scholarly journals Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks

2021 ◽  
Author(s):  
Payam Dibaeinia ◽  
Saurabh Sinha

Abstract Deciphering the sequence-function relationship encoded in enhancers holds the key to interpreting non-coding variants and understanding mechanisms of transcriptomic variation. Several quantitative models exist for predicting enhancer function and underlying mechanisms; however, there has been no systematic comparison of these models characterizing their relative strengths and shortcomings. Here, we interrogated a rich data set of neuroectodermal enhancers in Drosophila, representing cis- and trans- sources of expression variation, with a suite of biophysical and machine learning models. We performed rigorous comparisons of thermodynamics-based models implementing different mechanisms of activation, repression and cooperativity. Moreover, we developed a convolutional neural network (CNN) model, called CoNSEPT, that learns enhancer ‘grammar’ in an unbiased manner. CoNSEPT is the first general-purpose CNN tool for predicting enhancer function in varying conditions, such as different cell types and experimental conditions, and we show that such complex models can suggest interpretable mechanisms. We found model-based evidence for mechanisms previously established for the studied system, including cooperative activation and short-range repression. The data also favored one hypothesized activation mechanism over another and suggested an intriguing role for a direct, distance-independent repression mechanism. Our modeling shows that while fundamentally different models can yield similar fits to data, they vary in their utility for mechanistic inference. CoNSEPT is freely available at: https://github.com/PayamDiba/CoNSEPT.

2021 ◽  
Author(s):  
Payam Dibaeinia ◽  
Saurabh Sinha

AbstractDeciphering the sequence-function relationship encoded in enhancers holds the key to interpreting non-coding variants and understanding mechanisms of transcriptomic variation. Several quantitative models exist for predicting enhancer function and underlying mechanisms; however, there has been no systematic comparison of these models characterizing their relative strengths and shortcomings. Here, we interrogated a rich data set of neuroectodermal enhancers in Drosophila, representing cis- and trans- sources of expression variation, with a suite of biophysical and machine learning models. We performed rigorous comparisons of thermodynamics-based models implementing different mechanisms of activation, repression, and cooperativity. Moreover, we developed a convolutional neural network (CNN) model, called CoNSEPT, that learns enhancer “grammar” in an unbiased manner. CoNSEPT is the first general-purpose CNN tool for predicting enhancer function in varying conditions, and we show that such complex models can suggest interpretable mechanisms. We found model-based evidence for mechanisms previously established for the studied system, including cooperative activation and short-range repression. The data also favored one hypothesized activation mechanism over another and suggested an intriguing role for a direct, distance-independent repression mechanism. Our modeling shows that while fundamentally different models can yield similar fits to data, they vary in their utility for mechanistic inference. CoNSEPT is freely available at: https://github.com/PayamDiba/CoNSEPT.


2019 ◽  
Vol 14 (2) ◽  
pp. 148-156
Author(s):  
Nighat Noureen ◽  
Sahar Fazal ◽  
Muhammad Abdul Qadir ◽  
Muhammad Tanvir Afzal

Background: Specific combinations of Histone Modifications (HMs) contributing towards histone code hypothesis lead to various biological functions. HMs combinations have been utilized by various studies to divide the genome into different regions. These study regions have been classified as chromatin states. Mostly Hidden Markov Model (HMM) based techniques have been utilized for this purpose. In case of chromatin studies, data from Next Generation Sequencing (NGS) platforms is being used. Chromatin states based on histone modification combinatorics are annotated by mapping them to functional regions of the genome. The number of states being predicted so far by the HMM tools have been justified biologically till now. Objective: The present study aimed at providing a computational scheme to identify the underlying hidden states in the data under consideration. </P><P> Methods: We proposed a computational scheme HCVS based on hierarchical clustering and visualization strategy in order to achieve the objective of study. Results: We tested our proposed scheme on a real data set of nine cell types comprising of nine chromatin marks. The approach successfully identified the state numbers for various possibilities. The results have been compared with one of the existing models as well which showed quite good correlation. Conclusion: The HCVS model not only helps in deciding the optimal state numbers for a particular data but it also justifies the results biologically thereby correlating the computational and biological aspects.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kip D. Zimmerman ◽  
Mark A. Espeland ◽  
Carl D. Langefeld

