bluuebunny/crossref_metadata_2025 huggingface dataset:
Growth Factor Independence (GFI) 1B-mediated transcriptional repression and lineage allocation require Lysine Specific Demethylase (LSD)1-dependent recruitment of the BHC complex
Authors: McClellan David , Casey Mattie J. , Bareyan Diana , Lucente Helena , Ours Christopher , Velinder Matthew , Singer Jason , Lone Mehraju Din , Sun Wenxiang , Coria Yunuen , Mason Clinton , Engel Michael E.
Published: January 2019

Growth Factor Independence (GFI)1B coordinates assembly of transcriptional repressor complexes comprised of co-repressors and histone modifying enzymes to control gene expression programs governing lineage allocation in hematopoiesis. Enforced expression of GFI1B in K562 erythroleukemia cells favors erythroid over megakaryocytic differentiation, providing a platform to define molecular determinants of binary fate decisions triggered by GFI1B. We deployed proteome-wide proximity labeling to identify factors whose inclusion in GFI1B complexes depends upon GFI1B’s obligate effector, Lysine Specific Demethylase (LSD)1. We show that GFI1B preferentially recruits core and putative elements of the BRAF-histone deacetylase (HDAC) (BHC) chromatin remodeling complex (LSD1, RCOR1, HMG20A, HMG20B, HDAC1, HDAC2, PHF21A, GSE1, ZMYM2 and ZNF217) in an LSD1-dependent manner to control erythroid fate specification. Among these, depletion of both HMG20A and HMG20B, or GSE1 block GFI1B-mediated erythroid differentiation, phenocopying impaired differentiation brought on by LSD1 depletion or disruption of GFI1B—LSD1 binding. These findings demonstrate the central role of the GFI1B—LSD1 interaction as a determinant of BHC complex recruitment to enable cell fate decisions driven by GFI1B.
Repertoire-Based Diagnostics Using Statistical Biophysics
Authors: Arora Rohit , Kaplinsky Joseph , Li Anthony , Arnaout Ramy
Published: January 2019

A fundamental challenge in immunology is diagnostic classification based on repertoire sequence. We used the principle of maximum entropy (MaxEnt) to build compact representations of antibody (IgH) and T-cell receptor (TCRβ) CDR3 repertoires based on the statistical biophysical patterns latent in the frequency and ordering of repertoires’ constituent amino acids. This approach results in substantial advantages in quality, dimensionality, and training speed compared to MaxEnt models based solely on the standard 20-letter amino-acid alphabet. Descriptor-based models learn patterns that pure amino-acid-based models cannot. We demonstrate the utility of descriptor models by successfully classifying influenza vaccination status (AUC=0.97, p=4×10-3), requiring only 31 samples from 14 individuals. Descriptor-based MaxEnt modeling is a powerful new method for dissecting, encoding, and classifying complex repertoires.
Direct Coupling Analysis of Epistasis in Allosteric Materials
Authors: Bravi Barbara , Ravasio Riccardo , Brito Carolina , Wyart Matthieu
Published: January 2019

In allosteric proteins, the binding of a ligand modifies function at a distant active site. Such al-losteric pathways can be used as target for drug design, generating considerable interest in inferring them from sequence alignment data. Currently, different methods lead to conflicting results, in particular on the existence of long-range evolutionary couplings between distant amino-acids mediating allostery. Here we propose a resolution of this conundrum, by studying epistasis and its inference in models where an allosteric material is evolved in silico to perform a mechanical task. We find four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range and have a simple mechanical interpretation. We perform a Direct Coupling Analysis (DCA) and find that DCA predicts well mutation costs but is a rather poor generative model. Strikingly, it can predict short-range epistasis but fails to capture long-range epistasis, in agreement with empirical findings. We propose that such failure is generic when function requires subparts to work in concert. We illustrate this idea with a simple model, which suggests that other methods may be better suited to capture long-range effects.

Author summary

Allostery in proteins is the property of highly specific responses to ligand binding at a distant site. To inform protocols of de novo drug design, it is fundamental to understand the impact of mutations on allosteric regulation and whether it can be predicted from evolutionary correlations. In this work we consider allosteric architectures artificially evolved to optimize the cooperativity of binding at allosteric and active site. We first characterize the emergent pattern of epistasis as well as the underlying mechanical phenomena, finding four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range. The numerical evolution of these allosteric architectures allows us to benchmark Direct Coupling Analysis, a method which relies on co-evolution in sequence data to infer direct evolutionary couplings, in connection to allostery. We show that Direct Coupling Analysis predicts quantitatively mutation costs but underestimates strong long-range epistasis. We provide an argument, based on a simplified model, illustrating the reasons for this discrepancy and we propose neural networks as more promising tool to measure epistasis.
Genetic Risk for Rheumatoid Arthritis is Associated with Increased Striatal Volume in Healthy Young Adults
Authors: Avinun Reut , Nevo Adam , Hariri Ahmad R.
Published: January 2019

