bluuebunny/crossref_metadata_2025 huggingface dataset:
Varying co-factor requirements for MAML1-dependent transcription at different Notch-responsive target genes
Authors: Rogers Julia M. , Guo Bingqian , Egan Emily D. , Aster Jon C. , Adelman Karen , Blacklow Stephen C.
Published: January 2020

Mastermind proteins are required for transcription of Notch target genes, yet the molecular basis for mastermind function remains incompletely understood. Previous work has shown that Notch can induce transcriptional responses by binding to promoters, but more often by binding to enhancers, with HES4 and DTX1 as representative mammalian examples of promoter and enhancer responsiveness, respectively. Here, we show that mastermind dependence of the Notch response at these loci is differentially encoded in Jurkat T-ALL cells. Knockout of Mastermind-like1 (MAML1) eliminates Notch responsive activation of both these genes, and reduced target gene expression is accompanied by a decrease in H3K27 acetylation, consistent with the importance of MAML1 for p300 activity. Add-back of defined MAML1 constructs in knockout cells identifies residues 151-350 of MAML1 as essential for expression of either Notch-responsive gene. Fusion of the Notch-binding region of MAML1 to the HAT domain of p300 rescues expression of HES4 but not DTX1, suggesting that an additional activity of MAML1 is needed for gene induction at a distance. Together, these studies establish the functional importance of the MAML1151-350 region for Notch-dependent transcriptional induction, and reveal differential requirements for MAML1-dependent recruitment activities at different Notch responsive loci, highlighting the molecular complexity of NTC-stimulated transcription.
Loss of the Er81 Transcription Factor in Cholinergic Cells Alters Striatal Activity and Habit Formation
Authors: Ranjbar-Slamloo Yadollah , Ahmed Noorya Yasmin , Al Abed Alice Shaam , Gao Lingxiao , Sontani Yovina , Gauthier Alexandre R’Com-H Cheo , Arabzadeh Ehsan , Dehorter Nathalie
Published: January 2020

The finely-tuned activity of cholinergic interneurons (CINs) in the striatum is key for motor control, learning, and habit formation. Yet, the molecular mechanisms that determine their unique functional properties remain poorly explored. Using a combination of genetic and biochemical assays,in vitroandin vivophysiological characterisation, we report that selective ablation of the Er81 transcription factor leads to prominent changes in CIN molecular, morphological and electrophysiological features. In particular, the lack of Er81 amplifies intrinsic delayed-rectifier and hyperpolarization-activated currents, which subsequently alters the tonic and phasic activity of CINs. We further demonstrate that these alterations enhance their pause and time-locked responses to sensorimotor inputs in awake mice. Finally, this study reveals an Er81-dependent developmental mechanism in CINs essential for habit formation in adult mice.

Highlights

- The Er81 transcription factor is expressed in striatal cholinergic interneurons (CINs)

- Conditional deletion of Er81 alters key molecular, morphological and electrophysiological properties of CINs in adult mice

- Deletion of Er81 reduces the intrinsic excitability of CINs by upregulating delayed rectifier and hyperpolarization-activated currents

- Deletion of Er81 altersin vivostriatal activity and habit formation
The origin of domestication genes in goats
Authors: Zheng Zhuqing , Wang Xihong , Li Ming , Li Yunjia , Yang Zhirui , Wang Xiaolong , Pan Xiangyu , Gong Mian , Zhang Yu , Guo Yingwei , Wang Yu , Liu Jing , Cai Yudong , Chen Qiuming , Okpeku Moses , Colli Licia , Cai Dawei , Wang Kun , Huang Shisheng , Sonstegard Tad S. , Esmailizadeh Ali , Zhang Wenguang , Zhang Tingting , Xu Yangbin , Xu Naiyi , Yang Yi , Han Jianlin , Chen Lei , Lesur Joséphine , Daly Kevin G. , Bradley Daniel G. , Heller Rasmus , Zhang Guojie , Wang Wen , Chen Yulin , Jiang Yu
Published: January 2020

Goat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here we analyze the genomes of worldwide domestic goats, wild caprid species and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the MUC6 gene which encodes a gastrointestinally secreted mucin. Experiments revealed that the nearly fixed introgressed haplotype confers enhanced immune resistance to gastrointestinal pathogens. Another locus with a strong signal of selection may be related to behavior. The selected alleles at these two loci emerged in domestic goats at least 7,200 and 8,100 years ago, respectively, and increased to high frequencies concurrent with the expansion of the ubiquitous modern mitochondrial haplogroup A. Tracking these archaeologically cryptic evolutionary transformations provides new insights into the mechanism of animal domestication.

