title: Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

authors: Oliveira, Sandra

abstract: Previous research indicates that human genetic diversity in Wallacea—islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves—has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter–gatherer communities. Yet, inferences based on present-day groups proved insufficient to disentangle this region’s demographic movements and admixture timings. Here, we investigate the spatio-temporal patterns of variation in Wallacea based on genome-wide data from 16 ancient individuals (2600–250 years BP) from the North Moluccas, Sulawesi and East Nusa Tenggara. While ancestry in the northern islands primarily reflects contact between Austronesian- and Papuan-related groups, ancestry in the southern islands reveals additional contributions from Mainland Southeast Asia that seem to predate the arrival of Austronesians. Admixture time estimates further support multiple and/or continuous admixture involving Papuan- and Asian-related groups throughout Wallacea. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.

text: Ancient genomes from the last three millennia support multiple human dispersals into Wallacea Previous research indicates that human genetic diversity in Wallacea—islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves—has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter–gatherer communities. Yet, inferences based on present-day groups proved insufficient to disentangle this region’s demographic movements and admixture timings. Here, we investigate the spatio-temporal patterns of variation in Wallacea based on genome-wide data from 16 ancient individuals (2600–250 years BP) from the North Moluccas, Sulawesi and East Nusa Tenggara. While ancestry in the northern islands primarily reflects contact between Austronesian- and Papuan-related groups, ancestry in the southern islands reveals additional contributions from Mainland Southeast Asia that seem to predate the arrival of Austronesians. Admixture time estimates further support multiple and/or continuous admixture involving Papuan- and Asian-related groups throughout Wallacea. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.

year: 2022

title: Determination of ribonuclease sequence-specificity using Pentaprobes and mass spectrometry

authors: McKenzie, Joanna Leigh

subjects: Mycobacteria

abstract: The VapBC toxin-antitoxin (TA) family is the largest of nine identified TA families. The toxin, VapC, is a metal-dependent ribonuclease that is inhibited by its cognate antitoxin, VapB. Although the VapBCs are the largest TA family, little is known about their biological roles. Here we describe a new general method for the overexpression and purification of toxic VapC proteins and subsequent determination of their RNase sequence-specificity. Functional VapC was isolated by expression of the nontoxic VapBC complex, followed by removal of the labile antitoxin (VapB) using limited trypsin digestion. We have then developed a sensitive and robust method for determining VapC ribonuclease sequence-specificity. This technique employs the use of Pentaprobes as substrates for VapC. These are RNA sequences encoding every combination of five bases. We combine the RNase reaction with MALDI-TOF MS to detect and analyze the cleavage products and thus determine the RNA cut sites. Successful MALDI-TOF MS analysis of RNA fragments is acutely dependent on sample preparation methods. The sequencespecificity of four VapC proteins from two different organisms (VapCPAE0151 and VapCPAE2754 from Pyrobaculum aerophilum, and VapCRv0065 and VapCRv0617 from Mycobacterium tuberculosis) was successfully determined using the described strategy. This rapid and sensitive method can be applied to determine the sequence-specificity of VapC ribonucleases along with other RNA interferases (such as MazF) from a range of organisms. Published by Cold Spring Harbor Laboratory Press.

text: Determination of ribonuclease sequence-specificity using Pentaprobes and mass spectrometry The VapBC toxin-antitoxin (TA) family is the largest of nine identified TA families. The toxin, VapC, is a metal-dependent ribonuclease that is inhibited by its cognate antitoxin, VapB. Although the VapBCs are the largest TA family, little is known about their biological roles. Here we describe a new general method for the overexpression and purification of toxic VapC proteins and subsequent determination of their RNase sequence-specificity. Functional VapC was isolated by expression of the nontoxic VapBC complex, followed by removal of the labile antitoxin (VapB) using limited trypsin digestion. We have then developed a sensitive and robust method for determining VapC ribonuclease sequence-specificity. This technique employs the use of Pentaprobes as substrates for VapC. These are RNA sequences encoding every combination of five bases. We combine the RNase reaction with MALDI-TOF MS to detect and analyze the cleavage products and thus determine the RNA cut sites. Successful MALDI-TOF MS analysis of RNA fragments is acutely dependent on sample preparation methods. The sequencespecificity of four VapC proteins from two different organisms (VapCPAE0151 and VapCPAE2754 from Pyrobaculum aerophilum, and VapCRv0065 and VapCRv0617 from Mycobacterium tuberculosis) was successfully determined using the described strategy. This rapid and sensitive method can be applied to determine the sequence-specificity of VapC ribonucleases along with other RNA interferases (such as MazF) from a range of organisms. Published by Cold Spring Harbor Laboratory Press.

year: 2012

title: Using a digital library as a Māori language learning resource: Issues and possibilities

authors: Mato, Paora James

subjects: Digital Library

abstract: The development of electronic language learning resources, founded on digital library technology, is a capability that, to date, is largely unrealised. The Flexible Language Acquisition (FLAX) project is a digital library initiative at the University of Waikato in New Zealand. The current FLAX activities provide practice for students who are learning English as an additional language. The prospect of extending this resource to include te reo Māori is as exciting as it is groundbreaking. The outcomes of this research inform the issues and possibilities involved in creating such resources.