Rheumatoid arthritis (RA), an autoimmune disease, has recently been associated with increased striatal volume and decreased intracranial volume (ICV) in longstanding patients. As inflammation has been shown to precede the clinical diagnosis of RA and it is a known moderator of neuro- and gliogenesis, we were interested in testing whether these brain morphological changes appear before the clinical onset of disease in healthy young adult volunteers, as a function of relative genetic risk for RA. Genetic and structural MRI data were available for 516 healthy non-Hispanic Caucasian university students (275 women, mean age 19.78±1.24 years). Polygenic risk scores were computed for each individual based on a genome-wide association study of RA, so that higher scores indicated higher risk. Striatal volume (sum of caudate, putamen, and nucleus accumbens volumes) and ICV were derived for each individual from high-resolution T1-weighted images. After controlling for sex, age, genetic components of ethnicity, socioeconomic status, and depressive symptoms, we found that higher RA polygenic risk scores were associated with increased striatal volume, but not decreased ICV. Our findings suggest that increased striatal volume may be linked to processes that precede disease onset, such as inflammation, while decreased ICV may relate to disease progression.
Modeling the dynamics of Let-7-coupled gene regulatory networks linking cell proliferation to malignant transformation
Authors: Gérard Claude , Lemaigre Frédéric , Gonze Didier
Published: January 2019

The microRNA Let-7 controls the expression of proteins that belong to two distinct gene regulatory networks, namely a cyclin-dependent kinases (Cdks) network driving the cell cycle and a cell transformation network which can undergo an epigenetic switch between a non-transformed and a malignant transformed cell state.

Using mathematical modeling and transcriptomic data analysis, we here investigate how Let-7 controls the cdk-dependent cell cycle network, and how it couples the latter with the transformation network. We also determine whether the two networks can be combined into a larger entity that impacts on cancer progression.

Our analysis shows that the switch from a quiescent to a cycling state depends on the relative levels of Let-7 and several cell cycle activators. Numerical simulations further indicate that the Let-7-coupled cell cycle and transformation networks control each other, and our model identifies key players for this mutual control. Transcriptomic data analysis from the The Cancer Genome Atlas (TCGA) suggest that the two networks are activated in cancer, in particular in gastrointestinal cancers, and that the activation levels vary significantly among patients affected with a same cancer type. Our mathematical model, when applied to a heterogeneous cell population, suggests that heterogeneity among tumors results from stochastic switches between a non-transformed cell state with low proliferative capability and a transformed cell state with high proliferative property. The model further predicts that Let-7 may reduce tumor heterogeneity by decreasing the occurrence of stochastic switches towards a transformed, proliferative cell state.

In conclusion, we identified the key components responsible for the qualitative dynamics of two GRNs interconnected by Let-7. The two GRNs are heterogeneously involved in several cancers, thereby stressing the need to consider patient’s specific GRN characteristics to optimize therapeutic strategies.
Attentional modulation of neural phase is enhanced by short-term training and linked to musical experience
Authors: Laffere Aeron , Dick Fred , Tierney Adam
Published: January 2019

How does the brain follow a sound that is mixed with others in a noisy environment? A possible strategy is to allocate attention to task-relevant time intervals while suppressing irrelevant intervals - a strategy that could be implemented by aligning neural modulations with critical moments in time. Here we tested whether selective attention to non-verbal sound streams is linked to shifts in the timing of attentional modulations of EEG activity, and investigated whether this neural mechanism can be enhanced by short-term training and musical experience. Participants performed a memory task on a target auditory stream presented at 4 Hz while ignoring a distractor auditory stream also presented at 4 Hz, but with a 180-degree shift in phase. The two attention conditions were linked to a roughly 180-degree shift in phase in the EEG signal at 4 Hz. Moreover, there was a strong relationship between performance on the 1-back task and the timing of the EEG modulation with respect to the attended band. EEG modulation timing was also enhanced after several days of training on the selective attention task and enhanced in experienced musicians. These results support the hypothesis that modulation of neural timing facilitates attention to particular moments in time and indicate that phase timing is a robust and reliable marker of individual differences in auditory attention. Moreover, these results suggest that nonverbal selective attention can be enhanced in the short term by only a few hours of practice and in the long term by years of musical training.
Rice annexin OsANN4 interacting with OsCDPK24, reduces root aerenchyma formation by modulating H2O2 under ABA treatment
Authors: Zhang Qian , Song Tao , Guan Can , Gao Yingjie , Ma Jianchao , Qi Zhiguang , Liu Jingze , Zhu Ying , Zhu Zhengge
Published: January 2019

Plant annexins are calcium- and lipid-binding proteins that have multiple functions, and a significant amount of research on plant annexins has been reported in recent years. However, the functions of annexins in diverse biological processes in rice are largely unclear. Herein, we report that OsANN4, a calcium-binding rice annexin protein, is a substrate for OsCDPK24, and the OsANN4 phosphorylation site is the 13th serine, which is a key site for phosphorylation. Most strikingly, abscisic acid (ABA) promotes the interaction between OsANN4 and OsCDPK24. Moreover, knocking down OsANN4 by RNA interference resulted in visible and invisible phenotypes with exogenous ABA treatment, such as shorter shoots of seedlings, less lateral roots, earlier root aerenchyma formation and so on. The further analyzed results showed that decreased superoxide dismutase (SOD) and catalase (CAT) activity of the RNAi lines, which control H2O2 accumulation for redox homeostasis, and further promoted earlier aerenchyma formation of the root. These results suggest that a proposed molecular mechanism exists between OsANN4 and H2O2 production to response ABA.

