bluuebunny/crossref_metadata_2025 huggingface dataset:
Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids’ di-symbiotic systems
Authors: Manzano-Marín Alejandro , d’acier Armelle Coeur , Clamens Anne-Laure , Orvain Céline , Cruaud Corinne , Barbe Valérie , Jousselin Emmanuelle
Published: February 2019

Many insects with a nutrient-restricted diet depend on obligate mutualistic bacteria for the provisioning of essential nutrients lacking from their food source, namely essential amino acids and B vitamins. Most aphids (Hemiptera: Aphididae), whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera for the supply of the aforementioned compounds. However, in some aphid lineages Buchnera have lost the capability of producing these nutrients and thus the symbiotic consortium has accommodated an extra bacterial partner to supplement Buchnera’s deficiencies. In this work, we explore the di-symbiotic nutritional endosymbiosis of a group of Cinara aphids which has been found to harbour both Buchnera and an Erwinia-related symbiont. Using fluorescence in situ hybridisation, we have located this symbiont to the bacteriome where it inhabits its own bacteriocytes. Through whole-genome sequencing of the endosymbionts of 9 species of Erwinia-associated Cinara aphids, we have found that Ewrinia genomes are highly syntenic and all show significant genome reduction. Additionally, Erwinia symbionts display phylogenetic congruency with Buchnera, suggesting long-term co-divergence. Most significantly, we found that not only is Erwinia capable of complementing Buchnera’s auxotrophies, but that the genes involved in the biosynthesis of two B vitamins have actually been horizontally acquired from a Sodalis-related bacterium. Finally, this B-vitamin biosynthetic genes have been further transferred to a new Hamiltonella co-obligate symbiont in a specific Cinara lineage, thus displaying a tri-symbiotic system. These results highlight the important role horizontal gene transfer plays in the establishment of new obligate nutritional symbionts.
Early life DNA methylation profiles are indicative of age-related transcriptome changes
Authors: Hadad Niran , Masser Dustin R. , Blanco-Berdugo Laura , Stanford David R. , Freeman Willard M.
Published: February 2019

Alterations to cellular and molecular programs with brain aging result in cognitive impairment and susceptibility to neurodegenerative disease. Changes in DNA methylation patterns, an epigenetic modification required for various CNS functions, are observed with aging and can be prevented by anti-aging interventions, but the functional outcomes of altered methylation on transcriptome profiles are poorly understood with brain aging. Integrated analysis of the hippocampal methylome and transcriptome with aging of male and female mice demonstrates that age-related differences in methylation and gene expression are anti-correlated within gene bodies and enhancers, but not promoters. Methylation levels at young age of genes altered with aging are positively associated with age-related expression changes even in the absence of significant changes to methylation with aging, a finding also observed in mouse Alzheimer’s models. DNA methylation patterns established in youth, in combination with other epigenetic marks, are able to predict changes in transcript trajectories with aging. These findings are consistent with the developmental origins of disease hypothesis and indicate that epigenetic variability in early life may explain differences in age-related disease.
ANP32A and ANP32B are key factors in the Rev dependent CRM1 pathway for nuclear export of HIV-1 unspliced mRNA
Authors: Wang Yujie , Zhang Haili , Na Lei , Du Cheng , Zhang Zhenyu , Zheng Yong-Hui , Wang Xiaojun
Published: February 2019

The nuclear export receptor CRM1 is an important regulator involved in the shuttling of various cellular and viral RNAs between the nucleus and the cytoplasm. HIV-1 Rev interacts with CRM1 in the late phase of HIV-1 replication to promote nuclear export of unspliced and single spliced HIV-1 transcripts. However, the knowledge of cellular factors that are involved in the CRM1-dependent viral RNA nuclear export remains inadequate. Here, we identified that ANP32A and ANP32B mediate the export of unspliced or partially spliced viral mRNA via interacting with Rev and CRM1. We found that double, but not single, knockout of ANP32A and ANP32B, significantly decreased the expression of gag protein. Reconstitution of either ANP32A or ANP32B restored the viral production equally. Disruption of both ANP32A and ANP32B expression led to a dramatic accumulation of unspliced viral mRNA in the nucleus. We further identified that ANP32A and ANP32B interact with both Rev and CRM1 to promote RNA transport and that this function is Rev/RRE-dependent, but not CTE-dependent. Together our data suggests that ANP32A and ANP32B are required for HIV-1 unspliced RNA export in the Rev-CRM1 pathway.

Author summary

Posttranscriptional regulation of HIV-1 genome is very important for viral protein expression and viral replication. HIV-1 Rev protein bind to RRE structure of viral RNA and interacts with the mammalian nuclear export factor Chromosomal Maintenance 1 (CRM1) in the late phase of HIV-1 replication to promote nuclear export of unspliced and single spliced HIV-1 transcripts. The REV/RRE-CRM1 pathway has been investigated for years and many host factors have been reported to be involved, but the complicated complex and procedure remain largely unknown. Here the authors report that two host proteins, ANP32A and ANP32B, are novel key factors that support export of unspliced and partial spliced viral RNA from the nucleus to the cytosol. ANP32A/B can interact with both Rev and CRM1, and this interaction is necessary for Rev/RRE-CRM1 dependent viral RNA export. These results suggest that ANP32A and ANP32B are important in viral replication and could be potential targets for novel antiviral strategy.
Growth Phase Dependent Chromosome Condensation and H-NS Protein Redistribution in E. coli Under Osmotic Stress
Authors: Rafiei Nafiseh , Cordova Martha , Navarre William Wiley , Milstein Joshua N.
Published: February 2019

