Three-dimensional model of an ancient Egyptian falcon mummy skeleton

Published ArticlePurpose – The purpose of this paper is to present the first detailed three-dimensional (3D) print from micro-computed tomography data of the skeleton of an ancient Egyptian falcon mummy. Design/methodology/approach – Radiographic analysis of an ancient Egyptian falcon mummy housed at Iziko Museums of South Africa was performed using non-destructive x-ray micro-computed tomography. A 1:1 physical replica of its skeleton was printed in a polymer material (polyamide) using 3D printing technology. Findings – The combination of high-resolution computed tomography scanning and rapid prototyping allowed us to create an accurate 1:1 model of a biological object hidden by wrappings. This model can be used to study skeletal features and morphology and also enhance exhibitions hosted within the museum. Originality/value – This is the first replica of its kind made of an ancient Egyptian falcon mummy skeleton. The combination of computed tomography scanning and 3D printing has the potential to facilitate scientific research and stimulate public interest in Egyptology

Identification of growth related quantitative Trait Loci within the abalone using comparative microsatellite bulked segregant analysis

Thesis (PhD (Genetics))--Stellenbosch University, 2010.ENGLISH ABSTRACT: The South African abalone, Haliotis midae, is a commercially valuable mollusc and is mostly exported to the Far East. Genetics research on H. midae has increased substantially since a genetic improvement programme was introduced in 2006 by collaboration between Stellenbosch University, government and industry partners. The development of molecular markers, QTL-mapping, gene-expression and genome manipulations are the main focuses of the research currently being conducted. The end goal is to create high quality and fast growing animals for the industry. The present study focused on the development of microsatellite markers and the detection of quantitative trait loci (QTL) affecting growth traits (shell length, shell width, wet weight) in this species. A combination of three methods, namely selective genotyping and bulked segregant analysis (pooling analysis), single marker regression and interval mapping were used to identify putative QTL in two full-sib families from two different farmed locations. Additional methods and protocols were developed that can assist the industry in other molecular research aspects. A total of 125 microsatellite loci were characterised. A total of 82 of these loci were isolated using second generation sequencing, a first for any abalone species. A preliminary, low-density framework linkage map was constructed containing 50 loci that mapped to 18 linkage groups. The observed genome length was 148.72cm with coverage of ±47%. QTL analyses revealed two putative QTL for shell width and wet weight, with 17% and 15% variance explained, that mapped on one linkage group in the first family and three putative QTL, for shell length, shell width and wet weight, with 33%, 28.5% and 31.5% variance explained, that mapped on one linkage group in the second family. Additional methods and protocols developed include an automated high-throughput DNA isolation protocol, a real-time PCR assay for H. midae x H. spadicea hybrid verification, a triploid verification microsatellite assay and a pre- and post-PCR multiplex setup and optimisation protocol. Future studies focussing on QTL and marker assisted selection (MAS) should verify the QTL found in this study and also utilise additional family structures and determine QTL-marker phase within the commercial populations.AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse perlemoen, Haliotis midae, is ’n kommersieel waardevolle weekdier en word hoofsaaklik na die Verre-Ooste uitgevoer. Genetiese navorsing op H. midae het aansienlik toegeneem sedert ’n genetiese verbeteringsprogram in 2006 deur samewerking tussen die Universiteit van Stellenbosch, die regering en industrievennote ingebring is. Die ontwikkeling van molekulêre merkers, KEL-kartering, geen-uitdrukking en genoom manipulasies is die hooffokusse van die navorsing wat tans uitgevoer word. Die einddoel is om hoë kwaliteit en snelgroeiende diere vir die industrie te skep. Die huidige studie het op die ontwikkeling van mikrosatelliet merkers en die opsporing van groeiverwante (skulplengte, -breedte en nat gewig) kwantitatiewe eienskap lokusse (KEL) in hierdie spesie gefokus. ’n Kombinasie van drie metodes, naamlik selektiewe genotipering en versamelde segregaat analise (samevoegingsanalise), enkel merker regressie en intervalkartering is gebruik om waarskynlike KEL in twee vol-sibbe families van twee verskillende produksiegebiede te identifiseer. Aanvullende metodes en protokolle is ontwikkel wat die industrie in ander molekulêre navorsingsaspekte kan ondersteun. ’n Totaal van 125 mikrosatelliet lokusse is beskryf. ’n Totaal van 82 van hierdie lokusse is deur die gebruik van derde generasie volgordebepaling geïsoleer, ’n eerste vir enige perlemoen spesie. ’n Voorlopige, laedigtheid raamwerkkoppelingskaart is saamgestel met 50 lokusse wat op 18 koppelingsgroepe gekarteer is. Die waarneembare genoomlengte was 148.72cm met ’n dekking van ±47%. KEL-analises het twee waarskynlike KEL vir skulpbreedte en nat gewig blootgelê wat 17% en 15% variasie verduidelik en is op een koppelingsgroep in die eerste familie gekarteer asook drie waarskynlike KEL, vir skulplengte, -breedte en nat gewig wat 33%, 28.5% en 31.5% variasie verduidelik en is op een koppelingsgroep in die tweede familie gekarteer. Aanvullende metodes en protokolle wat ontwikkel is, sluit ’n geoutomatiseerde hoë-deurgang DNS-isolasieprotokol, ’n intydse PKR-proef vir H. midae x H. spadicea hibried verifikasie, ’n triploïed verifikasie mikrosatellietproef en veelsoortige pre- en post-PKR opstelling en optimaliseringsprotokol in. Toekomstige studies wat fokus op KEL en merker ondersteunde seleksie (MOS) behoort die KEL wat in hierdie studie gevind is te verifieer en ook bykomende familie strukture te benut om KEL-merker fases binne die kommersiële populasie te bepaal