One Sentence Summary

Goat domestication mainly focused on immune and neural genes, with adaptive leaps driven by introgression and selection.
A Pathway and Network Oriented Approach to Enlighten Molecular Mechanisms of Type 2 Diabetes Using Multiple Association Studies
Authors: Bakir-Gungor Burcu , Yazici Miray Unlu , Goy Gokhan , Temiz Mustafa
Published: January 2020

Diabetes Mellitus (DM) is a group of metabolic disorder that is characterized by pancreatic dysfunction in insulin producing beta cells, glucagon secreting alpha cells, and insulin resistance or insulin in-functionality related hyperglycemia. Type 2 Diabetes Mellitus (T2D), which constitutes 90% of the diabetes cases, is a complex multifactorial disease. In the last decade, genome-wide association studies (GWASs) for type 2 diabetes (T2D) successfully pinpointed the genetic variants (typically single nucleotide polymorphisms, SNPs) that associate with disease risk. However, traditional GWASs focus on the ‘the tip of the iceberg’ SNPs, and the SNPs with mild effects are discarded. In order to diminish the burden of multiple testing in GWAS, researchers attempted to evaluate the collective effects of interesting variants. In this regard, pathway-based analyses of GWAS became popular to discover novel multi-genic functional associations. Still, to reveal the unaccounted 85 to 90% of T2D variation, which lies hidden in GWAS datasets, new post-GWAS strategies need to be developed. In this respect, here we reanalyze three meta-analysis data of GWAS in T2D, using the methodology that we have developed to identify disease-associated pathways by combining nominally significant evidence of genetic association with the known biochemical pathways, protein-protein interaction (PPI) networks, and the functional information of selected SNPs. In this research effort, to enlighten the molecular mechanisms underlying T2D development and progress, we integrated different in-silico approaches that proceed in top-down manner and bottom-up manner, and hence presented a comprehensive analysis at protein subnetwork, pathway, and pathway subnetwork levels. Our network and pathway-oriented approach is based on both the significance level of an affected pathway and its topological relationship with its neighbor pathways. Using the mutual information based on the shared genes, the identified protein subnetworks and the affected pathways of each dataset were compared. While, most of the identified pathways recapitulate the pathophysiology of T2D, our results show that incorporating SNP functional properties, protein-protein interaction networks into GWAS can dissect leading molecular pathways, which cannot be picked up using traditional analyses. We hope to bridge the knowledge gap from sequence to consequence.
The Nonequilibrium Mechanism of Noise Enhancer synergizing with Activator in HIV Latency Reactivation
Authors: Guo Xiaolu , Tang Tao , Duan Minxuan , Zhang Lei , Ge Hao
Published: January 2020

Reactivating HIV latency and then simultaneously eliminating it by antiretroviral therapy has become a leading strategy in curing HIV. Recently, single-cell screening experiments have shown the drug synergy between two categories of biomolecules, Activators (AC) and Noise Enhancers (NE): NE can amplify the reactivation of latent HIV induced by AC, although NE itself cannot reactivate HIV latency. Based on an established LTR-two-state effective model, we uncover two necessary conditions for this type of drug synergy: The decreasing of the turning-on rate of LTR induced by NE is highly inhibited when presented with AC; The timescale of LTR turning off without AC/NE presented should be no slower than the timescale of Tat transactivation. Then we propose a detailed LTR-four-state mechanistic model with both AC/NE regulation kinetics and Tat transactivation circuit. We show that, in order to achieve drug synergy, the system of HIV gene state transition must operate out of thermodynamic equilibrium, which is caused by energy input. The direction of energy input determines whether the inhibition of NE upon the reactivation rate of LTR-off states (unbinding of RNAP) can be successfully prevented in the presence of AC. The drug synergy can also be significantly enhanced if the energy input is appropriately distributed to more than one reaction. Our model reveals a generic nonequilibrium mechanism underpinning the noise enhanced drug synergy, which may apply to identify the same drug synergy on reactivating a diverse class of lentivirus latency.

Significance Statement

The “kick and kill” strategy has become a promising way to cure HIV by eliminating latent HIV reservoirs, the main barrier to a clinical cure. Two categories of biomolecules, Activators (AC) and Noise Enhancers (NE), have been found to have synergy on reactivating latent HIV (kick strategy). We uncover the underlying non-equilibrium mechanism of such drug synergy by developing mathematical models based on genetic regulatory kinetics. We find that controlling the magnitude and direction of energy input into genetic regulatory kinetics can prevent NE from reducing the turn-on rate of the inactivated gene state in the presence of AC, which produces the synergy. This general nonequilibrium mechanism can be useful for identifying other drug synergies on lentivirus latency reactivation.
SETD7-mediated lysine monomethylation is abundant on non-hyperphosphorylated nuclear Tau
Authors: Bichmann Maria , Prat Oriol Nuria , Ercan-Herbst Ebru , Schöndorf David C. , Gomez Ramos Borja , Schwärzler Vera , Haberkant Per , Gasparini Laura , Ehrnhoefer Dagmar E.
Published: January 2020

Human tauopathies including Alzheimer’s disease (AD) are characterized by alterations in the post-translational modification (PTM) pattern of Tau, leading to the formation of insoluble aggregates, neuronal dysfunction and degeneration. Using a mass spectrometry approach, we identified multiple sites of lysine monomethylation on Tau isolated from a detergent-soluble fraction of human brain, some of which were increased in early AD samples. Brain tissues derived from a mouse model of tauopathy demonstrate an age-dependent increase in methylation at specific sites, with methylated Tau enriched in the soluble nuclear fraction and not associated with hyperphosphorylated, insoluble Tau species. Furthermore, we show that the protein lysine methyltransferase SETD7 methylates Tau at K132 and demonstrate an interaction with K130, an additional methylation site in close vicinity. These findings shed light on the function of a novel type of PTM on Tau that provide a potential signal for its translocation to different subcellular sites. Since the mislocalization and depletion of Tau from axons is associated with tauopathies, our findings may furthermore provide insight into this disease-associated phenomenon.
Molecular signatures of local adaptation to light in Norway Spruce: role of lignin mediated immunity
Authors: Ranade Sonali Sachin , García-Gil María Rosario
Published: January 2020