The heat-stable nucleoid-structuring (H-NS) protein is a global transcriptional regulator implicated in coordinating the expression of over 200 genes in E. coli bacteria. We have applied super-resolved microscopy to quantify the intracellular, spatial reorganization of H-NS in response to osmotic stress. We find that H-NS shows a growth phase dependent response to hyperosmotic shock. In stationary phase, H-NS detaches from a tightly compacted bacterial chromosome and is excluded from the nucleoid volume over an extended period of time. This behaviour is absent during rapid growth but may be induced by exposing the osmotically stressed culture to the DNA gyrase inhibitor, coumermycin. This compaction/H-NS exclusion phenomenon occurs in the presence of either potassium or sodium ions and is independent of the stress responsive sigma factor RpoS, or the H-NS paralog StpA.
Big root approximation of site-scale vegtation water uptake
Authors: Bouda Martin
Published: February 2019

Land surface model (LSM) predictions of soil moisture and transpiration under water-limited conditions suffer from biases due to a lack of mechanistic process description of vegetation water uptake. Here, I derive a ‘big root’ approach from the porous pipe equation for root water uptake and compare its predictions of soil moistures during the 2010 summer drought at the Wind River Crane site to two previously used Ohm’s law analogue plant hydraulic models. Structural error due to inadequate representation of root system architecture (RSA) in both Ohm’s law analogue models yields significant and predictable moisture biases. The big root model greatly reduces these as it better represents RSA effects on pressure gradients and flows within the roots. It represents a major theoretical advance in understanding vegetation water limitation at site scale with potential to improve LSM predictions of soil moisture, temperature and surface heat, water, and carbon fluxes.
Nanoparticle-mediated transformation expands horizon of organism engineering
Authors: French Katherine E.
Published: February 2019

Our ability to engineer organisms will unlock new discoveries in how cellular processes work and enable new advances in biotechnology. However, many organisms are recalcitrant to traditional transformation methods. Here, we describe a new nanoparticle-based method of transformation which can be used to transform bacteria, plants, algae and diatoms.
Cytoskeleton dynamics control early events of lateral root initiation in Arabidopsis
Authors: Barro Amaya Vilches , Stöckle Dorothee , Thellmann Martha , Ruiz-Duarte Paola , Bald Lotte , Louveaux Marion , Born Patrick von , Denninger Philipp , Goh Tatsuaki , Fukaki Hidehiro , Vermeer Joop EM , Maizel Alexis
Published: February 2019

How plant cells re-establish differential growth to initiate organs is poorly understood. Morphogenesis of lateral roots relies on the tightly controlled radial expansion and asymmetric division of founder cells. The cellular mechanisms that license and ensure these features are unknown. Here, we quantitatively analyse F-actin and microtubule dynamics during LR initiation. Using mutants, pharmacological and tissue-specific genetic perturbations, we show that dynamic reorganisation of both microtubule and F-actin networks is required for the asymmetric expansion of the founder cells. This cytoskeleton remodelling intertwine with auxin signalling in the pericycle and endodermis in order for founder cells to acquire a basic polarity required for initiating LR development. Our results reveal the conservation of cell remodelling and polarisation strategies between the Arabidopsis zygote and lateral root founder cells. We propose that coordinated, auxin-driven reorganisation of the cytoskeleton licenses asymmetric cell growth and divisions during embryonic and post-embryonic organogenesis.

HIGHLIGHTS

Failure for lateral root founder cells to undergo asymmetric radial expansion before division, leads to aberrant organ formation.

Cortical microtubules arrays reorganise to facilitate this asymmetric expansion and F-actin the asymmetric division.

Cytoskeletal reorganisation depends on auxin signalling.

New genetic tools allow to perturb microtubules or actin in an inducible and cell-type specific manner.
SAXSDom: Modeling multi-domain protein structures using small-angle X-ray scattering data
Authors: Hou Jie , Adhikari Badri , Tanner John J. , Cheng Jianlin
Published: February 2019

Many proteins are composed of several domains that pack together into a complex tertiary structure. Some multidomain proteins can be challenging for protein structure modeling, particularly those for which templates can be found for the domains but not for the entire sequence. In such cases, homology modeling can generate high quality models of the domains but not for the assembled protein. Small-angle X-ray scattering (SAXS) reports on the solution structural properties of proteins and has the potential for guiding homology modeling of multidomain proteins. In this work, we describe a novel multi-domain protein assembly modeling method, SAXSDom, that integrates experimental knowledge from SAXS profiles with probabilistic Input-Output Hidden Markov model (IOHMM). Four scoring functions to account for the energetic contribution of SAXS restraints for domain assembly were developed and tested. The method was evaluated on multi-domain proteins from two public datasets. Based on the results, the accuracy of domain assembly was improved for 40 out of 46 CASP multi-domain proteins in terms of RMSD and TM-score when SAXS information was used. Our method also achieved higher accuracy for at least 45 out of 73 multi-domain proteins according to RMSD and TM-score metrics in the AIDA dataset. The results demonstrate that SAXS data can provide useful information to improve the accuracy of domain-domain assembly. The source code and tool packages are available athttp://github.com/multicom-toolbox/SAXSDom.
Cholesterol Myth and the Imperative Role of Functional Evaluation of Lipoproteins in Atherosclerotic Risk Prediction Strategies
Authors: Bhavani Ravi Divya , Ashokkumar Srinivasan , Prema Velusamy , Kishore Kumar S Narasimhan , Narasimhan Chakrapani Lakshmi , Singh Abhilasha , Thangarajeswari Mohan , Thiruvengadam Kannan , Arumugam Moongilpatti Angappa , Kalaiselvi Periandavan
Published: February 2019