Highlight

OsANN4 enhances SOD and CAT activities to scavenge H2O2 to alleviate the formation of aerenchyma under ABA treatment. OsCDPK24 interacts with and phosphorylates OsANN4, this interaction strengthened under ABA treatment.
Early urinary protein changes in the tumor-forming process of the NuTu-19 lung metastasis
Authors: Wei Jing , Ni Na , Meng Wenshu , Huan Yuhang , Gao Youhe
Published: January 2019

The early detection of cancer is essential for effective intervention. Urine, which lacks homeostatic control, has been used to reflect early systemic changes in subcutaneous cancer models. However, urine has not been used to predict whether tumors will be formed in animal models. In this study, a cancer model was established by the tail-vein injection of 2 million NuTu-19 tumor cells. Approximately half of the rats formed lung metastatic carcinoma tumors. Urine samples were randomly selected from 4 tumor-forming rats and 4 non-tumor-forming rats on day 0/12/27/39/52 and analyzed by label-free proteomic quantitative analysis. Compared to day 0, a total of 180 and 118 urinary proteins in tumor-forming and non-tumor-forming rats, respectively, showed significant changes. Functional enrichment analysis of the differential proteins in tumor-forming rats revealed similar events during cancer metastasis cascades and tumor progression, such as the migration of tumor cell lines, coagulation system, TGF-β signaling, the STAT3 pathway and the adhesion of myeloid cells and alveolar macrophages. The differential proteins in non-tumor-forming rats were associated with agranulocyte/granulocyte adhesion and diapedesis, glutathione biosynthesis, IL-12 signaling and vitamin metabolism. After validation by parallel reaction monitoring (PRM) targeted proteomics quantitative analysis, a total of 22 urinary proteins showed significant changes in the early phase of the lung tumor formation process, 5 of which have been associated with the mechanisms of lung cancer, while 3 have been suggested as lung cancer biomarkers. Another 14 urinary proteins showed significant changes in the early phase in non-tumor-forming rats. Our results indicate that urine proteins could differentiate early tumor-forming and non-tumor-forming status.
Many unreported crop pests and pathogens are probably already present
Authors: Bebber Daniel P. , Field Elsa , Heng Gui , Mortimer Peter , Holmes Timothy , Gurr Sarah J.
Published: January 2019

Biotic invasions threaten global biodiversity and ecosystem function. Such incursions present challenges to agriculture where invasive pest species cause significant production losses require major economic investment to control and can cause significant production losses. Pest Risk Analysis (PRA) is key to prioritizing agricultural biosecurity efforts, but is hampered by incomplete knowledge of current crop pest and pathogen distributions. Here we develop predictive models of current pest distributions and test these models using new observations at sub-national resolution. We apply generalized linear models (GLM) to estimate presence probabilities for 1739 crop pests in the CABI pest distribution database. We test model predictions for 100 unobserved pest occurrences in the People’s Republic of China (PRC), against observations of these pests abstracted from the Chinese literature. This resource has hitherto been omitted from databases on global pest distributions. Finally, we predict occurrences of all unobserved pests globally. Presence probability increases with host presence, presence in neighbouring regions, per capita GDP, and global prevalence. Presence probability decreases with mean distance from coast and known host number per pest. The models were good predictors of pest presence in Provinces of the PRC, with area under the ROC curve (AUC) values of 0.75 – 0.76. Large numbers of currently unobserved, but probably present pests (defined here as unreported pests with a predicted presence probability > 0.75), are predicted in China, India, southern Brazil and some countries of the former USSR. Our results shows that GLMs can predict presences of pseudo-absent pests at sub-national resolution. The Chinese scientific literature has been largely inaccessible to Western academia but contains important information that can support PRA. Prior studies have often assumed that unreported pests in a global distribution database represents a true absence. Our analysis provides a method for quantifying pseudo-absences to enable improved PRA and species distribution modelling.
Evaluation of the novel culture-based FAST-T system allowing selection of optimal antibiotics for critically ill patients within 4 h (for other than bloodstream infectious).
Authors: Tetz George , Tetz Victor
Published: January 2019

Rapid diagnostic tests are needed to improve patient care, particularly in immunocompromised hosts. Here, we describe the validation of a new phenotypic culture-based FAST-T method for rapid selection of antibiotics in vitro using specimens with mono- and polybacterial infections. FAST-T approach, which can be applied to any type of non-blood tissue, does not require isolation of pure bacterial cultures. FAST-T-selected antibiotics are those that can completely eliminate mixed bacterial infections in specimens. The method uses a novel FASM-T medium that allows more rapid bacterial growth of gram-positive and gram-negative monoisolates compared with that achieved with conventional laboratory media. The application of the FAST-T method in 122 bacterial species demonstrated overall sensitivity, specificity, positive predictive value, and negative predictive value of 99.6%, 98.1%, 98.5%, and 99.4%, respectively, already after 4 h. The overall category agreement with the outcome of standard testing was 98.9% with very major errors and major errors being detected in 1.2% and 0.6% of cases. The use of FASM-T medium in 20 clinical polymicrobial samples allowed culturing a more diverse set of bacteria, including fastidious species, compared with that achieved with the standard laboratory diagnostic and enabled, already within 4 h, accurate selection of the antibiotics that completely eliminated all cultivatable bacteria from clinical samples. In conclusion, FAST-T system may be a valuable tool in improving phenotypic-based antibiotic selection, enabling targeted empirical therapy and accurate antibiotic replacement, which is especially important in high-risk patients.
Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning
Authors: Luo Yunan , Ma Jianzhu , Zhao Xiaoming , Su Yufeng , Liu Yang , Ideker Trey , Peng Jian
Published: January 2019