Study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. However, it is challenging to determine the genetic basis of adaptive variation especially in forest trees which have large and complex genomes. Norway spruce is a shade tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. In the current work, hypocotyl-length followed a latitudinal cline in response to SHADE (low red:far-red ratio). RNA-sequencing revealed differential gene expression in response to SHADE, between a southern and a northern natural population in Sweden. Exome capture included analysis of uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway and cold acclimation, and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation and immunity. Findings from this work primarily suggests that the northern populations of Norway spruce are better adapted towards disease resistance under shade by up-regulation of lignin pathway that is linked to immunity and it forms concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.
Generalized calibration across LC-setups for generic prediction of small molecule retention times
Authors: Bouwmeester Robbin , Martens Lennart , Degroeve Sven
Published: January 2020

Motivation

Accurate prediction of liquid chromatographic retention times from small molecule structures is useful for reducing experimental measurements and for improved identification in targeted and untargeted MS. However, different experimental setups (e.g. differences in columns, gradients, solvents, or stationary phase) have given rise to a multitude of prediction models that only predict accurate retention times for a specific experimental setup. In practice this typically results in the fitting of a new predictive model for each specific type of setup, which is not only inefficient but also requires substantial prior data to be accumulated on each such setup.

Results

Here we introduce the concept of generalized calibration, which is capable of the straightforward mapping of retention time models between different experimental setups. This concept builds on the database-controlled calibration approach implemented in PredRet, and fits calibration curves on predicted retention times instead of only on observed retention times. We show that this approach results in significantly higher accuracy of elution peak prediction than is achieved by setup-specific models.
Informed dimension reduction of clinically-related genome-wide association summary data characterises cross-trait axes of genetic risk
Authors: Burren Oliver S , Reales Guillermo , Wong Limy , Bowes John , Lee James C , Barton Anne , Lyons Paul A , Smith Kenneth GC , Thomson Wendy , Kirk Paul DW , Wallace Chris
Published: January 2020

Integration of genome-wide association study (GWAS) data has been used to generate new hypotheses of biological mechanism, aetiological relationships between traits, or test causality of one factor for another. However, such approaches have typically been limited to pairwise comparisons of traits. We propose a generally applicable method, that exploits ideas from Bayesian genetic fine mapping to define a “lens” that focuses relevant variants before dimension reduction of a set of related GWAS summary statistics. We applied this technique to immune-mediated diseases, deriving 13 components which summarise the multidimensional patterns of genetic risk. Projection of independent datasets demonstrated the specificity and accuracy of our reduced dimension basis, enabled us to functionally characterise individual components, identify disease-discriminating components and suggest novel associations in rare diseases where classical GWAS approaches are challenging. Our approach summarises the genetic architectures underlying any range of aetiologically-related traits in fewer dimensions, facilitating more nuanced multidimensional comparative analyses.
Canonical Wnt-signaling modulates the tempo of dendritic growth of adult-born hippocampal neurons
Authors: Heppt Jana , Wittmann Marie-Theres , Zhang Jingzhong , Vogt-Weisenhorn Daniela , Prakash Nilima , Wurst Wolfgang , Taketo Makoto Mark , Lie D. Chichung
Published: January 2020

In adult hippocampal neurogenesis neural stem/progenitor cells generate new dentate granule neurons that contribute to hippocampal plasticity. The establishment of a morphologically defined dendritic arbor is central to the functional integration of adult-born neurons. Here, we investigated the role of canonical Wnt/β-catenin-signaling in dendritogenesis of adult-born neurons. We show that canonical Wnt-signaling follows a biphasic pattern, with high activity in stem/progenitor cells, attenuation in early immature neurons, and re-activation during maturation, and demonstrate that the biphasic activity pattern is required for proper dendrite development. Increasing β-catenin-signaling in maturing neurons of young adult mice transiently accelerated dendritic growth, but eventually resulted in dendritic defects and excessive spine numbers. In middle-aged mice, in which protracted dendrite and spine development was paralleled by lower canonical Wnt-signaling activity, enhancement of β-catenin-signaling restored dendritic growth and spine formation to levels observed in young adult animals. Our data indicate that precise timing and strength of β-catenin-signaling is essential for the correct functional integration of adult-born neurons and suggest Wnt/β-catenin-signaling as a pathway to ameliorate deficits in adult neurogenesis during aging.
Symmetry breaking andde-novoaxis formation inhydraspheroids: the microtubule cytoskeleton as a pivotal element
Authors: Sander Heike , Pasula Aravind , Sander Mathias , Giri Varun , Terriac Emmanuel , Lautenschlaeger Franziska , Ott Albrecht
Published: January 2020

