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INDONESIA
Jurnal Biodjati
Published by Universitas Islam Negeri Sunan Gunung Djati Bandung
ISSN : 25481606     EISSN : 25414208     DOI : 10.15575/biodjati
Core Subject : Science,
Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences
Arjuna Subject : -
Articles 15 Documents
 1   2 
Search results for , issue "Vol 8, No 1 (2023): May" : 15 Documents clear
In Silico Analysis of Catechin, Galangin, and Hesperidin as Competitors of the SARS-CoV-2 Spike Protein Astuti Kusumorini; Nisrina Hasna; Yani Suryani; Opik Taufiqurrahman4
Jurnal Biodjati Vol 8, No 1 (2023): May
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/biodjati.v8i1.24521

Abstract

Currently, Covid-19 has become endemic. However, the development of Covid-19 drugs continues to be carried out to suppress the growth of the Sars-Cov-2 virus. Some compounds with antiviral activity are catechin, galangin, and hesperidin. Angiotensin-converting enzyme-2 (ACE-2) is a protein that enters viruses into the cell. Based on that, ACE-2 can be used as a primary target to suppress the development of the Sars-Cov-2 virus. This study aimed to test the catechin, galangin, and hesperidin compounds in inhibiting the SARS CoV-2 virus from attaching to ACE-2 by trying the interactions of catechin, galangin, and hesperidin compounds with ACE-2 using the in-silico method. The material used was the three-dimensional structure of the compounds catechin, galangin hesperidin, and ACE-2. The tools used were FAF-Drugs4, Discovery Studio, and Pyrex software. Low-affinity energy values (kcal/mol) indicate promising results. The results showed that the energy affinity value of catechin was -6.2 kcal/mol, galangin was -6.3 kcal/mol, and hesperidin was -8.3 kcal/mol. This value is lower than the control affinity energy (chloroquine and favipiravir), which is  -5.2 kcal/mol and -4.8 kcal/mol, respectively. Based on this, catechin, galangin, and hesperidin can be used as inhibitors/competitors for the Sars-Cov-2 to attach to ACE-2.
Genetic Characteristics of Chloropsis cochinchinensis Gmelin, 1789 Based on The Mitochondrial DNA COI Gene Jarulis Jarulis; Apin Saputra; Risky Hadi Wibowo
Jurnal Biodjati Vol 8, No 1 (2023): May
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/biodjati.v8i1.20260

Abstract

The rate of illegal poaching of blue-winged leafbirds (Chloropsis cochinchinensis) throughout Indonesia, particularly Bengkulu, is quite high. However, only minimal molecular information is available for this species. We performed mtDNA COI gene sequencing to explore genetic characters (conservative site, variable site, parsimony site, and singleton site) of blue-winged leafbirds. Using Qiagen's DNeasy® Blood and Tissue Kit based on the Spin-Column Protocol, total DNA was isolated, and PCR amplification methods were performed. DNA derived from a PCR reaction was forwarded to PT. First Base Malaysia for sequencing. Using MEGA 10.0 and BIOEDIT, the COI gene nucleotide sequence data were assembled, edited, and analyzed to explore of single nucleotide polymorphism, genetic distance, and phylogeny. The 616 bp COI genes contained 566 conservative sites (C), 50 variation sites (V), 24 information parsimony sites (Pi), and 26 singleton sites (S), as indicated by the results. The greatest nucleotide base composition was cytosine (34.1–34.9%), while the lowest was guanine (15.7–16.2%). The proportion of adenine-thymine nucleotide base pairs was greater than that of guanine-cytosine (50.3%). There were 26 barcode-specific mutation sites, 17 transition substitution mutation sites, and 9 transverse substitution mutation sites. The average genetic distance between C. cochinchinensis individuals was 2.2%, but the average genetic difference between species was 9.0%. All C. cochinchinensis individuals in our sample clustered within the same clade and were distinguished from other species within the same genus. The COI gene sequences of C. cochinchinensis that we acquired are novel and can be utilized for molecular identification of the species.
Vegetation Structure and Composition of Coffee Agroforestry in Kalibaru District Titanio Auditya Pribadi; Mufidah Afiyanti; Luchman Hakim
Jurnal Biodjati Vol 8, No 1 (2023): May
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/biodjati.v8i1.23826