A plethora of biological functions are performed through various types of protein-peptide binding. Prime examples include the protein kinase phosphorylation on peptide substrates and the binding of major histocompatibility complex to neoantigens in the immune system. Understanding the specificity of protein-peptide interactions is critical for unraveling the architectures of functional pathways and the mechanisms of cellular processes in human cells. Despite mass-spectrometric techniques were developed for the identification of protein-peptide interactions, our understanding of the preferences of proteins on their binding peptides is still rudimentary. As a complementary direction, a line of computational prediction methods has been recently proposed to predict protein-peptide bindings which efficiently provide rich functional annotations on a large scale. To achieve a high prediction accuracy, these computational methods require a sufficient amount of data to build the prediction model. However, the number of experimentally verified protein-peptide bindings is often limited in real cases. For example, a majority of protein kinases have very few experimentally verified phosphorylation sites (e.g., less than 30 sites) in existing databases. These methods are thus limited to building accurate prediction models for only well-characterized proteins with a large volume of known binding peptides and cannot be extended to predict new binding peptides for less-studied proteins. In this paper, we introduce a generic framework to address this issue of data scarcity in protein binding prediction. We demonstrate the applicability of our framework in predicting kinase-specific phosphorylation sites. Our method uses an effective training strategy to build a prediction model with robust transferability. The model is able to predict the phosphorylation sites of a less-studied kinase, even if there is only a small number of phosphorylation sites known for this kinase. To achieve this, we train the model via a meta-learning phase followed by a few-shot learning phase. We demonstrate our framework has better transferability than state-of-the-art methods and is effective in utilizing limited data to accurately predict phosphorylation sites for less-characterized kinases. The implementation of our framework is available athttps://github.com/luoyunan/MetaKinase.
Stereotyped large amplitude cortical LFP events can be clustered and reveal precisely ordered phase-locking in neuronal populations
Authors: Mitelut Catalin C. , Spacek Martin A. , Chan Allen W. , Murphy Tim H. , Swindale Nicholas V.
Published: January 2019

During quiet wakefulness, slow-wave sleep and anesthesia, mammalian cortex exhibits a synchronised state during which transient changes in the local field potential (LFP) accompany periods of increased single neuron firing, known as UP-states. While UP-state genesis is still debated (Crunelli and Hughes, 2010) such transitions may constitute the default activity pattern of the entire cortex (Neske, 2016). Recent findings of preserved firing order between UP-state transitions and stimulus processing in high-firing rate (>2Hz) rat auditory and barrel cortex neurons (Luczak et al., 2015) support this hypothesis. Yet it is unknown whether UP-states are homogeneous and whether neurons with firing rates <2Hz in visual cortex or other species exhibit spiking order. Using extracellular recordings during anesthetized states in cat visual cortex and mouse visual, auditory and barrel cortex, we show that UP-states can be tracked and clustered based on the shape of the LFP waveform. We show that LFP event clusters (LECs) have current-source-density profiles that are common across different recordings or animals and using simultaneous electrophysiology and widefield voltage and calcium imaging in mouse we confirm that LEC transitions are cortex-wide phenomena. Individual LEC events can be resolved in time to within 1 – 4 ms and they elicit synchronous firing of over 75% of recorded neurons with most neurons synchronizing their firing to within ±5 – 15 ms relative LECs. Firing order of different neurons during LEC events was preserved over periods of ~30 minutes enabling future studies of UP-state transitions and firing order with near millisecond precision.

Significant Statement

During sleep and anesthetic states mammalian cortex undergoes substantial changes from awake active states. Recent studies show that single neurons in some cortical areas in rats undergo increased spiking during sleep and anesthetic states (called UP-state transitions) with some neurons firing in an order similar to awake states. This suggests that sensory processing may be similar across all states and that firing order is important for stimulus processing. Yet UP-state transitions remain poorly understood and it is unclear whether firing order is present in other cortical areas or species. Here we describe multiple classes of UP-state transitions and show most neurons in visual cortex in cats and visual, barrel and auditory cortex in mice exhibit firing order during such transitions.
A statistical modeling framework to assess cross-frequency coupling while accounting for confounding effects
Authors: Nadalin Jessica , Martinet Louis-Emmanuel , Blackwood Ethan , Lo Meng-Chen , Widge Alik S. , Cash Sydney S. , Eden Uri T. , Kramer Mark A.
Published: January 2019

