Biogenesis: Jurnal Ilmiah Biologi最新文献_第8页

Prediction of SARS-CoV-2 3C-like protease (3CLpro) crystal structure to provide COVID-19 inhibitor design through computational studies 通过计算研究预测SARS-CoV-2 3c样蛋白酶(3CLpro)晶体结构，为COVID-19抑制剂设计提供依据

Biogenesis: Jurnal Ilmiah Biologi Pub Date : 2021-12-30 DOI: 10.24252/bio.v9i2.24520

T. M. Fakih, D. Ramadhan

{"title":"Prediction of SARS-CoV-2 3C-like protease (3CLpro) crystal structure to provide COVID-19 inhibitor design through computational studies","authors":"T. M. Fakih, D. Ramadhan","doi":"10.24252/bio.v9i2.24520","DOIUrl":"https://doi.org/10.24252/bio.v9i2.24520","url":null,"abstract":"Infectious diseases have lately become pandemic, posing a threat to global public health with the introduction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously provisionally named 2019 novel coronavirus or 2019-nCoV). Technological advancements have increased the possibility of discovering natural inhibitor candidates capable of preventing and controlling COVID-19 infections. The SARS-CoV-2 3C-like protease (3CLpro) is critical for SARS-CoV-2 replication and is a prospective therapeutic target. This study aims to identify, evaluate, and explore the 3CLpro macromolecular structures from SARS-CoV and SARS-CoV-2, as well as their impact on angiotensin-converting enzyme 2 (ACE-2). The discovery of the two 3CLpro macromolecules revealed structural similarities in several regions. These findings were subsequently confirmed by performing protein-protein docking simulations to observe the interaction of 3CLpro with the active site ACE-2. With an ACE score of 701.41 kJ/mol, SARS-COV-2 3CLpro forms the strongest binding with ACE-2. As a result, the findings of this research can be used to guide the development of potential SARS-CoV-2 3CLpro inhibitors for the treatment of COVID-19 infectious diseases.","PeriodicalId":8911,"journal":{"name":"Biogenesis: Jurnal Ilmiah Biologi","volume":"37 1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90665749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Analysis of genetic diversity of bacteria Xanthomonas oryzae pv. oryzae causes leaf blight in North Sumatra 水稻黄单胞菌遗传多样性分析。米曲菌在北苏门答腊岛引起叶枯萎病

Biogenesis: Jurnal Ilmiah Biologi Pub Date : 2021-12-30 DOI: 10.24252/bio.v9i2.24092

Zulheri Noer, M. Maimunah, Erwin Pane, E. Prasetya

{"title":"Analysis of genetic diversity of bacteria Xanthomonas oryzae pv. oryzae causes leaf blight in North Sumatra","authors":"Zulheri Noer, M. Maimunah, Erwin Pane, E. Prasetya","doi":"10.24252/bio.v9i2.24092","DOIUrl":"https://doi.org/10.24252/bio.v9i2.24092","url":null,"abstract":"Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight on rice plants, which is responsible for crop failure, resulting in economic losses. Control of Xoo bacteria can be accomplished through the use of Xoo-resistant rice varieties. Due to the shifting genetic structure and environmental conditions of Xoo bacteria, it is difficult to identify them according to their pathotype. This study aims to determine the genetic diversity of Xoo bacteria using the polymerase chain reaction (PCR) method and the IS1112-based RAPD marker, which is known to contain repetitive sequences. DNA was isolated from 52 isolates collected from 15 districts and cities in North Sumatra province and then used to amplify the IS1112 sequence. Dendrogram analysis revealed that cluster analysis of PCR findings classified isolates into 15 groups with a 90% similarity value. Genetic variation among Xoo isolates from North Sumatra ranged between 51% and 100%. North Sumatra Xoo isolates exhibited a high degree of genetic diversity. This findings can be used as a resource for future management of the Xoo bacteria by expediting disease-resistant rice breeding projects in various rice producing countries.","PeriodicalId":8911,"journal":{"name":"Biogenesis: Jurnal Ilmiah Biologi","volume":"101 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80848025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparising DNA extraction from environmental DNA samples to reveal the diversity of freshwater metazoans 比较环境DNA样本的DNA提取，揭示淡水后生动物的多样性

Biogenesis: Jurnal Ilmiah Biologi Pub Date : 2021-12-30 DOI: 10.24252/bio.v9i2.24390

