism in European orthopterans
Authors: Schielzeth Holger
Published: April 2020

The green-brown polymorphism among polyneopteran insects represents one of the most penetrant color polymorphisms in any group of organisms. Yet systematic overviews are lacking. I here present analyses of the phylogenetic, geographic and habitat distribution of the green-brown polymorphism across the complete European orthopteran fauna. Overall, 30% of European orthopterans are green-brown polymorphic. Polymorphic species are scattered across the entire phylogenetic tree, including roughly equal proportions of Ensifera and Caelifera. A few taxonomic groups, however, include only brown species. Polymorphic species occur more frequently in clades that contain monomorphic green species than in those without green species. The relative abundance of color morphs in polymorphic species is skewed towards green, and in particular rare/exceptional brown morphs are more common in predominantly green species than rare/exceptional green morphs in predominantly brown species. The patterns of abundances support the hypothesis that loss-of-function mutations play a role in creating polymorphic populations from green species. Polymorphic species are particularly common in moist to mesic grasslands, alpine and arboreal habitats. Dry, open, rocky and cave habitats as well as nocturnal lifestyles are dominated by monomorphic brown species. The proportion of polymorphic species increases from southern to northern latitudes. These marked habitat-dependencies also show that coloration is affected by natural selection and/or environmental filtering. Overall, the results illustrate that the occurrence of the polymorphism is phylogenetically, geographically and ecologically widespread and they suggest that polymorphism is thus potentially in mutation-selection balance across a large number of species.
Lipid droplets disrupt mechanosensing in human hepatocytes
Authors: Chin LiKang , Theise Neil D. , Loneker Abigail E. , Janmey Paul A. , Wells Rebecca G.
Published: April 2020

Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer death in the world. Although most cases occur in stiff, cirrhotic livers, and stiffness is a significant risk factor, HCC can also arise in non-cirrhotic livers in the setting of non-alcoholic fatty liver disease (NAFLD). We hypothesized that lipid droplets in NAFLD might apply mechanical forces to the nucleus, functioning as mechanical stressors akin to stiffness. We investigated the effect of lipid droplets on cellular mechanosensing and found that primary human hepatocytes loaded with the fatty acids oleate and linoleate exhibited decreased stiffness-induced cell spreading and disrupted focal adhesions and stress fibers. The presence of large lipid droplets in hepatocytes resulted in increased nuclear localization of the mechano-sensor Yes-associated protein (YAP). In cirrhotic livers from patients with NAFLD, hepatocytes filled with large lipid droplets showed significantly higher nuclear localization of YAP as compared to cells with small lipid droplets. This work suggests that lipid droplets induce a mechanical signal that disrupts the ability of the hepatocyte to sense its underlying matrix stiffness, and that the presence of lipid droplets can induce intracellular mechanical stresses.

GRAPHICAL ABSTRACT
Molecular Docking Analysis Of Some Phytochemicals On Two SARS-CoV-2 Targets: Potential Lead Compounds Against Two Target Sites of SARS-CoV-2 Obtained from Plants
Authors: Ubani Amaka , Agwom Francis , RuthMorenikeji Oluwatoyin , Nathan Shehu , Luka Pam , Umera Arinze , Umar Usal , Omale Simeon , Nnadi Nnaemeka Emmanuel , Aguiyi John Chineye
Published: April 2020

COV spike (S) glycoprotein and Mproare two key targets that have been identified for vaccines and drug development against the COVID-19 disease. Virtual screening of some compounds of plants origin that have shown antiviral activities were carried out on the two targets, 6lu7 and 6vsb by docking with the PyRx software. The binding affinities were compared with other compounds and drugs already identified as potential ligands for 6lu7 and 6vsb as well as Chloroquine and hydroxychloroquine. The docked compounds with best binding affinities were also filtered for drug likeness using the SwissADME and PROTOX platforms on the basis of Physicochemical properties and toxicity respectively. The docking results revealed that scopodulcic acid and dammarenolic acid had the best binding affinity on the s-glycoprotein and Mproprotein targets respectively. Silybinin also demonstrated a good binding affinity to both protein targets making it a potential candidate for further evaluation as repurposed candidate for SARS COV2 with likelihood of having a multitarget activity.
Decision making and best practices for taxonomy-free eDNA metabarcoding in biomonitoring using Hill numbers
Authors: Mächler Elvira , Walser Jean-Claude , Altermatt Florian
Published: April 2020

