bluuebunny/crossref_metadata_2025 huggingface dataset:
GENis, an open-source multi-tier forensic DNA information system
Authors: Chernomoretz Ariel , Balparda Manuel , Grutta Laura La , Calabrese Andres , Martinez Gustavo , Escobar Maria Soledad , Sibilla Gustavo
Published: June 2020

GENis is an open source multi-tier information system developed to run a forensic DNA database at local, regional and national levels.1It was conceived as a highly customizable system, enforcing several security policies including: data encryption, double factor identification, structure of user’s roles and permissions, system-wide secure log auditing, non-repudiation protocols and a blockchain-based option to reinforce genetic profile’s integrity. GENis is able to perform genetic profile queries of autosomal STR’s and its design follows ENFSI2and ISFG3standards and recommendations. In this work, we present a summary of GENis architecture, the implemented matching rule definitions, and the Bayesian framework used to provide statistical significance of cold hits, that includes a new strategy to identify common contributors in mixture pairs.
Impacts of landscape-scale windthrow and subsequent, variable reforestation on bird communities in Central Europe
Authors: Kamp Johannes , Trappe Johanna , Dübbers Luca , Funke Stephanie
Published: June 2020

With climate change, the area affected by and the intensity of forest disturbances such as windthrow, insect outbreaks and fire will be increasing. Post-disturbance forest management will be varied, and it is difficult to predict how much natural succession will be allowed in comparison to reforestation. Both, disturbance and reforestation will affect forest biodiversity globally, but potential shifts in species distribution, abundance and community composition are poorly understood.

We studied the response of breeding bird communities to windthrow and different reforestation strategies in one of Central Europe’s largest contiguous windthrow areas created by storm Kyrill in 2007. A decade after the disturbance, we compared bird species diversity, population densities and community composition on plots in replanted beech, replanted conifers and secondary succession (all salvage-logged after the storm), with undisturbed old Norway sprucePicea abiesas a control, in the setting of a natural experiment.

Of the stands blown down, 95% were Norway Spruce. Reforestation strategies varied, with Spruce and non-native conifers planted on twice the area that was replanted with European BeechFagus sylvestris. Large areas were still dominated by successional tree species a decade after the storm, especially birch, mirroring recommendations of sub-national forestry agencies to include secondary succession in future forest development. Birds responded strongly to windthrow, with a pronounced community turnover. Species associated with high conifer stands reached significantly lower densities on sample plots in disturbed areas. Replanted areas were characterized by mostly ubiquitous bird species. Areas dominated by secondary succession, especially birchBetula spp., were characterized by high densities of long-distance migrants (often species of conservation concern) and shrubland species, among them several indicator species.

Our results suggest that an increase of forest disturbance across Central Europe will lead to a pronounced reorganisation of biodiversity. Strategies that allow more secondary succession, and avoid replanting allochthonous tree species are likely to benefit populations of depleted bird species, even at salvage-logged and cleared disturbance sites.
Multimodal small-molecule screening for human prion protein binders
Authors: Reidenbach Andrew G , Mesleh Michael F , Casalena Dominick , Vallabh Sonia M , Dahlin Jayme L , Leed Alison J , Chan Alix I , Usanov Dmitry L , Yehl Jenna B , Lemke Christopher T , Campbell Arthur J , Shah Rishi N , Shrestha Om K , Sacher Joshua R , Rangel Victor L , Moroco Jamie A , Sathappa Murugappan , Nonato Maria Cristina , Nguyen Kong T , Wright S Kirk , Liu David R , Wagner Florence F , Kaushik Virendar K , Auld Douglas S , Schreiber Stuart L , Minikel Eric Vallabh
Published: June 2020

Prion disease is a rapidly progressive neurodegenerative disorder caused by misfolding and aggregation of the prion protein (PrP), and there are currently no therapeutic options. PrP ligands could theoretically antagonize prion formation by protecting the native protein from misfolding or by targeting it for degradation, but no validated small-molecule binders have been discovered to date. We deployed a variety of screening methods in an effort to discover binders of PrP, including19F-observed and saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy, differential scanning fluorimetry (DSF), DNA-encoded library selection, andin silicoscreening. A single benzimidazole compound was confirmed in concentration-response, but affinity was very weak (Kd> 1 mM), and it could not be advanced further. The exceptionally low hit rate observed here suggests that PrP is a difficult target for small-molecule binders. While orthogonal binder discovery methods could yield high affinity compounds, non-small-molecule modalities may offer independent paths forward against prion disease.
Tissue-autonomous phenylpropanoid production is essential for establishment of root barriers
Authors: Andersen Tonni Grube , Molina David , Kilian Joachim , Franke Rochus , Ragni Laura , Geldner Niko
Published: June 2020