D. S. Yudha, D. Priyono, Rahma Izzati, Aulia Sigit Ardianto, Ananto Puradi, Nainggolan Nainggolan

{"title":"Comparising DNA extraction from environmental DNA samples to reveal the diversity of freshwater metazoans","authors":"D. S. Yudha, D. Priyono, Rahma Izzati, Aulia Sigit Ardianto, Ananto Puradi, Nainggolan Nainggolan","doi":"10.24252/bio.v9i2.24390","DOIUrl":"https://doi.org/10.24252/bio.v9i2.24390","url":null,"abstract":"Environmental DNA (eDNA) monitoring has gained popularity in the last decade as one of the most sensitive and cost-effective monitoring methods. However, information regarding the type of DNA extraction used still needs to be studied, especially for metazoan in fresh water samples. This parameter is also critical for a project's experimental design. This study aims to compare the effectiveness of two extraction kits between DNeasy® Blood & Tissue Kit (Qiagen) silica column-based and ZymoBIOMICS 96 MagBead DNA Kit (Zymo Research) magnetic bead-based. The quantity of DNA extracts was measured using a spectrophotometer at 260/280 nm. Following that, we continued the metazoa PCR procedure. Qiagen has higher mean value of DNA concentration (88.48 ng/μl) than Zymo (20.89 ng/μl). For DNA purity, Zymo has higher mean value of DNA purity (1.84) than the Qiagen (1.59). However, both kits were equally successful in amplifying universal metazoan primers. We recommend that the use of these types of kits appears to be the least important consideration. Other important factors that may have a major impact on DNA extraction such as water volume, membrane type, sampling strategy need to be investigated in freshwater samples.","PeriodicalId":8911,"journal":{"name":"Biogenesis: Jurnal Ilmiah Biologi","volume":"125 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77103147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Evaluation of antimicrobial activity and phytochemical screening of red Kamboja (Plumeria rubra L.) extracts 红色Kamboja (Plumeria rubra L.)提取物抑菌活性评价及植物化学筛选

Biogenesis: Jurnal Ilmiah Biologi Pub Date : 2021-12-30 DOI: 10.24252/bio.v9i2.25409

N. Sari, N. W. Deswiniyanti, P. Wiradana

{"title":"Evaluation of antimicrobial activity and phytochemical screening of red Kamboja (Plumeria rubra L.) extracts","authors":"N. Sari, N. W. Deswiniyanti, P. Wiradana","doi":"10.24252/bio.v9i2.25409","DOIUrl":"https://doi.org/10.24252/bio.v9i2.25409","url":null,"abstract":"Natural antimicrobial sources such as red Kamboja (Plumeria rubra L.) flower extract can be utilized to treat infectious disorders caused by Staphylococcus aureus, Escherichia coli, and Candida albicans. This study aims to determine evaluate the effectiveness of methanol and ethanol extracts of P. rubra floral against E. coli, S. aureus, and C. albicans growth, as well as the amount of secondary metabolites in P. rubra extract. The study's findings indicate that the highest DIZ value of P. rubra methanol extract was 7.40 mm, 7.36 mm, and 7.30 mm for S. aureus ATCC25923 at 5%, 10%, and 20%, respectively, while the highest DIZ value for C. albicans ATCC10231 at 10%, 10%, and 20% was 25.08 mm, and 25.04 mm, respectively. The DIZ value of the P. rubra flower ethanol extract against E. coli strain was 5.26 mm at 5%, and 7.30 mm at 20%. Secondary metabolites of saponins, tannins, alkaloids, flavonoids, steroids, and phenols were present in the methanol and ethanol extracts of P. rubra flowers. In summary, our findings highlight the use of P. rubra flower extract as a biological source with antibacterial properties for the control of human infectious illnesses.","PeriodicalId":8911,"journal":{"name":"Biogenesis: Jurnal Ilmiah Biologi","volume":"132 25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86422549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A modified high-fat diet and its effect on histopathological features of mice liver as an alternative diet for animal model of liver cell damage 改良高脂饮食对肝细胞损伤动物模型小鼠肝脏组织病理学的影响

Biogenesis: Jurnal Ilmiah Biologi Pub Date : 2021-12-30 DOI: 10.24252/bio.v9i2.24081

