Genetic Association and Expression of Myoglobin Gene Related to Mineral Content in IPB-D2 Chickens

Myoglobin (MB) gene encodes the protein of myoglobin, which is a protein found in muscle tissues that plays a crucial role in binding and storing oxygen. This study aimed to analyze the polymorphism of the MB gene, examine its relationship with the meat mineral content, and analyze its expression in the liver and thigh muscle tissue of IPB-D2 chicken. A total of 55 IPB-D2 chickens were used in this study. Identification of the gene polymorphism, quantification of the mineral content, and gene expression were performed using the direct sequencing method, the Atomic Absorption Spectroscopy (AAS) method, and the qRT-PCR, respectively. Chicken thigh muscle and liver tissues were used as the source of mRNA in this study. The statistical analysis methods used were the chi-square test to test Hardy-Weinberg equilibrium, and the T-test for mineral association analysis and gene expression analysis. IPB-D2 chicken on average contains 17.81, 0.22, 16.50, and 0.34 mg/kg of Fe, Se, Zn, and Mn, respectively. Two SNPs were found in 5’UTR of the MB gene, namely SNP g.17 G>T and SNP g.25 T>C. Genotype TT (g.17 G>T) and genotype CC (g.25 T>C) were significantly (P<0.05) associated with high Fe content in IPB-D2 chicken. The gene expression analysis showed that MB mRNA expression in the liver was not statistically different between high Fe (TT/CC) and low Fe (GG/TT and GT/TC) genotype combination. Meanwhile, in the thigh muscle, MB mRNA expression in TT/CC genotype combination was significantly higher than GG/TT and GT/TC genotype combination (P<0.05). These results suggest that the identified polymorphisms in the IPB-D2 MB gene could serve as references for investigating similar gene in other chicken breeds, especially regarding Fe, Se, Zn, and Mn mineral content

East African origins for Madagascan chickens as indicated by mitochondrial DNA

Published 22 March 2017The colonization of Madagascar by Austronesian-speaking people during AD 50–500 represents the most westerly point of the greatest diaspora in prehistory. A range of economically important plants and animals may have accompanied the Austronesians. Domestic chickens (Gallus gallus) are found in Madagascar, but it is unclear how they arrived there. Did they accompany the initial Austronesian-speaking populations that reached Madagascar via the Indian Ocean or were they late arrivals with Arabian and African sea-farers? To address this question, we investigated the mitochondrial DNA control region diversity of modern chickens sampled from around the Indian Ocean rim (Southeast Asia, South Asia, the Arabian Peninsula, East Africa and Madagascar). In contrast to the linguistic and human genetic evidence indicating dual African and Southeast Asian ancestry of the Malagasy people, we find that chickens in Madagascar only share a common ancestor with East Africa, which together are genetically closer to South Asian chickens than to those in Southeast Asia. This suggests that the earliest expansion of Austronesian-speaking people across the Indian Ocean did not successfully introduce chickens to Madagascar. Our results further demonstrate the complexity of the translocation history of introduced domesticates in Madagascar.Michael B. Herrera, Vicki A. Thomson, Jessica J.Wadley, Philip J. Piper, Sri Sulandari, Anik Budhi Dharmayanthi, Spiridoula Kraitsek, Jaime Gongora and Jeremy J. Austi

Intensitas Serangan Spodoptera Frugiperda J.E. Smith (Lepidoptera: Noctuidae) pada Pertanaman Jagung di Kabupaten Garut dan Tasikmalaya, Jawa Barat

The presence of Spodoptera frugiperda J.E. Smith or fall armyworm (FAW) have now detected in West Java. However, no information is available on their attack intensity even though the data is crucial for the implementation of appropriate control methods. The investigations were carried out in Garut (Limbangan, Wanaraja, dan Banyuresmi) and Tasikmalaya (Sukaratu) Regencies from 25 to 27 February 2020. At each location, 100 plants were selected for recording observations on leaf damage following the Davis Scale. The results showed the attack intensity in Wanaraja (34,78%), Banyuresmi (34.78%), and Sukaratu (39.89%) showed moderate damage. On the other hand, Limbangan one of the corn production center, showed high damage with the intensity of the pest up to 52.78%. The attack intensity of FAW tends to correlate with their attack level. This means that plant damage levels increasing at higher attack levels

East African origins for Madagascan chickens as indicated by mitochondrial DNA

The colonization of Madagascar by Austronesian-speaking people during AD 50–500 represents the most westerly point of the greatest diaspora in prehistory. A range of economically important plants and animals may have accompanied the Austronesians. Domestic chickens (Gallus gallus) are found in Madagascar, but it is unclear how they arrived there. Did they accompany the initial Austronesian-speaking populations that reached Madagascar via the Indian Ocean or were they late arrivals with Arabian and African sea-farers? To address this question, we investigated the mitochondrial DNA control region diversity of modern chickens sampled from around the Indian Ocean rim (Southeast Asia, South Asia, the Arabian Peninsula, East Africa and Madagascar). In contrast to the linguistic and human genetic evidence indicating dual African and Southeast Asian ancestry of the Malagasy people, we find that chickens in Madagascar only share a common ancestor with East Africa, which together are genetically closer to South Asian chickens than to those in Southeast Asia. This suggests that the earliest expansion of Austronesian-speaking people across the Indian Ocean did not successfully introduce chickens to Madagascar. Our results further demonstrate the complexity of the translocation history of introduced domesticates in Madagasca

ESM Table 2. Genetic diversity measures for each chicken population from Indonesia, South Asia, Continental Africa, and Madagascar from East African origins for Madagascan chickens as indicated by mitochondrial DNA

