Comparative Analysis of Genes Induced by Respiratory Syncytial Virus and DsRNA in Human Epithelial Cells

Epithelial cells are the primary target of respiratory viral infections and play a pivotal role in virusinducedlung infl ammation and in anti viral immune response. A common signal for the presence of viralinfections and induction of infl ammation is recognition of double stranded RNA (dsRNA). Thus far, therehas not been a high-throughput transcrptome analysis of RSV- or dsRNA-induced genes in primary humanbronchial epithelial cells (PHBE), nor there has been a comparison between dsRNA- and RSV-inducedgenes. To establish the transcriptome profi les and to determine the contribution of dsRNA in the inductionof infl ammation during respiratory virus infection, we compared the gene expression profi les of PHBE cellsthat were infected with Respiratory Syncytial Virus (RSV) or were treated with dsRNA. Our transcriptomeanalysis showed that RSV infection and and dsRNA treatment induced up-regulation of 2024 and 159 genesin PHBE respectively. Comparison of genes revealed that RSV and dsRNA commonly induced 75 genes inPHBE cells. The common up-regulated genes were functionally grouped in multiple response pathwaysinvolved in infl ammation and immune responses. Interestingly, there were several previously unreportedgenes that were up-regulated in primary human epithelial cells that are relevant to a TH2 allergic phenotype.This comparison of a high-throughput gene expression study offers a comprehensive view of transcriptionalchanges induced by dsRNA and RSV, and importantly compares dsRNA-induced genes with RSV-inducedgenes in PHBE cells. Keywords: RSV, dsRNA, transcriptome, immune response, infl ammatio

Comparative Analysis of Genes Induced by Respiratory Syncytial Virus and DsRNA in Human Epithelial Cells

Epithelial cells are the primary target of respiratory viral infections and play a pivotal role in virusinducedlung infl ammation and in anti viral immune response. A common signal for the presence of viralinfections and induction of infl ammation is recognition of double stranded RNA (dsRNA). Thus far, therehas not been a high-throughput transcrptome analysis of RSV- or dsRNA-induced genes in primary humanbronchial epithelial cells (PHBE), nor there has been a comparison between dsRNA- and RSV-inducedgenes. To establish the transcriptome profi les and to determine the contribution of dsRNA in the inductionof infl ammation during respiratory virus infection, we compared the gene expression profi les of PHBE cellsthat were infected with Respiratory Syncytial Virus (RSV) or were treated with dsRNA. Our transcriptomeanalysis showed that RSV infection and and dsRNA treatment induced up-regulation of 2024 and 159 genesin PHBE respectively. Comparison of genes revealed that RSV and dsRNA commonly induced 75 genes inPHBE cells. The common up-regulated genes were functionally grouped in multiple response pathwaysinvolved in infl ammation and immune responses. Interestingly, there were several previously unreportedgenes that were up-regulated in primary human epithelial cells that are relevant to a TH2 allergic phenotype.This comparison of a high-throughput gene expression study offers a comprehensive view of transcriptionalchanges induced by dsRNA and RSV, and importantly compares dsRNA-induced genes with RSV-inducedgenes in PHBE cells.Keywords: RSV, dsRNA, transcriptome, immune response, infl ammation</div

