Biology subjects

Mattison, S.

Publications and source records attributed to Mattison, S..

3 recordsLinked to original sources

bioRxiv2020

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic

The COVID-19 pandemic spread very fast around the world. A few days after the first detected case in South Africa, an infection started a large hospital outbreak in Durban, KwaZulu-Natal. Phylogenetic analysis of SARS-CoV-2 genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. In this manuscript, we outline the obstacles we encountered in order to genotype SARS-CoV-2 in real-time during an urgent outbreak investigation. In this process, we encountered problems with the length of the original genotyping protocol, reagent stockout and sample degradation and storage. However, we managed to set up three different library preparation methods for sequencing in Illumina. We also managed to decrease the hands on library preparation time from twelve to three hours, which allowed us to complete the outbreak investigation in just a few weeks. We also fine-tuned a simple bioinformatics workflow for the assembly of high-quality genomes in real-time. In order to allow other laboratories to learn from our experience, we released all of the library preparation and bioinformatics protocols publicly and distributed them to other laboratories of the South African Network for Genomics Surveillance (SANGS) consortium.

genomics↗

bioRxiv2018

The expendable male hypothesis

Matrilineal descent confers lineage membership via the female line. In matrilineal descent systems, men share lineage membership not with their own children, but with their sisters children. The theoretically influential concept of the matrilineal puzzle posits that men experience tension between the desire to exert control over their natal kin (i.e., the lineage to which they belong) and over their affinal kin (i.e., their spouses and their biological children). The rationale for this puzzle rests on two fundamental assumptions: (i) that men are always in positions of authority over women; and (ii) that men are interested in the outcomes of parenting. In this paper, we suggest that the matrilineal puzzle does not exist from an evolutionary perspective. Instead, we examine what ecological conditions might render men expendable within local kinship configurations-specifically when (i) women, without significant assistance from men, are capable of meeting the subsistence needs of their families; and (ii) men have little to gain from parental investment in children. We conclude that the expendable male hypothesis may explain the evolution of matrilineal descent in numerous cases, and by noting that female-centered approaches that call into doubt assumptions inherent to male-centered models of kinship are justified in evolutionary perspective.\n\nO_QD\"...for some females there exist important advantages for male care ... For many females male parental care has small or negligible effects on female reproductive success, suggesting that as a general explanation for social monogamy, the Male Care is Essential Hypothesis is inadequate.\" - Gowaty 1996 [1]\n\nC_QD

animal behavior and cognition↗

bioRxiv2018

High altitude adaptation mitigates anemia risk associated with diabetes among the Mosuo of Southwest China

Human populations native to high altitude regions ([≥]2500 m) exhibit numerous adaptations to hypoxic stress. On the Tibetan Plateau, these include modifications of the hypoxia inducible factor (HIF) pathway to essentially uncouple erythropoiesis (red blood cell production) and blood hemoglobin (Hb) concentration--which normally increase in response to low oxygen--from hypoxia. Uncoupling of erythropoiesis and hypoxia is also observed among people with diabetes due to damage to kidney tissues. This is hypothesized to result in elevated risk for anemia among diabetics, which increases risk for cardiovascular disease and death. We tested the hypothesis that the independence of erythropoiesis from HIF among high-altitude adapted populations of the Tibetan Plateau may protect against diabetes-associated anemia. We investigated this hypothesis among the Mosuo, a population living in Yunnan Province, China (at ~2800 m altitude) that is undergoing rapid market integration and lifestyle change, with concomitant increase in risk for type 2 diabetes. We found that, although diabetes (glycated hemoglobin, HbA1c [≥]6.5%) is associated with anemia (females: Hb<12g/dl; males: Hb<13g/dl) among the Chinese population as a whole (N: 5,606; OR: 1.48; p: 0.008), this is not the case among the Mosuo (N: 316; OR: 1.36; p: 0.532). Both pathways uncoupling hypoxia from erythropoiesis (diabetic disease and high altitude adaptation) are incompletely understood; their intersection in protecting Mosuo with diabetes from anemia may provide insight into the mechanisms underlying each. Further, these findings point to the importance of understanding how high-altitude adaptations interact with chronic disease processes, as populations like the Mosuo experience rapid market integration.

evolutionary biology↗