Abstract

Agroforestry is a form of sustainable agriculture; the present threat of agroforestry is a change in agroforestry landforms that have switched to a less sustainable form. Coffee plays a role in the agroforestry ecosystem, Kalibaru is one of the Banyuwangi District coffee centers managed by the local community. The objective of this study was to determine the vegetation structure and analyze the effect of that on environmental parameters. Data was collected by vegetation analysis and soil parameter analysis with PAST 2020 Software version 4.05. In total, 15 research plots were used, consisting of 5 complex agroforestry, 5 simple agroforestry, and 5 monoculture plots. The results showed 20 species in complex agroforestry, 24 species in simple agroforestry, and 18 species in monoculture  were found. The highest important index level in complex agroforestry: Durio zibethinus 63.87%  for trees, the Swietenia mahagoni 64.43%  for poles, and Coffee canephora 128.87% for shrubs. In simple agroforestry : Cocos nucifera 72.83% for trees, Leucaena leucocephala  80.70%  for poles, and the Coffea canephora 137.57%  for shrubs. In monoculture agroforestry: Hibiscus similis 82.99%  for trees, Leucaena leucocephala 209.22% for poles, and Coffea canephora 130.96% for shrubs. Agroforestry in Kalibaru was categorized  in the moderate diversity. The diversity index (H') in complex agroforestry showed H' trees 2.21, pole 2.03 and. shrubs 1.60. Simple agroforestry shows H' tree 2.00, pole 2.49, and shrubs 1.50. Monoculture shows H' tree 1.98, pole 0.64, and shrubs 1.54. Agroforestry a role in maintaining soil moisture and temperature, complex agroforestry: temperature 24 0C, and Moist 5.82, simple: temperature 24.2 0C, Moist 5.42, and Monoculture temperature 26 0C, Moist 4.54.
Diversity and Epidermal Characteristic of Lauraceae Leaf in Two Forest Locations, Bogor Regency, West Java Nurul amalia fadhila; Sulistijorini Sulistijorini; Nina Ratna Djuita
Jurnal Biodjati Vol 8, No 1 (2023): May
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/biodjati.v8i1.24406

Abstract

Lauraceae is a group of tropical plants with a wide distribution. The abundance and species richness of the Lauraceae family includes the under to the upper canopy of the forest. The Lauraceae family can be utilized in various sectors, especially economically. Limiting characters as a significance in the Lauraceae classification was needed to provide additional information regarding taxon grouping. This research aimed to study epidermal characteristics, leaf venation variations, and the diversity of Lauraceae species under different forest environmental conditions. The research procedure involved: collecting ecological field data and morphological identification using a purposive sampling method based on the presence of species. Soil sampling and environmental microclimate were measured on each plot. The anatomical process was carried out by recording characters. Correlation between environmental factors and plant targets used canonical correspondence analysis. The kinship between members of Lauraceae was expressed in a dendrogram. The result of this study showed that Lauraceae could live at various elevations. The analysis data indicated differences in environmental factors that affect the existence of Lauraceae species. Leaf venation studies support clustering in the family using characters such as primary, secondary, tertiary veins, and areola. Observation of leaf venation can be used as a taxonomic significance in the family Lauraceae. Epidermal cell walls in leaf samples are straight, curved shallow, deep, and sharp. Other characters that can be found are anomocytic, laterocytic, and brachyparasitic types of stomata, with stellate and glandless trichomes The anatomical dendrogram separated Lauraceae into clusters on a similarity coefficient scale.
Genetic Variation of Structural and Functional Genes of SARS-CoV-2 Isolates Circulating in Banyumas (Indonesia) Anwar Rovik; Clearensia Ade Bina Noviani
Jurnal Biodjati Vol 8, No 1 (2023): May
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/biodjati.v8i1.25132

Abstract

Scientists are performing various measurements to overcome the COVID-19 pandemic. The genomic mutations of SARS-CoV-2 can change their pathogenicity, infectivity, transmission, and antigenicity. This present study aimed to know a) the genetic variation of structural and functional genes of SARS-CoV-2 circulating in Banyumas and b) the potential of the Cilacap’s Harbour as a human mobility portal on the genetic variations of SARS-CoV-2 circulating in Banyumas, Central Java (Indonesia). Genomic sequence of SARS-CoV-2 isolates were taken from the Global Initiative on Sharing All Influenza Data (GISAID) and the National Center for Biotechnology Information (NCBI) online platforms. A gene cut was carried out from Wuhan reference isolate, fifteen isolates from Banyumas, and two isolates from Cilacap (Central Java) using Unipro UGENE v. 33.0 software, considering the annotation of the Wuhan-1 isolate. Genetic variations were detected among SARS-CoV-2 isolates circulating in Banyumas. The structural protein (envelope, membrane, nucleocapsid) encoding gene and the RdRp gene were highly conserved to Wuhan reference genome (Wuhan-Hu-1). Meanwhile, the ORF and the spike-encoding genes were less identical to the Wuhan reference genome. This study also proposed that human mobility from outside Central Java through Cilacap’s Harbour did not affect the genetic variation of SARS-CoV-2 isolates circulating in Banyumas (Central Java).
Effective Combination of Nigella sativa and Trigonella foenum-graecum Seed Extract on Wound Healing in Diabetic Mice Retno Susilowati; Ulfa Maynisa Rohmanningrum
Jurnal Biodjati Vol 8, No 1 (2023): May
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/biodjati.v8i1.19968