The World Wide Web has allowed an everyday access to the Internet, but finding and retrieving pertinent information is often a convoluted and time-consuming exercise. The normal outcome is that users are unable to take full advantage of the available resources. Digital libraries have an unprecedented power in terms of organising and storing vast amounts of information and, with built-in retrieval functionality, serve as ideal repositories. The ability to focus the information within these repositories is extremely significant because there is no longer the chaff that normally results from Internet searches. Purposeful learning activities can be presented exploiting an assortment of media and drawing on stored information that can be assembled in a range of formats. Such capacity, flexibility and diversity is normally only encountered at traditional, physical libraries.

The research includes an overview of digital libraries and some of the language learning resources that are currently available on the Internet. Since the target language is te reo Māori, a critical review on the features of kaupapa Māori theory, pedagogy and Māori pedagogy is undertaken. Using the concepts discussed in this review, the language learning activities associated with the FLAX project are analysed to determine their suitability for learning te reo Māori. Further feedback was provided by a sample group following their testing of a selection of activities that were based on text written in te reo Māori. 
 

The analysis suggests the current range of FLAX activities have more benefit to students as tools that allow practice of the learning that has been delivered in face-to-face classroom settings, rather than as a standalone language learning resource. In their present form, the main benefits of the activities predominantly rest in the way they were performed rather than in the activities themselves. Furthermore, commentary from the testing group regarded the activities as more beneficial for practicing sentence structures, grammar and punctuation, rather than actual language learning. The group generally agreed, however, that combining the activities with methods of oral and aural transmission, in te reo Māori, would certainly result in more effective language learning outcomes.

The legitimacy of digital library-based language learning activities lies in designs that promote learner-centred interaction that is consistent with best practice communicative learning theory. When the target language is te reo Māori, it is of the utmost importance that the activities are tailored to embrace a Māori world view in ways that promote the learning rather than the activity or the content.

text: Using a digital library as a Māori language learning resource: Issues and possibilities The development of electronic language learning resources, founded on digital library technology, is a capability that, to date, is largely unrealised. The Flexible Language Acquisition (FLAX) project is a digital library initiative at the University of Waikato in New Zealand. The current FLAX activities provide practice for students who are learning English as an additional language. The prospect of extending this resource to include te reo Māori is as exciting as it is groundbreaking. The outcomes of this research inform the issues and possibilities involved in creating such resources.

The World Wide Web has allowed an everyday access to the Internet, but finding and retrieving pertinent information is often a convoluted and time-consuming exercise. The normal outcome is that users are unable to take full advantage of the available resources. Digital libraries have an unprecedented power in terms of organising and storing vast amounts of information and, with built-in retrieval functionality, serve as ideal repositories. The ability to focus the information within these repositories is extremely significant because there is no longer the chaff that normally results from Internet searches. Purposeful learning activities can be presented exploiting an assortment of media and drawing on stored information that can be assembled in a range of formats. Such capacity, flexibility and diversity is normally only encountered at traditional, physical libraries.

The research includes an overview of digital libraries and some of the language learning resources that are currently available on the Internet. Since the target language is te reo Māori, a critical review on the features of kaupapa Māori theory, pedagogy and Māori pedagogy is undertaken. Using the concepts discussed in this review, the language learning activities associated with the FLAX project are analysed to determine their suitability for learning te reo Māori. Further feedback was provided by a sample group following their testing of a selection of activities that were based on text written in te reo Māori. 
 

The analysis suggests the current range of FLAX activities have more benefit to students as tools that allow practice of the learning that has been delivered in face-to-face classroom settings, rather than as a standalone language learning resource. In their present form, the main benefits of the activities predominantly rest in the way they were performed rather than in the activities themselves. Furthermore, commentary from the testing group regarded the activities as more beneficial for practicing sentence structures, grammar and punctuation, rather than actual language learning. The group generally agreed, however, that combining the activities with methods of oral and aural transmission, in te reo Māori, would certainly result in more effective language learning outcomes.

The legitimacy of digital library-based language learning activities lies in designs that promote learner-centred interaction that is consistent with best practice communicative learning theory. When the target language is te reo Māori, it is of the utmost importance that the activities are tailored to embrace a Māori world view in ways that promote the learning rather than the activity or the content.

year: 2009