Plants deposit polymeric barriers in their root cell walls to protect against external stress and facilitate selective nutrient uptake. The compounds that make up these barriers originate from the fatty acid- and phenylpropanoid biosynthetic pathways. Although the machinery responsible for production of the barrier constituents is well-char-acterized, our pathway models lack spatiotemporal resolution – especially in roots - and the source tissue is often not clear due to the apoplastic nature of barriers. Insights into how the individual root tissues or cells contribute to forming apoplastic barriers is important for elucidation of their ultrastructure, function and development. Manipulation of the associated biosynthesis is delicate, as mutants often display pleiotropic phenotypes due to the broad role of the underlying metabolites. Here, we address these issues by creating a genetic tool that allows in vivo repression of the phenylpropanoid pathway with both spatial and temporal control. We provide strong evidence that tissue-auton-omous production of phenylpropanoids is essential for establishment of the endodermal Casparian strip. Moreover, we find that in order to maintain deposition and attachment of a coherent suberin matrix to the cell wall, cells require continuous production of aromatic constituents. This process is especially crucial in the suberized endodermis where we find that repression of phenylpropanoid production leads to active removal of suberin.
“A Novel Therapeutic Approach to Corneal Alkaline Burn Model by Targeting Fidgetin-like 2, a Microtubule Regulator”
Authors: Wang Jessie , Dey Abhinav , Kramer Adam , Miao Yuan , Liu Juan , Baker Lisa , Friedman Joel , Nacharaju Parimala , Chuck Roy , Zhang Cheng , Sharp David J.
Published: June 2020

Purpose

To determine the efficacy of nanoparticle-encapsulated FL2 siRNA (FL2-NPsi), a novel therapeutic agent targeting the Fidgetin-like 2 (FL2) gene, for the treatment of corneal alkaline chemical injury.

Methods

Eighty 12-week-old, male Sprague-Dawley rats were divided evenly into 8 treatment groups: prednisolone, empty nanoparticles, control-NPsi (1 μM, 10 μM, 20 μM) and FL2-NPsi (1 μM, 10 μM, 20 μM). An alkaline burn was induced onto the cornea of each rat, which was then treated for 14 days according to group assignment. Clinical (N=10 per group), histopathologic (N=6 per group), and immunohistochemical (N=4 per group) analyses were conducted to assess for wound healing. FL2-NPsi-mediated knockdown of FL2 was confirmed byin vitroqPCR. Toxicity assays were performed to assess for apoptosis (TUNEL assay, N=3 per group) and nerve damage (whole mount immunochemical staining, N=2 per group). Statistical analyses were performed using student’s t-test and ANOVA.

Results

Compared to controls, FL2-NPsi-treated groups demonstrated enhanced corneal wound healing, with the 10 and 20 μM FL2-NPsi-treated groups demonstrating maximum rates of corneal re-epithelialization (p=0.0003 at Day 4 and p<0.0001 at Day 8) as assessed by ImageJ software, enhanced corneal transparency, and improved stromal organization on histology. Immunohistochemical analysis of vascular endothelial cells, macrophages, and neutrophils did not show significant differences between treatment groups. FL2-NPsi was not found to be toxic to nerves or induce apoptosis (p=0.917).

Conclusion

Dose-response studies found both 10 and 20 μM FL2-NPsi to be efficacious in this rat model. FL2-NPsi may offer a novel treatment for corneal alkaline chemical injuries.
Transcriptomic analysis of four cerianthid (Cnidaria, Ceriantharia) venoms
Authors: Klompen Anna M. L. , Macrander Jason , Reitzel Adam M. , Stampar Sérgio N.
Published: June 2020

Tube anemones, or cerianthids, are a phylogenetically informative group of cnidarians with complex life histories, including a pelagic larval stage and tube-dwelling adult stage, both known to utilize venom in stinging-cell rich tentacles. Cnidarians are an entirely venomous group that utilize their proteinaceous-dominated toxins to capture prey and defend against predators, in addition to several other ecological functions, including intraspecific interactions. At present there are no studies describing the venom for any species within cerianthids. Given their unique development, ecology, and distinct phylogenetic-placement within Cnidaria, our objective is to evaluate the venom-like gene diversity of four species of cerianthids from newly collected transcriptomic data. We identified 525 venom-like genes between all four species. The venom-gene profile for each species was dominated by enzymatic protein and peptide families, which is consistent with previous findings in other cnidarian venoms. However, we found few toxins that are typical of sea anemones and corals, and furthermore, three of the four species express toxin-like genes closely related to potent pore-forming toxins in box jellyfish. Our study is the first to provide a survey of the putative venom composition of cerianthids, and contributes to our general understanding of the diversity of cnidarian toxins.
GardeninA confers neuroprotection against environmental toxin in aDrosophilamodel of Parkinson’s disease
Authors: Maitra Urmila , Harding Thomas , Liang Qiaoli , Ciesla Lukasz
Published: June 2020

Parkinson’s disease (PD) is an age-associated neurodegenerative disorder characterized by the progressive loss of dopaminergic neurons from the midbrain. Epidemiological studies have implicated exposures to environmental toxins like the herbicide, paraquat (PQ) as major contributors to PD etiology in both mammalian and invertebrate models. We have employed a PQ-induced PD model inDrosophilaas an inexpensivein vivoplatform to screen therapeutics from natural products. We have identified the polymethoxyflavonoid, GardeninA, with neuroprotective potential against PQ-induced parkinsonian symptoms involving reduced survival, mobility defects, and loss of dopaminergic neurons. GardeninA-mediated neuroprotection is not solely dependent on its antioxidant activities but also involves modulation of the neuroinflammatory and cellular death responses. Furthermore, we have successfully detected GardeninA bioavailability in the fly heads after oral administration using ultra-performance liquid chromatography and mass spectrometry. Our findings reveal a molecular mechanistic insight into GardeninA-mediated neuroprotection against environmental toxin-induced PD pathogenesis for novel therapeutic intervention.
Honeyweed (Leonurus sibiricus) and Buckwheat (Fagopyrum esculentum) supplemented diet improve growth performance, lipid profile and hematological values of broiler chicks
Authors: Abedin M.T. , Rahman S.T. , Islam M.M. , Hayder S. , Ashraf M.A. , Pelc J. , Sayed M.A.
Published: June 2020

