S-D614G Mutation Reveals the Euro-America and East-Asia Origin SARS-CoV-2 Virus Spread in Indonesia

COVID-19 is a pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The first case was found in the city of Wuhan, Hubei province, China. The first case in Indonesia was reported in March 2020 and currently there are 0.5 million cases with a death rate of 3.1%. This rapid increase in cases is thought to due to presence of the mutant strain S-D614G, which causes a faster rate of infection and spread. The purpose of this study was to determine the presence of S-D614G mutations in Indonesian samples in order to find the origin of COVID-19 which was spread in Indonesia based on the Spike gene sequences and the RdRp genes from 25 countries, and one control sequence China/Wuhan-Hu-1 obtained from the NCBI and GISAID databases. Mutation analysis was carried out through multiple alignments using BioEdit software. Phylogenetic tree reconstruction using MEGA6 software with the Neighbor Joining method. This study found mutation of S-D614G in one Indonesian sample, namely the Indonesian/SBY9 sample along with 23 samples from Europe, America, and Africa. The phylogenetic tree reconstruction confirmed these findings; the mutated samples were closely related to samples from these continents, while the non-mutated Indonesian samples were closely related to sample from East Asia. These findings indicate that the origin of the SARS-CoV-2 virus in Indonesia possibly came from the East Asia cluster and the European-American cluster.

Optimization of Various ITS rDNA Amplification Protocol of Yeast Isolated from Giant Honey Beehives (Apis dorsata)

Indonesia is a country with high variability of microorganisms, including bacteria, yeast, and fungi. Yeast isolates could be isolated from the honeycomb of Apis dorsata. Molecular approaches were used to identify yeast using ribosomal DNA gene sequences, called the ITS gene. The optimum condition for DNA extractions and amplifications are needed for the successfully of molecular identification. Therefore, it is necessary to optimize the DNA extraction and amplification of several protocols to obtain good identification results. This study aimed to compare the effects of DNA extraction with various temperatures and different amplification protocols. LIPI reference DNA extraction protocol with the boiling method and variations in incubation time of 10, 15, and 20 minutes at a temperature of 98° C. Meanwhile, for the amplification of yeast DNA using a variety of different amplification protocols. The results showed the optimal time of incubation was 10 minutes in K1 isolates with DNA purity of 1.896. meanwhile, for isolates K2, K3, and K4 each with a purity of 2.246, 2.335, and 1.748. optimal DNA amplification results were indicated by the presense of DNA bands for each sample K1, K2, K3, and K4, namely 503, 542, 492, and 526 bp. In this study, it can be concluded that the optimal incubation time for the extraction process is 10 minutes. In addition, the optimal amplification protocol was shown in the DNA bands in all sample.

Variation and Phenetic Relationship of Tobacco (Nicotiana tabacum L.) In Central Java and Yogyakarta Based on Morphological Characters

Tobacco (Nicotiana tabacum L.) is a plant used as a mixture of cigarettes, and recreational media especially for men. This study aimed to identify variations, and determine the relationship between tobacco cultivars in Central Java and Yogyakarta based on macromorphological and micromorphological characters. Sampling locations are determined by surveying locations in both regions. Tobacco samples found include 5 cultivars in Central Java namely 'Mantili', 'Uler Magetan', 'Garut', ‘Gober Boyolali’, 'Manila', and 3 cultivars in Yogyakarta namely 'Siluk', 'Java', and 'Virginia'. Characterization with 23 qualitative macromorphological characters including leaves, and stems, with 9 qualitative and quantitative micromorphological characters including trichome and stomata. Descriptive data analysis is done to obtain the typical character of each cultivar, followed by numerical analysis including scoring characters processed with MVSP (Multi Variate Statistical Package), clustering with UPGMA (Unweighted Pair Group Method with Averages), and calculation of similarity coefficients with Simple matching formula. The results showed variations in the macromorphological characters including the shape of the leaf lamina, the base of the leaf, the absence of leaf stalks, and type of leaf venation. Tobacco has anisositic stomata, and varies in terms of length, width, and density of stomata. Tobacco trichomes are glandular. The result dendrograms form two clusters (A and B) with the similarity index of each cluster above 0.80. Cultivars with close relationships such as 'Siluk'-'Java', and far relationship like 'Java'-'Manila'.