AbstractCells from the same individual share common genetic and environmental backgrounds and are not statistically independent; therefore, they are subsamples or pseudoreplicates. Thus, single-cell data have a hierarchical structure that many current single-cell methods do not address, leading to biased inference, highly inflated type 1 error rates, and reduced robustness and reproducibility. This includes methods that use a batch effect correction for individual as a means of accounting for within-sample correlation. Here, we document this dependence across a range of cell types and show that pseudo-bulk aggregation methods are conservative and underpowered relative to mixed models. To compute differential expression within a specific cell type across treatment groups, we propose applying generalized linear mixed models with a random effect for individual, to properly account for both zero inflation and the correlation structure among measures from cells within an individual. Finally, we provide power estimates across a range of experimental conditions to assist researchers in designing appropriately powered studies.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ryan B. Patterson-Cross ◽  
Ariel J. Levine ◽  
Vilas Menon

Abstract Background Generating and analysing single-cell data has become a widespread approach to examine tissue heterogeneity, and numerous algorithms exist for clustering these datasets to identify putative cell types with shared transcriptomic signatures. However, many of these clustering workflows rely on user-tuned parameter values, tailored to each dataset, to identify a set of biologically relevant clusters. Whereas users often develop their own intuition as to the optimal range of parameters for clustering on each data set, the lack of systematic approaches to identify this range can be daunting to new users of any given workflow. In addition, an optimal parameter set does not guarantee that all clusters are equally well-resolved, given the heterogeneity in transcriptomic signatures in most biological systems. Results Here, we illustrate a subsampling-based approach (chooseR) that simultaneously guides parameter selection and characterizes cluster robustness. Through bootstrapped iterative clustering across a range of parameters, chooseR was used to select parameter values for two distinct clustering workflows (Seurat and scVI). In each case, chooseR identified parameters that produced biologically relevant clusters from both well-characterized (human PBMC) and complex (mouse spinal cord) datasets. Moreover, it provided a simple “robustness score” for each of these clusters, facilitating the assessment of cluster quality. Conclusion chooseR is a simple, conceptually understandable tool that can be used flexibly across clustering algorithms, workflows, and datasets to guide clustering parameter selection and characterize cluster robustness.


1999 ◽  
Vol 55 (7) ◽  
pp. 1365-1367 ◽  
Author(s):  
Tiina A. Salminen ◽  
Yvonne Nymalm ◽  
Jussi Kankare ◽  
Jarmo Käpylä ◽  
Jyrki Heino ◽  
...  

Integrin α1β1 is one of the main collagen receptors in many cell types. A fast large-scale production, purification and crystallization method for the integrin α1 I domain is reported here. The α1 I domain was crystallized using the vapour-diffusion method with a reservoir solution containing a mixture of PEG 4000, sodium acetate, glycerol and Tris–HCl buffer. The crystals beong to the C2 space group, with unit-cell parameters a = 74.5, b = 81.9, c = 37.3 Å, α = γ = 90.0, β = 90.8°. The crystals diffract to 2.0 Å and a 94.2% complete data set to 2.2 Å has been collected from a single crystal with an R merge of 5.8%.


2014 ◽  
Vol 69 (7-8) ◽  
pp. 346-356 ◽  
Author(s):  
Andréa S. G. Figueiredo-Rinhel ◽  
Everton O. L. Santos ◽  
Luciana M. Kabeya ◽  
Ana Elisa C. S. Azzolini ◽  
Livia M. C. Simões-Ambrosio ◽  
...  

Stimulated human neutrophils exhibit increased net oxygen consumption (NOC) due to the conversion of O2 into the superoxide anion by the NADPH oxidase enzymatic complex during the respiratory burst. In several inflammatory diseases, overproduction of these oxidants causes tissue damage. The present study aims to: (a) optimize the experimental conditions used to measure the NOC in serum-opsonized zymosan (OZ)-and insoluble immune complex (i-IC)-stimulated human and rabbit neutrophils; and (b) compare the effect of four flavonols (quercetin, myricetin, kaempferol, and galangin) on this activity. We used a Clark-type oxygen electrode to measure the NOC of stimulated neutrophils. Eliciting the neutrophil respiratory burst with OZ and i-IC yielded similar maximum O2 uptake levels within the same species, but the human neutrophil NOC was almost four times higher than the rabbit neutrophil NOC. The optimal experimental conditions established for both cell types were 4·106 neutrophils mL-1, 2 mg mL-1 OZ, and 240 µg mL-1 i-IC. Upon stimulation with OZ or i-IC, the tested flavonols reduced the human and rabbit neutrophil NOC in the same order of potency - quercetin and galangin were the most and the least potent, respectively. These compounds were around four times more effective in inhibiting the rabbit as compared to the human neutrophil NOC, respectively. The four flavonols were not toxic to human or rabbit neutrophils. The experimental conditions used are suitable for both the determination of human and rabbit neutrophil NOC and for the assessment of the modulatory effects of natural compounds on these activities. The relationship between the level of NOC and the inhibitory potency of the flavonols suggests that rabbit neutrophils can be useful experimental models to predict the effect of drugs on immune complexstimulated human neutrophils.