The establishment of polarity in cells and tissues is one of the first steps in multicellular development. The ‘eternal embryo’hydracan completely regenerate from a disorganized cell cluster or a small fragment of tissue of about 10, 000 cells. During regeneration, the cells first form a hollow cell spheroid, which then undergoesde-novosymmetry breaking to irreversibly polarize. Here, we address the symmetry-related shape changes. Prior to axis establishment, the spheroid of regenerating cells presents inflation oscillations on several timescales that are isotropic in space. There are transient periods of fluctuations in defined arbitrary directions, until these undergo a clearly identified, irreversible transition to directed fluctuations along the future main axis of the regeneratinghydra. Stabilized cytosolic actin structures disappear during thede-novopolarization, while polymerized microtubules remain. In our observations applied drugs that depolymerize actin filaments accelerate the symmetry breaking process, while drug-stabilized actin filaments prevent it. Nocodazole-depolymerized microtubules prevent symmetry breaking, but regeneration can be rescued by the microtubule-stabilizing drug paclitaxel at concentrations where microtubular structures start to reappear. We discuss the possibility that mechanical fluctuations induce the orientation and position of microtubules, which contribute toβ-catenin nuclear translocation, to increase the organizer-forming-potential of the cells. Our data suggest that in regeneratinghydraspheroids, microtubules play a pivotal role in the cooperative polarization process of the self-organizinghydraspheroid.
Gapless assembly of maize chromosomes using long read technologies
Authors: Liu Jianing , Seetharam Arun S , Chougule Kapeel , Ou Shujun , Swentowsky Kyle William , Gent Jonathan Isaiah , Llaca Victor , Woodhouse Margaret , Manchanda Nancy , Presting Gernot G , Kudrna David , Alabady Magdy , Hirsch Candice , Fengler Kevin , Ware Doreen , Michael Todd , Hufford Matthew , Dawe Kelly
Published: January 2020

Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We used long read technologies and an optical map based approach to produce a maize genome assembly composed of only 63 contigs. The B73-Ab10 genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), multiple highly repetitive centromeres and heterochromatic knobs, and 53 Mb of the Ab10 meiotic drive haplotype.
Moderating Effect of Social Support on Role Conflict and Job Satisfaction among Nurses with Multiple Roles
Authors: Li Caifu , Song Rhayun , Fan Xing , Xu Lijuan
Published: January 2020

Registered nurses perform multiple roles in their lives at work, at home, and at school when they decide to pursue various types of advanced degrees. Work-family conflict was found to be negatively correlated with job satisfaction among nurses. This study aimed to determine the moderating effect of social support on the relationship between role conflicts and job satisfaction among registered nurses in mainland China. The study had a cross-sectional correlational design. Convenience sampling was applied to recruit 320 nurses with multiple roles from 8 nursing universities and 3 hospitals in China between January and August 2017. SPSS (version 20.0) software and PROCESS program was used to examine to moderating effect of social support between the relationship of role conflicts and job satisfaction. It was found that role conflicts were negatively correlated with job satisfaction. Support from work and support from family negatively moderated the relationship between role conflicts and job satisfaction. These findings suggest that support from family, coworkers and nursing administrators, and the implementation of school- and family-friendly policies would help nurses who are pursuing further nursing degrees to handle their multiple roles and improve their job satisfaction.
Evaluation of modulators of cAMP-response in terms of their impact on cell cycle and mitochondrial activity ofLeishmania donovani
Authors: Saha Amrita , Bhattacharjee Anindita , Vij Amit , Das Pijush K. , Bhattacharya Arijit , Biswas Arunima
Published: January 2020

With the identification of novel cAMP binding effecter molecules inTrypanosoma, role of cAMP in kinetopalstida parasites gained an intriguing break through. Despite earlier demonstrations of role of cAMP in survival ofLeishmaniaduring macrophage infection, there is essential need to specifically clarify involvement of cAMP in various cellular processes in the parasite. In this context, we sought to gain a comprehensive understanding of the effect of cAMPanalogs and cAMP-phosphodiesterase (PDE) inhibitors on proliferation of log phase parasites. Administration of both hydrolysable (8-pCPT-cAMP) and non-hydrolysable analogs (Sp-8-pCPT-cAMPS) of cAMP resulted in significant decrease ofLeishmaniaproliferation. Amongst the various PDE inhibitors, etazolate was found to be potently anti-proliferative. BrdU cell proliferation and K/N/F-enumeration microscopic study revealed that both cAMP analogues and selective PDE inhibitors resulted in significant cell cycle arrest at G1phase with reduced S-phase population. Furthermore, careful examination of the flagellar motility patterns revealed significantly reduced coordinated forward flagellar movement of the promastigotes with a concomitant decrease in cellular ATP levels. Alongside, 8-pCPT-cAMP and PDE inhibitors etazolate and trequinsin showed marked reduction in mitochondrial membrane potential. Treatment of etazolate at subcytotoxic concentration to infected macrophages significantly reduced parasite burden and administration of etazolate toLeishmania-infected BALB/c mice showed reduced liver and spleen parasite burden. Collectively, these results imply involvement of cAMP in various crucial processes paving the avenue for developing potent anti-leishmanial agent.