Diversity of Butterflies (Hexapoda: Lepidoptera: Rhopalocera) Around Campus 4 of Universitas Ahmad Dahlan

The conversion of land functions can result in a decrease of environmental quality, which can reduce the diversity of butterflies. This study aimed to determine the diversity level and to find the most abundant and less abundant butterfly species around campus 4 UAD. The sampling was done at campus area, vacant land, rice fields and housing sites. Each of these sites had 2 plots and consisted of 5 subplots, respectively. Sampling was carried out four times, which was done in the morning at 08.00 - 11.00 and in the afternoon at 15.00 - 17.00. Butterflies caught using a sweep net. The data were analyzed by inferential analysis, namely Pearson correlation test. The calculation of the diversity level of butterflies was carried out by calculating the importance value index, the diversity Shannon-Wiener index, and the Simpson dominance index. The results showed that the diversity level of Shannon Wiener index of butterflies around the campus 4 UAD showed a low level (0.67). The species of butterflies found around campus 4 UAD were Acraea violae, Aphrissa statira, Appias libythea, Appias olferna, Catopsilia pyranthe, Catopsilia Scylla, Danaus Chrysippus, Elymnias hypermnestra, Junonia almana, and Junonia atlites. The most abundant butterfly was C. pyranthe with 125 individuals whereas the least abundant was A. libythea with 1 individual. This suggested that the ecosystem around campus 4 UAD is disturbed category; causing instability of the diversity that exists, including butterflies.

Diversity of Lepidoptera: Rhopalocera at Selorejo Waterfall Area, Ponorogo District, East Java, Indonesia

Selorejo Waterfall is a natural tourist area that is directly adjacent to the Sigogor Mountain Nature Reserve and has a beautiful and natural environment. This makes the Selorejo Waterfall area has a good environment for the sustainability of various species of butterflies. This research aimed to find out the diversity and abundance of butterflies in the Selorejo Waterfall area. This research was conducted using the Visual Day Flaying method by following the trail in the Selorejo Waterfall area. This study found 26 species belongs 4 families with 109 individuals in total. The value of the species diversity index at the location of H'= 2.81 moderate category. The diversity of butterflies in the Selorejo Waterfall area was influenced by the availability of host plants and feed as well as abiotic factors.

The population of Sanderling (Calidris alba) in 2020 Migration on the South Coast of Puger, Getem, Jember

Sanderling (Calidris alba) is a type of shorebird that migrates from the northern hemisphere to the southern hemisphere. Indonesia is a migration route for East Asia-Australasia. The southern coastal area of the Jember Regency, one of the wetlands, especially in East Java, has become an air route and a stopover for shorebirds every year. The research objective was to determine the population of Sanderling (Calidris alba) on the southern coast of Puger and Getem, Jember Regency. Method of collecting encounter rates. Bird watching is carried out in the morning at 06.00-08.00 and in the afternoon at 15.30-17.30. Data recording includes species, number of birds, and other supporting data. Identification using the book by Mac Kinnon et al. (2010) and Bhushan, B., et al. (1993). Tools used for binocular observation, monocular, camera, and GPS. Data analysis used the density index for individual bird species using the formula method (Alikodra, 1990). The results of the study were a total of 445 individuals. Data analysis of Muara Sungai population density was the location with the four other survey locations' highest number.

Design of the env-su Gene Coding for Surface Unit Protein as a Vaccine Candidate for Jembrana Disease Virus in In Silico

Bali cattle are superior meat producers, but they are susceptible to Jembrana disease. The injection of the crude vaccine was considered ineffective, so the env-su gene was selected to express the Jembrana Surface Unit (JSU) protein as a candidate for the Jembrana vaccine. This study aimed to analyze the potential of the JSU protein as a candidate for the Jembrana vaccine and analyze the increase in the env-su gene expression which codon has been optimized in silico. Vaccine design was carried out through in silico including the selection of the SU protein sequences of the genus Lentivirus and sequence alignment of UniProt. The construction phylogeny tree of SU protein using MEGA-X program, optimization of env-su gene codon with preference codon Esherichia coli str. K-12 substr. MG1655 using Optimizer. The optimized env-su gene was inserted into the plasmid pET-21a (+) using GenScript. The result of sequence alignment showed that there is no SU protein that has a percent identity value of more than 30% with JSU protein. The SU JDV and BIV proteins are monophyletic groups and have a percent identity of 20.57%. Codon optimization showed an increase in CAI by 1,000 and GC 54.5%, and a decrease in ENc to 22 and AT 45.5%. EcoR1 and HindIII can recognize the gene target and MCS cut regions on the plasmid so that the env-su gene can be inserted into the pET-21a (+) plasmid. The JSU protein has the potential to be a candidate for the Jembrana vaccine, but it needs further research in vitro and in vivo.