The study was conducted to investigate the combined effects of honeyweed (HW) and buckwheat (BW) supplemented diets on the growth, feed intake, serum lipid profile and blood parameters in broiler chicks. One hundred fifty (150) day old chicks (Cobb-500) were divided into five groupsviz. T1 (Commercial control, CC), T2 (FF+10% BW), T3 (FF+10% BW +5% (w/v) HW powder), T4 (FF+10% BW +10% (w/v) HW powder), T5 (FF+10% BW +15% (w/v) HW powder) in complete randomized design with five (5) replications, each of which contain six (6) birds. The CC feed and the FF with HW and BW supplemented diet fed on broiler for 30 days. At the end of the study, the body weight gain, FCR and mortality rate were calculated. It was found that T3 (FF+10% BW +5% (w/v) HW powder) diet significantly (p <0.05) showed the good FCR, mortality rate and body weight gain. Interestingly, T3 decreased the serum cholesterol, triglycerides (TG), low density lipoprotein (LDL), increased high density lipoprotein (HDL) and improves blood parameters significantly (p < 0.05). Our results suggested that this newly formulated feed T3 (FF+10% BW +5% (w/v) HW powder) could be considered as an alternative natural feed additive to hazardous synthetic antibiotics.
Estimation of sinking velocities using free-falling dynamically scaled models: foraminifera as a test case
Authors: Walker Matthew , Humphries Stuart , Schuech Rudi
Published: June 2020

The velocity of settling particles is an important determinant of distribution in extinct and extant species with passive dispersal mechanisms, such as plants, corals, and phytoplankton. Here we adapt dynamic scaling, borrowed from engineering, to determine settling velocities. Dynamic scaling leverages physical models with relevant dimensionless numbers matched to achieve similar dynamics to the original object. Previous studies have used flumes, wind tunnels, or towed models to examine fluid flows around objects with known velocities. Our novel application uses free-falling models to determine the unknown sinking velocities of planktonic foraminifera – organisms important to our understanding of the Earth’s current and historic climate. Using enlarged 3D printed models of microscopic foraminifera tests, sunk in viscous mineral oil to match their Reynolds numbers and drag coefficients, we predict sinking velocities of real tests in seawater. This method can be applied to study other settling particles such as plankton, spores, or seeds.

Summary Statement

We developed a novel method to determine the sinking velocities of biologically important microscale particles using 3D printed scale models.
SLAP2 adaptor binding disrupts c-CBL autoinhibition to activate ubiquitin ligase function
Authors: Wybenga-Groot Leanne E. , Tench Andrea J. , Simpson Craig D. , Germain Jonathan St. , Raught Brian , Moran Michael F. , McGlade C. Jane
Published: June 2020

CBL is a RING type E3 ubiquitin ligase that functions as a negative regulator of tyrosine kinase signaling and loss of CBL E3 function is implicated in several forms of leukemia. The Src-like adaptor proteins (SLAP/SLAP2) bind to CBL and are required for CBL-dependent downregulation of antigen receptor, cytokine receptor, and receptor tyrosine kinase signaling. Despite the established role of SLAP/SLAP2 in regulating CBL activity, the nature of the interaction and the mechanisms involved are not known. To understand the molecular basis of the interaction between SLAP/SLAP2 and CBL, we solved the crystal structure of CBL tyrosine kinase binding domain (TKBD) in complex with SLAP2. The carboxy-terminal region of SLAP2 adopts an α-helical structure which binds in a cleft between the 4H, EF-hand, and SH2 domains of the TKBD. This SLAP2 binding site is remote from the canonical TKBD phospho-tyrosine peptide binding site but overlaps with a region important for stabilizing CBL in its autoinhibited conformation. In addition, binding of SLAP2 to CBLin vitroactivates the ubiquitin ligase function of autoinhibited CBL. Disruption of the CBL/SLAP2 interface through mutagenesis demonstrated a role for this protein-protein interaction in regulation of CBL E3 ligase activity in cells. Our results reveal that SLAP2 binding to a regulatory cleft of the TKBD provides an alternative mechanism for activation of CBL ubiquitin ligase function.
Comparative Genomic Analysis of Fifty-TwoStaphylococcus aureusIsolates Identified from Uncharacterized Staphylococcus Genomes in the NCBI database
Authors: Abouelkhair Mohamed A.
Published: June 2020

Background

Staphylococcus aureusis a major bacterial pathogen that causes a variety of diseases, ranging from wound infections to severe bacteremia or food poisoning. The course and severity of the disease are mainly dependent on the bacterium genotype as well as host factors. Whole-genome sequencing (WGS) is currently the most extensive genotyping method available, followed by bioinformatic sequence analysis.

Methods

A total of 253 uncharacterized staphylococcus genome sequences were downloaded from the National Center for Biotechnology Information (NCBI) (August 2012 to March 2020) from different studies. Samples were clustered based on core and accessory pairwise distances between isolates and then analyzed by multilocus sequence typing tool (MLST). Staphylococcal Cassette Chromosomemec(SCCmec), spa typing, variant calling, core genome alignment, and recombination sites prediction were performed on detectedS. aureusisolates.S. aureusisolates were also analyzed for the presence of genes coding for virulence factors and antibiotic resistance.