Author Summary

Leishmania donovaniis the causative agent of fatal Visceral Leishmaniasis. The current available medications are toxic, expensive and require long term daily administrations. With an aim to develop improved therapeutic, components of cAMP homeostasis, particularly cAMP-phosphodiesteares, has been targeted forLeishmaniaand other kinetoplastid pathogens. cAMP plays diverse roles in functional processes involved in cell division, transition into different stages of the life cycle ofLeishmaniaand motility. In this study, the authors found administration of both hydrolysable and non-hydrolysable analogs of cAMP and certain PDE inhibitors resulted in remarkable decrease proliferation with considerable cytopathic impact on promastigotes. The mammalian phosphodiestearse inhibitor etazolate caused significant reduction in parasite load inL. donovaniinfected macrophages and demonstrated considerable reduction of liver and spleen parasite burden inin vivomouse infection model. The study suggested that etazolate, with its slightest impact on mammalian host, can be repurposed for developing effective anti-leishmanials.
Nobiletin Affects Circadian Rhythms and Oncogenic Characteristics in a Cell-Dependent Manner
Authors: Lellupitiyage Don Sujeewa S. , Robertson Kelly L. , Lin Hui-Hsien , Labriola Caroline , Harrington Mary E. , Taylor Stephanie R. , Farkas Michelle E.
Published: January 2020

The natural product nobiletin is a small molecule, widely studied with regard to its therapeutic effects, including in models of cancer. Recently, nobiletin has also been shown to affect circadian rhythms via their enhancement, resulting in protection against metabolic syndrome. We hypothesized that nobiletin’s anti-oncogenic effects are correspondingly accompanied by modulation of circadian rhythms. Concurrently, we wished to determine whether the circadian and anti-oncogenic effects of nobiletin differed across cell culture models of cancer. In this study, we assessed nobiletin’s circadian and therapeutic characteristics to ascertain whether these effects depend on cell line, which here also vary in terms of baseline circadian rhythmicity. Three cell culture models where nobiletin’s anti-cancer effects have been studied previously were evaluated here: U2OS (bone osteosarcoma), which possesses robust circadian rhythms; MCF7 (breast adenocarcinoma), which has weak circadian rhythms; and MDA-MB-231 (breast adenocarcinoma), which is arrhythmic. We found that both circadian and anti-cancer effects following nobiletin treatment were subtle in the U2OS and MCF7 cells. On the other hand, changes were clear in MDA-MB-231s, where nobiletin rescued rhythmicity, and substantially reduced oncogenic features. Based on these results and those previously described, we posit that a positive correlation exists between nobiletin’s circadian and therapeutic effects.
Roles of sarcoplasmic reticulum Ca2+ATPase pump in the impairments of lymphatic contractile activity in a metabolic syndrome rat model
Authors: Lee Yang , Chakraborty Sanjukta , Muthuchamy Mariappan
Published: January 2020

The intrinsic lymphatic contractile activity is necessary for proper lymph transport. Mesenteric lymphatic vessels from high-fructose diet-induced metabolic syndrome (MetSyn) rats exhibited impairments in its intrinsic phasic contractile activity; however, the molecular mechanisms responsible for the weaker lymphatic pumping activity in MetSyn conditions are unknown. Several metabolic disease models have shown that dysregulation of sarcoplasmic reticulum Ca2+ATPase (SERCA) pump is one of the key determinants of the phenotypes seen in various muscle tissues. Hence, we hypothesized that a decrease in SERCA pump expression and/or activity in lymphatic muscle influences the diminished lymphatic vessel contractions in MetSyn animals. Results demonstrated that SERCA inhibitor, thapsigargin, significantly reduced lymphatic phasic contractile frequency and amplitude in control vessels, whereas, the reduced MetSyn lymphatic contractile activity was not further diminished by thapsigargin. While SERCA2a expression was significantly decreased in MetSyn lymphatic vessels, myosin light chain 20, MLC20phosphorylation was increased in these vessels. Additionally, insulin resistant lymphatic muscle cells exhibited elevated intracellular calcium and decreased SERCA2a expression and activity. The SERCA activator, CDN 1163 increased phasic contractile frequency in the vessels from MetSyn, thereby, partially restored lymph flow. Thus, our data provide the first evidence that SERCA2a modulates the lymphatic pumping activity by regulating phasic contractile amplitude and frequency, but not the lymphatic tone. Diminished lymphatic contractile activity in the vessels from the MetSyn animal is associated with the decreased SERCA2a expression and impaired SERCA2 activity in lymphatic muscle.
The synergistic actions of hydrolytic genes reveal the mechanism ofTrichoderma harzianumfor cellulose degradation
Authors: Almeida Déborah Aires , Crivelente Horta Maria Augusta , Ferreira Filho Jaire Alves , Murad Natália Faraj , de Souza Anete Pereira
Published: January 2020