Cross frequency coupling (CFC) is emerging as a fundamental feature of brain activity, correlated with brain function and dysfunction. Many different types of CFC have been identified through application of numerous data analysis methods, each developed to characterize a specific CFC type. Choosing an inappropriate method weakens statistical power and introduces opportunities for confounding effects. To address this, we propose a statistical modeling framework to estimate high frequency amplitude as a function of both the low frequency amplitude and low frequency phase; the result is a measure of phase-amplitude coupling that accounts for changes in the low frequency amplitude. We show in simulations that the proposed method successfully detects CFC between the low frequency phase or amplitude and the high frequency amplitude, and outperforms an existing method in biologically-motivated examples. Applying the method to in vivo data, we illustrate how CFC evolves during seizures and is affected by electrical stimuli.
Age-related kinematic performance must be considered during fast head-neck rotation target task in individuals aged from 8 to 85 years old
Authors: Hage Renaud , Dierick Frédéric , Roussel Nathalie , Pitance Laurent , Detrembleur Christine
Published: January 2019

Rationale

Kinematic behavior during fast cervical rotations is a useful parameter for assessing sensorimotor control performances in neck-pain patients. However, in asymptomatic individuals from children to seniors, the influence of age still needs to be explored.

Aim and method

We assessed the impact of age on sensorimotor control performance of the head-neck with execution time and kinematic variables (time of task, mean speed/acceleration/deceleration, overshoots, minimum/maximum speed) during standardized fast rotation target task using the DidRen Laser test. Eighty volunteers were stratified in four different age-groups: Children [8-14y]: n=16; Young Adults [18-35y]: n=29; Old Adults [36-64y]: n=18; Seniors [65-85y]: n=17.

Results

To perform the test, Children were slower compared to Young Adults (p<0.001) and Old Adults (p<0.001). It was also slower in Seniors compared to Young Adults (p<0.013). Mean speed was slower in Children and Seniors compared to Young Adults (p<0.001) and Old Adults (p<0.001). Mean acceleration was slower for Children compared to Young Adults (p<0.016) and Old Adults (p<0.015). Mean deceleration was slower for Children compared to Young Adults (p<0.001) and Old Adults (p<0.003).

Conclusion

The DidRen Laser test allows us to discriminate age-specific performances for mean speed, acceleration and deceleration. Seniors and Children needed to be slower to become as precise as Young and Old people, no difference was observed for overshoots which assesses accuracy of movement. Age must therefore be considered as a key parameter when analyzing execution time and kinematic results during DidRen Laser test.
3D-printing Enabled Micro-assembly of Microfluidic Electroporation System for 3D Tissue Engineering
Authors: Zhu Qingfu , Hamilton Megan , He Mei
Published: January 2019

Electro-transfection is an essential workhorse tool for regulating cellular responses and engineering cellular materials in tissue engineering. However, existing approaches, including microfluidic platforms and bench top methods, are only able to study monolayer cell suspensionsin vitro, and are incapable of clinical translation withinin vivotissue microenvironment. Knowledge regarding the three-dimensional (3D) electric field distribution and mass transport in a tissue microenvironment is lacking. However, building a 3D electro-transfection system that is compatible with 3D cell culture for mimickingin vivotissue microenvironment is challenging, due to the substantial difficulties in control of 3D electric field distribution as well as the cellular growth. To address such challenges, we introduce a novel 3D micro-assembling strategy assisted by 3D printing, which enables the molding of 3D microstructures as LEGO®parts from 3D-printed molds. The molded PDMS LEGO®bricks are then assembled into a 3D-cell culture chamber interconnected with vertical and horizontal perfusion microchannels as a 3D channel network. Such 3D perfusion microchannel network is unattainable by direct 3D printing or other microfabrication approaches, which can facilitate the high-efficient exchange of nutrition and waste for 3D cell growth. Four flat electrodes are mounted into the 3D culture chamber via a 3D-printed holder and controlled by a programmable power sequencer for multi-directional electric frequency scanning (3D μ-electro-transfection). This multi-directional scanning not only can create transient pores all over the cell membrane, but also can generate local oscillation for enhancing mass transport and improving cell transfection efficiency. As a proof-of-concept, we electro-delivered pAcGFP1-C1 vector to 3D cultured HeLa cells within peptide hydrogel scaffolding. The expressed GFP level from transfected HeLa cells reflects the transfection efficiency. We found two key parameters including electric field strength and plasmid concentration playing more important roles than manipulating pulse duration and duty cycles. The results showed an effective transfection efficiency of ~15% with ~85% cell viability, which is a 3-fold increase compared to the conventional benchtop 3D cell transfection. This 3D μ-electrotransfection system was further used for genetically editing 3D-cultured Hek-293 cells via direct delivery of CRISPR/Cas9 plasmid which showed successful transfection with GFP expressed in the cytoplasm as the reporter. The 3D-printing enabled micro-assembly allows facile creation of novel 3D culture system for electro-transfection which can be employed for versatile gene delivery and cellular engineering, as well as buildingin-vivolike tissue models for fundamentally studying cellular regulatory mechanisms.
Alveolar macrophage chromatin is modified to orchestrate host response toMycobacterium bovisinfection
Authors: Hall Thomas Jonathan , Vernimmen Douglas , Browne John Andrew , Mullen Michael P. , Gordon Stephen Vincent , MacHugh David Evan , O’Doherty Alan Mark
Published: January 2019

Background

Bovine tuberculosis is caused by infection withMycobacterium bovis, which can also cause disease in a range of other mammals, including humans. Alveolar macrophages are the key immune effector cells that first encounterM. bovisand how the macrophage epigenome responds to mycobacterial pathogens is currently not well understood.