Results and conclusion

Uncategorized genome sequences were clustered into 24 groups. About 182 uncharacterized Staphylococcus genomes were identified at the species level based on MLST, including 32S. lugdunensisgenome sequence, thus doubling the number of the publicly accessibleS. lugdunensisgenome sequence in Genbank. MLST identified another four species (S. epidermidis(33/253),S. lugdunensis(32/253),S. haemolyticus(41/253),S. hominis(24/253)and S. aureus(52/253)). Among the 52S. aureusisolates, 21 (40.38%) isolates carriedmecA gene, with 57.14% classified as SCCmecIV. The results of this study provide knowledge that facilitates evolutionary studies of staphylococcal species and other bacteria at the genome level.
The influence of axial length upon the retinal ganglion cell layer of the human eye
Authors: Chen Min , Nofziger Jill , Datta Ritobrato , Gee James C. , Morgan Jessica , Aguirre Geoffrey K
Published: June 2020

Purpose

We examined the relationship between axial length and the thickness and volume of the ganglion cell layer (GCL) of the retina, and related these measures to the size of the optic chiasm.

Methods

We used optical coherence tomography to measure the thickness of the GCL over a 50° extent of the horizontal meridian in 50 normally-sighted participants with a wide range of axial lengths. Using a model eye informed by individual biometry, we converted GCL thickness to tissue volume per square degree. The volume of the optic chiasm was measured for 40 participants using magnetic resonance imaging.

Results

While GCL thickness decreases with increasing axial length, there is a positive relationship between GCL tissue volume and axial length, leading us to conclude that increasing axial length is associated with decreased retinal ganglion cell packing, increased cell size, or both. We characterize how retinal ganglion cell tissue varies systematically in volume and spatial distribution as a function of axial length. This model allows us to remove the effect of axial length from individual difference measures of GCL volume. We find that variation in GCL volume correlates well with the size of the optic chiasm as measured using magnetic resonance imaging.

Conclusions

Our results provide the volume of ganglion cell tissue in the retina, adjusted for the effects of axial length upon ganglion cell size and/or packing. The resulting volume measure accounts for individual differences in the size of the optic chiasm, supporting its use to characterize the post-retinal visual pathway.
A synthetic peptide rescues rat cortical neurons from anesthetic-induced cell death and modulation of growth and synaptic assembly
Authors: Iqbal Fahad , Pehar Marcus , Thompson Andrew J. , Azeem Urva , Jahanbakhsh Kiana , Jimenez-Tellez Nerea , Sabouny Rasha , Batool Shadab , Syeda Atika , Chow Jennifer , Machiraju Pranav , Shutt Timothy , Yusuf Kamran , Shearer Jane , Rice Tiffany , Syed Naweed I.
Published: June 2020

Anesthetics, although necessary for many modern procedures, exert neurotoxic effects in various experimental models; the underlying mechanisms, however, remain unknown. In the absence of this information, anyin vivomitigation strategy would be challenging. To help address these gaps, we sought to determine whether preserving mitochondrial network integrity with a non-toxic, short-life synthetic peptide, P110, could protect cortical neurons against both inhalational and intravenous anesthetic-induced neurotoxicity. This study provides the first direct comparative account of three key general anesthetics (desflurane, propofol, and ketamine) under identical conditions and demonstrates their impact on cellular viability, neurite outgrowth, and synaptic network assembly on neonatal rat cortical neurons. Further, we discovered that the inhibition of Fis1 receptor-mediated fission reverses anesthetic-induced aberrations in an agent-specific manner. Our data thus underscore the importance of a reductionist approach, offering unique opportunities to explore non-toxic, mitochondria-based therapeutic tools for mitigating anesthetic-induced harm to the developing brain.
Evidence of Superior and Inferior Sinoatrial Nodes in the Mammalian Heart
Authors: Brennan Jaclyn A. , Chen Qing , Gams Anna , Dyavanapalli Jhansi , Mendelowitz David , Peng Weiqun , Efimov Igor R.
Published: June 2020

The initiation of rhythmic heartbeat is the earliest manifestation of new life after conception. A normal heartbeat originates as an action potential in a group of pacemaker cells of the sinoatrial node (SAN)1. Pacemaker cells are evident since early embryogenesis when the entire sinus venosus exhibits electric automaticity and possesses specific gene expression profile distinct from that of working myocardium2,3. During the subsequent looping and ballooning stages of cardiac development, pacemaker cells eventually localize into SAN near the superior vena cava (SVC) when the two horns of the sinus venosus coil in formation of the atria2. The heart rate and anatomical site of origin of pacemaker activity dynamically change in response to various physiological input such as autonomic stimuli and pharmacological interventions4. However, the mechanisms of dominant pacemaker shift are not well understood. Here, we present functional and molecular evidence of two competing right atrial pacemakers localized near the SVC and the inferior vena cava (IVC), which we call the superior and inferior SANs: sSAN and iSAN. Usingex vivooptical mapping techniques and RNA sequencing of rat and human hearts, we demonstrate that sSAN and iSAN preferentially control the fast and slow heart rates during sympathetic or parasympathetic stimulation, respectively. RNAseq confirmed unique transcriptional profiles of sSAN and iSAN, which differs from both atria and ventricles. We speculate that the anatomical locations of sSAN and iSAN are a result of the way the two horns of the sinus venosus twist into a mature chambered heart. We anticipate these findings would clarify previously observed migration of dominant pacemaker and corresponding changes in P-wave morphology in many species. Furthermore, we expect these findings will shed light onto pathogenesis of aberrant pacemakers responsible for life-threatening arrhythmias near orifices of other major vessels: SVC and IVC, coronary sinus, pulmonary veins, aorta and the right ventricular outflow tract.
Using rat operant delayed match-to-sample task to identify neural substrates recruited with increased working memory load
Authors: Gobin Christina , Wu Lizhen , Schwendt Marek
Published: June 2020