Bioprospecting genes and proteins related to plant biomass degradation is an attractive approach for the identification of target genes for biotechnological purposes, especially genes with potential applications in the biorefinery industry that can enhance second-generation ethanol production technology.Trichoderma harzianumis a potential candidate for cellulolytic enzyme prospection and production. Herein, the enzymatic activities, transcriptome, exoproteome, and coexpression networks of theT. harzianumstrain CBMAI-0179 were examined under biomass degradation conditions. We used RNA-Seq to identify differentially expressed genes (DEGs) and carbohydrate-active enzyme (CAZyme) genes related to plant biomass degradation and compared them with the genes of strains from congeneric species (T. harzianumIOC-3844 andT. atrovirideCBMAI-0020).T. harzianumCBMAI-0179 harbors strain- and treatment-specific CAZyme genes and transcription factors. We detected important proteins related to biomass degradation, including β-glucosidases, endoglucanases, cellobiohydrolases, lytic polysaccharide monooxygenases, endo-1,4-β-xylanases and β-mannanases, in the exoproteome under cellulose growth conditions. Coexpression networks were constructed to explore the relationships among the genes and corresponding secreted proteins that act synergistically for cellulose degradation. An enriched cluster with degradative enzymes was described, and the subnetwork of CAZymes revealed strong correlations among the secreted proteins (AA9, GH6, GH10, GH11 and CBM1) and differentially expressed CAZyme genes (GH45, GH7, AA7 and GH1). Our results provide valuable information for future studies on the genetic regulation of plant cell wall-degrading enzymes. This knowledge can be exploited for the improvement of enzymatic reactions in biomass degradation for bioethanol production.

Key points

Different biotechnological approaches were used to understand the mechanism of cellulose degradation ofTrichodermaspp.

T. harzianumCBMAI-0179 is a potential candidate for the production of cellulolytic enzymes.

Coexpression networks revealed genes and proteins acting synergistically for cellulose hydrolysis.
Early metazoan origin and multiple losses of a novel clade of RIM pre-synaptic calcium channel scaffolding protein homologues
Authors: Piekut Thomas , Wong Yuen Yan , Walker Sarah E. , Smith Carolyn L. , Gauberg Julia , Harracksingh Alicia N. , Lowden Christopher , Mary Cheng Hai-Ying , Spencer Gaynor E. , Senatore Adriano
Published: January 2020

The precise localization of CaV2 voltage-gated calcium channels at the synapse active zone requires various interacting proteins, of which,Rab3 interactingmolecule or RIM is considered particularly important. In vertebrates, RIM interacts with CaV2 channelsin vitrovia a PDZ domain that binds to the extreme C-termini of the channels at acidic ligand motifs of D/E-D/E/H-WC-COOH, and knockout of RIM in vertebrates and invertebrates disrupts CaV2 channel synaptic localization and synapse function. Here, we describe a previously uncharacterized clade of RIM proteins bearing homologous domain architectures as known RIM homologues, but some notable differences including key amino acids associated with PDZ domain ligand specificity. This novel RIM emerged near the stem lineage of metazoans and underwent extensive losses, but is retained in select animals including the early-diverging placozoanTrichoplax adhaerens, and molluscs. RNA expression and localization studies inTrichoplaxand the mollusc snailLymnaea stagnalisindicate differential regional/tissue type expression, but overlapping expression in single isolated neurons fromLymnaea. Ctenophores, the most early-diverging animals with synapses, are unique among animals with nervous systems in that they lack the canonical RIM, bearing only the newly identified homologue. Through phylogenetic analysis, we find that CaV2 channel D/E-D/E/H-WC-COOHlike PDZ ligand motifs were present in the common ancestor of cnidarians and bilaterians, and delineate some deeply conserved C-terminal structures that distinguish CaV1 from CaV2 channels, and CaV1/CaV2 from CaV3 channels.
Learning to Encode Cellular Responses to Systematic Perturbations with Deep Generative Models
Authors: Xue Yifan , Ding Michael Q. , Lu Xinghua
Published: January 2020

Components of cellular signaling systems are organized as hierarchical networks, and perturbing different components of the system often leads to transcriptomic profiles that exhibit compositional statistical patterns. Mining such patterns to investigate how cellular signals are encoded is an important problem in systems biology. Here, we investigated the capability of deep generative models (DGMs) for modeling signaling systems and learning representations for transcriptomic profiles derived from cells under diverse perturbations. Specifically, we show that the variational autoencoder and the supervised vector-quantized variational autoencoder can accurately regenerate gene expression data. Both models can learn representations that reveal the relationships between different classes of perturbagens and enable mappings between drugs and their target genes. In summary, DGMs can adequately depict how cellular signals are encoded. The resulting representations have broad applications in systems biology, such as studying the mechanism-of-action of drugs.
Molecular Pathways Resultant in Fever due to Inhibitory Effects of Binding PGE2 to Glucocorticoid Receptors
Authors: Schaper Charles D.
Published: January 2020

Thermoregulation is crucial to homeostasis, but the mechanisms of its dysfunction are still largely mysterious, including fever, which is generally the most disconcerting sign of a serious infection or disease. Theories on body temperature dynamics that aim to explain a fever, such as changes in an internal setpoint, have been proposed, but none can identify the fundamental molecular pathways that produce a fever. Moreover, causative substances, pyrogens such as prostaglandin E2 (PGE2), have not been associated with receptors at the hypothalamus, which is responsible for autonomic control of temperature, and therefore no molecular path has been previously identified that can elucidate the causative reason for fever. Here, molecular pathways resultant in fever are identified for the first time. Based on recent developments made by this lab, which has shown that PGE2 possesses similar binding affinity as the hormone cortisol (CORT) at the critical ligand binding domain (LBD) of glucocorticoid receptors (GR); mathematical modeling and a case study for validation is used to present that competitive inhibition of CORT by PGE2 as the fundamental reason for dysfunctional dynamics of body temperature, including fever. The model characterizing temperature is in the form of a multivariable feedback controller comprised of a superposition of proportional and derivative terms of temperature, CORT, and PGE2 concentration at the hypothalamus thereby linking the cardiovascular, immune, and neural systems. The model constitutes a framework of linear equations that describes a closed-loop system of body temperature effects in response to infectious agents, triggering events, and other causal factors. The model is validated by examination of the transient and spectral characteristics of a three-day case history involving temperature trajectories after physical activity protocols in response to a standard vaccination of pneumococcal and influenza species. The framework for the development of the molecular pathways of fever is further proposed as extensible to other signs and symptoms of disease and emotional dysfunction whose causative source is competitive inhibition of PGE2 and CORT at the LBD of GR.

