bluuebunny/crossref_metadata_2025 huggingface dataset:
Elements and Evolutionary Determinants of Genomic Divergence Between Paired Primary and Metastatic Tumors
Authors: Sun Ruping , Nikolakopoulos Athanasios N.
Published: August 2020

Can metastatic-primary (M-P) genomic divergence measured from next generation sequencing reveal the natural history of metastatic dissemination? This remains an open question of utmost importance in facilitating a deeper understanding of metastatic progression, and thereby, improving its prevention. Here, we utilize mathematical and computational modeling to tackle this question as well as to provide a framework that illuminates the fundamental elements and evolutionary determinants of M-P divergence. Our framework facilitates the integration of sequencing detectability of somatic variants, and hence, paves the way towards bridging the measurable between-tumor heterogeneity with analytical modeling and interpretability. We show that the number of somatic variants of the metastatic seeding cell that are experimentally undetectable in the primary tumor, can be characterized as the path of the phylogenetic tree from the last appearing variant of the seeding cell back to the most recent detectable variant. We find that the expected length of this path is principally determined by the decay in detectability of the variants along the seeding cell’s lineage; and thus, exhibits a significant dependence on the underlying tumor growth dynamics. A striking implication of this fact, is that dissemination from an advanced detectable subclone of the primary tumor can lead to an abrupt drop in the expected measurable M-P divergence, thereby breaking the previously assumed monotonic relation between seeding time and M-P divergence. This is emphatically verified by our single cell-based spatial tumor growth simulation, where we find that M-P divergence exhibits a non-monotonic relationship with seeding time when the primary tumor grows under branched and linear evolution. On the other hand, a monotonic relationship holds when we condition on the dynamics of progressive diversification, or by restricting the seeding cells to always originate from undetectable subclones. Our results highlight the fact that a precise understanding of tumor growth dynamics is thesine qua nonfor exploiting M-P divergence to reconstruct the chronology of metastatic dissemination. The quantitative models presented here enable further careful evaluation of M-P divergence in association with crucial evolutionary and sequencing parameters.

Graphical Abstract

Highlights

Depth of most recent detectable variant characterizes Metastatic-Primary divergence

Decay in variant detectability determines the expected M-P divergence

Dissemination from late detectable subclone leads to an abrupt drop in M-P divergence

Spatial model verifies growth mode governs M-P divergence dependency on seeding time
Genome-wide diversity and differentiation of two novel multidrug-resistant populations ofPasteurella multocidatype B:2 from fowl cholera
Authors: Saha Otun , Islam M. Rafiul , Rahman M. Shaminur , Hoque M. Nazmul , Hossain M. Anwar , Sultana Munawar
Published: August 2020

Pasteurella multocidais the etiologic agent of fowl cholera (FC), a highly contagious and severe disease in poultry with higher mortality and morbidity. Twenty-twoP. multocidastrains isolated from the FC outbreaks were subjected to phenotypic and genotypic characterization. The isolates were grouped into two distinct RAPD biotypes harboring a range of pathogenic genes;exbB,ompH,ptfA,nanB,sodC, andhgbA. Among these strains, 90.90% and 36.37% were multidrug-resistant and strong biofilm formers, respectively. Whole genome sequencing of the two representative RAPD isolates confirmed asP. multocida typeB:L2:ST122 harboring a number of virulence factors, and antimicrobial resistance genes. Pan-genome analysis revealed 90 unique genes in these genomes associated with versatile metabolic functions, pathogenicity, virulence, and antimicrobial resistance. This study for the first time reports the association ofP. multocidagenotype B:L2:ST122 in the pathogenesis of FC, and provides a genetic context for future researches onP. multocidastrains.
Frequency shapes the quality of tactile percepts evoked through electrical stimulation of the nerves
Authors: Graczyk Emily L. , Christie Breanne P. , He Qinpu , Tyler Dustin J. , Bensmaia Sliman J.
Published: August 2020

Abstract

Touch is critical for our ability to manipulate objects, as evidenced by the deficits incurred when touch is absent. To restore the sense of touch via electrical stimulation of the peripheral nerves requires that we understand how the parameters of stimulation shape the evoked sensation. To this end, we investigated the sensory consequences of changing the frequency of pulse trains (PF) delivered to the peripheral nerves of humans chronically implanted with multi-channel nerve cuff electrodes. We found that increases in PF led to systematic increases in perceived frequency, up to about 50 Hz, at which point further changes in PF had little to no impact on sensory quality. Above this transition frequency, ratings of perceived frequency levelled off, the ability to discriminate changes in PF was abolished, and verbal descriptors selected to characterize the sensation changed abruptly. We conclude that the quality of electrically evoked tactile sensations can be shaped by imposing temporal patterns on a fixed neural population, but this temporal patterning can only be resolved up to about 50 Hz. These findings highlight the importance of spike timing in shaping the quality of a sensation and will contribute to the development of encoding strategies for conveying touch feedback through bionic hands and feet.
Human ACE2 peptide mimics block SARS-CoV-2 Pulmonary Cells Infection
Authors: Karoyan Philippe , Vieillard Vincent , Odile Estelle , Denis Alexis , Guihot Amélie , Luyt Charles-Edouard , Gómez-Morales Luis , Grondin Pascal , Lequin Olivier
Published: August 2020