2012 ◽  
Vol 72 (1) ◽  
pp. 134-167 ◽  
Author(s):  
SHEILAGH OGILVIE ◽  
MARKUS KÜPKER ◽  
JANINE MAEGRAITH

The “less-developed” interior of early modern Europe, especially the rural economy, is often regarded as financially comatose. This article investigates this view using a rich data set of marriage and death inventories for seventeenth-century Germany. It first analyzes the characteristics of debts, examining borrowing purposes, familial links, communal ties, and documentary instruments. It then explores how borrowing varied with gender, age, marital status, occupation, date, and asset portfolio. It finds that ordinary people, even in a “less-developed” economy in rural central Europe, sought to invest profitably, smooth consumption, bridge low liquidity, and hold savings in financial form.


2009 ◽  
Vol 14 (9) ◽  
pp. 1054-1066 ◽  
Author(s):  
Keith A. Houck ◽  
David J. Dix ◽  
Richard S. Judson ◽  
Robert J. Kavlock ◽  
Jian Yang ◽  
...  

The complexity of human biology has made prediction of health effects as a consequence of exposure to environmental chemicals especially challenging. Complex cell systems, such as the Biologically Multiplexed Activity Profiling (BioMAP) primary, human, cell-based disease models, leverage cellular regulatory networks to detect and distinguish chemicals with a broad range of target mechanisms and biological processes relevant to human toxicity. Here the authors use the BioMAP human cell systems to characterize effects relevant to human tissue and inflammatory disease biology following exposure to the 320 environmental chemicals in the Environmental Protection Agency’s (EPA’s) ToxCast phase I library. The ToxCast chemicals were assayed at 4 concentrations in 8 BioMAP cell systems, with a total of 87 assay endpoints resulting in more than 100,000 data points. Within the context of the BioMAP database, ToxCast compounds could be classified based on their ability to cause overt cytotoxicity in primary human cell types or according to toxicity mechanism class derived from comparisons to activity profiles of BioMAP reference compounds. ToxCast chemicals with similarity to inducers of mitochondrial dysfunction, cAMP elevators, inhibitors of tubulin function, inducers of endoplasmic reticulum stress, or NFκB pathway inhibitors were identified based on this BioMAP analysis. This data set is being combined with additional ToxCast data sets for development of predictive toxicity models at the EPA. ( Journal of Biomolecular Screening 2009:1054-1066)


1995 ◽  
Vol 268 (4) ◽  
pp. C1067-C1074 ◽  
Author(s):  
M. E. O'Donnell ◽  
J. D. Brandt ◽  
F. R. Curry

The trabecular meshwork (TM) of the eye plays a critical role in modulating intraocular pressure (IOP) through regulation of aqueous humor outflow, although the underlying mechanisms remain unknown. Ethacrynic acid, an agent known to inhibit Na-K-Cl cotransport of a number of cell types, recently has been reported to increase aqueous outflow and lower IOP through an unknown effect on the TM. In vascular endothelial cells and a variety of other cell types, the Na-K-Cl cotransporter functions to regulate intracellular volume. The present study was conducted to evaluate TM cells for the presence of Na-K-Cl cotransport activity and to test the hypothesis that modulation of cotransport activity alters intracellular volume and, consequently, permeability of the TM. We demonstrate here that bovine and human TM cells exhibit robust Na-K-Cl cotransport activity that is inhibited by bumetanide and by ethacrynic acid. Our studies also show that TM cell Na-K-Cl cotransport is modulated by a variety of hormones and neurotransmitters. Inhibition of the cotransporter either by bumetanide, ethacrynic acid, or inhibitory hormones reduces TM intracellular volume, whereas stimulatory hormones increase cell volume. In addition, shrinkage of the cells by hypertonic media stimulates cotransport activity and initiates a subsequent regulatory volume increase. Permeability of TM cell monolayers, assessed as transmonolayer flux of [14C]sucrose, is increased by hypertonicity-induced cell shrinkage and by bumetanide. These findings suggest that Na-K-Cl cotransport of TM cells is of central importance to regulation of intracellular volume and TM permeability. Defects of Na-K-Cl cotransport may underlie the pathophysiology of glaucoma.


