Exploring genomes with a game engine

2014 ◽  
Vol 169 ◽  
pp. 443-453 ◽  
Author(s):  
Jeremiah J. Shepherd ◽  
Lingxi Zhou ◽  
William Arndt ◽  
Yan Zhang ◽  
W. Jim Zheng ◽  
...  

More and more evidence indicates that the 3D conformation of eukaryotic genomes is a critical part of genome function. However, due to the lack of accurate and reliable 3D genome structural data, this information is largely ignored and most of these studies have to use information systems that view the DNA in a linear structure. Visualizing genomes in real time 3D can give researchers more insight, but this is fraught with hardware limitations since each element contains vast amounts of information that cannot be processed on the fly. Using a game engine and sophisticated video game visualization techniques enables us to construct a multi-platform real-time 3D genome viewer. The game engine-based viewer achieves much better rendering speed and can handle much larger amounts of data compared to our previous implementation using OpenGL. Combining this viewer with 3D genome models from experimental data could provide unprecedented opportunities to gain insight into the conformation–function relationships of a genome.

2021 ◽  
Author(s):  
◽  
Christopher Wratt

<p>In video games, audio is often a vital element in the creation of immersive gaming experiences. One set of techniques that are particularly well suited to attaining this immersion are procedural audio techniques. These techniques enable enhanced immersion through supporting close synchronisation between player and game state in ways that are difficult to achieve with other game audio techniques. While this is the case, there is a lack of GUI and script-based tools that support the use of such techniques. This thesis explores this lack, and documents the development of two new video game tools for the creation of procedurally generated audio.  The first of these tools is a Musical Instrument Digital Interface (MIDI) library that supports the playback and real-time manipulation of MIDI files in the Unity game engine. The tool achieves real-time procedural audio, yet fails to meet required levels of time accuracy and is only a partial success. The second tool developed is a plugin hosting application that enables the use of the popular audio plugin format, VST2, in the Unity game engine. The tool succeeds in achieving VST2 effect plugin loading and, at the time of the completion of this thesis, is the only tool capable of embedding such plugins into applications developed in a major game engine. This will be of significant benefit to game developers who wish to achieve a high degree of immersivity in the music and sound design in their games.</p>


2021 ◽  
Author(s):  
◽  
Christopher Wratt

<p>In video games, audio is often a vital element in the creation of immersive gaming experiences. One set of techniques that are particularly well suited to attaining this immersion are procedural audio techniques. These techniques enable enhanced immersion through supporting close synchronisation between player and game state in ways that are difficult to achieve with other game audio techniques. While this is the case, there is a lack of GUI and script-based tools that support the use of such techniques. This thesis explores this lack, and documents the development of two new video game tools for the creation of procedurally generated audio.  The first of these tools is a Musical Instrument Digital Interface (MIDI) library that supports the playback and real-time manipulation of MIDI files in the Unity game engine. The tool achieves real-time procedural audio, yet fails to meet required levels of time accuracy and is only a partial success. The second tool developed is a plugin hosting application that enables the use of the popular audio plugin format, VST2, in the Unity game engine. The tool succeeds in achieving VST2 effect plugin loading and, at the time of the completion of this thesis, is the only tool capable of embedding such plugins into applications developed in a major game engine. This will be of significant benefit to game developers who wish to achieve a high degree of immersivity in the music and sound design in their games.</p>


2020 ◽  
Vol 48 (22) ◽  
pp. 12604-12617
Author(s):  
Pengpeng Long ◽  
Lu Zhang ◽  
Bin Huang ◽  
Quan Chen ◽  
Haiyan Liu

Abstract We report an approach to predict DNA specificity of the tetracycline repressor (TetR) family transcription regulators (TFRs). First, a genome sequence-based method was streamlined with quantitative P-values defined to filter out reliable predictions. Then, a framework was introduced to incorporate structural data and to train a statistical energy function to score the pairing between TFR and TFR binding site (TFBS) based on sequences. The predictions benchmarked against experiments, TFBSs for 29 out of 30 TFRs were correctly predicted by either the genome sequence-based or the statistical energy-based method. Using P-values or Z-scores as indicators, we estimate that 59.6% of TFRs are covered with relatively reliable predictions by at least one of the two methods, while only 28.7% are covered by the genome sequence-based method alone. Our approach predicts a large number of new TFBs which cannot be correctly retrieved from public databases such as FootprintDB. High-throughput experimental assays suggest that the statistical energy can model the TFBSs of a significant number of TFRs reliably. Thus the energy function may be applied to explore for new TFBSs in respective genomes. It is possible to extend our approach to other transcriptional factor families with sufficient structural information.


Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 246
Author(s):  
Xiaomeng Chen ◽  
Rui Li ◽  
Yonglin Wang ◽  
Aining Li

An emerging poplar canker caused by the gram-negative bacterium, Lonsdalea populi, has led to high mortality of hybrid poplars Populus × euramericana in China and Europe. The molecular bases of pathogenicity and bark adaptation of L. populi have become a focus of recent research. This study revealed the whole genome sequence and identified putative virulence factors of L. populi. A high-quality L. populi genome sequence was assembled de novo, with a genome size of 3,859,707 bp, containing approximately 3434 genes and 107 RNAs (75 tRNA, 22 rRNA, and 10 ncRNA). The L. populi genome contained 380 virulence-associated genes, mainly encoding for adhesion, extracellular enzymes, secretory systems, and two-component transduction systems. The genome had 110 carbohydrate-active enzyme (CAZy)-coding genes and putative secreted proteins. The antibiotic-resistance database annotation listed that L. populi was resistant to penicillin, fluoroquinolone, and kasugamycin. Analysis of comparative genomics found that L. populi exhibited the highest homology with the L. britannica genome and L. populi encompassed 1905 specific genes, 1769 dispensable genes, and 1381 conserved genes, suggesting high evolutionary diversity and genomic plasticity. Moreover, the pan genome analysis revealed that the N-5-1 genome is an open genome. These findings provide important resources for understanding the molecular basis of the pathogenicity and biology of L. populi and the poplar-bacterium interaction.


Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 76
Author(s):  
Matthias T. Ochmann ◽  
Zoltán Ivics

Sleeping Beauty (SB) is a transposon system that has been widely used as a genetic engineering tool. Central to the development of any transposon as a research tool is the ability to integrate a foreign piece of DNA into the cellular genome. Driven by the need for efficient transposon-based gene vector systems, extensive studies have largely elucidated the molecular actors and actions taking place during SB transposition. Close transposon relatives and other recombination enzymes, including retroviral integrases, have served as useful models to infer functional information relevant to SB. Recently obtained structural data on the SB transposase enable a direct insight into the workings of this enzyme. These efforts cumulatively allowed the development of novel variants of SB that offer advanced possibilities for genetic engineering due to their hyperactivity, integration deficiency, or targeting capacity. However, many aspects of the process of transposition remain poorly understood and require further investigation. We anticipate that continued investigations into the structure–function relationships of SB transposition will enable the development of new generations of transposition-based vector systems, thereby facilitating the use of SB in preclinical studies and clinical trials.


Insects ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 97
Author(s):  
Nace Kranjc ◽  
Andrea Crisanti ◽  
Tony Nolan ◽  
Federica Bernardini

The increase in molecular tools for the genetic engineering of insect pests and disease vectors, such as Anopheles mosquitoes that transmit malaria, has led to an unprecedented investigation of the genomic landscape of these organisms. The understanding of genome variability in wild mosquito populations is of primary importance for vector control strategies. This is particularly the case for gene drive systems, which look to introduce genetic traits into a population by targeting specific genomic regions. Gene drive targets with functional or structural constraints are highly desirable as they are less likely to tolerate mutations that prevent targeting by the gene drive and consequent failure of the technology. In this study we describe a bioinformatic pipeline that allows the analysis of whole genome data for the identification of highly conserved regions that can point at potential functional or structural constraints. The analysis was conducted across the genomes of 22 insect species separated by more than hundred million years of evolution and includes the observed genomic variation within field caught samples of Anopheles gambiae and Anopheles coluzzii, the two most dominant malaria vectors. This study offers insight into the level of conservation at a genome-wide scale as well as at per base-pair resolution. The results of this analysis are gathered in a data storage system that allows for flexible extraction and bioinformatic manipulation. Furthermore, it represents a valuable resource that could provide insight into population structure and dynamics of the species in the complex and benefit the development and implementation of genetic strategies to tackle malaria.


2016 ◽  
Vol 90 (13) ◽  
pp. 5860-5875 ◽  
Author(s):  
Eva Maria Borst ◽  
Rudolf Bauerfeind ◽  
Anne Binz ◽  
Thomas Min Stephan ◽  
Sebastian Neuber ◽  
...  