Objective

To arrive at apposite risk prediction strategies in identifying markers that could delineate patients susceptible for atherosclerotic progression from other diabetic patient population thus circumventing undesirable drug exposure or conversely inadequate treatment.

Research Design and Methods

The study was designed to assess and compare the biochemical parameters along with lipoprotein ratios assessed in structural and functional aspects between the probable risk factor groups for CAD(diabetics with no symptoms for CAD) and untreated CAD patients (on admission for CAD) in a total of 593 participants. Anthropometric measurements were made and serum fasting glucose, lipid peroxide levels, lipid and lipoprotein ratio assessments were carried out. In addition to these basic parameters, oxidized LDL (Ox-LDL) and serum paraoxonase (PON) activity were also measured in this study. To ascertain the diagnostic accuracy of the individual markers, receiver operating characteristic curve analysis was carried out.

Results

Serum levels of blood lipids, lipid peroxides were higher in the diabetic and the cardiovascular patients with a concomitant decrease in the levels of HDL. Increased median levels of Ox-LDL and decreased PON activity was observed in the cardiovascular patients both with and without diabetes.

Conclusion

This study proposes Ox-LDL/PON assessment would be more functional than the traditional LDL-c/HDL-c to categorize the risk group of patients into prospective atherosclerotic predisposed and non-predisposed population, thus enabling the former to get treated with appropriate medication.
Allometric Scaling of physiologically-relevant organoids
Authors: Magliaro Chiara , Rinaldo Andrea , Ahluwalia Arti
Published: February 2019

The functional and structural resemblance of organoids to mammalian organs suggests that they might follow the same allometric scaling rules. However, despite their remarkable likeness to downscaled organs, non-luminal organoids are often reported to possess necrotic cores due to oxygen diffusion limits. To assess their potential as physiologically relevant in vitro models, we determined the range of organoid masses in which quarter power scaling as well as a minimum threshold oxygen concentration is maintained. Using data on brain organoids as a reference, computational models were developed to estimate oxygen consumption and diffusion at different stages of growth. The results show that mature brain (or other non-luminal) organoids generated using current protocols must lie within a narrow range of masses to maintain both quarter power scaling and viable cores. However, micro-fluidic oxygen delivery methods could be designed to widen this range, ensuring a minimum viable oxygen threshold throughout the constructs and mass dependent metabolic scaling. The results provide new insights into the significance of the allometric exponent in systems without a resource-supplying network and may be used to guide the design of more predictive and physiologically relevant in vitro models, providing an effective alternative to animals in research.
Grey matter volume changes and corresponding cellular metrics identified in a longitudinalin vivoimaging approach
Authors: Asan Livia , Falfan-Melgoza Claudia , Weber-Fahr Wolfgang , Beretta Carlo , Kuner Thomas , Knabbe Johannes
Published: February 2019

Magnetic resonance imaging (MRI) of the brain combined with voxel-based morphometry (VBM) has revealed structural changes of grey and white matter in a range of neurological and psychiatric disorders. However, the cellular basis of volume changes observed with VBM has remained unclear. We devised an approach to systematically correlate changes in grey matter volume (GMV) with cellular composition. Mice were alternately examined with structural MRI and two-photonin vivomicroscopy at three time points, taking advantage of age-dependent changes in brain structure. We chose to image fluorescently labelled cell nuclei, because these can be readily imaged in large tissue volumes and allow inferences on several structural parameters: (1) the physical volume as determined from a subset of nuclei used to generate a geometrically defined space, (2) the number of cells, (3) the nearest neighbour distance measured between all nuclei as an indicator of cell clustering, and (4) the volume of the cell nuclei. Using this approach, we found that physical volume did not significantly correlate with GMV change, whereas mean nuclear volume was inversely correlated. When focusing on layers within the imaging volume, positive correlations of GMV were found with cell number near the cortical surface and nearest neighbour distance in deeper layers. Thus, the novel approach introduced here provided new insights into the factors underlying grey matter volume changes.
Orthogonal Drug Pooling Enhances Phenotype-based Discovery of Ocular Anti-angiogenic Drugs in Zebrafish Larvae
Authors: Ohnesorge Nils , Sasore Temitope , Hillary Daniel , Alvarez Yolanda , Carey Michelle , Kennedy Breandán N.
Published: February 2019