Dzul Fithria Mumtazah, H. Busman, M. Kanedi, G. Pratami

{"title":"A modified high-fat diet and its effect on histopathological features of mice liver as an alternative diet for animal model of liver cell damage","authors":"Dzul Fithria Mumtazah, H. Busman, M. Kanedi, G. Pratami","doi":"10.24252/bio.v9i2.24081","DOIUrl":"https://doi.org/10.24252/bio.v9i2.24081","url":null,"abstract":"Researchers attempted to obtain animal models that experienced hypercholesterolemia and led to liver damage to determine the performance of the liver. Rats were chosen because of the ease of handling, collecting organ and blood samples. Still, their high price and availability that are more difficult to find have made some researchers look for alternatives to other animal models such as mice. This study aims to determine the role of a modified high-fat diet as an alternative diet for mice to experience hepar damage. Male mice treated for four and eight weeks with a modified high-fat diet were sacrificed for their liver, then they were tested for histopathology using the paraffin method and HE staining. The characterization of hepar damage traits was carried out to score the degree of parenchymal degeneration, hydropic degeneration, and necrosis. The results showed that the control group, four and eight weeks of atherogenic diet had more than 50% cell damage, presumably due to the role of the starch mixture in feed as a source of carbohydrates through the mechanism of converting carbohydrate pathways into fat which damages liver cells.","PeriodicalId":8911,"journal":{"name":"Biogenesis: Jurnal Ilmiah Biologi","volume":"101 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77326356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Efficacy of knockdown insecticide based on Permot (Passiflora foetida L.) leaf extract against mortality of German cockroach (Blattella germanica L.) 柿子叶提取物击倒型杀虫剂对德国小蠊的杀伤效果研究

Biogenesis: Jurnal Ilmiah Biologi Pub Date : 2021-12-30 DOI: 10.24252/bio.v9i2.24100

R. Susilowati, Flora Rumiati

{"title":"Efficacy of knockdown insecticide based on Permot (Passiflora foetida L.) leaf extract against mortality of German cockroach (Blattella germanica L.)","authors":"R. Susilowati, Flora Rumiati","doi":"10.24252/bio.v9i2.24100","DOIUrl":"https://doi.org/10.24252/bio.v9i2.24100","url":null,"abstract":"Chemical insecticides have a detrimental effect on not only the target species, but also on non-target species and the environment. Transfluthrin is a pyrethroid class II insecticide that is considered to be safe for humans. However, repeated use over an extended period of time can result in cockroach resistance. For this reason, this study sought out alternative materials, specifically Permot leaf (Passiflora foetida L.). This study aims to determine the neurotoxic efficacy of insecticides derived from Permot leaf extract on German cockroach knockdown time and death. A total of 120 German cockroaches and was replicated three times. After 1 h of exposure to insecticides containing transfluthrin 3000 ppm and Permot leaf extract up to a dose of 4000 ppm, knockdown time and cockroach death were observed. The probit test was used to determine the cockroach knockdown time. The study's findings indicated that when cockroaches were exposed to insecticides derived from Permot leaves at a dose of 4000 ppm, the knockdown efficacy was KT50 for 8 min and KT90 for 30 min. The blocking test on German cockroach spiracles established that exposure via cockroach spiracles was more effective than exposure via other cockroach organs in killing.","PeriodicalId":8911,"journal":{"name":"Biogenesis: Jurnal Ilmiah Biologi","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77473821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tillering response of liquid organic fertilizer and monosodium glutamate supplementation on Ganyong (Canna discolor Lindl.) 液体有机肥和谷氨酸钠对甘庸美人蕉分蘖的响应

Biogenesis: Jurnal Ilmiah Biologi Pub Date : 2021-12-30 DOI: 10.24252/bio.v9i2.24196