In the light of the recent accumulated knowledge on SARS-CoV-2 and its mode of human cells invasion, the binding of viral spike glycoprotein to human Angiotensin Converting Enzyme 2 (hACE2) receptor plays a central role in cell entry. We designed a series of peptides mimicking the N-terminal helix of hACE2 protein which contains most of the contacting residues at the binding site and have a high helical folding propensity in aqueous solution. Our best peptide mimics bind to the virus spike protein with high affinity and are able to block SARS-CoV-2 human pulmonary cell infection with an inhibitory concentration (IC50) in the nanomolar range. These first in class blocking peptide mimics represent powerful tools that might be used in prophylactic and therapeutic approaches to fight the coronavirus disease 2019 (COVID-19).
Binary decision between asymmetric and symmetric cell division is defined by the balance of PAR proteins inC. elegansembryos
Authors: Lim Yen Wei , Wen Fu-Lai , Shankar Prabhat , Shibata Tatsuo , Motegi Fumio
Published: August 2020

Coordination between cell differentiation and proliferation during development requires the balance between asymmetric and symmetric modes of cell division. However, the cellular intrinsic cue underlying the binary choice between these two division modes remains elusive. Here we show evidence inCaenorhabditis elegansthat the invariable lineage of the division modes is programmed by the balance between antagonizing complexes of partitioning-defective (PAR) proteins. By uncoupling unequal inheritance of PAR proteins from that of fate determinants during zygote division, we demonstrated that changes in the balance between PAR-2 and PAR-6 are sufficient to re-program the division modes from symmetric to asymmetric andvice versain two-cell stage embryos. The division mode adopted occurs independently of asymmetry in cytoplasmic fate determinants, cell-size asymmetry, and cell-cycle asynchrony between the sister cells. We propose that the balance between antagonizing PAR proteins represents an intrinsic self-organizing cue for binary specification of the division modes during development.
StackPDB: predicting DNA-binding proteins based on XGB-RFE feature optimization and stacked ensemble classifier
Authors: Zhang Qingmei , Liu Peishun , Han Yu , Zhang Yaqun , Wang Xue , Yu Bin
Published: August 2020

DNA binding proteins (DBPs) not only play an important role in all aspects of genetic activities such as DNA replication, recombination, repair, and modification but also are used as key components of antibiotics, steroids, and anticancer drugs in the field of drug discovery. Identifying DBPs becomes one of the most challenging problems in the domain of proteomics research. Considering the high-priced and inefficient of the experimental method, constructing a detailed DBPs prediction model becomes an urgent problem for researchers. In this paper, we propose a stacked ensemble classifier based method for predicting DBPs called StackPDB. Firstly, pseudo amino acid composition (PseAAC), pseudo position-specific scoring matrix (PsePSSM), position-specific scoring matrix-transition probability composition (PSSM-TPC), evolutionary distance transformation (EDT), and residue probing transformation (RPT) are applied to extract protein sequence features. Secondly, extreme gradient boosting-recursive feature elimination (XGB-RFE) is employed to gain an excellent feature subset. Finally, the best features are applied to the stacked ensemble classifier composed of XGBoost, LightGBM, and SVM to construct StackPDB. After applying leave-one-out cross-validation (LOOCV), StackPDB obtains high ACC and MCC on PDB1075, 93.44% and 0.8687, respectively. Besides, the ACC of the independent test datasets PDB186 and PDB180 are 84.41% and 90.00%, respectively. The MCC of the independent test datasets PDB186 and PDB180 are 0.6882 and 0.7997, respectively. The results on the training dataset and the independent test dataset show that StackPDB has a great predictive ability to predict DBPs.
Causal Understanding of the Stone Dropping Task in Two Species of Macaw
Authors: O’Neill Laurie , Picaud Anthony , Hastings Ronan , Buffenoir Nina , Gahr Manfred , von Bayern Auguste M.P.
Published: August 2020

Causal understanding in animal cognition can be divided into two broad categories (Woodward, 2011): learned associations between cause and effect (Le Pelley et al., 2017) and understanding based on underlying mechanisms (Johnson and Ahn, 2017). One experiment that gives insight to animals’ use of causal mechanisms is the stone-dropping task. In this, subjects are given an opportunity to push a platform to make it collapse and are then required to innovate dropping a stone tool to recreate the platform collapsing (von Bayern et al., 2009). We describe how 16/18 subjects of two species of macaw (n=18; Ara ambiguus (n=9) & Ara glaucogularis (n=9)) were able to innovate the solution in this task. Many of the subjects were able to innovate the behaviour through exploratory object combination, but it is also possible that a mechanistic understanding of the necessity for contact with the platform influenced some subjects’ behaviour. All the successful subjects were able to recreate their novel stone-dropping behaviour in the first or second trial after innovation (and all trials thereafter) and they were also able to do the behaviour increasingly faster. This suggests they also rely on learned associations of cause and effect. However, in a transfer task in which subjects had to guide a stick tool to make it touch a differently positioned platform, all but one of the subjects failed. This would suggest that the majority of the subjects were not using an understanding of platform contact to solve the task, although the subjects’ difficulty with using stick tools may have also affected their performance in this transfer.
Methods for detecting PER2::LUCIFERASE bioluminescence rhythms in freely moving mice
Authors: Martin-Burgos B. , Wang W. , William I. , Tir S. , Mohammad I. , Javed R. , Smith S. , Cui Y. , Smith C.B. , van der Vinne V. , Molyneux P.C. , Miller S.C. , Weaver D. R. , Leise T.L. , Harrington M.E.
Published: August 2020

