Biology subjects

Inta, A.

Publications and source records attributed to Inta, A..

4 recordsLinked to original sources

bioRxiv2024

Identification of Southeast Asian Anopheles mosquito species with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using a cross-correlation approach

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is proposed for mosquito species identification. The absence of public repositories for sharing mass spectra and of open-source data analysis pipelines for fingerprint matching to mosquito species limits widespread use of this technology. The objective of this study was to develop an open-source data analysis pipeline for Anopheles species identification with MALDI-TOF MS. Malaria mosquitos were captured in 33 villages in Karen (Kayin) state in Myanmar. 359 specimens were identified with DNA barcodes and assigned to 21 sensu stricto species and 5 sibling species pairs or complexes. 3584 mass spectra of the head of these specimens identified with DNA barcoding were acquired and the similarity between mass spectra was quantified using a cross-correlation approach adapted from the published literature. A simulation experiment was carried out to evaluate the performance of species identification with MALDI-TOF MS at varying thresholds of cross-correlation index for the algorithm to output an identification result and with varying numbers of technical replicates for the tested specimens, considering PCR identification results as the reference. With one spot and a threshold value of -14 for the cross-correlation index on the log scale, the sensitivity was 0.99 (95%CrI: 0.98 to 1.00), the predictive positive value was 0.99 (95%CrI: 0.98 to 0.99) and the accuracy was 0.98 (95%CrI: 0.97 to 0.99). It was not possible to directly estimate the sensitivity and negative predictive value because there was no true negative in the assessment. In conclusion, the modified cross-correlation approach can be used for matching mass spectral fingerprints to predefined taxa and MALDI-TOF MS is a valuable tool for rapid, accurate and affordable identification of malaria mosquitos.

bioinformatics↗

bioRxiv2024

Under the name of "Lua": Revisiting Genetic Heterogeneity and Population Ancestry of Austroasiatic speakers in Northern Thailand Through Genomic Analysis

Austroasiatic (AA)-speaking populations in northern Thailand are of significant interest due to their status as indigenous descendants and their location at the crossroads of AA prehistoric distribution across Southern China, the Indian Subcontinent, and Mainland Southeast Asia. However, the complexity of ethnic identification can result in inaccuracies regarding the origin and migration history of these populations. To address this, we conducted a genome-wide SNP analysis on 89 individuals from two Lavue- and three Lwa-endonym populations and combined them with previously published data to elucidate the genetic diversity and clustering of AA groups in northern Thailand. Our findings align with linguistic classifications, revealing distinct genetic structure among the three branches of the Mon-Khmer subfamily within the AA family: Monic, Khmuic, and Palaungic. Although the term "Lua" ethnicity is used confusingly to identify ethnic groups belonging to both Khmuic and Palaungic branches, our genomic data clarifies that the Khmuic-speaking Lua living on the eastern side of the region show genetic differentiation from the Palaungic-speaking Lavue and Lwa populations living on the western side. Within the Palaungic branch, the Dara-ang population stands out as genetically distinct, reflecting remnants of ancient ancestry. The Lavue populations, mainly inhabiting mountainous areas, exhibit a genetic makeup unique to the AA family, with a close genetic relationship to the Karenic subgroup of the ST family. Conversely, the Lwa and Blang populations, residing in lowland river valleys, display genetic signatures resulting from admixture with Tai-Kadai-speaking ethnic groups. Author summaryIn the past, many Austroasiatic speakers in northern Thailand concealed their identity due to perceptions of inferiority compared to the majority Tai-Kadai-speaking group in the region. However, attitudes have shifted in the modern era, with a greater appreciation for ethnic diversity and the unique aspects of different valuable cultures. This scenario provides an opportunity for us to use genetic insights to untangle the complexities of ethnic identification among these indigenous inhabitants of Mainland Southeast Asia. Through our genetic analysis, we aimed to shed light on the ancestry and diversity of the Austroasiatic people in northern Thailand, often collectively referred to as "Lua" or "Lawa", which is an exonym (a name of the ethnic group created by another group of people) commonly used in prior scientific reports. Our findings clearly indicate genetic distinctions among the Lua, Lavue, and Lwa ethnic groups. The intricate interplay of genetics, cultural heritage, and historical influences has shaped these ethnic communities. Our study underscores the importance of accurate ethnic classifications, emphasizing the use of self-identified endonyms, names created and used by the ethnic group themselves. This approach respects the Austroasiatic communities in northern Thailand and acknowledges their significant contributions to advancing our understanding of genetic anthropology.