The delayed match-to-sample task (DMS) is used to probe working memory (WM) across species. While the involvement of the PFC in this task has been established, limited information exists regarding the recruitment of broader circuitry, especially under the low- versus high-WM load. We sought to address this question by using a variable-delay operant DMS task. Male Sprague-Dawley rats were trained and tested to determine their baseline WM performance across all (0-24s) delays. Next, rats were tested in a single DMS test with either 0s or 24s fixed delay, to assess low-/high-load WM performance.c-FosmRNA expression was quantified within cortical and subcortical regions and correlated with WM performance. High WM load upregulated overallc-FosmRNA expression within the PrL, as well as within a subset of mGlu5+ cells, with load-dependent, local activation of protein kinase C as the proposed underlying molecular mechanism. The PrL activity negatively correlated with choice accuracy during high load WM performance. A broader circuitry, including several subcortical regions, was found to be activated under low and/or high load conditions. These findings highlight the role of mGlu5 and/or PKC dependent signaling within the PrL, and corresponding recruitment of subcortical regions during high-load WM performance.
Drosophilamodel of Anti-retroviral therapy Induced Peripheral Neuropathy and Nociceptive Hypersensitivity
Authors: Bush Keegan M. , Barber Kara R. , Martinez Jade A. , Tang Shao-Jun , Wairkar Yogesh P.
Published: June 2020

The success of antiretroviral therapy (ART) has improved the survival of HIV-infected patients significantly. However, significant numbers of patients on ART whose HIV disease is well controlled show peripheral sensory neuropathy (PSN), suggesting that ART may cause PSN. Although the nucleoside reverse transcriptase inhibitors (NRTIs), one of the vital components of ART, are thought to contribute to PSN, the mechanisms underlying the PSN induced by NRTIs are unclear. In this study, we developed aDrosophilamodel of NRTI-induced PSN that recapitulates the salient features observed in patients undergoing ART: PSN and nociceptive hypersensitivity. Furthermore, our data demonstrate that pathways known to suppress PSN induced by chemotherapeutic drugs are ineffective in suppressing the PSN or nociception induced by NRTIs. Instead, we found that increased dynamics of a peripheral sensory neuron may underlie NRTI-induced PSN and nociception. Our model provides a solid platform in which to investigate further mechanisms of ART-induced PSN and nociceptive hypersensitivity.
Phenome-scale causal network discovery with bidirectional mediated Mendelian randomization
Authors: Brown Brielin C. , Knowles David A.
Published: June 2020

Inference of directed biological networks from observational genomics datasets is a crucial but notoriously difficult challenge. Modern population-scale biobanks, containing simultaneous measurements of traits, biomarkers, and genetic variation, offer an unprecedented opportunity to study biological networks. Mendelian randomization (MR) has received attention as a class of methods for inferring causal effects in observational data that uses genetic variants as instrumental variables, but MR methods rely on assumptions that limit their application to complex traits at the biobank-scale. Moreover, MR estimates the total effect of one trait on another, which may be mediated by other factors. Biobanks include measurements of many potential mediators, in principle enabling the conversion of MR estimates into direct effects representing a causal network. Here, we show that this can be accomplished by a flexible two stage procedure we callbidirectional mediated Mendelian randomization(bimmer). First, bimmer estimates the effect of every trait on every other. Next, bimmer finds a parsimonious network that explains these effects using direct and mediated causal paths. We introduce novel methods for both steps and show via extensive simulations that bimmer is able to learn causal network structures even in the presence of non-causal genetic correlation. We apply bimmer to 405 phenotypes from the UK biobank and demonstrate that learning the network structure is invaluable for interpreting the results of phenome-wide MR, while lending causal support to several recent observational studies.
Environmental conditions define the energetics of bacterial dormancy and its antibiotic susceptibility
Authors: Mancini L , Pilizota T
Published: June 2020

Bacterial cells that stop growing but maintain viability and the capacity to regrow are termed dormant and have been shown to transiently tolerate high concentrations of antimicrobials. The proposed mechanism behind the enhanced survival capabilities of these cells is the reduced energy supply. However, not all reported results are in agreement, and the exact role of energetics remains unsolved. Because dormancy merely indicates growth arrest, which can be induced by various stimuli, we hypothesise that dormant cells may exist in a range of energetic states that depend on the environment. We first establish conditions that are capable of inducing dormancy, and subsequently measure the energy profiles they elicit in single dormant cells. Our simultaneous measurements of proton motive force (PMF), cytoplasmic pH and ATP concentrations confirm that dormant cells exhibit characteristic energetic profiles that can vary in level and dynamics, depending on the stimulus leading to growth arrest. We test whether the energetic makeup is associated with survival to antibiotics of different classes and find that, while growth arrest remains the dominant mechanism enabling survival, some correlations with cellular energetics exist. Our results pave the way to a classification of dormant states based on energy profiles, support a novel relationship between environment and drug susceptibility of dormant cells and suggest that knowledge of the conditions present at the infection site is necessary to design appropriate treatments.
Functional Characterization of the Lin28/let-7 Circuit during Forelimb Regeneration inAmbystoma mexicanumand its Influence on Metabolic Reprogramming
Authors: Varela-Rodríguez Hugo , Abella-Quintana Diana G. , Varela-Rodríguez Luis , Gomez-Zepeda David , Espinal-Centeno Annie , Caballero-Pérez Juan , Ordaz-Ortiz José Juan , Cruz-Ramírez Alfredo
Published: June 2020