Results

Here, we have used chromatin immunoprecipitation sequencing (ChIP-seq), RNA-seq and miRNA-seq to examine the effect ofM. bovisinfection on the bovine alveolar macrophage (bAM) epigenome. We show that H3K4me3 is more prevalent, at a genome-wide level, in chromatin fromM. bovis-infected bAM compared to control non-infected bAM; this was particularly evident at the transcriptional start sites of genes that determine programmed macrophage responses to mycobacterial infection (e.g. M1/M2 macrophage polarisation). This pattern was also supported by the distribution of RNA Polymerase II (PolII) ChIP-seq results, which highlighted significantly increased transcriptional activity at genes demarcated by permissive chromatin. Identification of these genes enabled integration of high-density GWAS data, which revealed genomic regions associated with resilience to infection withM. bovisin cattle.

Conclusions

Through integration of these data, we show that bAM transcriptional reprogramming occurs through differential distribution of H3K4me3 and PolII at key immune genes. Furthermore, this subset of genes can be used to prioritise genomic variants from a relevant GWAS data set.
Inferring wildlife poaching in Southeast Asia with multispecies dynamic occupancy models
Authors: Marescot Lucile , Lyet Arnaud , Singh Rohit , Carter Neil , Gimenez Olivier
Published: January 2019

Determining the ‘space race’ between sympatric species is crucial to understand the effects of interspecific interactions on the extinction risk of species threatened by poachers, predators, pathogens, and invasive competitors. Dynamic two-species occupancy models provide a flexible framework to decompose complex species interaction patterns while accounting for imperfect detection. In particular, these models can describe poachers-wildlife interactions by considering the occupancy, the extinction and colonisation probabilities of wildlife conditional on the presence or absence of poachers and vice versa. We apply our model to a case study on wildlife poaching in the Eastern plains of Cambodia. We used co-occurrence data extracted from the database of the SMART partnership to study the distribution dynamics between poachers and six ungulate species regarded as main prey of tigers. We used 4 years of survey data reporting the locations of ranger patrols on the detection of snares with visual detections or presence signs of the ungulates. Our results showed that a substantial proportion of the sites occupied by ungulate species went extinct over the years of the study while the proportion of sites colonised by poachers increased. We also showed, for the first time, that spatio-temporal heterogeneity in the patrolling effort explains a great deal of the variation in the detection of poachers and ungulates. Our approach provides practitioners with a flexible and robust tool to assess conservation status of species and extinction risk of wildlife populations. It can assist managers in better evaluating, learning and adapting the patrolling strategies of rangers.
Follicle-stimulating hormone and luteinizing hormone increase Ca2+ in the granulosa cells of mouse ovarian follicles1
Authors: Egbert Jeremy R. , Fahey Paul G. , Reimer Jacob , Owen Corie M. , Evsikov Alexei V. , Nikolaev Viacheslav O. , Griesbeck Oliver , Ray Russell S. , Tolias Andreas S. , Jaffe Laurinda A.
Published: January 2019

In mammalian ovarian follicles, follicle stimulating hormone (FSH) and luteinizing hormone (LH) signal primarily through the G-protein Gs to elevate cAMP, but both of these hormones can also elevate Ca2+ under some conditions. Here we investigate FSH- and LH-induced Ca2+ signaling in intact follicles of mice expressing genetically encoded Ca2+ sensors, Twitch-2B and GCaMP6s. At a physiological concentration (1 nM), FSH elevates Ca2+ within the granulosa cells of preantral and antral follicles. The Ca2+ rise begins several minutes after FSH application, peaks at ~10 minutes, remains above baseline for another ~10 minutes, and depends on extracellular Ca2+. However, suppression of the FSH-induced Ca2+ increase by reducing extracellular Ca2+ does not inhibit FSH-induced phosphorylation of MAP kinase, estradiol production, or the acquisition of LH responsiveness. Like FSH, LH also increases Ca2+, when applied to preovulatory follicles. At a physiological concentration (10 nM), LH elicits Ca2+ oscillations in a subset of cells in the outer mural granulosa layer. These oscillations continue for at least 6 hours and depend on the activity of Gq family G-proteins. Suppression of the oscillations by Gq inhibition does not inhibit meiotic resumption, but does delay the time to 50% ovulation by about 3 hours. In summary, both FSH and LH increase Ca2+ in the granulosa cells of intact follicles, but the functions of these Ca2+ rises are only starting to be identified.