The First Investigation of Microplastics Contamination in Estuarine Located in Puger District, Jember Regency, Indonesia

Microplastics are harmful to the ecosystem and need to solve immediately. Detection of microplastic contamination is the first step to reduce plastics pollution. Estuarine in Puger has a high potential for microplastic pollution related to the multifunction of waters as ports, tourism, fish market, fish processing, and human settlements. However, there are no studies related to microplastic contamination in the area. The objectives of this research were to determine microplastic contamination in the estuarine located in Puger District, Jember Regency, Indonesia. The research results were the first evidence to inform the society and local government about the actual condition of plastic pollution, especially in the aquatic ecosystem. The sampling sites were determined by purposive sampling. Fifty liters of water from each station (with three repetitions) were taken using a 24V water pump and then filtered using stainless steel filter (mesh 5 mm and 0.2 mm). The filtered samples were placed in a sterile bottle sample, stored at 4 ± 20C. Microplastics were counted and categorized according to size, color, and type under a microscope stereo. Microplastic abundance was calculated based on the number of microplastic particles identified per liter of sample water (particle/liter). The result showed that the study area was contaminated by microplastics throughout site sampling, with abundances varying from 0.03 particles/liter to 0.19 particles/liter. The highest microplastic abundance found near the fishery market. The microplastics also vary in size, color, and type. According to characterization, the sources of microplastic contamination come from human-based activities.

Distribution Patterns of Exotic Plant Chromolaena odorata, in Rehabilitation Zone at Donglo Block, Resort of Wonoasri, Meru Betiri National Park

Exotic plants are plants that are introduced intentionally or unintentionally from their original habitat to a new habitat. One of the exotic plants that is potentially invasive is Chromolaena odorata. These plants are found a lot especially in the rehabilitation zone at Donglo Block Resort of Wonoasri, Meru Betiri National Park (MBNP). An initial effort to determine whether this exotic plant was potentially invasive was to use the distribution pattern of a plant population. This study aimed to determine the distribution pattern and area of cover of exotic plants C. odorata in rehabilitation zone at Donglo Block, Resort of Wonoasri MBNP. The sampling of C. odorata used the transect plot method systematically, which carried out in Donglo Block Resort of Wonoasri MBNP. Data analyzed using Morisita index. The map of distribution pattern of C. odorata was created using the Geographic Information System (GIS). Based on the results of the Morisita index, the value (Iδ) = 12.39, which means that C. odorata has a clumped distribution pattern. The distribution pattern of C. odorata can also be seen from the visualization of the spatial distribution map, which shows that the growth of C. odorata in plants or overlaps with each other, hence that it looks clustered. The coverage area of C. odorata in the study location was 596,5 m2 or 29.24% of the total area of the study (20,400 m2). Based on the results of the coverage area of C. odorata, it was indicated that this exotic species is not yet classified as an invasive species in the area.

Diversity and Community Structure of Dragonfly and Damselfly (Odonata) at the Selorejo Waterfall Area, Ponorogo Regency, East Java Indonesia

Selorejo Waterfall is a natural tourism area that is quite far from downtown Ponorogo and directly adjacent to the Gunung Sigogor Nature Reserve. Hence, this area has the potential as a natural habitat for dragonfly and damselfly. The presence of dragonfly and damselfly species is determined by the type of habitat, canopy conditions, vegetation diversity, and the microclimate that exists in a location. This study aimed to determine the diversity of dragonfly and damselfly and to determine the community structure of dragonflies in Selorejo Waterfall. The sampling method was Visual Day Flying. The results of research conducted in two streams showed that there were 12 species from 6 families with a total of 230 individuals. The value of species diversity at this location is H '= 2.05. In the community structure at the Selorejo Waterfall dragonfly, there are differences in the number of species and individuals in the two streams in Selorejo Waterfall Area. The large stream, eight species from four families, 151 individuals in total. Meanwhile, in small stream, there were nine species from six families, 79 individuals in total. The differences in the number of species and individual dragonflies in the two streams at Selorejo Waterfall can be used to describe the diversity and structure of the Odonata community in the area.