The colonization of Madagascar by Austronesian-speaking people during AD 50–500 represents the most westerly point of the greatest diaspora in prehistory. A range of economically important plants and animals may have accompanied the Austronesians. Domestic chickens (<i>Gallus gallus</i>) are found in Madagascar, but it is unclear how they arrived there. Did they accompany the initial Austronesian-speaking populations that reached Madagascar via the Indian Ocean or were they late arrivals with Arabian and African sea-farers? To address this question, we investigated the mitochondrial DNA control region diversity of modern chickens sampled from around the Indian Ocean rim (Southeast Asia, South Asia, the Arabian Peninsula, East Africa and Madagascar). In contrast to the linguistic and human genetic evidence indicating dual African and Southeast Asian ancestry of the Malagasy people, we find that chickens in Madagascar only share a common ancestor with East Africa, which together are genetically closer to South Asian chickens than to those in Southeast Asia. This suggests that the earliest expansion of Austronesian-speaking people across the Indian Ocean did not successfully introduce chickens to Madagascar. Our results further demonstrate the complexity of the translocation history of introduced domesticates in Madagascar

ESM Table 1. Samples used in the study from East African origins for Madagascan chickens as indicated by mitochondrial DNA

The colonization of Madagascar by Austronesian-speaking people during AD 50–500 represents the most westerly point of the greatest diaspora in prehistory. A range of economically important plants and animals may have accompanied the Austronesians. Domestic chickens (<i>Gallus gallus</i>) are found in Madagascar, but it is unclear how they arrived there. Did they accompany the initial Austronesian-speaking populations that reached Madagascar via the Indian Ocean or were they late arrivals with Arabian and African sea-farers? To address this question, we investigated the mitochondrial DNA control region diversity of modern chickens sampled from around the Indian Ocean rim (Southeast Asia, South Asia, the Arabian Peninsula, East Africa and Madagascar). In contrast to the linguistic and human genetic evidence indicating dual African and Southeast Asian ancestry of the Malagasy people, we find that chickens in Madagascar only share a common ancestor with East Africa, which together are genetically closer to South Asian chickens than to those in Southeast Asia. This suggests that the earliest expansion of Austronesian-speaking people across the Indian Ocean did not successfully introduce chickens to Madagascar. Our results further demonstrate the complexity of the translocation history of introduced domesticates in Madagascar

ESM Figure 2. Median-joining network depicting the relationship of the E haplotypes observed in East Africa and Madagascar (blue), South Asia (black) and Indonesia (green) from East African origins for Madagascan chickens as indicated by mitochondrial DNA

The colonization of Madagascar by Austronesian-speaking people during AD 50–500 represents the most westerly point of the greatest diaspora in prehistory. A range of economically important plants and animals may have accompanied the Austronesians. Domestic chickens (<i>Gallus gallus</i>) are found in Madagascar, but it is unclear how they arrived there. Did they accompany the initial Austronesian-speaking populations that reached Madagascar via the Indian Ocean or were they late arrivals with Arabian and African sea-farers? To address this question, we investigated the mitochondrial DNA control region diversity of modern chickens sampled from around the Indian Ocean rim (Southeast Asia, South Asia, the Arabian Peninsula, East Africa and Madagascar). In contrast to the linguistic and human genetic evidence indicating dual African and Southeast Asian ancestry of the Malagasy people, we find that chickens in Madagascar only share a common ancestor with East Africa, which together are genetically closer to South Asian chickens than to those in Southeast Asia. This suggests that the earliest expansion of Austronesian-speaking people across the Indian Ocean did not successfully introduce chickens to Madagascar. Our results further demonstrate the complexity of the translocation history of introduced domesticates in Madagascar

SARS-CoV-2 genetic variation and bacterial communities of naso-oropharyngeal samples in middle-aged and elderly COVID-19 patients in West Java, Indonesia

الملخص: أهدف البحث: تعكس عدد حالات كورونا في إندونيسيا خطورة الأمراض وانتشارها بسرعة. تم إجراء الرصد الجينومي لفيروس كورونا المستجد والتحقيق في المجتمعات البكتيرية للجهاز التنفسي العلوي في غرب جاوة كرد فعل للتهديد المتزايد حيث يمكن أن يؤثر تفاوت التوازن في الميكروبات في الجهاز التنفسي العلوي بشكل سلبي على حالة المرضى. طرق البحث: استخدمنا منصة تسلسل النانوبور لتحليل 43 عينة من التغيرات الجينية لفيروس كورونا المستجد و11 عينة مختارة لتسلسل الجينات عبر الريبوزوم 16، تم جمعهم في الفترة من مايو إلى أغسطس 2021. النتائج: خمسة أنواع فيروسية في السكان (أ.ي.23؛ أ.ي.24؛ أ.ي.26؛ أ.ي.42؛ ب.1.1.7) كانت تهيمن على وجود النوع أ.ي.23 (82%) predominated among five virus lineages in the populations (AY.23, AY.24, AY.26, AY.42, B.1.1.7). The region in the SARS-CoV-2 genome found to have the highest number of mutations was the spike (S) protein (>20%). There was no association between SARS-CoV-2 lineages, mutation frequency, patient profile, and COVID-19 rapid spread-categorized cases. There was no association of bacterial relative abundance, alpha-beta diversity, and linear discriminant analysis effect size analysis with patient profile and rapid spread cases. MetagenomeSeq analysis showed eight differential abundance species in individual patient profiles, including Pseudomonas aeruginosa and Haemophilus parainfluenzae. Conclusions: The data demonstrated relevant AY.23 dominance (the Delta variant) in West Java during that period supporting the importance of surveillance program in monitoring disease progression. The inconsistent results of the bacterial communities suggest that a complex multifactor process may contribute to the progression of bacterial-induced disease in each patient