Molecular analysis of genetic variation and relationships within the population of abalone (Haliotis midae) at the Sea Plant Products abalone hatchery, Hermanus, R.S.A.

Thesis (MSc)--University of Stellenbosch, 2004.ENGLISH ABSTRACT: The species Haliotis midae is the only commercially exploitable abalone species of the six found in the South African coastal waters. This species is under substantial pressure from both legal and illegal harvesters, to such an extent that it could be commercially extinct within four years. Efforts to alleviate the pressures on the natural populations of both illegal and legal harvesting are being made. The genetic management systems for abalone farming and ranching activities should be carefully evaluated. The loss of genetic diversity and the risks of contaminating the gene pools of natural populations in the vicinity of a farm should be minimized. Genetic evaluation studies will be at great importance to acquire the necessary data needed for genetic diversity and differentiation analysis. The aim at this study was to develop species-specific microsatellite DNA markers to assess the genetic diversity and differentiation within and between the brood stock and commercial stock of the Sea Plant Products abalone farm (Hermanus, Republic of South Africa) and natural populations related to the brood stock. The species-specific DNA markers were also used for parentage assignments within the tarm population (first for abalone) and preliminary OTL (quantitative trait loci)-discovery analysis studying growth rate segregation. Samples were taken of the farm's brood stock and commercial stock (Rows 2, 3, 4) as well as from two natural populations (Saldanha Bay and Black Rock) related to the brood stock. Various statistical parameters and software packages were used to assess genetic diversity and differentiation, to infer parentage and to look for OTL's. Eight species-specific microsatellite DNA markers were designed and used for data analysis. Data analysis showed a loss at genetic diversity from the brood stock to the commercial stock caused by the subdivision of the original brood stock into rows and the differential contributions of parents to the offspring. No genetic differentiation (Fst) was detected between the farm and natural populations, except for the offspring of Row2. levels of inbreeding (ns) were high for all loci within the populations. Thirty-eight percent of all studied offspring were confidently assigned to a couple. The preliminary QTldiscovery suggested the segregation of a number of alleles and genotypes with growth rate. The study concluded that the commercial abalone population of the Sea Plant Products abalone farm holds no threat to the disruption of the genetic diversity of the natural populations. It is proposed that the farm implement a rotational breeding program to increase the genetic diversity of the commercial population. Any newly acquired brood stock must be profiled before their introduction into the breeding program to assess the influence of the animals on the current levels of genetic diversity within the farm. The accuracy and reliability of parentage assignments and QTl-discovery need to be optimised by adding more loci and sampling more animals or even by trying and developing new methods.AFRIKAANSE OPSOMMING: Van die ses perlemoen spesies wat langs die Suid-Afrikaanse kus