Environmental DNA (eDNA) metabarcoding raises expectations for biomonitoring to cover organisms that have hitherto been neglected or excluded. To bypass current limitations in taxonomic assignments due to incomplete or erroneous reference data bases, taxonomic-free approaches are proposed for biomonitoring at the level of operational taxonomic unites (OTUs). However, this is challenging, because OTUs cannot be annotated and directly compared to classically derived data. The application of good stringency treatments to infer validity of OTUs and the clear understanding of the consequences to such treatments is thus especially relevant for biodiversity assessments. We investigated how common practices of stringency filtering affect diversity estimates based on Hill numbers derived from eDNA samples. We collected eDNA at 61 sites across a 740 km2river catchment, reflecting a spatially realistic scenario in biomonitoring. After bioinformatic processing of the data, we studied how different stringency treatments affect conclusions with respect to biodiversity at the catchment and site levels. The applied stringency treatments were based on the consistent appearance of OTUs across filter replicates, a relative abundance cut-off and rarefaction. We detected large differences in diversity estimates when accounting for presence/absence only, such that the detected diversity at the catchment scale differed by an order of magnitude between the treatments. These differences disappeared between the stringency treatments with increasing weighting of the OTUs’ abundances. Our study demonstrated the usefulness of Hill numbers for comparisons between data sets with large differences in diversity, and suggests best practice for data stringency filtering for biomonitoring.
Regulation of polyphosphate glucokinase gene expression through co-transcriptional processing inMycobacterium tuberculosisH37Rv
Authors: Bokolia Naveen Prakash , Khan Inshad Ali
Published: April 2020

Transcription is the process that allows the simultaneous folding of RNA molecules, known as co-transcriptional folding. This folding determines the functional properties of RNA molecules and possibly having a critical role during the synthesis as well. This functioning includes the characterized properties of riboswitches and ribozymes as well, which is significant when the transcription rate is comparable to the cellular environment. This study aims to discover a novel non-coding region that is important in the genetic expression ofMycobacterium tuberculosis. In this work, we identified a novel non-coding element of polyphosphate glucokinase (ppgk) gene that undergoes cleavage activity during the transcriptional process inMycobacterium tuberculosis. We revealed that cleavage occurs within the nascent RNA, and the resultant cleaved 3’RNA fragment carries the Shine-Dalgarno (SD) sequence and expression platform. Site-specific mutations provide a strong correlation between the disruption of cleavage activity and expression ofppgkgene. We concluded that co-transcriptional processing at the noncoding region as the required mechanism forppgkexpression that remains constitutive within the bacterial environment. The underlying reason forppgkmRNA processing and expression is correlated because the non-coding counterpart adopts a hairpin domain that sequesters ribosomal binding site. Thus, the mRNA processing at the immediate upstream of Shine-Dalgarno sequence is required to prevent this sequestration and subsequent expression as well. This study defines the molecular mechanism that is dependent on the transient but highly active structural features of the nascent RNA.
Single-molecule imaging reveals translation of mRNAs localized to stress granules
Authors: Mateju Daniel , Eichenberger Bastian , Eglinger Jan , Roth Gregory , Chao Jeffrey A.
Published: April 2020

Cellular stress leads to reprogramming of mRNA translation and formation of stress granules (SGs), membraneless organelles consisting of mRNA and RNA-binding proteins. Although the function of SGs remains largely unknown, it is widely assumed they contain exclusively nontranslating mRNA. Here we re-examine this hypothesis using single-molecule imaging of mRNA translation in living cells. While our data confirms that non-translating mRNAs are preferentially recruited to SGs, we find unequivocal evidence for translation of mRNA localized to SGs. Our data indicate that SG-associated translation is not rare and that the entire translation cycle (initiation, elongation and termination) can occur for these transcripts. Furthermore, translating mRNAs can be observed transitioning between the cytosol and SGs without changing their translational status. Together, these results argue against a direct role for SGs in inhibition of mRNA translation.
Echocardiography-guided percutaneous left ventricular intracavitary injection as a cell delivery approach in infarcted mice
Authors: Nong Yibing , Guo Yiru , Tomlin Alex , Zhu Xiaoping , Wysoczynski Marcin , Li Qianhong , Bolli Roberto
Published: April 2020

Background

In the field of cell therapy for heart disease, a new paradigm of repeated dosing of cells has recently emerged. However, the lack of a repeatable cell delivery method in preclinical studies in rodents is a major obstacle to investigating this paradigm.