Circadian rhythms are driven by daily oscillations of gene expression. An important tool for studying cellular and tissue rhythms is the use of a gene reporter, such as bioluminescence from the reporter gene luciferase controlled by a rhythmically expressed gene of interest. Here we describe methods that allow measurement of bioluminescence from a freely-moving mouse housed in a standard cage. Using a LumiCycleIn Vivo(Actimetrics), we determined conditions that allow detection of circadian rhythms of bioluminescence from the PER2 reporter, PER2::LUC, in freely behaving mice. We tested delivery of D-luciferin via a subcutaneous minipump and in the drinking water. Further, we demonstrate that a synthetic luciferase substrate, CycLuc1, can support circadian rhythms of bioluminescence, even when delivered at a lower concentration than D-luciferin. We share our analysis scripts and suggestions for further improvements in this method. This approach will be straightforward to apply to mice with tissue-specific reporters, allowing insights into responses of specific peripheral clocks to perturbations such as environmental or pharmacological manipulations.
SARS-CoV-2 neutralizing human antibodies protect against lower respiratory tract disease in a hamster model
Authors: Haagmans Bart L. , Noack Danny , Okba Nisreen M.A. , Li Wentao , Wang Chunyan , Bestebroer Theo , de Vries Rory , Herfst Sander , de Meulder Dennis , van Run Peter , Lamers Mart M. , Rijnders Bart , Rokx Casper , van Kuppeveld Frank , Grosveld Frank , Drabek Dubravka , GeurtsvanKessel Corine , Koopmans Marion , Bosch Berend Jan , Kuiken Thijs , Rockx Barry
Published: August 2020

Effective clinical intervention strategies for COVID-19 are urgently needed. Although several clinical trials have evaluated the use of convalescent plasma containing virus-neutralizing antibodies, the effectiveness has not been proven. We show that hamsters treated with a high dose of human convalescent plasma or a monoclonal antibody were protected against weight loss showing reduced pneumonia and pulmonary virus replication compared to control animals. However, a ten-fold lower dose of convalescent plasma showed no protective effect. Thus, variable and relatively low levels of virus neutralizing antibodies in convalescent plasma may limit their use for effective antiviral therapy, favouring concentrated, purified (monoclonal) antibodies.
Synchrony between daily rhythms of malaria parasites and hosts is driven by an essential amino acid
Authors: Prior Kimberley F. , Middleton Benita , T.Y. Owolabi Alíz , Westwood Mary L. , Holland Jacob , O’Donnell Aidan J. , Blackman Mike , Skene Debra J. , Reece Sarah E.
Published: August 2020

Rapid asexual replication of blood stage malaria parasites is responsible for the severity of disease symptoms and fuels the production of transmission forms. That malaria parasite species coordinate their cycles of asexual replication with daily rhythms of their host was discovered in the Hippocratic era, but how and why this occurs is enigmatic. Here, we demonstrate that thePlasmodium chabaudi’sschedule for asexual replication can be orchestrated by a isoleucine, metabolite provided to the parasite in periodic manner due to the host’s rhythmic intake of food. First, we identify nutrients with daily rhythms in the blood that match the timing of rhythms in both host feeding and the developmental schedule of asexually replicating parasites. We hypothesise that if parasites set their own developmental schedule, they should use a time-of-day cue that is a factor they cannot generate endogenously at any time-of-day, or scavenge in a round-the-clock manner. Our large-scale metabolomics experiment reveals that only one metabolite - the amino acid isoleucine – fits these criteria. Second, further experiments reveal that parasites alter the developmental schedule of asexual stages in response to isoleucine provision and withdrawal in the manner consistent with it acting as a time-cue. Specifically, parasites respond to isoleucine loss by slowing development. This is a parasite strategy rather than the consequences of an imposed constraint, because unlike when parasites are deprived of other essential nutrients, they suffer no apparent costs in the absence of isoleucine. Overall, our data suggest parasites can use the daily rhythmicity of blood-isoleucine concentration to synchronise asexual development with the availability of isoleucine, and potentially other resources, that arrive in the blood in a periodic manner due to the host’s daily feeding-fasting cycle. Identifying both how and why parasites keep time opens avenues for interventions; interfering with the parasite’s time-keeping mechanism may stall replication, increasing the efficacy of drugs and immune responses, and could also prevent parasites from entering dormancy to tolerate drugs.
Learning epistatic gene interactions from perturbation screens
Authors: Elmes Kieran , Schmich Fabian , Szczurek Ewa , Jenkins Jeremy , Beerenwinkel Niko , Gavryushkin Alex
Published: August 2020