Summary sentence

Both FSH and LH increase Ca2+ in the granulosa cells of intact ovarian follicles from mice expressing genetically encoded sensors.
Genome-wide dynamics of RNA synthesis, processing and degradation without RNA metabolic labeling
Authors: Furlan Mattia , Galeota Eugenia , Del Gaudio Nunzio , Dassi Erik , Caselle Michele , de Pretis Stefano , Pelizzola Mattia
Published: January 2019

The kinetic rates of RNA synthesis, processing and degradation determine the dynamics of transcriptional regulation by governing both the abundance and the responsiveness to modulations of premature and mature RNA species. The study of RNA dynamics is largely based on the integrative analysis of total and nascent transcription, with the latter being quantified through RNA metabolic labeling. We describe here INSPEcT-, a computational method based on mathematical modeling of intronic and exonic expression, able to derive the dynamics of transcription from steady state or time course profiling of just total RNA, without requiring any information on nascent transcripts. Our approach closely recapitulates the kinetic rates obtained through RNA metabolic labeling, improves the ability to detect changes in transcripts half-lives, reduces the cost and complexity of the experiments, and can be adopted to study experimental conditions where nascent transcription cannot be readily profiled. Finally, we applied INSPEcT- to the characterization of post-transcriptional regulation landscapes in dozens of physiological and disease conditions. This approach was included in the INSPEcT Bioconductor package, which can now unveil RNA dynamics from steady state or time course data, with or without the profiling of nascent RNA.
Biotic interactions and climate in species distribution modelling
Authors: Bebber Daniel P. , Gurr Sarah J.
Published: January 2019

Species have preferred environmental niches 1 and their geographical distributions respond to global climate change 2. Predicting range shifts under climate change has profound implications for conservation of biodiversity 3, provision of ecosystem services, and in the management of invasive species 4. Species distribution modelling (SDM) has largely focussed on climate variations, but biotic interactions, such as predation and competition, can alter potential distributions 5,6 and affect migration rates 7. However, a lack of data on biotic interactions has restricted consideration of these factors for many species 1. Here, we compare the power of biotic and climatic factors as predictors of global distributions of hundreds of crop pests and pathogens (CPPs), for which host preferences are known. We show that host availability is a more important predictor of endobiotic pathogen distributions (fungi, oomycetes, bacteria, viruses and nematodes) than of epibiotic pest distributions (insect herbivores). Conversely, climatic variables are better predictors of epibiotic pest distributions. These results are robust to statistical controls for varying observational capacity among countries. Our findings demonstrate that life history affects global scale species distributions and that SDM should incorporate biotic interactions as well as climate.
Genetic Variability and Correlation Coefficients of Major Traits in Early Maturing Rice under Rainfed Lowland Environments of Nepal
Authors: Tiwari Dev Nidhi , Tripathi Santosh Raj , Tripathi Mahendra Prasad , Khatri Narayan , Bastola Bishwas Raj
Published: January 2019

Genetic variability is the fundamental requirement of any crop breeding program to develop superior cultivars. The objective of this study was to estimate the genetic variability and find out the correlation among the different quantitative traits of rainfed early lowland rice. The experiment was conducted consecutively two years during 2015 and 2016 in wet season across the four different locations in Regional Agricultural Research Station, Khajura, National Wheat Research Program, Bhairahawa, National Maize Research Program, Rampur and National Rice Research Program, Hardinath along the Terai region of Nepal representing sub-tropical agro-climate. Seven genotypes including Hardinath-1 as standard check variety were evaluated in the randomized complete block design with three replications. Various quantitative traits were measured to investigate the variability and correlation coefficients. All the genotypes and locations showed significant variations for all the traits considered. Genotypic coefficient of variation was lower than phenotypic coefficient of variation for all traits studied. The magnitudes of genotypic coefficient of variations were relatively higher for grain yield, 1000-grain weight and days to heading. The highest broad sense heritability of 94% was recorded in days to maturity and the lowest heritability of 16% was observed in plant height. Positive and highly significant correlations were found both in genotypic and phenotypic levels between days to heading and days to maturity (rg=0.9999**, rp=0.997**), days to heading and grain yield (rg =0.9999**, rp= 0.9276**), days to maturity and grain yield (rg =0.9796**, rp=0.9174**). However, negative and highly significant genetic correlation was observed between plant height and 1000 grain weight (rg = -0.9999**). Thus results indicated that days to heading, days to maturity, grain yield, 1000 grain weight demonstrated higher heritability and remarkable genetic advance could be considered for the most appropriate traits for improvement and selection of trait to achieve stable and high yielding early rice genotypes under rainfed environments.
Plasticity versus stability across the human cortical visual connectome
Authors: Haak Koen V. , Beckmann Christian F.
Published: January 2019

Whether and how the balance between plasticity and stability varies across the brain is an important open question. Within a processing hierarchy, it is thought that plasticity is increased at higher levels of cortical processing, but direct quantitative comparisons between low- and high-level plasticity have not been made so far. Here, we addressed this issue for the human cortical visual system. By quantifying plasticity as the complement of the heritability of functional connectivity, we demonstrate a non-monotonic relationship between plasticity and hierarchical level, such that plasticity decreases from early to mid-level cortex, and then increases further of the visual hierarchy. This non-monotonic relationship argues against recent theory that the balance between plasticity and stability is governed by the costs of the “coding-catastrophe”, and can be explained by a concurrent decline of short-term adaptation and rise of long-term plasticity up the visual processing hierarchy.
Discovery of a redox-thiol switch regulating cellular energy metabolism
Authors: Gao Xing-Huang , Li Ling , Parisien Marc , Mcleod Matt , Wu Jing , Bederman Ilya , Gao Zhaofeng , Krokowski Dawid , Chirieleison Steven M , Diatchenko Luda , Abbott Derek , Yee Vivien , Hoppel Charles L. , Kibbey Richard G , Holyoak Todd , Willard Belinda , Arvan Peter , Hatzoglou Maria
Published: January 2019