The axolotl (Ambystoma mexicanum) is a caudate amphibian, which has an extraordinary ability to restore a wide variety of damaged structures by a process denominated epimorphosis. While the origin and potentiality of progenitor cells that take part during epimorphic regeneration are known to some extent, the metabolic changes experienced and their associated implications, remain unexplored. However, a circuit with a potential role as a modulator of cellular metabolism along regeneration is that formed by Lin28/let-7. In this study, we report two Lin28 paralogs and eight mature let-7 microRNAs encoded in the axolotl genome. Particularly, in the proliferative blastema stage amxLin28B is more abundant in the nuclei of blastemal cells, while the microRNAs amx-let-7c and amx-let-7a are most downregulated. Functional inhibition of Lin28 factors increase the levels of most mature let-7 microRNAs, consistent with an increment of intermediary metabolites of the Krebs cycle, and phenotypic alterations in the outgrowth of the blastema. In summary, we describe the primary components of the Lin28/let-7 circuit and their function during axolotl regeneration, acting upstream of metabolic reprogramming events.
Crinet: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions
Authors: Kesimoglu Ziynet Nesibe , Bozdag Serdar
Published: June 2020

To understand driving biological factors for complex diseases like cancer, regulatory circuity of genes needs to be discovered. Recently, a new gene regulation mechanism called competing endogenous RNA (ceRNA) interactions has been discovered. Certain genes targeted by common microRNAs (miRNAs) “compete” for these miRNAs, thereby regulate each other by making others free from miRNA regulation. Several computational tools have been published to infer ceRNA networks. In most existing tools, however, expression abundance sufficiency, collective regulation, and groupwise effect of ceRNAs are not considered. In this study, we developed a computational tool named Crinet to infer genome-wide ceRNA networks addressing critical drawbacks. Crinet considers all mRNAs, lncRNAs, and pseudogenes as potential ceRNAs and incorporates a network deconvolution method to exclude the spurious ceRNA pairs. We tested Crinet on breast cancer data in TCGA. Crinet inferred reproducible ceRNA interactions and groups, which were significantly enriched in the cancer-related genes and processes. We validated the selected miRNA-target interactions with the protein expression-based benchmarks and also evaluated the inferred ceRNA interactions predicting gene expression change in knockdown assays. The hub genes in the inferred ceRNA network included known suppressor/oncogene lncRNAs in breast cancer showing the importance of non-coding RNA’s inclusion for ceRNA inference. The source code of Crinet could be accessed on Github athttps://github.com/bozdaglab/crinet.
Highly multiplexed immune profiling throughout adulthood reveals kinetics of lymphocyte infiltration in the aging mouse prostate
Authors: Fox Jonathan J. , Hashimoto Takao , Navarro Héctor I. , Garcia Alejandro J. , Shou Benjamin L. , Goldstein Andrew S.
Published: June 2020

Aging is a significant risk factor for cancer in several tissues, including the prostate. Defining the kinetics of age-related changes in these tissues is critical for identifying regulators of aging and evaluating interventions to slow the aging process and reduce disease risk. An altered microenvironment is characteristic of prostatic aging in mice. Whether features of aging in the prostate emerge predominantly in old age or earlier in adulthood has not previously been established. Using comprehensive immune profiling and time-course analysis, we show that populations of T and B lymphocytes increase in the mouse prostate between 6 and 12 months of age. When comparing the prostate to other urogenital tissues, we found similar features of age-related inflammation in the mouse bladder. In summary, our study offers new insight into the kinetics of prostatic inflammaging and the window when interventions to slow down age-related changes may be most effective.
Microbial dark matter filling the niche in hypersaline microbial mats
Authors: Wong Hon Lun , MacLeod Fraser I. , White Richard Allen , Visscher Pieter T. , Burns Brendan P.
Published: June 2020