gevind word, is die spesie Haliotis midae die enigste een wat van kommersiële belang is. Wettige, sowel as onwettige versameling, plaas hierdie spesie onder sulke geweldige druk dat dit dalk binne vier jaar verlore kan wees vir die kommersiële bedryf. Verskeie strategieë word tans geïmplimenteer om hierdie druk te verlig. Die genetiese bestuurstrategieë binne perlemoen plase moet deeglik ondersoek word. Die verlies aan genetiese diversiteit en die moontlikheid vir die kontaminering van die natuurlike populasies in die omgewing van die plaas se geenpoel, moet uitgeskakel word. Genetiese evaluasies sal van groot belang wees om die nodige data vir genetiese diversiteit- en differensiasie-analises te verkry. Die doel van die studie was om spesies-spesifieke mikrosatelliet DNA merkers te ontwikkel wat gebruik sou word om die genetiese diversiteit en differensiasie binne en tussen die broei diere en die kommersiële diere van Sea Plant Products se perlemoen plaas (Hermanus, Republiek van Suid- Afrika) en die natuurlike populasies wat verwant is aan die broei diere, te bepaal. Die spesies-spesifieke DNA merkers is ook vir ouerskap-bepalings binne die plaas se populasie gebruik, asook vir voorlopige OTL (quantitative trait locI) - ontdekking met betrekking tot groeitempo segregasie. Monsters van die plaas se broei diere en kommersiële diere (Ry 2, 3, 4) asook van twee natuurlike populasies (Saldanha Baai en Black Rock) wat verwant is aan die broei diere, is geneem. 'n Verskeidenheid van statistiese parameters en sagteware pakette is vir die genetiese diversiteit- en differensiasie-analises, vir ouerskap-bepalings en vir die opspoor van OTL's gebruik. Agt spesies-spesifieke mikrosatelliet DNA merkers is ontwerp en toe gebruik vir die data analises. 'n Verlies aan genetiese diversiteit vanaf die broei diere na die kommersiële diere is deur die data analises uitgewys. Dit is veroorsaak deur die verdeling van die oorspronklike broei diere in rye en die differensiële bydraes deur die ouers na die nageslag. Geen genetiese differensiasie (Fst) is tussen die plaas se populasie en die natuurlike populasies gevind nie, maar die nageslag van Ry 2 het wel differensiasie getoon. Die vlakke van inteling (Fis) was hoog oor alle lokusse binne alle populasies. Agt-en-dertig persent van die nageslag wat bestudeer is, was suksesvol met 'n ouerpaartjie geassosieer. Die voorlopige OTL-ontdekking studie toon die potesiële segregasie van 'n aantal allele en genotipes saam met groeitempo. Die bevindinge van die studie is dat die kommersiële populasie op die Sea Plant Products perlemoen plaas, geen bedreiging vir die versteuring van die natuurlike populasies se genetiese diversiteit inhou nie. Daar is voorgestel dat die plaas 'n rotasie-basis broeiprogram moet implimenteer om sodoende die genetiese diversiteit van die kommersiële populasie te verhoog. Enige nuwe broei diere se genetiese profiel moet ook voor die tyd ondersoek word om te sien wat se effek hierdie diere op die huidige genetiese diversiteit van die kommersiële populasie sal hê. Die akkuraatheid en betroubaarheid van die ouerskap-bepalings en OTL-ontdekking moet optimiseer word deur of meer lokusse te bestudeer, of meer diere in analises te gebruik of selfs om nuwe tegnieke te probeer of te ontwikkel

Whats your mummy doing? An overview of the status of mummy research with reference to the 8th world congress