Methods and Results

We have established and standardized a method of echocardiography-guided percutaneous left ventricular intracavitary injection (echo-guided LV injection) as a cell delivery approach in infarcted mice. Here, we describe the method in detail and address several important issues regarding it. First, by integrating anatomical and echocardiographic considerations, we have established strategies to determine a safe anatomical window for injection in infarcted mice. Second, we summarize our experience with this method (734 injections). The overall survival rate was 91.4%. Previous studies results suggest that 1×106cells delivered via this method yielded similar retention in the heart at 24 h as 1×105cells delivered via intracoronary or intramyocardial injection. Lastly, we examined the efficacy of this cell delivery approach. Compared with vehicle treatment, cardiac mesenchymal cells (CMCs) delivered via this method improved cardiac function assessed both echocardiographically and hemodynamically. Furthermore, repeated injections of CMCs via this method yielded greater cardiac function improvement than single dose administration.

Conclusion

Echo-guided LV injection is a feasible, reproducible, relatively less invasive and effective delivery method for cell therapy in heart disease. It is an important approach that could move the field of cell therapy forward, especially with regard to repeated cell administrations.
A recombinant gp145 Env glycoprotein from HIV-1 expressed in two different cell lines: effects on glycosylation and antigenicity
Authors: González-Feliciano José A. , Akamine Pearl , Capó-Vélez Coral M. , Delgado-Vélez Manuel , Dussupt Vincent , Krebs Shelly J. , Wojna Valerie , Polonis Victoria R. , Baerga-Ortiz Abel , Lasalde-Dominicci José A.
Published: April 2020

The envelope glycoprotein (Env) of the human immunodeficiency virus (HIV), has been the primary target for the development of a protective vaccine against infection. The extensiveN-linked glycosylation on Env is an important consideration as it may affect efficacy, stability, and expression yields. The expression host has been shown to influence the extent and type of glycosylation that decorates the protein target. Here, we report the glycosylation profile of the candidate subtype C immunogen CO6980v0c22 gp145 produced in two different host cells: CHO-K1 and Expi293F. The amino acid sequence for both glycoproteins was confirmed to be identical by peptide mass fingerprinting. However, the isoelectric point of the proteins differed; 4.5-5.5 and 6.0-7.0 for gp145 produced in CHO-K1 and Expi293F, respectively. These differences in pI were eliminated by enzymatic treatment with sialidase, indicating a large difference in the incorporation of sialic acid between hosts. This dramatic difference in the number of sialylated glycans between hosts was confirmed by analysis of PNGase F-released glycans using MALDI-ToF MS. These differences in glycosylation, however, did not greatly translate into differences in antibody recognition. Biosensor assays showed that gp145 produced in CHO-K1 had similar affinity toward the broadly neutralizing antibodies, 2G12 and PG16, as the gp145 produced in Expi293F. Additionally, both immunogens showed the same reactivity against plasma of HIV-infected patients. Taken together, these results support the notion that there are sizeable differences in the glycosylation of Env depending on the expression host. How these differences translate to vaccine efficacy remains unknown.
Adipose depot-specific upregulation of Ucp1 or mitochondrial oxidative complex proteins are early consequences of genetic insulin reduction in mice
Authors: Botezelli Jose Diego , Overby Peter , Lindo Lorenzo , Wang Su , Haïda Obélia , Lim Gareth E. , Templeman Nicole M. , Pauli Jose Rodrigo , Johnson James D.
Published: April 2020

Hyperinsulinemia plays a causal role in adipose tissue expansion. Mice with reduced insulin have increased energy expenditure, but the mechanisms remained unclear. Here we investigated the effects of genetically reducing insulin production on uncoupling and oxidative mitochondrial proteins in liver, skeletal muscle, white adipose tissue (WAT), and brown adipose tissue (BAT). Male Ins1+/+ or Ins1+/- littermates were fed either a low-fat diet (LFD) or a high-fat diet (HFD) for 4 weeks, starting at 8 weeks of age. Replicating our previous observations, HFD increased fasting hyperinsulinemia, and Ins1+/- mice had significantly lower circulating insulin compared with Ins1+/+ littermates. Fasting glucose and body weight were not different between genotypes. We did not observe significant differences in liver in skeletal muscle. In mesenteric WAT, Ins1+/- mice had reduced Ndufb8 and Sdhb. Ucp1 was increased in the context of the HFD, and HFD alone had a dramatic inhibitory effect on Pparg abundance. In inguinal WAT, Ins1+/- mice exhibited significant increases in oxidative complex proteins, independent of diet, without affecting Ucp1, Pparg, or Prdm16:Pparg association. In BAT, lowered insulin increased Sdhb protein levels that had been reduced by HFD. Ucp1 protein, Prdm16:Pparg association, and Sirt3 abundance were all increased in the absence of diet-induced hyperinsulinemia. Our data show that reducing insulin upregulates oxidative proteins in inguinal WAT without affecting Ucp1, while in mesenteric WAT and BAT, reducing insulin upregulates Ucp1 in the context of HFD. Preventing hyperinsulinemia has early depot-specific effects on adipose tissue metabolism and help explain the increased energy expenditure previously reported in Ins1+/- mice.
Helminth infection in a suburban ungulate population is driven more by age than landscape variables
Authors: Vannatta J. Trevor
Published: April 2020