Shark Bay, Australia, harbours one of the most extensive and diverse systems of living microbial mats, that are proposed to be analogs of some of the earliest ecosystems on Earth. These ecosystems have been shown to possess a substantial abundance of uncultivable microorganisms. These enigmatic groups - ‘microbial dark matter’ (MDM) - are hypothesised to play key roles in microbial mats. We reconstructed 115 metagenome-assembled genomes (MAGs) affiliated to MDM, spanning 42 phyla within the bacterial and archaeal domains. We classified bacterial MDM from the PVC group, FCB group, Microgenomates, Parcubacteria, and Peregrinibacteria, as well as a high proportion of archaeal MDM under the TACK, DPANN, Altiarchaeales, and Asgard archaea. The latter includes the first putative Heimdallarchaeota MAG obtained from any microbial mat system. This study reports novel microorganisms (Zixibacterial order GN15) putatively taking part in dissimilatory sulfate reduction in surface hypersaline settings, as well as novel eukaryote signature proteins in the Asgard archaea. Despite possessing reduced-size genomes, the MDM MAGs are capable of fermenting and degrading organic carbon, suggesting a role in recycling organic carbon. Several forms of RuBisCo were identified, allowing putative CO2incorporation into nucleotide salvaging pathways, which may act as an alternative carbon and phosphorus source. High capacity of hydrogen production was found among Shark Bay MDM. Putative schizorhodopsins were also identified in Parcubacteria, Asgard archaea, DPANN archaea, and Bathyarchaeota, allowing these members to potentially capture light energy. Diversity-generating retroelements were prominent in DPANN archaea that likely facilitate the adaptation to a dynamic, host-dependent lifestyle. In light of our findings, we propose H2, ribose and CO/CO2as the main energy currencies of the MDM community in these mat systems.
A single dose of recombinant VSV-ΔG-spike vaccine provides protection against SARS-CoV-2 challenge
Authors: Yahalom-Ronen Yfat , Tamir Hadas , Melamed Sharon , Politi Boaz , Shifman Ohad , Achdout Hagit , Vitner Einat B. , Israeli Ofir , Milrot Elad , Stein Dana , Cohen-Gihon Inbar , Lazar Shlomi , Gutman Hila , Glinert Itai , Cherry Lilach , Vagima Yaron , Lazar Shirley , Weiss Shay , Ben-Shmuel Amir , Avraham Roy , Puni Reut , Lupu Edith , Bar David Elad , Sittner Assa , Erez Noam , Zichel Ran , Mamroud Emanuelle , Mazor Ohad , Levy Haim , Laskar Orly , Yitzhaki Shmuel , Shapira Shmuel C. , Zvi Anat , Beth-Din Adi , Paran Nir , Israely Tomer
Published: June 2020

The COVID-19 pandemic caused by SARS-CoV-2 that emerged in December 2019 in China resulted in over 7.8 million infections and over 430,000 deaths worldwide, imposing an urgent need for rapid development of an efficient and cost-effective vaccine, suitable for mass immunization. Here, we generated a replication competent recombinant VSV-ΔG-spike vaccine, in which the glycoprotein of VSV was replaced by the spike protein of the SARS-CoV-2. In vitro characterization of the recombinant VSV-ΔG-spike indicated expression and presentation of the spike protein on the viral membrane with antigenic similarity to SARS-CoV-2. A golden Syrian hamster in vivo model for COVID-19 was implemented. We show that vaccination of hamsters with recombinant VSV-ΔG-spike results in rapid and potent induction of neutralizing antibodies against SARS-CoV-2. Importantly, single-dose vaccination was able to protect hamsters against SARS-CoV-2 challenge, as demonstrated by the abrogation of body weight loss of the immunized hamsters compared to unvaccinated hamsters. Furthermore, whereas lungs of infected hamsters displayed extensive tissue damage and high viral titers, immunized hamsters’ lungs showed only minor lung pathology, and no viral load. Taken together, we suggest recombinant VSV-ΔG-spike as a safe, efficacious and protective vaccine against SARS-CoV-2 infection.
A dispensable role of mitochondrial fission protein 1 (Fis1) in the erythrocytic development ofPlasmodium falciparum
Authors: Maruthi Mulaka , Ling Liqin , zhou Jing , Ke Hangjun
Published: June 2020

Malaria remains a huge global health burden and control of this disease has run into a severe bottleneck. To defeat malaria and reach the goal of eradication, a deep understanding of parasite biology is urgently needed. The mitochondrion of the malaria parasite is essential throughout the parasite’s lifecycle and has been validated as a clinical drug target. In the asexual development ofPlasmodium spp., the single mitochondrion grows from a small tubular structure to a complex branched network. At the end of schizogony when 8-32 merozoites are produced, the branched mitochondrion is precisely divided, distributing one mitochondrion to each forming daughter merozoite. In mosquito and liver stages, the giant mitochondrial network is split into thousands of pieces then daughter mitochondria are segregated into individual progeny. Despite the significance of mitochondrial fission inPlasmodium, the underlying mechanism is largely unknown. Studies of mitochondrial fission in model eukaryotes have revealed that several mitochondrial fission adaptor proteins are involved in recruiting dynamin GTPases to physically split mitochondrial membranes. Apicomplexan parasites, however, share no identifiable homologs of mitochondrial fission adaptor proteins of yeast or human, except for Fis1. Here, we investigated the localization and essentiality of the Fis1 homolog inPlasmodium falciparum, PfFis1 (PF3D7_1325600), during the asexual lifecycle. We found that PfFis1 requires an intact C-terminus for mitochondrial localization but is not essential for parasite development or mitochondrial fission. The dispensable role of PfFis1 indicatesPlasmodiumcontains additional fission adaptor proteins on the mitochondrial outer membrane that could be essential for mitochondrial fission.