Unbiased screening of large randomized chemical libraries in vivo is a powerful tool to find new drugs and targets. However, forward chemical screens in zebrafish can be time consuming and usually >99% of test compounds have no significant effect on the desired phenotype. Here, we sought to find bioactive drugs more efficiently and to comply with the 3R principles of replacement, reduction and refinement of animals in research. We investigated if pooling of drugs to simultaneously test 8-10 compounds in zebrafish larvae can increase the screening efficiency of an established assay that identifies drugs inhibiting developmental angiogenesis in the eye. In a phenotype-based screen, we tested 1760 small molecule compounds from the ChemBridge DIVERSet™ chemical library for their ability to inhibit the formation of distinct primary hyaloid vessels in the eye. Applying orthogonal pooling of the chemical library, we treated zebrafish embryos from 3 to 5 days post fertilization with pools of 8 or 10 compounds at 10 μM each. This reduced the number of tests from 1760 to 396. In 63% of cases, treatment showed sub-threshold effects of <40% reduction of primary hyaloid vessels. From 18 pool hits, we identified 8 compounds that reduce hyaloid vessels in the larval zebrafish eye by at least 40%. Compound 4-[4-(1H-benzimidazol-2-yl)phenoxy]aniline ranked as the most promising candidate with reproducible and dose-dependent effects. To our knowledge, this is the first report of a self-deconvoluting matrix strategy applied to drug screening in zebrafish. We conclude that the orthogonal drug pooling strategy is a cost-effective, time-saving and unbiased approach to discover novel inhibitors of developmental angiogenesis in the eye. Ultimately, this approach may identify new drugs or targets to mitigate disease caused by pathological angiogenesis in the eye e.g. diabetic retinopathy or age-related macular degeneration wherein blood vessel growth and leaky vessels lead to vision impairment or clinical blindness.
Interaction of NPC2 protein with Lysobisphosphatidic Acid is required for normal endolysosomal cholesterol trafficking
Authors: McCauliff Leslie A. , Langan Annette , Li Ran , Ilnytska Olga , Bose Debosreeta , Kahn Peter C. , Storch Judith
Published: February 2019

Unesterified cholesterol accumulation in the late endosomal/lysosomal (LE/LY) compartment is the cellular hallmark of Niemann-Pick C (NPC) disease, caused by defects in the genes encoding NPC1 or NPC2. We previously reported the dramatic stimulation of NPC2 cholesterol transport rates by the LE/LY phospholipid lysobisphosphatidic acid (LBPA) and in these studies sought to determine their functional relationship in normal LE/LY cholesterol egress. Here we demonstrate that NPC2 interacts directly with LBPA and identify the NPC2 hydrophobic knob domain as the site of interaction. Using its precursor phosphatidylglycerol (PG), we show that PG-induced LBPA enrichment results in clearance of accumulated cholesterol from NPC1-deficient cells but is ineffective in cells lacking functional NPC2. Together these studies reveal a heretofore unknown aspect of intracellular cholesterol trafficking, in which NPC2 and LBPA function together in an obligate step of sterol egress from the LE/LY compartment, which appears to be independent of NPC1.
Transitions in filament geometry drive ESCRT-III-mediated membrane remodelling and fission
Authors: Harker-Kirschneck Lena , Baum Buzz , Šarić Andela
Published: February 2019

ESCRT-III is an evolutionarily conserved membrane remodeling machinery that, with the Vps4 ATPase, forms filaments able to cut biological membranes from the cytosolic side. This activity of ESCRT-III is essential for the final stage of cell division in archaea and in many eukaryotes, the formation of vesicles, the creation of exosomes, the release of viruses such as HIV-1 and Ebola, and for the repair and sealing of cellular membranes. While there has been recent rapid progress in describing the biochemical and cell biology details of different ESCRT-III functions, we lack an understanding of the physical mechanism involved in ESCRT-III-mediated membrane remodelling. Here, through the development of coarse-grained molecular dynamic simulations, we present a minimal model that captures the ability of ESCRT-III to induce experimentally reported cases of ESCRT-III driven membrane sculpting, including the formation of cones and tubules, and membrane scission. This model suggests a universal physical mechanism of action, that differs from that of other cytoskeletal elements, whereby a change in the twist of membrane bound ESCRT-III filaments drives transitions between a flat spiral and a 3D helix to induce membrane deformation and scission. We expect the mechanistic principles revealed here to be useful in manipulating ESCRT-III-driven processes in cells and in guiding the engineering of synthetic membrane-sculpting systems.
Phylogenetic relationships among the clownfish-hosting sea anemones
Authors: Titus Benjamin M. , Benedict Charlotte , Laroche Robert , Gusmão Luciana C. , Deusen Vanessa Van , Chiodo Tommaso , Meyer Christopher P. , Berumen Michael L. , Bartholomew Aaron , Yanagi Kensuke , Reimer James D. , Fujii Takuma , Daly Marymegan , Rodríguez Estefanía
Published: February 2019