Please cite as follows: Slabbert, R., Swanepoel, L. & Cornelius, I. 2015. Wat maak jou mummie? ’n Oorsig van die stand van mummienavorsing aan die hand van die 8ste wêreldkongres. Tydskrif vir Geesteswetenskappe, 55(1):1-14, doi.10.17159/2224-7912/2015/v55n1a1.The original publication is available at http://www.scielo.org.za/scielo.php?script=sci_issuetoc&pid=0041-475120150001&lng=en&nrm=isoDie doel van hierdie artikel is om opsommend al die temas en studierigtings te beskryf wat by die 8ste Wêreldkongres oor Mummienavorsing aangebied is om die huidige stand van die bestudering van mummies aan te dui. Mummies is unieke bronne van inligting oor die verlede en die studie van mummies gee ons insig in die lewens van mense uit vervloë dae en van vele kulture. Mummies het nog altyd bekoor, selfs vandag nog. Die 8ste Wêreldkongres oor Mummienavorsing is vanaf 6 tot 9 Augustus 2013 in Rio de Janeiro, Brasilië, gehou. Hierdie kongres bring wetenskaplikes bymekaar wat mummies en hul toebehore bestudeer. Die 8ste kongres het verskeie internasionaal erkende navorsers se werk deur middel van 99 referate en 45 plakkaataanbiedings ten toon gestel. Twee plakkate het selfs oor werk gehandel wat in Suider-Afrika gedoen word, naamlik die studie van antieke Egiptiese dieremummies in Iziko Museums van Suid-Afrika (Kaapstad) en die studie van die Tuli-mummie wat in Botswana gevind is. Die wetenskaplike studie van mummies is goed gevestig en toon merkwaardige groei. Die enigste kritiek teen die kongres is egter die oordrewe klem op suiwer wetenskaplike studie en dat die kulturele en sosiale interpretasie van die mummies grootliks agterweë gelaat is. Die natuur-, mediese en chemiese wetenskappe is goed verteenwoordig en die data is waardevol, maar die ware integrasie van hierdie en die sosiale wetenskappe is nog onvoldoende. ’n Meer gebalanseerde kombinasie van die verskillende dissiplines sal die waarde van so ’n kongres aansienlik verhoog.The aim of this article is to summarise the current state of mummy research by describing all the themes and fields of study which were covered during the 8th World Congress on Mummy Studies. Mummies are exceptional and unique sources of information about the past. The study of mummies gives us insight into the lives of peoples from bygone eras and their cultures. A mummy is the preserved body of either a human or an animal and includes skin, hair and flesh, regardless of whether it was created by natural processes or artificial methods. The best-known mummies are those from ancient Egypt, but mummies are found all over the world, from Europe to South America and even Australia. Mummification is the process whereby a mummy is created. A distinction is made between natural mummification and artificial or rather intentional mummification. Both the technical and religious aspects of mummification are of great importance when studying the funeral practices of ancient societies. Mummies have always fascinated the scientific community as well as everyday folk, a trend that continues to this day. The study of mummies and the processes and mechanisms responsible for mummification has a long and varied history. Modern mummy research is an interdisciplinary field which makes use of highly advanced experimental and analytical methodologies. Anthropologists, anatomists, chemists, physicists, biologists, geneticists and other specialists are working together to reveal the secrets of mummies. To facilitate this atmosphere of collaboration the 8th World Congress on Mummy Studies was held in Rio de Janeiro in Brazil from 6 to 9 August 2013. This congress brought together a number of scientists who work on mummies and their paraphernalia. The 8th congress exhibited the work of various internationally recognised researchers – in the form of 99 papers and 45 posters. Two posters even presented work that was done in Southern Africa, namely the study of ancient Egyptian animal mummies in Iziko Museums of South Africa (Cape Town) and the study of the Tuli mummy which was found in Botswana. Other work that was presented at this congress covered a number of scientific disciplines. The study of ancient DNA has grown in popularity as the advances in technology increased. Ancient DNA is useful in studying human population history and the evolution of diseases such as tuberculosis. Techniques such as gas chromatography-mass spectrometry (GC-MS) and high performance liquid chromatography (HPLC) are also popular when studying ancient pathogens. The most popular technique used by scientists presenting at the congress was computed tomography, better known as CT-scanning. This technology uses x-rays to create cross-sections or whole threedimensional images of both organic and inorganic samples. This technique is perfect for nondestructive and non-invasive studies of mummified materials. Researchers can use this technology to perform a virtual autopsy on valuable specimens without cutting or removing anything. Information can be gathered on the health status of the mummy. The presence of tuberculosis lesions, heart disease, skeletal deformities and dental pathologies can be studied using CT-scanning technologies. Other objects associated with mummies and mummy burials can also be examined with CT-scanning. Amulets, jewellery and other known or unidentified trinkets found in mummy bundles can be seen in the scanning data and isolated to be studied in more detail. The congress showed that the scientific study of mummies is a healthy and growing field. However, the only criticism about the congress is the excessive emphasis on the pure scientific studies while the cultural and social interpretation of the data and the mummies are being neglected to a great extent. The natural, medical and chemical sciences are well represented and the data are valuable, but a true integration of the social sciences and natural sciences is still insufficient. The importance and scientific value of the congress, if such a balanced combination can be achieved in future, will increase greatly.Publishers' Versio