Abstract

The treatment of complex diseases often relies on combinatorial therapy, a strategy where drugs are used to target multiple genes simultaneously. Promising candidate genes for combinatorial perturbation often constitute epistatic genes, i.e., genes which contribute to a phenotype in a non-linear fashion. Experimental identification of the full landscape of genetic interactions by perturbing all gene combinations is prohibitive due to the exponential growth of testable hypotheses. Here we present a model for the inference of pairwise epistatic, including synthetic lethal, gene interactions from siRNA-based perturbation screens. The model exploits the combinatorial nature of siRNA-based screens resulting from the high numbers of sequence-dependent off-target effects, where each siRNA apart from its intended target knocks down hundreds of additional genes. We show that conditional and marginal epistasis can be estimated as interaction coefficients of regression models on perturbation data. We compare two methods, namelyglinternetandxyz, for selecting non-zero effects in high dimensions as components of the model, and make recommendations for the appropriate use of each. For data simulated from real RNAi screening libraries, we show thatglinternetsuccessfully identifies epistatic gene pairs with high accuracy across a wide range of relevant parameters for the signal-to-noise ratio of observed phenotypes, the effect size of epistasis and the number of observations per double knockdown.xyzis also able to identify interactions from lower dimensional data sets (fewer genes), but is less accurate for many dimensions. Higher accuracy ofglinternet, however, comes at the cost of longer running time compared toxyz. The general model is widely applicable and allows mining the wealth of publicly available RNAi screening data for the estimation of epistatic interactions between genes. As a proof of concept, we apply the model to search for interactions, and potential targets for treatment, among previously published sets of siRNA perturbation screens on various pathogens. The identified interactions include both known epistatic interactions as well as novel findings.
The 3’UTR of theorb2gene encoding theDrosophilaCPEB translation factor plays a critical role in spermatogenesis
Authors: Gilmutdinov Rudolf A. , Kozlov Eugene N. , Olenina Ludmila V. , Kotov Alexei A. , Barr Justinn , Zhukova Mariya V. , Schedl Paul , Shidlovskii Yulii V.
Published: August 2020

CPEB proteins are conserved translation regulators involved in multiple biological processes. One of these proteins inDrosophila, Orb2, is a principal player in spermatogenesis. It is required for meiosis and spermatid differentiation. During the later processorb2mRNAs and proteins are localized within the developing spermatid. To evaluate the role oforb2mRNA 3’UTR in spermatogenesis, we used the CRISPR/Cas9 system to generate a deletion of theorb23’UTR,orb2R. This deletion disrupts the process of spermatid differentiation, but has no apparent effect on meiosis. While this deletion appears to destabilize theorb2mRNA and reduce the levels of Orb2 protein, this is not the primary cause of the differentiation defects. Instead, differentiation appears to be disrupted becauseorb2mRNAs and proteins are not properly localized within the differentiating spermatids. Other transcripts and proteins involved in spermatogenesis are also mislocalized inorb2Rspermatids.

Author summary

The conserved family of cytoplasmic polyadenylation element binding (CPEB) proteins can activate or repress translation of target mRNAs, depending on the specific biological context, through interaction with special cytoplasmic polyadenylation element (CPE) sequences. These proteins function mainly in highly polarized cells. Orb2, one of the twoDrosophila melanogasterCPEB proteins, is predominantly expressed in the testes and is crucial for spermatogenesis. The 3’UTR oforb2transcript contains multiple CPE-like motifs, which is indicative oforb2self-regulation. We have generated a deletion that removes the greater portion of 3’UTR. While this deletion causes a reduction in the levels oforb2mRNA and the protein, this does not appear to be responsible for the defects in spermatogenesis observed in the deletion mutant. Instead, it is the mislocalization of the mRNA and protein in the developing spermatids.
Protected areas network is not adequate to protect a critically endangered East Africa Chelonian: Modelling distribution of pancake tortoise, Malacochersus tornieri under current and future climates
Authors: Eustace Abraham , Esser Luíz Fernando , Mremi Rudolf , Malonza Patrick K. , Mwaya Reginald T.
Published: August 2020

While the international pet trade and habitat destruction have been extensively discussed as major threats to the survival of the pancake tortoise (Malacochersus tornieri), the impact of climate change on the species remains unknown. In this study, we used species distribution modelling to predict the current and future distribution of pancake tortoises in Zambezian and Somalian biogeographical regions. We used 224 pancake tortoise occurrences obtained from Tanzania, Kenya and Zambia to estimate suitable and stable areas for the pancake tortoise in all countries present in these regions. We also used a protected area network to assess how many of the suitable and stable areas are protected for the conservation of this critically endangered species. Our model predicted the expansion of climatically suitable habitats for pancake tortoises from four countries and a total area of 90,668.75 km2to ten countries in the future and an area of 343,459.60 - 401,179.70 km2. The model also showed that a more significant area of climatically suitable habitat for the species lies outside of the wildlife protected areas. Based on our results, we can predict that pancake tortoises may not suffer from habitat constriction. However, the species will continue to be at risk from the international pet trade, as most of the identified suitable habitats remain outside of protected areas. We suggest that efforts to conserve the pancake tortoise should not only focus on protected areas but also areas that are unprotected, as these comprise a large proportion of the suitable and stable habitats available following predicted future climate change.
Comparison of antimicrobial activity between intraoperatively soaked bacitracin sutures and triclosan coated suture
Authors: Musick Shane T. , Adkins Jeremy M. , Al-Ahmar Roy , Yu Hongwei D. , Alberico Anthony M.
Published: August 2020