The clownfish-sea anemone symbiosis has been a model system for understanding fundamental evolutionary and ecological processes. However, our evolutionary understanding of this symbiosis comes entirely from studies of clownfishes. A holistic understanding of a model mutualism requires systematic, biogeographic, and phylogenetic insight into both partners. Here, we conduct the largest phylogenetic analysis of sea anemones (Order Actiniaria) to date, with a focus on expanding the biogeographic and taxonomic sampling of the 10 nominal clownfish-hosting species. Using a combination of mtDNA and nuDNA loci we test 1) the monophyly of each clownfish-hosting family and genus, 2) the current anemone taxonomy that suggests symbioses with clownfishes evolved multiple times within Actiniaria, and 3) whether, like the clownfishes, there is evidence that host anemones have a Coral Triangle biogeographic origin. Our phylogenetic reconstruction demonstrates widespread poly-and para-phyly at the family and genus level, particularly within the family Stichodactylidae and genus Sticodactyla, and suggests that symbioses with clownfishes evolved minimally three times within sea anemones. We further recover evidence for a Tethyan biogeographic origin for some clades. Our data provide the first evidence that clownfish and some sea anemone hosts have different biogeographic origins, and that there may be cryptic species of host anemones. Finally, our findings reflect the need for a major taxonomic revision of the clownfish-hosting sea anemones.
The impact of pro-inflammatory cytokines on the β-cell regulatory landscape provides new insights into the genetics of type 1 diabetes
Authors: Ramos-Rodríguez M. , Raurell-Vila H. , Colli ML. , Alvelos MI. , Subirana M. , Juan-Mateu J. , Norris R. , Turatsinze JV. , Nakayasu ES. , Webb-Robertson BJ. , Inshaw JRJ. , Marchetti P. , Piemonti L. , Esteller M. , Todd JA. , Metz TO. , Eizirik DL. , Pasquali L.
Published: February 2019

Early stages of type 1 diabetes (T1D) are characterized by local autoimmune inflammation and progressive loss of insulin-producing pancreatic β cells. We show here that exposure to pro-inflammatory cytokines unmasks a marked plasticity of the β-cell regulatory landscape. We expand the repertoire of human islet regulatory elements by mapping stimulus-responsive enhancers linked to changes in the β-cell transcriptome, proteome and 3D chromatin structure. Our data indicates that the β cell response to cytokines is mediated by the induction of novel regulatory regions as well as the activation of primed regulatory elements pre-bound by islet-specific transcription factors. We found that T1D-associated loci are enriched of the newly mapped cis-regulatory regions and identify T1D-associated variants disrupting cytokine-responsive enhancer activity in human β cells. Our study illustrates how β cells respond to a pro-inflammatory environment and implicate a role for stimulus-response islet enhancers in T1D.
Partial coherence and frustration in self-organizing spherical grids
Authors: Stella Federico , Urdapilleta Eugenio , Treves Alessandro
Published: February 2019

Nearby grid cells have been observed to express a remarkable degree of long-range order, which is often idealized as extending potentially to infinity. Yet their strict periodic firing and ensemble coherence are theoretically possible only in flat environments, much unlike the burrows which rodents usually live in. Are the symmetrical, coherent grid maps inferred in the lab relevant to chart their way in their natural habitat?

We consider spheres as simple models of curved environments and, waiting for the appropriate experiments to be performed, we use our adaptation model to predict what grid maps would emerge in a network with the same recurrent connections, which on the plane produce coherence among the units. We find that on the sphere such connections distort the maps that single grid units would express on their own, and aggregate them into clusters. When remapping to a different spherical environment, units in each cluster maintain only partial coherence, similar to what is observed in disordered materials, such as spin glasses.
Positive feedback loop of regulating ERK phosphorylation in mESCs mediated by Etv5-Tet2-Fgfr2 axis
Authors: Fan Chen , Zhu Kui , Liu Yuan , Zhang Mengyao , Cao Hongxia , Li Na , Wang Yan , Hua Jinlian , Wang Huayan , Zhang Shiqiang
Published: February 2019

Dynamic equilibrium of extracellular signal-regulated kinase (ERK) activity is regulated elaborately by multiple feedback loops to ensure the normal self-renewal of mouse embryonic stem cells (mESCs). Previous studies on mESCs have demonstrated that the negative feedback loops are engaged to prevent the overactivated ERK phosphorylation (pERK). It is not clear whether there is any positive feedback loop involved to maintain a minimum of pERK in mESCs. Here, we found that blocking fibroblast growth factor (FGF)-ERK pathway by chemical PD0325901 downregulated the transcription of E26 transformation-specific (ETS) family transcription factor Etv5 in mESCs. In turn, knockout (KO) of Etv5 by CRISPR/Cas9 decreased pERK. Moreover, Etv5 KO enhanced the DNA methylation at promoter of fibroblast growth factor receptor 2 (Fgfr2) by downregulating DNA hydroxylase Tet2, which further decreased the expression of Fgfr2 in mESCs. Collectively, a positive feedback loop of regulating pERK was revealed in mESCs, which was mediated by Etv5-Tet2-Fgfr2 axis. Our findings provide a new paradigm for pERK regulation in mESCs and will be useful to understand the cell fate determination during early embryo development.
Controllability of molecular pathways
Authors: Wuchty Stefan
Published: February 2019