Abstract

High levels of free radicals in diabetic wounds often cause chronic inflammation. Nigella sativa and Trigonella foenum-graecum seed extracts are rich in antioxidants and have anti-inflammatory effects. Trigonella foenum-graecum seed extracts can also accelerate the reepithelialization process in wound healing. This study aimed to determine the combination of ethanol extract of Nigella sativa and Trigonella foenum-graecum seeds on wound length and the number of neutrophils, macrophages, fibroblasts, and collagen density in the incision wound of diabetic mice induced by streptozotocin. T. This study used three types of controls, namely Normal (Normal mice,  HPMC 3%),  DM (Diabetic mice, HPMC 3%), and Iodine (Diabetic mice, Povidone Iodine 10%). Topical treatment with 70% ethanol extract ointment combined with Nigella sativa and Trigonella foenum-graecum in various variations, namely N (20%:0%), T (0%:10%), NT (10%:5%), Observations of the wound healing process were carried out on 3rd, 7th and 14th day. Data were analyzed using the One Way ANOVA and Duncan Multiple Range Test. The study's results by observing the morphology of the wound length on day 7th day showed that the combination treatment of extracts of Nigella sativa and Trigonella foenum-graecum resulted in the shortest wound, which was significantly different from the wound in untreated diabetic mice. In addition, diabetic wounds without treatment showed infection, and on the contrary, the infection did not occur in wounds treated with a combination of extracts of Nigella sativa and Trigonella foenum-graecum. The results of wound histology observations showed that the combination treatment of extracts of Nigella sativa and Trigonella foenum-graecum showed a decrease in inflammation which was indicated by a significant decrease in the number of neutrophil cells, macrophages, and accelerated reepithelialization of wound healing as indicated by a significant increase in the number of fibroblasts and collagen density since the third day of treatment.
Age Structure, Growth, and Mortality of Blue Swimming Crab (Portunus pelagicus Linnaeus,1758) in Banten Bay Waters Imadiah Aulia; Muta Ali Khalifa; Ani Rahmawati; Muhammad Syauqi; Mila Wahyuningsih; Syifa Jihan Raimahua; Wilda Akmalia
Jurnal Biodjati Vol 8, No 1 (2023): May
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/biodjati.v8i1.22884

Abstract

Blue swimming crab (BSC) (Portunus pelagicus) is the main fisheries commodity in Banten Bay, with the highest catch of catch occurring in the west monsoon. Increased fishing efforts have reduced the catch, as indicated by a decrease in the average size of carapace width. Overfishing might influence the life cycle and population structure of the BSC. This research aims to analyze the growth and mortality of the Blue Swimming Crab in Banten Bay, especially in the west monsoon. Blue swimming crab samples were obtained from the catch of fish trap and gillnet fishermen with landing sites around the Karangantu Archipelago Fishing Port. Growth, age, and mortality were predicted based on the measurement of total carapace width and body weight. Data were analyzed using Fisat II and Microsoft Excel. The frequency distribution of carapace showed one mode class which normally was distributed consisting of only one age structure group (cohort). The relationship between carapace width and weight of males or females resulted in a slope value (b>3) and was positive allometric, indicating that both sexes had a faster weight gain than the increase in carapace width. Growth parameters resulted asymptotic length (L∞); male 176.75 mm and female 176.46 mm. The growth was relatively fast, with a growth coefficient value of more than one. The mortality showed that the fishing mortality value (F);in males was 3.47 /year and in females 2.69/year was greater than the natural mortality value (M); males 1.25/year and females 1.22/year. Blue Swimming Crabs in Banten Bay had overfished as shown by the high fishing mortality value and there were still many BSC that were caught below the legal size allowed. Thus, catches should be controlled to keep the population and for sustainable fisheries.
Endemic Bamboo (Poaceae, Bambusoideae) of the Lesser Sunda Islands I Putu Gede P. Damayanto; Himmah Rustiami; Miftahudin Miftahudin; Tatik Chikmawati
Jurnal Biodjati Vol 8, No 1 (2023): May
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/biodjati.v8i1.25015