evolutionary biology↗

bioRxiv2024

Identification of Southeast Asian Anopheles mosquito species using MALDI-TOF mass spectrometry

Malaria control in South-East Asia remains a challenge, underscoring the importance of accurately identifying malaria mosquitoes to understand transmission dynamics and improve vector control. Traditional methods such as morphological identification require extensive training and cannot distinguish between sibling species, while molecular approaches are costly for extensive screening. Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and cost-effective tool for Anopheles species identification, yet its current use is limited to few specialized laboratories. This study aimed to develop and validate an online reference database for MALDI-TOF MS identification of Southeast Asian Anopheles species. The database, constructed using the in-house data analysis pipeline MSI2 (Sorbonne University), comprised 2046 head mass spectra from 209 specimens collected at the Thailand-Myanmar border. Molecular identification via COI and ITS2 DNA barcodes enabled the identification of 20 sensu stricto species and 5 sibling species complexes. The high quality of the mass spectra was demonstrated by a MSI2 median score (min-max) of 61.62 (15.94-77.55) for correct answers, using the best result of four technical replicates of a test panel. Applying an identification threshold of 45, 93.9% (201/214) of the specimens were identified, with 98.5% (198/201) consistency with the molecular taxonomic assignment. In conclusion, MALDI-TOF MS holds promise for malaria mosquito identification and can be scaled up for entomological surveillance in Southeast Asia. The free online sharing of our database on the MSI2 platform represents an important step towards the broader use of MALDI-TOF MS in malaria vector surveillance. Author summaryMosquito-borne diseases like malaria are on the rise globally, and climate change may exacerbate this global threat. Accurate identification of Anopheles mosquitoes, the malaria vectors, is crucial for understanding and controlling the disease. Unfortunately, morphological identification methods require extensive training and molecular methods can be time-consuming, especially when analyzing large samples. In this study, we established a reference database for identifying 25 species of Southeast Asian Anopheles using mass spectrometry, a rapid method based on protein fingerprinting. Using a test panel, we demonstrated the effectiveness of this innovative approach in identifying Southeast Asian Anopheles vectors. Importantly, the online sharing of our database marks an important step towards wider application of the tool, thereby contributing to the global effort to combat malaria.

microbiology↗

bioRxiv2021

Indian genetic heritage in Southeast Asian populations

The great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects multiple migration waves of people in the past. Deeply divergent East Eurasian hunter-gatherers were the first anatomically modern human population known to migrate to the region. Agriculturalists from South China migrated to the region and admixed with the local hunter-gatherers during the Neolithic period. During the Bronze and Iron Ages, the genetic makeup of people in MSEA changed again, indicating an additional influx of populations from South China. Maritime trading between MSEA and India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during the first millennium CE was strongly influenced by Indian culture, and this cultural influence is still prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and various populations in the country are likely to be descendants of people from those states. To systematically explore Indian genetic heritage in MSEA, we generated genome-wide SNP data (the HumanOrigins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and co-analyzed them with published data from MSEA using the PCA, ADMIXTURE, f3-statistics, qpAdm, and qpGraph methods. We found South Asian low-level admixture in various MSEA populations which are probably descendants of people from the ancient Indian-influenced states, but failed to find a South Asian genetic component in present-day hunter-gatherer groups and relatively isolated groups from highlands in Northern Thailand. Our results also support close genetic affinity between Kra-Dai-speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families. Author SummaryMainland Southeast Asia is a region with great ethnolinguistic diversity and complex population history. We studied genetic population history of present-day mainland Southeast Asian populations using genome-wide SNP data (the HumanOrigins array). We generated new data for 10 present-day ethnic groups from Thailand, which we further combined with published data from mainland and island Southeast Asians and worldwide populations. We revealed South Asian genetic admixture in various mainland Southeast Asian ethnic groups which are highly influenced by Indian culture, but failed to find it in groups who remained culturally isolated until recently. Our finding suggests that a massive migration of Indian people in the past was responsible for the spread of Indian culture in mainland Southeast Asia. We also found support for a close genetic affinity between Kra-Dai- and Austronesianspeaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.

genetics↗