PEMANFAATAN MATERIAL BIODEGRADABLE (BESE-ELEMENT) SEBAGAI MEDIA RESTORASI MANGROVE DI PESISIR NEGERI PASSO, KOTA AMBON

Mangrove ecosystems have potential both ecologically, economically, physically, and chemically. The abundance of this potential causes pressure from anthropogenic activities, which results in the degradation of mangrove ecosystems. Several mangrove ecosystems in the Ambon City area have experienced degradation, so restoration is necessary. The Passo State area has the potential for a dense mangrove ecosystem and can be used as a nursery area to support other ecosystems. Increasing the potential of mangrove ecosystems in the Passo State area can be done through restoration using biodegradable materials (BESE-Elements). Mangrove restoration is carried out through community service activities, a collaboration between the Maritime Center and Wardeen Burg Ecology – The Netherlands. The result of the activity is that mangrove ecosystem restoration is carried out in semi-enclosed areas using 10 BESE-Element. Each BESE-Element was planted with 10 mangrove seedlings consisting of 5 seedlings and 5 propagules. The mangrove species planted were Bruguiera gymnorrhiza, Rhizophora apicutala, and Rhizophora stylosa. Around BESE-Elements planted seedlings and mangrove propagules as a control for mangroves in BESE-Elements

Komposisi Jenis Karang Keras (Scleractinia) di Perairan Pantai Utara Pulau Ambon

Terumbu karang merupakan ekosistem pesisir yang secara ekologi paling produktif dengan keanekaragaman tinggi. Penelitian ini bertujuan untuk mengetahui komposisi jenis karang keras (Scleractinia) di perairan pantai utara Pulau Ambon. Pengambilan data dilakukan dengan menggunakan metode sistematik sampling. Data karang yang diperoleh kemudian diidentifikasi, proses identifikasi dilakukan dengan teknik analisa visual menggunakan beberapa referensi Veron (2000), Veron (1986), Suharsono (2017), Coral Finder edisi ketiga, dan Website Corals of The World (http://www.coralsoftheworld.org) untuk melihat jenis-jenis apa saja yang ada pada lokasi penelitian. Hasil penelitian menunjukkan bahwa berdasarkan komposisi taksa jumlah genus terbanyak dari famili Fungidae, jumlah spesies terbanyak dari genus Porites dan jumlah koloni terbanyak dari spesies Porites lutea

Correlation of some water quality parameters and Pb in sediment to gastropod diversity in Ambon Island Waters

The coastal waters of Ambon Island have quite diverse ecosystems that allow for the presence of various organisms, one of which is gastropods. This study aims to analyze the correlation of some water parameters and Pb in sediment to the diversity of gastropods. The research method was carried out by observing the density, water quality &nbsp;parameters, and Pb metal in sediments. Water parameters were measured in situ and analyzed in the laboratory. The distribution of gastropods was analyzed through Principal Component Analysis (PCA). At the same time, the correlation analysis was carried out using the Pearson correlation approach using SPSS v.16. The results showed that the types of gastropods with the highest density in the waters of Ambon Island were Terebralia sulcata, Hebra corticata, and Nerita patula. While the species with the lowest density value were Nassarius olivaceus, Polinices didyma, Lunella cinerea, Conus eburneus, Cypraea isabella, Vexillum plicarium, and Columbella scripta. The Shannon-Wienner Diversity Index ranges from 1.253–2.622, and the diversity index ranges from 0.083-0.207. It was included in the low category caused by the disturbance of water pollution and Pb metal in sediments. Meanwhile, the dominance index ranged from 0.098 to 0.511 indicating species dominance at several observation stations. The waters' physical-chemical parameters strongly correlating with gastropod diversity are DO and Pb, with respective correlation values ​​of r = 0.656 and r = -0.785. &nbsp

KONEKTIVITAS GENETIK Cephalopholis sexmaculata ANTARA DAERAH PENANGKAPAN DAN DAERAH KONSERVASI DI WILAYAH PENGELOLAAN PERIKANAN 714

