Ornithology of the Kelabit Highlands of Sarawak, Malaysia

The Kelabit Highlands played a key role in the development of modern Bornean ornithology. The Highlands consist of a plateau at 1000-1200 m with substantial wet rice paddy and surrounding taller mountains. These physical features lead to an unusual combination of montane, lowland, and migratory birds. This avifauna was studied in the 1940s to 1950s by two ornithologists whose collaboration helped usher in the modern era of Bornean ornithology: Tom Harrisson of the Sarawak Museum and Dean Amadon of the American Museum of Natural History. We examine their collaboration and explain how these men contributed to Bertram Smythies' milestone book, The Birds of Borneo (1960). Although the roles of Harrisson and Smythies in Bornean ornithology are well known, the contribution of Dean Amadon is not generally appreciated, and we clarify it. In the process, we also consider modern work on the Kelabit avifauna, including our own expedition in 2011, and the current status of Kelabit birds and issues relating to their conservation and potential for further stud

Using a machine learning technique to prospectively match Donor and Recipient pairs for bone marrow transplantation

Current matching procedures to select donors for transplantation are time consuming and expensive. We have developed a novel DNA based method of tissue typing termed MHC block matching. The technique not only matches the class I and II genes of the human Major Histocompatibility Complex (MHC) but also the alleles at yet undefined loci that affect transplantation outcome. The densitometric profile (obtained after PCR and scanning with a laser on a Corbett Research GS 2000 Gel Scanner) from donors are compared to that of potential recipients. Differences in the profiles of the donor and recipient are biologically relavent due to sequence differences in the MHC genes and they correlate to outcome. Our aim is to identify critical regions of the profile which have to be matched for successful transplant outcome. Thus, in an unrelated context, we are able to recognise permissible mismatches as well as important genes for transplantation. This presentation describes the use of a decision-trees, a feature-based machine learning technique, that learns from example the biological relavent regions in profile pairs that contribute to outcome. We will discuss the method of feature extraction to obtain a set of characteristic features for a given set of profile pairs and report on our initial results from constructing a decision tree and dealing with issues of noise in the training set

Identifying features from MHC block matching scans using artificial intelligence

No abstract availabl

Identifying features from MHC block matching profiles

No abstract availabl

The development of sequence-based-typing of myostatin (GDF-8) to identify the double muscling phenotype in the goat

Myostatin (or GDF-8) is a member of the TGF-β superfamily, which has been associated with carcass traits in beef breeds. Six polymorphisms within exons 2 and 3 of the cattle myostatin sequence results in a "loss of function" that give rise to a hyperplasia of skeletal muscle in a phenotype known as 'double muscling' (mh). As with beef producing breeds, goat meat breeds such as the South African Boer goat were selected on the basis of superior growth characteristics and carcass traits. The study was aimed at identifying polymorphisms found in the goat myostatin sequence. PCR and sequencing primers were designed for the goat based on information from nucleotide sequences of cattle myostatin in GenBank. The six polymorphisms that give rise to double muscling in cattle were not detected in the goat sequence. However, 38 nucleotide differences are described between the myostatin sequences in cattle and that of the goat. There were 25 non-synonymous changes and 13 synonymous changes. The ability to type for these polymorphisms provides an opportunity to assess further mutation in ruminants

Myostatin and its implications on animal breeding: a review

Myostatin, or growth and differentiation factor 8 (GDF8), has been identified as the factor causing a phenotype known as double muscling, in which a series of mutations render the gene inactive, and therefore, unable to regulate muscle fibre deposition. This phenotype occurs at a high frequency in some breeds of cattle such as Belgian Blue and Peidmontese. Phylogenetic analysis has shown that there has been positive selection pressure for non-synonymous mutations within the myostatin gene family, around the time of the divergence of cattle, sheep and goats, and these positive selective pressures on non-ancestral myostatin are relatively recent. To date, there have been reports of nine mutations in coding regions of myostatin that cause non-synonymous changes, of which three cause missense mutations. including two in exon 1 and one in exon 2. The remaining six mutations, located in exons 2 and 3, result in premature stop codons, which are the mutations responsible for the double-muscling phenotype. Unfortunately, breed management problems exist for double-muscled cattle, such as birthing difficulties, which can be overcome through genetically controlled breeding programmes, as shown in this review

MHC haplotype analysis by artificial neural networks

Conventional matching is based on numbers of alleles shared between donor and recipient. This approach, however, ignores the degree of relationship between alleles and haplotypes, and therefore the actual degree of difference. To address this problem, we have compared family members using a block matching technique which reflects differences in genomic sequences. All parents and siblings had been genotyped using conventional MHC typing so that haplotypes could be assigned and relatives could be classified as sharing 0, 1 or 2 haplotypes. We trained an Artificial Neural Network (ANN) with subjects from 6 families (85 comparisons) to distinguish between relatives. Using the outputs of the ANN, we developed a score, the Histocompatibility Index (HI), as a measure of the degree of difference. Subjects from a further 3 families (106 profile comparisons) were tested. The HI score for each comparison was plotted. We show that the HI score is trimodal allowing the definition of three populations corresponding to approximately 0, 1 or 2 haplotype sharing. The means and standard deviations of the three populations were found. As expected, comparisons between family members sharing 2 haplotypes resulted in high HI scores with one exception. More interestingly, this approach distinguishes between the 1 and 0 haplotype groups, with some informative exceptions. This distinction was considered too difficult to attempt visually. The approach provides promise in the quantification of degrees of histo-compatibility

Comparison of the milk quality of the South African Boer and Australian Rangeland goats

Milk composition studies on goats are limited and have mainly concentrated on traditional dairy breeds. Since goats have the advantage of producing larger volumes over a longer lactation period, systematic studies to define the quality of goats milk is warranted. There is anecdotal evidence amongst goat breeders suggesting that some breeds of goat produce highly nutritious milk. In this study, the milk composition of the South African Boer and the Australian Rangeland goats were evaluated. Milk from the Boer goat contained significantly higher fat concentration compared to the Australian Rangeland goat (7.1 versus 3.3% at week 6). There were significant differences in the milk protein levels in the early stages of lactation between the Boer and Rangeland goats (5.1 versus 3.6% at week 4), however the levels were similar at week 6. In contrast, there was no significant difference in Somatic Cell Counts between the milk from the two breeds of goat. The milk lactose level of the Australian Rangeland goat was significantly higher than in the Boer goat (5.0 versus 5.3% at week 4, and 5.4 versus 5.6% at week 6)

Evolution, ecology, and zoonotic transmission of Betacoronaviruses: A Review

Coronavirus infections have been a part of the animal kingdom for millennia. The difference emerging in the twenty-first century is that a greater number of novel coronaviruses are being discovered primarily due to more advanced technology and that a greater number can be transmitted to humans, either directly or via an intermediate host. This has a range of effects from annual infections that are mild to full-blown pandemics. This review compares the zoonotic potential and relationship between MERS, SARS-CoV, and SARS-CoV-2. The role of bats as possible host species and possible intermediate hosts including pangolins, civets, mink, birds, and other mammals are discussed with reference to mutations of the viral genome affecting zoonosis. Ecological, social, cultural, and environmental factors that may play a role in zoonotic transmission are considered with reference to SARS-CoV, MERS, and SARS-CoV-2 and possible future zoonotic events