With the easily available option for surgeons to soak their suture in anti-biotic irrigating solution intraoperatively in mind, this study was designed to evaluate the ability of suture soaked in bacitracin irrigating solution to inhibit the growth ofStaphylococcus aureusandMethicillin-resistant Staphylococcus aureus. Using standard experimental procedure, sterile suture was soaked in Bacitracin suture, and dried for 10 minutes or 6 hours, incubated for 24 h on inoculated plates, and examined for zone of inhibition around the suture. This was compared to control unsoaked suture and antimicrobial suture (AMS) currently on the market to determine if the minor intra operative procedural change of placing suture in antibiotic irrigation solution instead of on the sterile table could confer some antimicrobial activity. The study found the Bacitracin soaked suture (BSS) consistently inhibited the growth of the test organisms. For both organisms, the BSS exhibited a significantly larger zone of inhibition compared to the unsoaked control suture. However, the AMS currently on the market exhibited a larger zone of inhibition compared to the BSS. Placing sutures in a bacitracin irrigation solution intraoperatively instead of directly on the sterile table can achieve some of the in vitro antimicrobial effect seen from AMS currently on the market. This may result in reduced rates of SSIs and associated costs without major procedural change and at reduced overhead.
A compelling symmetry: The extended fetuses-at-risk perspective on modal, optimal and relative birthweight and gestational age
Authors: Joseph K.S.
Published: August 2020

Background

The relationship between several intriguing perinatal phenomena, namely, modal, optimal, and relative birthweight and gestational age, remains poorly understood, especially the mechanism by which relative birthweight and gestational age resolve the paradox of intersecting perinatal mortality curves.

Methods

Birthweight and gestational age distributions and birthweight- and gestational age-specific perinatal death rates of low- and high-risk cohorts in the United States, 2004-2015, were estimated using births-based and extended fetuses-at-risk formulations. The relationships between these births-based distributions and rates, and the first derivatives of fetuses-at-risk birth and perinatal death rates were examined in order to assess how the rate of change in fetuses-at-risk rates affects gestational age distributions and births-based perinatal death rate patterns.

Results

Modal gestational age typically exceeded optimal gestational age because both were influenced by the peak in the first derivative of the birth rate, while optimal gestational age was additionally influenced by the point at which the first derivative of the fetuses-at-risk perinatal death rate showed a sharp increase in late gestation. The clustering and correlation between modal and optimal gestational age within cohorts, the higher perinatal death rate at optimal gestational age among higher-risk cohorts, and the symmetric left-shift in births-based gestational age-specific perinatal death rates in higher-risk cohorts explained how relative gestational age resolved the paradox of intersecting perinatal mortality curves.

Conclusions

Changes in the first derivative the fetuses-at-risk birth and perinatal death rates underlie several births-based perinatal phenomena and this explanation further unifies the fetuses-at-risk and births-based models of perinatal death.
Profiles of expression pattern and tissue distribution of host defense peptides genes in different chicken (Gallus gallus) breeds related to body weight
Authors: Li Zhengtian , Ahmed Irfan , Xu Zhiqiang , Sun Shuai , Li Tao , Gu Dahai , Liu Yong , Zhang Xia , Yan Shixiong , Hu Wenyuan , Jiang Ziqing , Duan Xiaohua , Li Qihua , Liu Lixian , Rong Hua , Wang Kun , Abdulwahid Alsoufi Mohammed , Dou Tengfei , Wang Shanrong , Su Zhengchang , Ge Changrong , te Pas Marinus F.W. , Jia Junjing , Huang Ying
Published: August 2020

Host defense peptides(HDPs) are an important first line of defense with antimicrobial and immunomodulatory properties. Selection for increased body weight is suggested to be related to reduced immune response. We studied the relationships among body weight, age, and theHDPexpression patterns in intestine and immune organs. We used chickens with marked differences of body sizes. The non-selected Daweishan mini chickens showed the highest indexes of immune organs and the lowest concentrations of the plasma immune parameters C3, C4, IgA, and IgY, while the commercial Avian broiler showed the opposite results. The Daweishan mini chickens showed the highest mRNA expressions ofHDPgenes in small intestine followed by the semi-selected Wuding chickens. Compared with local breeds, broiler chickens showed higher mRNA expression ofHDPgenes in spleen, thymus, and bursa. Body weight andHDPexpression levels were negatively correlated in the intestine and positively in the immune organs. These results indicated that theHDPimmune regulatory roles in small intestine acted as first line of defense in innate immunity in local breeds, and as an adaptive immunity in broiler chickens. Selection was associated with the expression profiles ofHDPgenes in a chicken, age, and organ-specific manner.
Identification of split-GAL4 drivers and enhancers that allow regional cell type manipulations of theDrosophila melanogasterintestine
Authors: Ariyapala Ishara S. , Holsopple Jessica M. , Popodi Ellen M. , Hartwick Dalton G. , Kahsai Lily , Cook Kevin R. , Sokol Nicholas S.
Published: August 2020