The Fisheries Management Area (FMA 714) has great potential for reef fish with high diversity. However, exploitation of reef fish, especially grouper in FMA 714 is also high to meet national and international market demand. One of the species of grouper is Cephalopholis sexmaculata from the Serranidae family. This research was conducted with the aim to determine genetic distance and phylogenetic relationships as well as genetic diversity, population structure and genetic connectivity of the C. sexmaculata in conservation areas and fishing areas in FMA 714 using DNA barcoding. Samples of C. sexmaculata were collected using a survey method with analyzes carried out including molecular analysis, phylogenetic relationships as well as genetic diversity and connectivity. The results of the research show that the C. sexmaculata population in FMA 714 has a very close relationship with the the values of genetic distance ranging from 0-10.9%. The genetic diversity obtained also shows the value of 1 which is categorized as high in each population. The connectivity formed from the population structure of this species indicates the existence of genetic exchange between the C. sexmaculatapopulation in the conservation area and the fishing area in FMA 714. &nbsp; ABSTRAK Wilayah Pengelolaan Perikanan (WPP 714) memiliki potensi ikan karang yang besar dengan keragaman yang tinggi. Walaupun demikian, eksploitasi ikan karang terutama ikan kerapu di WPP 714 juga cukup tinggi untuk memenuhi permintaan pasar nasional dan internasional. Salah satu jenis ikan kerapu adalah Cephalopholis sexmaculata dari famili Serranidae. Penelitian ini dilakukan dengan tujuan untuk mengetahui jarak genetik dan hubungan filogenetik serta keragaman genetik, struktur populasi dan konektivitas genetik dari spesies C. sexmaculata antara daerah konservasi dan daerah penangkapan di WPP 714 dengan menggunakan DNA barcoding. Sampel ikan C. sexmaculata diperoleh menggunakan metode survei dengan analisis yang dilakukan meliputi analisis molekuler, hubungan kekerabatan atau filogenetik serta keragaman dan konektivitas genetik. Hasil penelitian menunjukan bahwa populasi C. sexmaculata di WPP 714 memiliki hubungan yang sangat dekat dengan jarak genetika yang diperoleh berkisar antara 0-10,9%. Nilai keragaman genetik yang diperoleh juga menunjukan angka 1 yang terkategori tinggi pada setiap populasi. Konektivitas yang terbentuk dari struktur populasi pada spesies ini menunjukan pendugaan terhadap adanya pertukaran genetik antara populasi C. sexmaculata di daerah konservasi dengan daerah penangkapan di WPP 714. Kata Kunci: WPP 714, Cephalopholis sexmaculata, penanda DNA, konektivitas, filogeneti

PENGENALAN JENIS TERIPANG EKONOMIS PENTING BAGI MASYARAKAT DESA SULI KABUPATEN MALUKU TENGAH

Pemanfaatan teripang semakin meningkat seiring dengan meningkatnya permintaan akan komoditi ini karena harganya yang tinggi. Pada beberapa tempat di Maluku, pemanfaatan teripang juga cukup tinggi, dan teripang masih ditemukan cukup melimpah di alam. Sedangkan pada beberapa lokasi lain, teripang justru tidak terlalu dimanfaatkan, karena masih rendahnya pengetahuan masyarakat akan manfaat dan nilai ekonomi dari komoditi ini. Pemanfaatan teripang juga masih terbatas pada beberapa spesies yang telah umum dikenal memiliki nilai jual, misalnya teripang pasir (Holothuria scabra), teripang susu (H. fuscogilva), dan teripang ananas (Thelenota ananas). Padahal, jenis teripang yang memiliki nilai ekonomis masih cukup banyak, dan sumberdayanya tersedia di perairan Maluku. Untuk itu, diperlukan upaya untuk mengenalkan jenis-jenis teripang bernilai ekonomis penting yang ada di Maluku. Desa Suli memiliki substrat pantai yang sesuai dengan habitat hidup teripang, namun pemanfaatannya masih sangat jarang. Sehingga dirasakan penting untuk melakukan kegiatan pengenalan jenis teripang ekonomis penting di Suli. Berdasarkan hasil kegiatan, dijumpai bahwa masih banyak masyarakat yang tidak mengetahui bahwa ada banyak teripang yang memiliki nilai ekonomis penting. Selain itu, masih rendah tingkat pemanfaatan teripang maupun upaya untuk mengelolanya, misalkan budidaya dan pengolahan teripang. Setelah kegiatan ini, masyarakat semakin mengenal jenis-jenis teripang yang memiliki nilai ekonomi, harga jual dan pasarnya