Previously, we reported that increased synthesis of the gas hydrogen sulfide (H2S) during the Integrated Stress Response (ISR) induced proteome-wide cysteine-sulfhydration with the predominant modified pathway being enzymes of cellular energy metabolism (Gao, et al. 2015). Using pancreatic beta cells and quantitative proteomics in this study, we identified a Redox Thiol Switch from S-glutathionylation to S-sulfhydration and we named it, RTSGS. About half of the identified proteins are involved in energy metabolism, and one novel target was the mitochondrial phosphoenolpyruvate carboxykinase 2 (PCK2) whose catalytic Cys306was targeted by both modifications. The enzymatic activity of PCK2 was inhibited by S-glutathionylation, and this inhibition was largely reversed by S-sulfhydration. S-sulfhydration also reversed the S-glutathionylation-mediated inhibition of glucose flux, indicating a broad metabolic significance. We propose that a Redox Thiol Switch from S-glutathionylation to S-sulfhydration is a key mechanism to fine tune cellular energy metabolism in response to different levels of oxidative stress.
Analytical expressions and physical principles for single-cell mRNA distributions of the lac operon of Escherichia coli
Authors: Choudhary Krishna , Narang Atul
Published: January 2019

Mechanistic models of stochastic gene expression are of considerable interest, but their complexity often precludes tractable analytical expressions for mRNA and protein distributions. The lac operon of E. coli is a model system with regulatory elements such as multiple operators and DNA looping that are shared by many operons. Although this system is complex, intuition suggests that fast DNA looping may simplify it by causing the repressor-bound states of the operon to equilibrate rapidly, thus ensuring that the subsequent dynamics are governed by slow transitions between the repressor-free and the equilibrated repressor-bound states. Here, we show that this intuition is correct by applying singular perturbation theory to a mechanistic model of lac transcription with the scaled time constant of DNA looping as the perturbation parameter. We find that at steady state, the repressor-bound states satisfy detailed balance and are dominated by the looped states; moreover, the interaction between the repressor-free and the equilibrated repressor-bound states is described by an extension of the Peccoud-Ycart two-state model in which both (repressor-free and repressor-bound) states support transcription. The solution of this extended two-state model reveals that the steady state mRNA distribution is a mixture of the Poisson and negative hypergeometric distributions which reflects mRNAs obtained by transcription from the repressor-bound and repressor-free states, respectively. Finally, we show that the physics revealed by perturbation theory makes it easy to derive the extended two-state model equations for complex regulatory architectures.
Quantitative Analysis of Global Protein Stability Rates in Tissues
Authors: McClatchy Daniel B. , Gao Yu , Lavallée-Adam Mathieu , Yates John R.
Published: January 2019

Protein degradation is an essential mechanism for maintaining homeostasis in response to internal and external perturbations. Disruption of this process is implicated in many human diseases, but quantitation of global stability rates has not yet been achieved in tissues. We have developed QUAD (Quantification of Azidohomoalanine Degradation), a technique to quantitate global protein degradation using mass spectrometry. Azidohomoalanine (AHA) is pulsed into mouse tissues through their diet. The mice are then returned to a normal diet and the decrease of AHA abundance can be quantitated in the proteome. QUAD analysis reveals that protein stability varied within tissues, but discernible trends in the data suggest that cellular environment is a major factor dictating stability. Within a tissue, different organelles, post-translation modifications, and protein functions were enriched with different stability patterns. Surprisingly, subunits of the TRIC molecular chaperonin possessed markedly distinct stability trajectories in the brain. Further investigation revealed that these subunits also possessed different subcellular localization and expression patterns that were uniquely altered with age and in Alzheimer’s disease transgenic mice, indicating a potential non-canonical chaperonin. Finally, QUAD analysis demonstrated that protein stability is enhanced with age in the brain but not in the liver. Overall, QUAD allows the first global quantitation of protein stability rates in tissues, which may lead to new insights and hypotheses in basic and translational research.

Protein degradation is an important component of the proteostasis network, but no techniques are available to globally quantitate degradation rates in tissues. In this study, we demonstrate a new method QUAD (Quantification of Azidohomoalanine Degradation) that can accurately quantitate degradation rates in tissues. QUAD analysis of mouse tissues reveal that unique degradation trends can define different tissue proteomes. Within a tissue, specific protein characteristics are correlated with different levels of protein stability. Further investigation of the TRIC chaperonin with strikingly different subunit stabilities suggests a non-canonical chaperonin in brain tissue. Consistent with the theory that the proteostasis network is compromised with age, we discovered that protein stability is globally enhanced in brains of old mice compared to young mice.