The Drosophila adult midgut is a model epithelial tissue composed of a few major cell types with distinct regional identities. One of the limitations to its analysis is the lack of tools to manipulate gene expression based on these regional identities. To overcome this obstacle, we applied the intersectional split-GAL4 system to the adult midgut and report 653 driver combinations that label cells by region and cell type. We first identified 424 split-GAL4 drivers with midgut expression from over 7,300 drivers screened, and then evaluated the expression patterns of each of these 424 when paired with three reference drivers that report activity specifically in progenitor cells, enteroendocrine cells, or enterocytes. We also evaluated a subset of the drivers expressed in progenitor cells for expression in enteroblasts using another reference driver. We show that driver combinations can define novel cell populations by identifying a driver that marks a distinct subset of enteroendocrine cells expressing genes usually associated with progenitor cells. The regional cell type patterns associated with the entire set of driver combinations are documented in a freely available website, providing information for the design of thousands of additional driver combinations to experimentally manipulate small subsets of intestinal cells. In addition, we show that intestinal enhancers identified with the split-GAL4 system can confer equivalent expression patterns on other transgenic reporters. Altogether, the resource reported here will enable more precisely targeted gene expression for studying intestinal processes, epithelial cell functions, and diseases affecting self-renewing tissues.
Olfactory host entry supports herpesvirus recombination
Authors: Xie Wanxiaojie , Bruce Kimberley , Farrell Helen E. , Stevenson Philip G.
Published: August 2020

Herpesvirus genomes record abundant recombination. Its impact on infection remains ill-defined. When co-infecting mice by the natural olfactory route, individually incapacitated Murid Herpesvirus-4 (MuHV-4) mutants routinely recombined to restore normal host colonization. Lung infection rescued much less well. Murine cytomegalovirus mutants deficient in salivary gland colonization also showed rescue via the nose but not the lungs. As nose and lung infections show similar spread, efficient recombination seemed specific to olfactory entry. Rescue of replication-deficient MuHV-4 implied co-infection of the first encountered cells, and this worked also with asynchronous inoculation, suggesting that latent virus could lie in wait for later reactivation. Inhaled MuHV-4 is commonly caught on respiratory mucus, which epithelial cilia push back towards the olfactory surface, and infection was correspondingly frequent at the anterior olfactory edge. Thus olfactory entry provides a general means for herpesviruses to meet.

Author summary

Inter-strain recombination allows viruses to optimise infection in diverse hosts. Many herpesviruses show past recombination. Yet they are ancient pathogens, so this past may be remote and recombination rare. Diverse herpesviruses enter new hosts via olfactory cells. We show that such entry routinely allows recombination between co-infecting virus strains, even when one strain cannot spread. Recombination was contrastingly rare after lung infection. Thus, entry via olfactory cells specifically supports frequent herpesvirus recombination.
Reconstructing the lineage histories and differentiation trajectories of individual cancer cells inJAK2-mutant myeloproliferative neoplasms
Authors: Van Egeren Debra , Escabi Javier , Nguyen Maximilian , Liu Shichen , Reilly Christopher R. , Patel Sachin , Kamaz Baransel , Kalyva Maria , DeAngelo Daniel J. , Galinsky Ilene , Wadleigh Martha , Winer Eric S. , Luskin Marlise R. , Stone Richard M. , Garcia Jacqueline S. , Hobbs Gabriela S. , Camargo Fernando D. , Michor Franziska , Mullally Ann , Cortes-Ciriano Isidro , Hormoz Sahand
Published: August 2020

Some cancers originate from a single mutation event in a single cell. For example, blood cancers known as myeloproliferative neoplasms (MPN) are thought to originate through the acquisition of a driver mutation (most commonlyJAK2-V617F) in a hematopoietic stem cell (HSC). However, when the mutation first occurs in individual patients and how it impacts the behavior of HSCs in their native context is not known. Here we quantified the impact of theJAK2-V617F mutation on the proliferation dynamics of HSCs and the differentiation trajectories of their progenies in individual MPN patients. We reconstructed the lineage history of individual HSCs obtained from MPN patients using the patterns of spontaneous somatic mutations accrued in their genomes over time. Strikingly, we found that theJAK2-V617F mutation occurred in a single HSC several decades before MPN diagnosis — at age 9±2 years in a 34-year-old patient, and at age 19±3 years in a 63-year-old patient. For each patient, we inferred the number of mutated HSCs over time and computed their fitness. The population ofJAK2-mutated HSCs grew exponentially by 63±15% and 44±13% every year in the two patients, respectively. To contrast the differentiation trajectories of theJAK2-mutated HSCs with those of healthy HSCs, we simultaneously measured the full transcriptome and somatic mutations in single hematopoietic stem and progenitor cells (HSPCs). We found that the fraction ofJAK2-mutant HSPCs varied significantly across different myeloid cell types within the same patient. The erythroid progenitor cells were often entirelyJAK2-mutant, even when the peripheral bloodJAK2-V617F allele burden was low. The novel biological insights uncovered by this work have implications for the prevention and treatment of MPN, as well as the accurate assessment of disease burden in patients. The technology platforms and computational frameworks developed here are broadly applicable to other types of hematological malignancies and cancers.
Induction of SARS-CoV-2 protein S-specific CD8+ T cells in the lungs of gp96-Ig-S vaccinated mice
Authors: Fisher Eva , Padula Laura , Podack Kristin , O’Neill Katelyn , Seavey Matthew M , Jayaraman Padmini , Jasuja Rahul , Strbo Natasa
Published: August 2020