Correlation of some water quality parameters and Pb in sediment to gastropod diversity in Ambon Island Waters

The coastal waters of Ambon Island have quite diverse ecosystems that allow for the presence of various organisms, one of which is gastropods. This study aims to analyze the correlation of some water parameters and Pb in sediment to the diversity of gastropods. The research method was carried out by observing the density, water quality  parameters, and Pb metal in sediments. Water parameters were measured in situ and analyzed in the laboratory. The distribution of gastropods was analyzed through Principal Component Analysis (PCA). At the same time, the correlation analysis was carried out using the Pearson correlation approach using SPSS v.16. The results showed that the types of gastropods with the highest density in the waters of Ambon Island were Terebralia sulcata, Hebra corticata, and Nerita patula. While the species with the lowest density value were Nassarius olivaceus, Polinices didyma, Lunella cinerea, Conus eburneus, Cypraea isabella, Vexillum plicarium, and Columbella scripta. The Shannon-Wienner Diversity Index ranges from 1.253–2.622, and the diversity index ranges from 0.083-0.207. It was included in the low category caused by the disturbance of water pollution and Pb metal in sediments. Meanwhile, the dominance index ranged from 0.098 to 0.511 indicating species dominance at several observation stations. The waters' physical-chemical parameters strongly correlating with gastropod diversity are DO and Pb, with respective correlation values ​​of r = 0.656 and r = -0.785.

Regeneration of Alveolar Type I and II Cells from Scgb1a1-Expressing Cells following Severe Pulmonary Damage Induced by Bleomycin and Influenza

The lung comprises an extensive surface of epithelia constantly exposed to environmental insults. Maintaining the integrity of the alveolar epithelia is critical for lung function and gaseous exchange. However, following severe pulmonary damage, what progenitor cells give rise to alveolar type I and II cells during the regeneration of alveolar epithelia has not been fully determined. In this study, we have investigated this issue by using transgenic mice in which Scgb1a1-expressing cells and their progeny can be genetically labeled with EGFP. We show that following severe alveolar damage induced either by bleomycin or by infection with influenza virus, the majority of the newly generated alveolar type II cells in the damaged parenchyma were labeled with EGFP. A large proportion of EGFP-expressing type I cells were also observed among the type II cells. These findings strongly suggest that Scgb1a1-expressing cells, most likely Clara cells, are a major cell type that gives rise to alveolar type I and II cells during the regeneration of alveolar epithelia in response to severe pulmonary damage in mice..Singapore. National Research FoundationSingapore–MIT Alliance for Research and Technology (Infectious Disease-IRG research programme

Combining environmental DNA and visual surveys can inform conservation planning for coral reefs

Environmental DNA (eDNA) metabarcoding has the potential to revolutionize conservation planning by providing spatially and taxonomically comprehensive data on biodiversity and ecosystem conditions, but its utility to inform the design of protected areas remains untested. Here, we quantify whether and how identifying conservation priority areas within coral reef ecosystems differs when biodiversity information is collected via eDNA analyses or traditional visual census records. We focus on 147 coral reefs in Indonesia’s hyper-diverse Wallacea region and show large discrepancies in the allocation and spatial design of conservation priority areas when coral reef species were surveyed with underwater visual techniques (fishes, corals, and algae) or eDNA metabarcoding (eukaryotes and metazoans). Specifically, incidental protection occurred for 55% of eDNA species when targets were set for species detected by visual surveys and 71% vice versa. This finding is supported by generally low overlap in detection between visual census and eDNA methods at species level, with more overlap at higher taxonomic ranks. Incomplete taxonomic reference databases for the highly diverse Wallacea reefs, and the complementary detection of species by the two methods, underscore the current need to combine different biodiversity data sources to maximize species representation in conservation planning