Graphical Abstract
Rerouting of an Esx substrate pair from the ESX-1 type VII secretion system to ESX-5 by modifying a PE/PPE substrate pair
Authors: Damen Merel P.M. , Phan Trang H. , Ummels Roy , Rubio-Canalejas Alba , Bitter Wilbert , Houben Edith N.G.
Published: January 2020

Type VII secretion systems (T7SSs) secrete a wide range of extracellular proteins that play important roles in bacterial viability and in host-pathogen interactions of pathogenic mycobacteria. There are five subtypes of mycobacterial T7SSs, called ESX-1 to ESX-5, and four classes of T7SS substrates, namely the Esx, PE, PPE and Esp proteins. At least some of these substrates are secreted as heterodimers. The ESX systems mediate the secretion of specific members of the Esx, PE and PPE proteins, raising the question how these substrates are recognized in a system-specific fashion. PE/PPE heterodimers interact with their cognate EspG chaperones, which recently has been shown to determine their designated secretion pathway. Both structural and pulldown analysis suggest that EspG is unable to interact with Esx proteins and therefore the determining factor for system-specificity of these substrates remains unknown. In this study, we have investigated the secretion specificity of the ESX-1 substrate pair EsxB_1/EsxA_1 (MMAR_0187/MMAR _0188) inMycobacterium marinum. While this substrate pair was hardly secreted when ectopically expressed, secretion was observed when EsxB_1/EsxA_1 was co-expressed together with PE35/PPE68_1 (MMAR_0185/MMAR_0186), which are encoded by the same operon. Surprisingly, co-expressing EsxB_1/EsxA_1 with a modified PE35/PPE68_1 version that carried the EspG5chaperone binding domain, previously shown to redirect this substrate pair to the ESX-5 system, also resulted in co-secretion of EsxB_1/EsxA_1 via ESX-5. Our data suggest a secretion model in which PE35/PPE68_1 is a determinant factor for the system-specific secretion of EsxB_1/EsxA_1.
Non-invasive monitoring of drug action: a new livein vitroassay design for Chagas’ disease drug discovery
Authors: Fesser Anna F. , Braissant Olivier , Olmo Francisco , Kelly John M. , Mäser Pascal , Kaiser Marcel
Published: January 2020

New assay designs are needed to improve the predictive value of theTrypanosoma cruzi in vitrotests used as part of the Chagas’ disease drug development pipeline. Here, we employed a green fluorescent protein (eGFP)-expressing parasite line and live high-content imaging to monitor the growth ofT. cruziamastigotes in mouse embryonic fibroblasts. A novel assay design allowed us to follow parasite numbers over 6 days, in four-hour intervals, while occupying the microscope for only 24 hours per biological replicate. Dose-response curves were calculated for each time point after addition of test compounds, revealing how EC50 values first decreased over the time of drug exposure, and then leveled off. However, we observed that parasite numbers could vary, even in the untreated controls, and at different sites in the same well, which caused variability in the EC50 values. To overcome this, we established that fold change in parasite number per hour is a more robust and informative measure of drug activity. This was calculated based on an exponential growth model for every biological sample. The net fold change per hour is the result of parasite replication, differentiation, and death. The calculation of this fold change enabled us to determine the tipping point of drug action, i.e. the point immediately before the fold change becomes negative, independent of the drug concentration and exposure time. This time-to-kill over drug concentration revealed specific pharmacodynamic profiles of the benchmark drugs benznidazole and posaconazole.

Author Summary

Chagas’ disease, caused byTrypanosoma cruzi, is a chronic debilitating infection occurring mostly in Latin America. There is an urgent need for new, well tolerated drugs. However, the latest therapeutic candidates have yielded disappointing outcomes in clinical trials, despite promising preclinical results. This demands new and more predictivein vitroassays. To address this, we have developed an assay design that enables the growth ofT. cruziintracellular forms to be monitored in real time, under drug pressure, for 6 days post-infection. This allowed us to establish the tipping point of drug action, when the parasites stop multiplying and start to die. The resulting pharmacodynamics profiles can provide robust and informative details on anti-chagasic candidates, as demonstrated for the benchmark drugs benznidazole and posaconazole.
A-to-I RNA editing in honeybees shows signals of adaptation and convergent evolution
Authors: Duan Yuange , Dou Shengqian , Porath Hagit T. , Huang Jiaxing , Eisenberg Eli , Lu Jian
Published: January 2020