Inputs to molecular pathways that are the backbone of cellular activity drive the cell to certain outcomes and phenotypes. Here, we investigated proteins that topologically controlled different human pathways represented as independent molecular interaction networks, suggesting that a minority of proteins control a high number of pathways and vice versa. Transcending different topological levels, proteins that controlled a large number of pathways also controlled a network of interactions when all pathways were combined. Furthermore, control proteins that were robust when interactions were rewired or inverted also increasingly controlled an increasing number of pathways. As for functional characteristics, such control proteins were enriched with regulatory and signaling genes, disease genes and drug targets. Focusing on evolutionary characteristics, proteins that controlled different pathways had a penchant to be evolutionarily conserved as equal counterparts in other organisms, indicating the fundamental role that control analysis of pathways plays for our understanding of regulation, disease and evolution.
Head motion predictability explains activity-dependent suppression of vestibular balance control
Authors: Dietrich H , Heidger F , Schniepp R , MacNeilage PR , Glasauer S , Wuehr M
Published: February 2019

Vestibular balance control is dynamically weighted during locomotion. This might result from a selective suppression of vestibular inputs in favor of a feed-forward balance regulation based on locomotor efference copies. The feasibility of such a feed-forward mechanism should however critically depend on the predictability of head movements (PHM) during locomotion. To test this, we studied in healthy subjects the differential impact of a stochastic vestibular stimulation (SVS) on body sway (center-of-pressure, COP) during standing and walking at different speeds using time-frequency analyses and compared it to activity-dependent changes in PHM. SVS-COP coupling decreased from standing to walking and further dropped with faster locomotion. Correspondingly, PHM increased with faster locomotion. Furthermore, SVS-COP coupling depended on the gait-cycle-phase with peaks corresponding to periods of least PHM. These findings support the assumption that during stereotyped human self-motion, locomotor efference copies selectively replace vestibular cues, similar to what was previously observed in animal models.
Calcium alginate entrapped Eupatorium adenophorum Sprengel stems powder for Chromium(VI) biosorption in aqueous medium
Authors: Aryal Mahendra
Published: February 2019

A novel biosorbent, Eupatorium adenophorum Sprengel was used for biosorption of chromium (VI) from aqueous solutions. Optimum pH, biomass concentration and contact time were estimated at 2.0, 1.0 g/L and 60 min respectively. Data obtained from batch studies confirmed well to the Langmuir model. It was found that the overall biosorption process was best described by pseudo second-order kinetics. The results demonstrated that intraparticle diffusion is not the sole rate-controlling step for the whole sorption process. In binary mixtures, biosorption efficiency of Cr(VI) was not significantly affected by the presence of ions up to 50 mg/L. Thermodynamic study showed that Cr(VI) biosorption on Eupatorium adenophorum-alginate beads was spontaneous, exothermic and physisorption in nature. Cr(VI) ions were recovered effectively from Eupatorium adenophorum-alginate beads using 0.5 M HNO3 solution.
LRRC33 is a novel binding and regulating protein of TGF-β1 function in human acute myeloid leukemia cells
Authors: Ma Wenjiang , Qin Yan , Chapuy Bjoern , Lu Chafen
Published: February 2019

Transforming growth factor – β1 (TGF-β1) is a versatile cytokine. It has context-dependent pro- and anti-cell proliferation functions. Activation of latent TGF-β1 requires release of the growth factor from pro-complexes and is regulated through TGF-β binding proteins. Two types of TGF-β binding partners, latent TGF-β-binding proteins (LTBPs) and leucine-rich-repeat-containing protein 32 (LRRC32), have been identified and their expression are cell specific. TGF-β1 also plays important roles in acute myeloid leukemia (AML) cells. However, the expression of LTBPs and LRRC32 are lacking in myeloid lineage cells and the binding protein of TGF-β1 in these cells are unknown. Here we show that a novel leucine-rich-repeat-containing protein family member, LRRC33, with high mRNA level in AML cells, to be the binding and regulating protein of TGF-β1 in AML cells. Using two representative cell lines MV4-11 and AML193, we demonstrate that the protein expression of LRRC33 and TGF-β1 are correlated. LRRC33 co-localizes and forms complex with latent TGF-β1 protein on the cell surface and intracellularly in these cells. Similar as in other cell types, the activation of TGF-β1 in MV4-11 and AML193 cells are also integrin dependent. We anticipate our study to be a starting point of more comprehensive research on LRRC33 as novel TGF-β regulating protein and potential non-genomic based drug target for AML and other myeloid malignancy.
Build a better mouse task – can an open-source rodent joystick enhance reaching behavior outcomes through improved monitoring of real-time spatiotemporal kinematics?
Authors: Belsey Parley , Nicholas Mark A. , Yttri Eric A
Published: February 2019

For decades, advanced behavioral tasks have only been used in human and non-human primates. However, with improved analytical and genetic techniques, there has been a growing drive to implement complex reaching, decision-making, and reaction time tasks – not in primates – but in rodents. Here, we assess the hypothesis that a mouse can learn a cued reaction time task. Moreover, we tested multiple training regimens and found that introducing elements of the reaction time task serially hindered, rather than helped task acquisition. Additionally, we include a step-by-step manual for inexpensive implementation and use of a rodent joystick for behavioral analysis. Task and analysis code for the evaluated behaviors are included such that they may be replicated and tested further. With these, we also include code for a probabilistic reward ‘two-arm bandit’ task. These various tasks, and the method to construct and implement them, will enable greatly improved study of the neural correlates of behavior in the powerful mouse model organism. In summary, we have tested and demonstrated that mice can learn sophisticated tasks with A joystick, and that targeted task design provides a significant advantage. These results of this study stand to inform the implementation of other sophisticated tasks using the mouse model.
Oncogenic Mutations in Histologically Normal Endometrium: The New Normal?
Authors: Lac Vivian , Nazeran Tayyebeh M. , Tessier-Cloutier Basile , Aguirre-Hernandez Rosalia , Albert Arianne , Lum Amy , Khattra Jaswinder , Praetorius Teresa , Mason Madeline , Chiu Derek , Köbel Martin , Yong Paul J. , Gilks Blake C. , Anglesio Michael S. , Huntsman David G.
Published: February 2019

