Using big data to understand evolutionary patterns in Geometridae and Erebidae, the two most diverse families of Lepidoptera

Lepidoptera (moths and butterflies) are one of the most diverse groups of organisms on earth. They have conquered all the continents apart from Antarctica. The reasons of such high diversity are still not clear. One of the first steps to study the causes of such evolutionary success is to have a clear idea of their phylogenetic relationships. In this thesis I focus on the diversity of two of the most diverse families of Lepidoptera, Geometridae with over 23,000 described species and Erebidae with over 24,000 species. In the case of Geometridae I focus in obtaining a robust phylogenetic hypothesis and then study the diversification dynamics and the biogeographical history which have shaped their actual diversity and distribution. In this project I used the most complete dataset of the family in order to study their evolutionary patterns. In the case of the Erebidae family, obtaining a robust phylogenetic hypothesis was more challenging. In the most complete study of the group up to date, using a multi locus Sanger based approach, it was not possible to resolve the deep phylogeny of the family. Therefore, I used high throughput sequencing (HTS) approaches to resolve the complex deep phylogenetic history of the group. In this project I used old DNA extracts of over 10 years old to explore the possibility of using this genetic resource for genomic studies. In addition, I evaluated the accuracy and range of resolution of the mitochondrial genomes in this family. And finally, I explored the alternative possibilities which the HTS approaches offer us to study the presence of symbiotic interactions using genomic data

Video Game Audio

Game sound is the last step in game production industries which plays an important role to enhance the sense of immersion or emotional involvement in most recent games. This feeling can be enhanced by adding ambience and interactive music with the correct transitions. Apart from providing sound materials, the role of a sound designer is to create smooth musical transitions for complex interactive events. Nowadays, the trend of game engines that can implement a real time transformation in acoustical and sound parameters has been increased [6,7,12]. Designing nonlinear sounds for video games can be challenging, especially when sound diversity for interactive scenes and characters is viable. This assignment has been scheduled to be complete individually. Although most of the audio materials have been created by author, some of the music and sound effects have been downloaded from online sources. The asset list and time schedule has been printed in appendices A and B

Final Proposal for Digital Audio Systems, DESC9115, 2018

Time Warp is a fantastic plugin that converts your digital audio workstation (DAW) to a powerful time stretcher system. The function offers a reliable algorithm based on Filter Bank (sum of sinusoids in frequency domain), the technique that can implement high-fidelity time scaling on a variety of sound sources such as synchronizing the audio with video content and tempo adjustment of the music

Sonification of Real-Time Physiological Data for Meditation Practice

Translating biophysical data to meaningful audible pieces has been under investigation in plants, animals and humans [2]. For example, the electrical signal resulting from changing the galvanic response of human skin (GSR) [3] by a physical or emotional stimulus can be used for mapping the parameters of a musical piece [6]. In a similar manner, the temperature change created by the human breath can be translated to audible signals. On this basis a scenario has been developed for a real-time sonification of breathing patterns and GSR data to create an audible reflection of the unconscious mind. This instrument can be a practical device to enhance the power of self-control in meditation practice as mapping the user’s psychophysical signals to musical notes can be a powerful way to control stress by enhancing mindfulness about internal layers of psychological patterns [1]

STI Measurement in The Car

In modern car industries, the intelligibility of sound inside the cabin of vehicles has been known as a factor of comfort [6]. One of the known objective methods for evaluating speech intelligibility inside cars is the speech transmission index STI which is the main subject of this report. The measurement aim is to predict the STI in a running car as a factor of speed (background noise). For this purpose, a series of audio- acoustical measurements have been conducted inside a five-door car (Mazda) based on the European standard IEC 60268-16 [4]. As the harshness of background noise in different speeds, compartment reverberation time and speech level are accounted for in the STI calculation, the resulting data can be interoperated as the quality of sound in the car [6]. Further investigations have been done for better understanding the effect of source spectrum and direction on the transmission index and finally the direct measurement method in aarae has been compared with a similar method in Arta (Audio Measurement and Analysis Software) in the room space