Abstract

More than 40 species of bamboo were known from the Lesser Sunda Islands (LSI), including several endemic species. Endemic species are often highly specialized, found in limited geographical areas, and vulnerable to extinction if their habitat is destroyed. This study aimed to provide an account of endemic bamboo species on the LSI. Fieldwork involved collecting samples of bamboo in the LSI. Herbarium specimens of bamboo deposited in the Herbarium Bogoriense (BO), collected from the LSI were examined, and endemic LSI species were recorded. The conservation status followed the International Union for Conservation of Nature (IUCN) red list categories and criteria. The conservation status of unassessed species was evaluated using IUCN red list categories and criteria. A spatial analysis was also conducted. Data were analyzed and presented descriptively. There are 10 endemic bamboo species in the LSI, namely Bambusa ooh Widjaja & Astuti from Bali (conservation status: endangered), Chloothamnus reholttumianus (Soenarko) Widjaja from Sumba (vulnerable), C. schmutzii (S.Dransf.) Widjaja from Sumbawa and Flores (near threatened), Dinochloa kostermansiana S.Dransf. from Sumba and Flores (near threatened), D. sepang Widjaja & Astuti from Bali (vulnerable), Fimbribambusa rifaiana Widjaja from Alor (near threatened), Gigantochloa aya Widjaja & Astuti from Bali (vulnerable), G. baliana Widjaja & Astuti from Bali (vulnerable), G. taluh Widjaja & Astuti from Bali (vulnerable), and Schizostachyum purpureum Damayanto & Widjaja from Sumba (data deficient). They can be found at an altitude of 20–1700 m in various habitats, including forests, bamboo forests, villages, botanical gardens, along a road, slopes, valleys, riverbanks, and around a lake.
Leaf Anatomy Profile of Begonia Section Platycentrum Sphenanthera Group From Java and Sumatera, Indonesia Intani Quarta Lailaty; Muhammad Efendi
Jurnal Biodjati Vol 8, No 1 (2023): May
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/biodjati.v8i1.20190

Abstract

Anatomical studies have been used in the classification and identification of Begonia species. However, the research on Indonesian native Begonia is still limited. This study focused to evaluate the importance of leaves’ anatomy character for the identification and classification purpose of the Sphenanthera group in Java and Sumatra. A total of six individuals of four Begonia species used in this study, namely Begonia multangula, B. longifolia, B. pseudoscottii, and B. robusta. This study aimed to describe the anatomical characters of the leaves that are useful in the identification and grouping of Begonia section Platycentrum–Sphenanthera. The anatomical preparations used the paraffin method for the cross-section of leaves and the semi-permanent method for paradermal observations. In general, the epidermal cells of paradermal Begonia leaves are polygonal in shape. Consistently, Begonias have single-type stomata with an anisocytic type which are only present on the abaxial leaves. Begonia Sphenanthera group has a thin cuticle (less than 2 µm), both in the abaxial and adaxial surfaces. The lower epidermis cells are smaller than the upper epidermis cells. The mesophyll is differentiated into palisade and spongy tissue. The number and form of mesophyll tissue are varied, therefore useful for diagnosing an important character in the grouping of Begonias from this section.
The Relationship of Sweet Potato Germplasm Based on Morphological Characters Wiwit Rahajeng; Joko Restuono; Febria C. Indriani
Jurnal Biodjati Vol 8, No 1 (2023): May
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/biodjati.v8i1.19331

Abstract

Information about the morphological and genetic characteristics of sweet potato (Ipomoea batatas) is important in the variety development program. This experiment aimed to determine the diversity and genetic relationship of sweet potato accessions from NTT based on morphological character data. The research was carried out at Kendalpayak Research Station, Malang, East Java  from April - September 2019. The materials used were seventy-one sweet potato germplasm from the ILETRI collection (collected from NTT). Each accession was planted on a 1 m × 5 m plot size, with a spacing of 100 × 20 cm (single row). Fertilization was carried out using a dose of “100 kg urea + 100 kg SP36 + 200 kg KCl ha-1”. The observed characters were the vines length, growth type, internode length, leaf length, leaf width, leaf size, leaf bone color, leaf shape, leaf characteristics, lobes number, lobe shape, mature leaf color, shoot color, pigmentation of petiole, young stems pigmentation (dominant and secondary color), young leaves feathers, tuber skin color, tuber flesh color, weight of canopy, number of tubers perplot, weight of tubers perplot, number and weight of tubers perplot. Cluster analysis was carried out using the Minitab 17 program. There was morphological diversity in seventy-one accessions of sweet potato germplasm from NTT. Principal component analysis resulted in seven main components with the proportion of diversity 76.3%. cluster analysis, seventy-one accessions of sweet potato germplasm were divided into fifteen accession groups on the basis of 80% degree. Characteristics of shoot color, mature leaf color, leaf size, petiole pigmentation, and leaf bone color contributed greatly to the total diversity.

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