The presence of somatic driver mutations in endometriosis has previously been believed to represent early events in transformation, however our group and others have described such mutations in roughly one-third of cases of deep infiltrating or iatrogenic endometriosis. These forms of endometriosis rarely progress to malignancy. Recent studies have also shown somatic driver mutations in normal skin, blood, peritoneal washings, and esophageal epithelium. Such findings prompt speculation on whether such mutations exist in the eutopic endometrium – the likely tissue of origin of endometriosis. In the current study we investigated the presence of somatic driver mutations in histologically normal endometrium from women lacking evidence of gynecologic malignancy or endometrial hyperplasia. Twenty-five women who underwent hysterectomies and 85 women who underwent endometrial biopsies were included in this study. Formalin-fixed, paraffin-embedded tissue specimens were analyzed by means of targeted sequencing followed by orthogonal validation with droplet digital PCR. PTEN and ARID1A immunohistochemistry (IHC) was also performed as surrogates for inactivating mutations in the respective genes. Overall, we observed somatic driver-like events in over 50% of histologically normal endometrial samples analyzed, which included hotspot mutations in KRAS, PIK3CA, and FGFR2 as well as PTEN-loss by IHC. Analysis of anterior and posterior samplings collected from women who underwent hysterectomies is consistent with the presence of somatic driver mutations within clonal pockets spread throughout the uterus. The prevalence of such oncogenic mutations also increased with age (OR: 1.05 (95% CI: 1.00 – 1.10), p = 0.035). These findings have implications on our understanding of aging and so-called “normal tissues”, thereby necessitating caution in the utilization of mutation-based early detection tools for endometrial or other cancers.
A Signaling Network based Computational Model to Uncover Loop as the Novel Molecular Mechanisms for Medulloblastoma
Authors: Xu Jielin , Li Fuhai
Published: February 2019

Medulloblastoma (MB) is the most common malignant brain tumor in children. Despite aggressive therapy, about one-third of patients with MB still die, and survivors suffer severe long-term side effects due to the treatments. The poor post-treatment outcomes are tightly linked to unpredictable drug resistance. Therefore, before developing robust single drug or drug combination recommendation algorithms, uncovering the underlying protein-protein interaction (PPI) network patterns that accurately explain and predict drug resistances for MB subtypes is essential and important. In this study, we hypothesize that the loop sub-structure within the PPI network can explain and predict drug resistance. Both static and dynamic models are built to evaluate this hypothesis for three MB subtypes. Specifically, a static model is created to first validate that many reported therapeutic targets are located topologically on highly deregulated loop sub-structure and then to characterize the loop for tumors without treatment. Next, with the after-treatment time-series genomics data, a dynamic hidden Markov model (HMM) with newly designed initialization scheme estimates the successful and unsuccessful occurrence probabilities for each given PPI and then re-delineates the loop for post-treatment tumors. Finally, the comparison of loop structures pre- and post-treatment distinguishes effective and ineffective treatment options, demonstrating that the loop sub-structure is capable of interpreting the mechanism of drug resistance. In summary, effective treatments show much stronger inhibition of cell cycle and DNA replication proteins when compared to ineffective treatments after considering the cross talk of multiple pathways (the loop).
Nonparametric expression analysis using inferential replicate counts
Authors: Zhu Anqi , Srivastava Avi , Ibrahim Joseph G. , Patro Rob , Love Michael I.
Published: February 2019

A primary challenge in the analysis of RNA-seq data is to identify differentially expressed genes or transcripts while controlling for technical biases present in the observations. Ideally, a statistical testing procedure should incorporate information about the inherent uncertainty of the abundance estimates, whether at the gene or transcript level, that arise from quantification of abundance. Most popular methods for RNA-seq differential expression analysis fit a parametric model to the counts or scaled counts for each gene or transcript, and a subset of methods can incorporate information about the uncertainty of the counts. Previous work has shown that nonparametric models for RNA-seq differential expression may in some cases have better control of the false discovery rate, and adapt well to new data types without requiring reformulation of a parametric model. Existing nonparametric models do not take into account the inferential uncertainty of the observations, leading to an inflated false discovery rate, in particular at the transcript level. Here we propose a nonparametric model for differential expression analysis using inferential replicate counts, extending the existing SAMseq method to account for inferential uncertainty, batch effects, and sample pairing. We compare our method, “SAMseq With Inferential Samples Helps”, or Swish, with popular differential expression analysis methods. Swish has improved control of the false discovery rate, in particular for transcripts with high inferential uncertainty. We apply Swish to a singlecell RNA-seq dataset, assessing sensitivity to recover DE genes between sub-populations of cells, and compare its performance to the Wilcoxon rank sum test.
Comparative analyses of phenotypic sequences using phylogenetic trees
Authors: Caetano Daniel S. , Beaulieu Jeremy M.
Published: February 2019