Importance

Malaria is responsible for over 230 million clinical cases and ∼ half a million deaths each year. The single mitochondrion of the malaria parasite functions as a metabolic hub throughout the parasite’s developmental cycle as well as a source of ATP in certain stages. To pass on its essential functions, the parasite’s mitochondrion needs to be properly divided and segregated into all progeny during cell division via a process named mitochondrial fission. Due to the divergent nature ofPlasmodium spp., molecular players involved in mitochondrial fission and their mechanisms of action remain largely unknown. We found that Fis1, the only identifiable mitochondrial fission adaptor protein evolutionarily conserved in the phylum of Apicomplexa, however, is not essential forPlasmodium falciparum. Our data suggest that malaria parasites use redundant fission adaptor proteins on the mitochondrial outer membrane to mediate the fission process.
Whole-Genome Sequence Typing shows extensive diversity ofListeria monocytogenesin the outdoor environment and poultry processing plants
Authors: Louha Swarnali , Meinersmann Richard J. , Abdo Zaid , Berrang Mark E. , Glenn Travis C.
Published: June 2020

A reliable and standardized classification ofListeria monocytogenes(Lm) is important for accurate strain identification during outbreak investigations. Current whole-genome sequencing (WGS) based approaches for strain characterization either lack standardization, rendering them less suitable for data exchange, or are not freely available. Thus, we developed a portable and open-source tool Haplo-ST to improve standardization and provide maximum discriminatory potential to WGS data tied to an MLST (multi locus sequence typing) framework. Haplo-ST performs whole-genome MLST (wgMLST) forLmwhile allowing for data exchangeability worldwide. This tool takes in (i) raw WGS reads as input, (ii) cleans the raw data according to user specified parameters, (iii) assembles genes across loci by mapping to genes from reference strains, (iv) assigns allelic profiles to assembled genes and provides a wgMLST subtyping for each isolate. Data exchangeability relies on the tool assigning allelic profiles based on a centralized nomenclature defined by the widely-used BIGSdb-Lmdatabase. Tests on Haplo-ST’s performance with simulated reads fromLmreference strains yielded a high sensitivity of 97.5%, and coverage depths of ≥ 20× was found to be sufficient for wgMLST profiling. We used Haplo-ST to characterize and differentiate between two groups ofLmisolates, derived from the natural environment and poultry processing plants. Phylogenetic reconstruction showed sharp delineation of lineages within each group and no lineage-specificity was observed with isolate phenotypes (transient vs. persistent) or origins. Genetic differentiation analyses between isolate groups identified 21 significantly differentiated loci, potentially enriched for adaptation and persistence ofLmwithin poultry processing plants.

IMPORTANCE

We have developed an open-source tool that provides allele-based subtyping ofLmisolates at the whole genome level. Along with allelic profiles, this tool also generates allele sequences, and identifies paralogs, which is useful for phylogenetic tree reconstruction and deciphering relationships between closely related isolates. More broadly, Haplo-ST is flexible and can be adapted to characterize the genome of any haploid organism simply by installing an organism-specific gene database. Haplo-ST also allows for scalable subtyping of isolates; fewer reference genes can be used for low resolution typing, whereas higher resolution can be achieved by increasing the number of genes used in the analysis. Our tool enabled clustering ofLmisolates into lineages and detection of potential loci for adaptation and persistence in food processing environments. Findings from these analyses highlights the effectiveness of Haplo-ST in subtyping and evaluating relationships among isolates for routine surveillance, outbreak investigations and source tracking.
Disruption of the MreB elongasome is overcome by mutations in the TCA cycle
Authors: Barton Brody , Grinnell Addison , Morgenstein Randy M.
Published: June 2020

The bacterial actin homolog, MreB, is highly conserved among rod-shaped bacteria and essential for growth under normal growth conditions. MreB directs the localization of cell wall synthesis and loss of MreB results in round cells and death. Using the MreB depolymerizing drug, A22, we show that changes to central metabolism through deletion of malate dehydrogenase from the TCA cycle results in cells with an increased tolerance to A22. We hypothesize that deletion of malate dehydrogenase leads to the upregulation of gluconeogenesis resulting in an increase in cell wall precursors. Consistent with this idea, metabolite analysis revealed thatmdhdeletion cells possess elevated levels of several glycolysis/gluconeogenesis compounds and the cell wall precursor, UDP-NAG. In agreement with these results, the increased A22 resistance phenotype can be recapitulated through the addition of glucose to the media. Finally, we show that this increase in antibiotic tolerance is not specific to A22 but also applies to the cell wall-targeting antibiotic, mecillinam.
Integrative omics data analysis uncovers biomarker genes and potential candidate drugs for G3 medulloblastoma
Authors: Guo Loreina , Cornick Kendall , Xu Vincent , Hao Tianyao , Ilagan Ma. Xenia G. , Buchser William , Rubin Joshua B. , Li Fuhai
Published: June 2020

Medulloblastoma (MB) is the most common malignant brain tumor in infants and children. Four molecular subtypes of MB are recognized: WNT, SHH, Group 3 (G3), and Group 4 (G4). Compared with WNT and SHH subtypes, G3 MBs exhibit significantly worse outcomes and higher metastatic rates, and there is no effective treatment yet. Moreover, G3 and G4 MBs are much more common in boys than girls, i.e., sex bias, which also plays important roles in cancer prognosis and drug response. However, the molecular mechanism of G3 remains unclear, and there are no well-identified biomarker genes associated with these phenotypes, i.e., worse survival rate, higher metastasis rate, and sex bias. In this exploratory study, we aim to identify potential biomarkers associated with the three phenotypes using integrative analysis of gene expression, methylation and copy number variation datasets. In the results, we identified a set of biomarker genes and linked them into a network signature. The network signature showed better performance in the separation of G3 MB patients into subtypes with a significant difference in terms of the three phenotypes. To identify potentially effective drugs for G3 MBs, a set of drugs with diverse targets were prioritized, which can potentially inhibit the network signature. These drugs or combinations thereof might be effective for G3 treatment.