Social insects exhibit extensive phenotypic diversities among the genetically similar individuals, suggesting a role for the epigenetic regulations beyond the genome level. The ADAR-mediated adenosine-to-inosine (A-to-I) RNA editing, an evolutionarily conserved mechanism, facilitates adaptive evolution by expanding proteomic diversities. Here, we characterize the A-to-I RNA editome of honeybees (Apis mellifera), identifying 407 high-confidence A-to-I editing sites. Editing is most abundant in the heads, and shows signatures for positive selection. Editing behavior differs between foragers and nurses, suggesting a role for editing in caste differentiation. Although only five sites are conserved between bees and flies, an unexpectedly large number of genes exhibit editing in both species, albeit at different locations, including the nonsynonymous auto-editing ofAdar. This convergent evolution, where the same target genes independently acquire recoding events in distant diverged clades, together with the signals of adaptation observed in honeybees alone, further supports the notion of recoding being adaptive.
Biodiversity Of Bacteriophages From Lysed Batch Culture Of RecombinantEscherichia ColiBL21(DE3) Examined By Anion Exchange Chromatography And TEM
Authors: Kushkina Alla , Tovkach Fedor
Published: January 2020

It was found that the phage population assaulted a batch culture of an industrial recombinant derivative ofE. coliBL21(DE3) was attenuated that manifested in producing pinprick-type plaques and their inability to propagation in subsequent passages. Because of this, the goals of the present research were to evaluate biodiversity and scrutinize the possible virion structural defects of the attenuated phage population prior to pure phage lines isolation. The anion exchange chromatography (AEC) was chosen as the principal method allowing to get a comparative phage population profile based on the virion net surface charge, as well as to treat the 5-liter virion-contained sample and collect high-quality concentrated and separated phage fractions to further analysis. The isolate consisted of a mix of two phages belonging toMyoviridae(A2-morphotype) andSiphoviridae(B1-morphotype) families. By restriction analysis, the main portion of this phage pool (about 99% of all virions) was identified as the primary population of myophage Lw1, which possessed its own intra-population biodiversity (heterogeneity). It consisted of a major and two minor subpopulations that differed by phage capsid size and shape. The subpopulation III consisted of aberrant tubby-phages with triprolate (expanded at both sides) capsids having low aspect ratio.
The conservation status and population decline of the African penguin deconstructed in space and time
Authors: Sherley Richard B. , Crawford Robert J. M. , de Blocq Andrew D. , Dyer Bruce M. , Geldenhuys Deon , Hagen Christina , Kemper Jessica , Makhado Azwianewi B. , Pichegru Lorien , Tom Desmond , Upfold Leshia , Visagie Johan , Waller Lauren J. , Winker Henning
Published: January 2020

Understanding changes in abundance is crucial for conservation, but population growth rates often vary over space and time. We use 40 years of count data (1979–2019) and Bayesian state-space models to assess the African penguinSpheniscus demersuspopulation under IUCN Red List Criterion A. We deconstruct the overall decline in time and space to identify where urgent conservation action is needed. The global African penguin population met the threshold forEndangeredwith a high probability (97%), having declined by almost 65% since 1989. An historical low of ~17,900 pairs bred in 2019. Annual declines were faster in the South African population (−4.2%, highest posterior density interval, HPDI: −7.8 to −0.6%) than the Namibian one (−0.3%, HPDI: −3.3 to +2.6%), and since 1999 were almost 10% at South African colonies north of Cape Town. Over the 40-year period, the Eastern Cape colonies went from holding ~25% of the total penguin population to ~40% as numbers decreased more rapidly elsewhere. These changes coincided with an altered abundance and availability of the main prey of African penguins. Our results underline the dynamic nature of population declines in space as well as time and highlight which penguin colonies require urgent conservation attention.
Assessing the adoption of sustainability practices in tourism industry
Authors: Islam Md. Farijul , Zhang Jing , Hasan Najmul
Published: January 2020

Purpose

The purpose of this study is to assess the key determinants of sustainability practices and policy adoption in small- and medium-sized tourism accommodation firms and its possible impact on the firm’s competitive advantages.

Design/methodology/approach

A combined model has been developed and tested with a set of relevant hypotheses based on primary data collected from tourism firm’s owners and personnel. Structural equation modeling has been used to test and validate the hypotheses.

Findings

The key results indicate that collaboration and innovation of tourism firms, employee culture, technological infrastructure, tourism intermediary’s sustainability practices and top management support have a significant impact on sustainability practices adoption, whereas government sustainable tourism policy and local’s attitude toward sustainability have an insignificant impact.

Practical implications

The findings assist managers and owners of tourism accommodation firms to re-address their policy and operational processes toward sustainability. This study is an endeavor to bridge the knowledge gap of current literature on sustainable practice adoption and tourism accommodation firm. This would be ensured through encouraging the economic aspect of sustainability practices and also facilitate social well-being, which is a real contribution that ought to practice to other countries where the tourist area is environmentally adverse tremendous.

Social implications

Considering sustainability is a social commitment, this study positively changes tourists’ behavioral approach reducing the undesirable use of social resources and maximizing the enduring socio-economic and environmental development for social well-being.

Originality/value

The novelty of this empirical study is that sustainability practices and policies adoption is entirely a new phenomenon. However, the mediating impact of the construct on the competitive advantage of small and medium tourism accommodation firms enhances the effectiveness of emerging tourism economy.