Given the aggressive spread of COVID-19-related deaths, there is an urgent public health need to support the development of vaccine candidates to rapidly improve the available control measures against SARS-CoV-2. To meet this need, we are leveraging our existing vaccine platform to target SARS-CoV-2. Here, we generated cellular heat shock chaperone protein, glycoprotein 96 (gp96), to deliver SARS-CoV-2 protein S (spike) to the immune system and to induce cell-mediated immune responses. We showed that our vaccine platform effectively stimulates a robust cellular immune response against protein S. Moreover, we confirmed that gp96-Ig, secreted from allogeneic cells expressing full-length protein S, generates powerful, protein S polyepitope-specific CD4+ and CD8+ T cell responses in both lung interstitium and airways. These findings were further strengthened by the observation that protein-S -specific CD8+ T cells were induced in human leukocyte antigen (HLA)-A2-02-01 transgenic mice thus providing encouraging translational data that the vaccine is likely to work in humans, in the context of SARS-CoV-2 antigen presentation.
Embedding covariate adjustments in tree-based automated machine learning for biomedical big data analyses
Authors: Manduchi Elisabetta , Fu Weixuan , Romano Joseph D. , Ruberto Stefano , Moore Jason H.
Published: August 2020

Background

A typical task in bioinformatics consists of identifying which features are associated with a target outcome of interest and building a predictive model. Automated machine learning (AutoML) systems such as the Tree-based Pipeline Optimization Tool (TPOT) constitute an appealing approach to this end. However, in biomedical data, there are often baseline characteristics of the subjects in a study or batch effects that need to be adjusted for in order to better isolate the effects of the features of interest on the target. Thus, the ability to perform covariate adjustments becomes particularly important for applications of AutoML to biomedical big data analysis.

Results

We present an approach to adjust for covariates affecting features and/or target in TPOT. Our approach is based on regressing out the covariates in a manner that avoids ‘leakage’ during the cross-validation training procedure. We then describe applications of this approach to toxicogenomics and schizophrenia gene expression data sets. The TPOT extensions discussed in this work are available athttps://github.com/EpistasisLab/tpot/tree/v0.11.1-resAdj.

Conclusions

In this work, we address an important need in the context of AutoML, which is particularly crucial for applications to bioinformatics and medical informatics, namely covariate adjustments. To this end we present a substantial extension of TPOT, a genetic programming based AutoML approach. We show the utility of this extension by applications to large toxicogenomics and differential gene expression data. The method is generally applicable in many other scenarios from the biomedical field.
An evolutionarily conserved Lhx2-Ldb1 interaction regulates the acquisition of hippocampal cell fate and regional identity
Authors: Kinare Veena , Iyer Archana , Padmanabhan Hari , Godbole Geeta , Khan Tooba , Khatri Zeba , Maheshwari Upasana , Muralidharan Bhavana , Tole Shubha
Published: August 2020

Protein cofactor Ldb1 regulates cell fate specification by interacting with LIM-homeodomain (LIM-HD) proteins in a tetrameric complex consisting of an LDB:LDB dimer that bridges two LIM-HD molecules, a mechanism first demonstrated in theDrosophilawing disc. Here, we demonstrate conservation of this interaction in the regulation of mammalian hippocampal development, which is profoundly defective upon loss of eitherLhx2orLdb1. Electroporation of a chimeric construct that encodes the Lhx2-HD and Ldb1-DD (dimerization domain) in a single transcript cell-autonomously rescues a comprehensive range of hippocampal deficits in the mouseLdb1mutant, including the acquisition of field-specific molecular identity and the regulation of the neuron-glia cell fate switch. This demonstrates that the LHX:LDB complex is an evolutionarily conserved molecular regulatory device that controls complex aspects of regional cell identity in the developing brain.

Summary statement

Similar to an Apterous-Chip mechanism that patterns the Drosophila wing blade, interaction between mammalian orthologs Lhx2 and Ldb1 regulates multiple aspects of hippocampal development in the mouse.
Multiscale virtual screening optimization for shotgun drug repurposing using the CANDO platform
Authors: Hudson Matthew L. , Samudrala Ram
Published: August 2020

Drug repurposing, the practice of utilizing existing drugs for novel clinical indications, has tremendous potential for improving human health outcomes and increasing therapeutic development efficiency. The goal of multidisease multitarget drug repurposing, also known as shotgun drug repurposing, is to develop platforms that assess the therapeutic potential of each existing drug for every clinical indication. Our Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multitarget repurposing implements several pipelines via large scale modelling and simulation of interactions between comprehensive libraries of drugs/compounds and protein structures. In these pipelines, each drug is described by an interaction signature that is then compared to all other signatures that are then sorted and ranked based on similarity. Pipelines within the platform are benchmarked based on their ability to recover known drugs for all indications in our library, and predictions are generated based on the hypothesis that (novel) drugs with similar signatures may be repurposed for the same indication(s). The drug-protein interactions in the platform used to create the drug-proteome signatures may be determined by any screening or docking method but the primary approach used thus far has been an in house similarity docking protocol. In this study, we calculated drug-proteome interaction signatures using the publicly available molecular docking method Autodock Vina and created hybrid decision tree pipelines that combined our original bio- and cheminformatic approach with the goal of assessing and benchmarking their drug repurposing capabilities and performance. The hybrid decision tree pipeline outperformed the corresponding two docking-based pipelines it was synthesized from, yielding an average indication accuracy of 13.3% at the top10 cutoff (the most stringent), relative to 10.9% and 7.1% for its constituent pipelines, and a random control accuracy of 2.2%. We demonstrate that docking based virtual screening pipelines have unique performance characteristics and that the CANDO shotgun repurposing paradigm is not dependent on a specific docking method. Our results also provide further evidence that multiple CANDO pipelines can be synthesized to enhance drug repurposing predictive capability relative to their constituent pipelines. Overall, this study indicates that pipelines consisting of varied docking based signature generation methods can capture unique and useful signal for accurate comparison of drug-proteome interaction signatures, leading to improvements in the benchmarking and predictive performance of the CANDO shotgun drug repurposing platform.
Gene set enrichment analysis for genome-wide DNA methylation data
Authors: Maksimovic Jovana , Oshlack Alicia , Phipson Belinda
Published: August 2020