Molecular markers to assist the South African abalone industry

CITATION: Roodt-Wilding, R. & Slabbert, R. 2006. Molecular markers to assist the South African abalone industry. South African Journal of Science, 102(3-4):99-102.The original publication is available at https://journals.co.zaHALIOTIS MIDAE (PERLEMOEN) IS THE ONLY southern African species of abalone to be commercially exploited. Commercial farms are currently producing 750 tons per annum, making this an economically viable enterprise. Increasing world demand and dwindling natural populations have, however, necessitated the adoption of genetic management practices on South African abalone farms to remain sustainable. This can be done by means of DNA markers, which are employed to investigate various phenomena from genetic diversity, parentage and broodstock contributions to linkage mapping and marker-assisted selection for genetic enhancement of the commercial species. The use of microsatellite markers for various abalone aquaculture applications is highlighted in this review.https://journals.co.za/content/sajsci/102/3-4/EJC96525Publisher's versio

Looking inside votive creatures : computed tomography (CT) scanning of ancient Egyptian mummified animals in Iziko Museums of South Africa : a preliminary report

Please cite as follows: Cornelius, I., Swanepoel, L. C., Du Plessis, A. & Slabbert, R. 2012. Looking inside votive creatures: computed tomography (CT) scanning of ancient Egyptian mummified animals in Iziko Museums of South Africa: a preliminary report. Akroterion, 57:129-148, doi:10.7445/57-0-135.The original publication is available at http://akroterion.journals.ac.zaThe ancient Egyptians mummified many more animals than humans. The study of ancient Egyptian animal mummies is varied and extensive. Currently new methodologies and modern technology are being used to unlock the secrets of animal mummies. Recently five animal mummies housed in the Egyptian collection of Iziko Museums of South Africa in Cape Town were scanned using a state of the art computed tomography (CT) scanner at Stellenbosch University. Preliminary results revealed two complete bird skeletons, a claw, a fake and the partial skeleton of what appears to be a cat.http://akroterion.journals.ac.za/pub/article/view/135Publisher's versio

Verification of authenticity and fraud detection in South African honey using NIR spectroscopy

The South African honey industry will benefit from a reliable method that can verify authenticity as well as detect fraudulence of honey that is on the market. This work presents the use of near-infrared (NIR) spectroscopy in combination with chemometrics as a fast and relatively inexpensive method to discriminate between authentic South African and imported and/or adulterated honey. A supervised chemometric approach was followed on NIR spectra collected from genuine South African honey, as well as intentionally adulterated honeys with sugar solutions (glucose and fructose) and also cheap imported honey. By using partial least squares discriminant analysis (PLS-DA), overall classification accuracies of between 93.3% and 99.9% were obtained when using three different NIR instruments (a laboratory instrument, as well as a portable and a mobile instruments). The usefulness of NIR spectroscopy for accurate honey classifications, regardless the instrument specifications, are demonstrated