Phenotypic sequences are a type of multivariate trait organized structurally, such as teeth distributed along the dental arch, or temporally, such as the stages of an ontogenetic series. However, unlike other multivariate traits, the elements of a phenotypic sequence are arranged along a vector, which allows for distinct evolutionary patterns between neighboring and distant positions. In fact, sequence traits share many characteristics with molecular sequences. We implement an approach to estimate rates of trait evolution that explicitly incorporates the sequence organization of traits. We apply models to study the temporal pattern evolution of cricket calling songs. We test whether songs show autocorrelation of rates (i.e., neighboring positions along a phenotypic sequence have correlated rates of evolution), or if they are best described by rate variation independent of sequence position. Our results show that models perform well when used with sequence phenotypes even under small sample sizes. We also show that silent regions of the songs evolve faster than chirp regions, which suggests that macroevolutionary changes are faster when associated with axes of variation less constrained by multiple sources of selection. Our approach is flexible and can be applied to any multivariate trait with units organized in a sequence-like structure.
Highly Efficient Repair of the ΔF508 Mutation in Airway Stem Cells of Cystic Fibrosis Patients with Functional Rescue of the Differentiated Epithelia
Authors: Vaidyanathan Sriram , Salahudeen Ameen A. , Sellers Zachary M. , Bravo Dawn T. , Choi Shannon S. , Batish Arpit , Le Wei , La O Sean De , Kaushik Milan P. , Galper Noah , Lee Ciaran M. , Bao Gang , Chang Eugene H. , Wine Jeffrey J. , Milla Carlos E. , Desai Tushar J. , Nayak Jayakar V. , Kuo Calvin J. , Porteus Matthew H.
Published: February 2019

Cystic fibrosis (CF) is a monogenic autosomal recessive disorder caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Cl- channel. CF results in multiorgan dysfunction and ultimately mortality from respiratory sequelae. Although pharmacologic approaches have demonstrated efficacy in reducing symptoms and respiratory decline, a curative treatment modality remains elusive. Gene therapy, a promising curative strategy, has been limited due to poor correction efficiencies both in vitro and in vivo. Here, we use Cas9 and adeno-associated virus 6 (AAV6) to correct the ΔF508 mutation (found in ∼70% of CF alleles and ∼90% of CF patients in North America) in upper airway basal stem cells (UABCs) obtained from CF and non-CF patients undergoing functional endoscopic sinus surgery (FESS). In UABCs from homozygous (ΔF508/ΔF508) and compound heterozygous (ΔF508/Other) CF patients, we achieved 28 ± 5 % and 42 ± 15% correction, respectively. In homozygous human bronchial epithelial cells (HBECs), we achieved 41± 4 % correction. Upon differentiation in air-liquid interface (ALI), cultures of corrected CF cells displayed partial restoration of CFTRinh-172 sensitive Cl- currents relative to non-CF controls: 31± 5 % in UABCs and 51 ± 3 % in HBECs (both from subjects homozygous for ΔF508 CFTR). Finally, gene edited cells embedded successfully and retained expression of cytokeratin 5 (KRT5), a basal cell marker, on a FDA-approved porcine small intestinal submucosal (pSIS) membrane previously shown to improve re-mucosalization after FESS. In summary, we present an efficient, feeder-free, selection-free and clinically compatible approach to generate cell-based therapies for CF from autologous airway stem cells. This approach represents a first step towards developing patient-specific autologous airway stem cell transplant as a curative treatment for CF.
Suppression of GABAergic transmission in the spinal dorsal horn induces pain-related behavior in a chicken model of spina bifida
Authors: Khan Md. Sakirul I , Nabeka Hiroaki , Islam Farzana , Shimokawa Tetsuya , Saito Shouichiro , Tachibana Tetsuya , Matsuda Seiji
Published: February 2019

Spina bifida aperta (SBA), one of the most common congenital malformations, causes various neurological disorders. Pain is a common complaint of patients with SBA. However, little is known about the neuropathology of SBA-related pain. Because loss of γ-aminobutyric acid (GABA)ergic neurons in the spinal cord dorsal horn is associated with pain, we hypothesized the existence of cross-talk between SBA-related pain and alterations in GABAergic transmission in the spinal cord. Therefore, we investigated the kinetics of GABAergic transmission in the spinal cord dorsal horn in a chicken model of SBA. Neonatal chicks with SBA exhibited various pain-like behaviors, such as an increased number of vocalizations with elevated intensity (loudness) and frequency (pitch), reduced mobility, difficulty with locomotion, and escape reactions. Furthermore, the chicks with SBA did not respond to standard toe-pinching, indicating disruption of the spinal cord sensorimotor networks. These behavioral observations were concomitant with loss of GABAergic transmission in the spinal cord dorsal horn. We also found apoptosis of GABAergic neurons in the superficial dorsal horn in the early neonatal period, although cellular abnormalization and propagation of neurodegenerative signals were evident at middle to advanced gestational stages. In conclusion, ablation of GABAergic neurons induced alterations in spinal cord neuronal networks, providing novel insights into the pathophysiology of SBA-related pain-like complications.