DNA methylation is one of the most commonly studied epigenetic marks, due to its role in disease and development. Illumina methylation arrays have been extensively used to measure methylation across the human genome. Methylation array analysis has primarily focused on preprocessing, normalisation and identification of differentially methylated CpGs and regions. GOmeth and GOregion are new methods for performing unbiased gene set testing following differential methylation analysis. Benchmarking analyses demonstrate GOmeth outperforms other approaches and GOregion is the first method for gene set testing of differentially methylated regions. Both methods are publicly available in themissMethylBioconductor R package.
Age-associated changes in lineage composition of the enteric nervous system regulate gut health and disease
Authors: Kulkarni Subhash , Saha Monalee , Slosberg Jared , Singh Alpana , Nagaraj Sushma , Becker Laren , Zhang Chengxiu , Bukowski Alicia , Wang Zhuolun , Liu Guosheng , Leser Jenna , Kumar Mithra , Bakhshi Shriya , Anderson Matthew , Lewandoski Mark , Vincent Elizabeth , Goff Loyal A. , Pasricha Pankaj Jay
Published: August 2020

The enteric nervous system (ENS), a collection of neural cells contained in the wall of the gut, is of fundamental importance to gastrointestinal and systemic health. According to the prevailing paradigm, the ENS arises from progenitor cells migrating from the neural crest and remains largely unchanged thereafter. Here, we show that the lineage composition of maturing ENS changes with time, with a decline in the canonical lineage of neural-crest derived neurons and their replacement by a newly identified lineage of mesoderm-derived neurons. Single cell transcriptomics and immunochemical approaches establish a distinct expression profile of mesoderm-derived neurons. The dynamic balance between the proportions of neurons from these two different lineages in the post-natal gut is dependent on the availability of their respective trophic signals, GDNF-RET and HGF-MET. With increasing age, the mesoderm-derived neurons become the dominant form of neurons in the ENS, a change associated with significant functional effects on intestinal motility which can be reversed by GDNF supplementation. Transcriptomic analyses of human gut tissues show reduced GDNF-RET signaling in patients with intestinal dysmotility which is associated with reduction in neural crest-derived neuronal markers and concomitant increase in transcriptional patterns specific to mesoderm-derived neurons. Normal intestinal function in the adult gastrointestinal tract therefore appears to require an optimal balance between these two distinct lineages within the ENS.
Morphometric reconstructions atlas shows insult-driven plasticity in cortical VIP/ChAT interneurons
Authors: Yayon Nadav , Amsalem Oren , Dudai Amir , Yakov Or , Adam Gil , Tessier-Lavigne Marc , Renier Nicolas , Segev Idan , London Michael , Soreq Hermona
Published: August 2020

We developed an automatic morphometric reconstruction pipeline, Pop-Rec, and used it to study the morphologies of cortical cholinergic VIP/ChAT interneurons (VChIs). Cholinergic networks control high cognitive functions, but their local modulation and stress-driven plasticity patterns remained elusive. Reconstructing thousands of local VChIs registered to their exact coordinates in multiple cleared murine cortices highlighted distinct populations of bipolar and multipolar VChIs which differed in their dendritic spatial organization. Following mild unilateral whisker deprivation, Pop-Rec found both ipsi-and contra-lateral VChI dendritic arborization changes. Furthermore, RNA-seq of FACS-sorted VChIs showed differentially expressed dendritic, synapse and axon-modulating transcripts in whisker-deprived mice. Indicating novel steady-state morphological roles, those genes also clustered distinctly in naïve single cell VChIs. This VChIs “morpheome” atlas is the first example of unbiased analysis of neuronal populations and holds the possibility to compare neuronal structure-function relationships across experimental conditions.
Complete mitogenome of Kashmir musk deer (Moschus cupreus) and its comparative phylogenetic relationships
Authors: Singh Bhim , Gautam Kumudani Bala , Sahoo Subhashree , Kumar Ajit , Gupta Sandeep Kumar
Published: August 2020

The endangered Kashmir musk deer (Moschus cupreus) is native to the high altitudinal region of the Himalayas. In this study, we sequenced, annotated and characterized the complete mitogenome ofM. cupreusto gain insight into the molecular phylogeny and evolution of musk deer. The mitogenome ofM. cupreus, which is 16,354 bp long comprised 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and non-coding control region. TheM. cupreusmitogenome composition was highly A+T biased 68.42%, and exhibited a positive AT skew (0.082) and negative GC skew (0.307). The phylogenetic analysis suggested that KMD is the most primitive extant species in the genusMoschuswhereas Alpine musk deer (M. chrysogaster) and Himalayan musk deer (M. leucogaster) are closely related. This result confirmed the placement ofM. cupreuswithin the monotypic family Moschidae of musk deer. This study provides a better understanding of lineage identification and musk deer evolution for further research.