2021 ◽  
Author(s):  
◽  
Ellen Yarrow

<p>This study explores the relationship between professional contractors and the permanent employees they work with at organisations in New Zealand. This thesis uses two concepts, organisational socialisation and the psychological contract, as lenses through which the working relationship is explored. The 20th century notion of standard employment has largely been eroded, giving way to different forms of non-standard work. Professional contractors are now found performing a variety of roles in many organisations across this country. Many are doing the work of permanent employees, but they are neither employees nor permanent. Professional contractors are a type of non-standard, transient worker. As part of a blended workforce, professional contractors work alongside permanent employees, but little is known about how they work together.  This qualitative study involves 49 face-to-face interviews with professional contractors, permanent employees and managers working in the Information Technology (IT) divisions of 10 organisations in three major cities in New Zealand. This research design results in a rich data set. The data collected was subject to analysis using the software NVIVO. This data was analysed in relation to the literature on organisational socialisation and the psychological contract to further explain the working relationship between professional contractors and permanent employees.  The findings reveal professional contractors’ experience of Van Maanen’s (1979) socialisation tactics were: collective, informal, variable, random and serial. It was found that an organisation’s policy sets the tone for the treatment (induction, inclusion and management) of professional contractors. According to the professional contractors interviewed, the Chao, O'Leary-Kelly, Wolf, Klein, and Gardner (1994) socialisation content dimensions that are important are structure, culture and values and language but history was not considered important. According to the managers interviewed, contractors need to know about the processes and procedures of the client organisation, have strong technical skills and industry, sector or domain knowledge. It was found that the indicator of adjustment ‘acceptance by insiders’ (Bauer & Erdogan, 2012) may be a sign that the contractor is adjusting to their new role but it is not essential. A new indicator of adjustment for professional contractors – output – clearly emerged from the data. The notion of ‘time to productivity’ is highly relevant to professional contractors and three factors affecting it are identified (contractor capability, role complexity and organisation readiness). Another important finding is that permanent employees play a key role as socialisation agents (Feldman, 1994; Jones, 1983; Van Maanen, 1978) in the socialisation of professional contractors. Surprisingly, it was found that other professional contractors also act as socialisation agents assisting the newcomer to adjust. It was found that proactive socialisation is particularly important for professional contractors. Together these findings establish the need to reconceptualise organisational socialisation for professional contractors specifically.  The second part of this thesis explores the psychological contract by asking interviewees about their mutual expectations. The expectations of each of the three parties (managers, professional contractors, and permanent employees) are subtly different, potentially influencing the psychological contract they develop. Permanent employees expect great things, professionalism and independence from professional contractors. Managers expect speed, professionalism and value for money from contractors. On the other hand, professional contractors simply expect to be treated with respect by their colleagues. Professional contractors expect to be given autonomy by their managers and support or guidance, should they require it. This study was not able to ascertain what type of psychological contract a professional contractor may develop. It is possible that a professional contractor develops a hybrid psychological contract. Alternatively, it is possible that a professional contractor’s psychological contract moves between the types developed by Rousseau (1995) over the course of their term with the client organisation. The insights gained by exploring the expectations of professional contractors, permanent employees and their managers are two-fold. Firstly, these expectations provide a valuable insight into the working relationship. Secondly, the exploration of a breach or violation of the psychological contract indicates that a malleable psychological contract (one that will shift or adjust) is less likely to manifest a breach or violation. Therefore, it is better for a professional contractor to develop and maintain a malleable rather than rigid psychological contract.  This study’s findings highlight the interrelationship between organisational socialisation and the psychological contract. This thesis asserts that the working relationship between professional contractors and permanent employees is specifically influenced by the socialisation of contractors as newcomers and in the mutual expectations, which form the psychological contract. As a result, it contributes to theorising and understanding of the working relationship between professional contractors and permanent employees. It identifies several tensions in the co-dependent working relationship, which are: time, team, treatment and training. This study has implications for Human Resource practitioners and managers because there is a need for corporate or HR policy relating to the treatment professional contractors. The use of organisational socialisation and the psychological contract as lenses with which the working relationship is explored is both original and meaningful.</p>


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