Nanotechnology in proteomics: Current status, promises and challenges

In genomics, the ability to amplify rare transcripts has enabled rapid advances in the understanding of gene expression patterns in human disease. The inability to increase the copy number and to detect the signal of rare proteins as unique species in biological samples has hindered the ability of proteomics to dissect human disease with the same complexity as genomic analyses. Advances in nanotechnology have begun to allow researchers to identify low-abundance proteins in samples through techniques that rely upon both nanoparticles and nanoscale devices. This review describes some of the physical and chemical principles underlying nanomaterials and devices and outlines how they can be used in proteomics; developments which are establishing nanoproteomics as a new field. Nanoproteomics will provide the platform for the discovery of next generation biomarkers. The most promising candidates for nanoproteomics, namely carbon nanotubes and nanowires, quantum dots and nanoscopic gold particles, offer several advantages such as high sensitivity, real-time measurements and improved reproducibility.

Properties of the amniotic membrane for potential use in tissue engineering

An important component of tissue engineering (TE) is the supporting matrix upon which cells and tissues grow, also known as the scaffold. Scaffolds must easily integrate with host tissue and provide an excellent environment for cell growth and differentiation. Most scaffold materials are naturally derived from mammalian tissues. The amniotic membrane (AM) is considered an important potential source for scaffolding material. The AM represents the innermost layer of the placenta and is composed of a single epithelial layer, a thick basement membrane and an avascular stroma. The special structure and biological viability of the AM allows it to be an ideal candidate for creating scaffolds used in TE. Epithelial cells derived from the AM have the advantages of stem cells, yet are a more suitable source of cells for TE than stem cells. The extracellular matrix components of the basement membrane of the AM create an almost native scaffold for cell seeding in TE. In addition, the AM has other biological properties important for TE, including anti-inflammatory, anti-microbial, anti-fibrosis, anti-scarring, as well as reasonable mechanical property and low immunogenicity. In this review, the various properties of the AM are discussed in light of their potential use for TE

Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera)

Models estimate that up to 80% of all butterfly and moth species host vertically transmitted endosymbiotic microorganisms, which can affect the host fitness, metabolism, reproduction, population dynamics, and genetic diversity, among others. The supporting empirical data are however currently highly biased towards the generally more colourful butterflies, and include less information about moths. Additionally, studies of symbiotic partners of Lepidoptera predominantly focus on the common bacterium Wolbachia pipientis, while infections by other inherited microbial partners have more rarely been investigated. Here, we mine the whole genome sequence data of 47 species of Erebidae moths, with the aims to both inform on the diversity of symbionts potentially associated with this Lepidoptera group, and discuss the potential of metagenomic approaches to inform on host associated microbiome diversity. Based on the result of Kraken2 and MetaPhlAn2 analyses, we found clear evidence of the presence of Wolbachia in four species. Our result also suggests the presence of three other bacterial symbionts (Burkholderia spp., Sodalis spp. and Arsenophonus spp.) in three other moth species. Additionally, we recovered genomic material from bracovirus in about half of our samples. The detection of the latter, usually found in mutualistic association to braconid parasitoid wasps, may inform on host-parasite interactions that take place in the natural habitat of the Erebidae moths, suggesting either contamination with material from species of the host community network, or horizontal transfer of members of the microbiome between interacting species.Peer reviewe

A new species of the genus Capoeta Valenciennes, 1842 from the Caspian Sea basin in Iran (Teleostei, Cyprinidae)

A new species of algae-scraping cyprinid of the genus Capoeta Valenciennes, 1842 is described from the Kheyroud River, located in the southern part of the Caspian Sea basin in Iran. The species differs from other members of this genus by a combination of the following characters: one pair of barbels; predorsal length equal to postdorsal length; maxillary barbel slightly smaller than eye¿s horizontal diameter and reach to posterior margin of orbit; intranasal length slightly shorter than snout length; lateral line with 46¿54 scales; 7¿9 scales between dorsal-fin origin and lateral line, and 6¿7 scales between anal-fin origin and lateral line.This research was funded by Tehran University and the Spanish Ministry of Economy and Competitiveness (project number CGL2016-75262-P).Peer Reviewe