Wildlife are increasingly common in suburban environments as towns and cities spread into surrounding rural areas. Many wildlife species have adapted to these new environments; however, we know comparatively little about how parasites respond urbanization of host habitats. Parasites are important members within ecological communities and alterations to transmission dynamics are known to alter host population dynamics. For complex life cycle parasites (parasites that use multiple different host species), suburban environments are thought to decrease transmission. Here, infection metrics of two parasites of white-tailed deer, giant liver flukes and thin-necked bladderworms, are examined to determine how successful these parasites are in a suburban environment. Additionally, land cover variables within suburban deer hunting areas are used to test if infection prevalence is associated with certain landscape level metrics. Results indicate that both parasites are common across the suburban landscape and are commonly found coinfecting the same hosts. Prevalence of neither parasite was strongly related to landscape variables within deer hunting areas, but fluke intensity was negatively correlated with the proportion of human development on the landscape. Overall, the scale of transmission events and host-parasite biology may explain why landscape metrics are weak predictors of infection risk in this system.
Nuclear Import of the HIV-1 Core Precedes Reverse Transcription and Uncoating
Authors: Selyutina Anastasia , Persaud Mirjana , Lee Kyeongeun , KewalRamani Vineet , Diaz-Griffero Felipe
Published: April 2020

HIV-1 particles contain a core formed by ~1500 capsid protein monomers housing viral RNA. HIV-1 core uncoating---disassembly---is required for infection. HIV-1 reverse transcription (RT) occurs before or during uncoating, but the cellular compartment where RT and uncoating occurs is unknown. Using imaging and biochemical assays to track HIV-1 capsids in nuclei during infection, we demonstrated that higher-order capsid complexes or complete cores containing viral genome are imported into nuclear compartments. Additionally, inhibition of RT that stabilizes the core during infection does not prevent capsid nuclear import; thus, RT may occur in nuclear compartments. We separated infected cells into cytosolic and nuclear fractions to measure RT during infection. Most observable RT intermediates were enriched in nuclear fractions, suggesting that most HIV-1 RT occurs in the nuclear compartment alongside uncoating. Thus, nuclear import precedes RT and uncoating, fundamentally changing our understanding of HIV-1 infection.
Demystifying “drop-outs” in single cell UMI data
Authors: Kim Tae , Zhou Xiang , Chen Mengjie
Published: April 2020

Analysis of scRNA-seq data has been challenging particularly because of excessive zeros observed in UMI counts. Prevalent opinions are that many of the detected zeros are “drop-outs” that occur during experiments and that those zeros should be accounted for through procedures such as normalization, variance stabilization, and imputation. Here, we extensively analyze publicly available UMI datasets and challenge the existing scRNA-seq workflows. Our results strongly suggest that resolving cell-type heterogeneity should be the foremost step of the scRNA-seq analysis pipeline because once cell-type heterogeneity is resolved, “drop-outs” disappear. Additionally, we show that the simplest parametric count model, Poisson, is sufficient to fully leverage the biological information contained in the UMI data, thus offering a more optimistic view of the data analysis. However, if the cell-type heterogeneity is not appropriately taken into account, pre-processing such as normalization or imputation becomes inappropriate and can introduce unwanted noise. Inspired by these analyses, we propose a zero inflation test that can select gene features contributing to cell-type heterogeneity. We integrate feature selection and clustering into iterative pre-processing in our novel, efficient, and straightforward framework for UMI analysis, HIPPO (Heterogeneity Inspired Pre-Processing tOol). HIPPO leads to downstream analysis with much better interpretability than alternatives in our comparative studies.