ABSTRACTSeveral essential viral proteins are proposed to participate in genome encapsidation of human cytomegalovirus (HCMV), among them pUL77 and pUL93, which remain largely uncharacterized. To gain insight into their properties, we generated an HCMV mutant expressing a pUL77-monomeric enhanced green fluorescent protein (mGFP) fusion protein and a pUL93-specific antibody. Immunoblotting demonstrated that both proteins are incorporated into capsids and virions. Conversely to data suggesting internal translation initiation sites within the UL93 open reading frame (ORF), we provide evidence that pUL93 synthesis commences at the first start codon. In infected cells, pUL77-mGFP was found in nuclear replication compartments and dot-like structures, colocalizing with capsid proteins. Immunogold labeling of nuclear capsids revealed that pUL77 is present on A, B, and C capsids. Pulldown of pUL77-mGFP revealed copurification of pUL93, indicating interaction between these proteins, which still occurred when capsid formation was prevented. Correct subnuclear distribution of pUL77-mGFP required pUL93 as well as the major capsid protein (and thus probably the presence of capsids), but not the tegument protein pp150 or the encapsidation protein pUL52, demonstrating that pUL77 nuclear targeting occurs independently of the formation of DNA-filled capsids. When pUL77 or pUL93 was missing, generation of unit-length genomes was not observed, and only empty B capsids were produced. Taken together, these results show that pUL77 and pUL93 are capsid constituents needed for HCMV genome encapsidation. Therefore, the task of pUL77 seems to differ from that of its alphaherpesvirus orthologue pUL25, which exerts its function subsequent to genome cleavage-packaging.IMPORTANCEThe essential HCMV proteins pUL77 and pUL93 were suggested to be involved in viral genome cleavage-packaging but are poorly characterized both biochemically and functionally. By producing a monoclonal antibody against pUL93 and generating an HCMV mutant in which pUL77 is fused to a fluorescent protein, we show that pUL77 and pUL93 are capsid constituents, with pUL77 being similarly abundant on all capsid types. Each protein is required for genome encapsidation, as the absence of either pUL77 or pUL93 results in a genome packaging defect with the formation of empty capsids only. This distinguishes pUL77 from its alphaherpesvirus orthologue pUL25, which is enriched on DNA-filled capsids and exerts its function after the viral DNA is packaged. Our data for the first time describe an HCMV mutant with a fluorescent capsid and provide insight into the roles of pUL77 and pUL93, thus contributing to a better understanding of the HCMV encapsidation network.


2021 ◽  
Author(s):  
Chingis Oshakbayev ◽  
Roman Romanov ◽  
Valentin Vlassenko ◽  
Simon Austin ◽  
Sergey Kovalev ◽  
...  

Abstract Currently drilling of horizontal wells is a common enhanced oil recovery method. Geosteering services are often used for accurate well placement, which makes it possible to achieve a significant increase in production at relatively low cost. This paper describes the result of using seismic data in three-dimensional visualization for high-quality geosteering using a deep boundary detection tool and multilayer inversion in real time. Crossing the top of the reservoir while drilling horizontal sections at the current oilfield is unacceptable, due to the presence of reactive mudstones. In case of crossing the top of reservoir, further work on running and installing the liner becomes impossible due to instability and may lead to well collapse. Based on prewell analysis of the structural data, the well was not supposed to approach the top of the target formation along the planned profile. However, while preparing geosteering model and analyzing seismic data it became possible to reveal that risk, elaborate its mitigation and eventually increase the length of the horizontal section. Such integrated analysis made it possible to maintain the wellbore within the target reservoirs, as well as to update the structural bedding of the top based on the multilayer inversion results.


Author(s):  
Jason Ginsberg Reitman

Elite video game competition provides a setting for studying how digitally connected teams handle massive amounts of information that no individual could manage on their own. This article discusses observations of the University of California, Irvine's scholarship League of Legends teams' practices and competitions from fall 2016 through spring 2017. The observations explore the nature of distributed cognition of time and temporal information in a high-pressure, competitive environment. The capacity and strategies of these teams to maintain high levels of coordination, while sitting at desktops for hours at a time, can provide insight into how other kinds of teams might learn to collaborate skillfully in networked settings.


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