Mahdalina Mursilati, A. Suprapto, Esna Dili Novianto

{"title":"Tillering response of liquid organic fertilizer and monosodium glutamate supplementation on Ganyong (Canna discolor Lindl.)","authors":"Mahdalina Mursilati, A. Suprapto, Esna Dili Novianto","doi":"10.24252/bio.v9i2.24196","DOIUrl":"https://doi.org/10.24252/bio.v9i2.24196","url":null,"abstract":"Ganyong (Canna discolor) is a plant that contains a high carbohydrate content, utilizing as alternative food for rice, especially in Indonesia. One of the factors affecting growth is the quantity of tillers, which affect the productivity of Ganyong's tuber. The purpose of this study was to discover the optimal combination of liquid organic fertilizer and monosodium glutamate to enhance the number of tillers. This study employed a randomized complete block design with a two-factor structure. The first factor to consider was the concentration of liquid organic fertilizer, which was specified as 0 ml/L, 2 ml/L, 3 ml/L, and 4 ml/L. The second factor was the monosodium glutamate dosage, which ranged from 0 to 3 g/plant, 6 g/plant, and 9 g/plant. Ganyong were cultivated for six months on farmland at an elevation of 460 m asl. Supplementation with liquid organic fertilizer resulted in a significant increase in the number of tillers. While monosodium glutamate supplementation had no significant effect on the formation of tillers. Combining liquid organic fertilizer at a concentration of 3 ml/L with monosodium glutamate 6 g/plant resulted in the optimal number of tillers.","PeriodicalId":8911,"journal":{"name":"Biogenesis: Jurnal Ilmiah Biologi","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80982430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PENGEMBANGAN MEDIA KOMIK PADA MATERI KEANEKARAGAMAN HAYATI BAGI SISWA KELAS X SMA 高中四年级学生漫画媒介的发展

Biogenesis: Jurnal Ilmiah Biologi Pub Date : 2021-08-23 DOI: 10.31258/biogenesis.17.2.94-100

A. Mandasari, L. MarianiNatalina, Nursal Nursal

引用次数: 0

ANALISIS MUTU IKAN PATIN (Pangasius sp.) SALAI DENGAN PEMBERIAN KITOSAN DAN LAMA PENGASAPAN SEBAGAI RANCANGAN LKPD BIOLOGI SMA

Biogenesis: Jurnal Ilmiah Biologi Pub Date : 2021-08-23 DOI: 10.31258/biogenesis.17.2.61-68

S. Wulandari, E. Febrita, Anugrah Tifanny

{"title":"ANALISIS MUTU IKAN PATIN (Pangasius sp.) SALAI DENGAN PEMBERIAN KITOSAN DAN LAMA PENGASAPAN SEBAGAI RANCANGAN LKPD BIOLOGI SMA","authors":"S. Wulandari, E. Febrita, Anugrah Tifanny","doi":"10.31258/biogenesis.17.2.61-68","DOIUrl":"https://doi.org/10.31258/biogenesis.17.2.61-68","url":null,"abstract":"The aims to determine the effect of chitosan concentration and smoking time on the quality of smoked catfish (Pangasius sp.) and produce Student Worksheet design. This research was divided into two step, there is experimental step and the Student Worksheet design. At the experimental step, used a factorial Completely Randomized Design (CRD). Factor I is the concentration of chitosan, and factor II is duration of smoking time. This study consisted of 12 treatments with 3 replications so that there were 36 experimental units. Parameters observed were protein content, fat content, water content and organoleptic on appearance, scent, taste and texture. The results showed that the effect of chitosan concentration and smoking time had an effect on treated with 3% chitosan and 3 days of smoking showed the best results, with the total protein content was 35.89%, fat content was 29.72% and water content was 15.27%. Meanwhile, the organoleptic test results of smoked catfish on the aspects of appearance, scent, taste and texture, the best treatment was also found in smoked catfish with 3% chitosan treatment and 3 days of smoking time. The results can be used as a student worksheet design on Food Additives material for class XI high school.","PeriodicalId":8911,"journal":{"name":"Biogenesis: Jurnal Ilmiah Biologi","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88733561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DAMPAK IMPLEMENTASI PEMBELAJARAN DARING PADA MASA PANDEMI COVID-19 COVID-19大流行期间在线学习的影响

Biogenesis: Jurnal Ilmiah Biologi Pub Date : 2021-08-23 DOI: 10.31258/biogenesis.17.2.88-93

Ayu Wahyuni, Cut Shaviatul Bayti, Aufa Rindu Purnama, Lidya Wahyundari

{"title":"DAMPAK IMPLEMENTASI PEMBELAJARAN DARING PADA MASA PANDEMI COVID-19","authors":"Ayu Wahyuni, Cut Shaviatul Bayti, Aufa Rindu Purnama, Lidya Wahyundari","doi":"10.31258/biogenesis.17.2.88-93","DOIUrl":"https://doi.org/10.31258/biogenesis.17.2.88-93","url":null,"abstract":"At current, the Covid-19 pandemic is a global health threat with confirmed cases and high mortality. WHO declared this outbreak a global pandemic because the transmission of this virus was very fast and most countries in the world also exposed to it. Recent data updating the number of confirmed patients worldwide is 23,491,520 positive cases. Indonesia is one of the countries that has been exposed to this virus the beginning of March until now on 25 August 2020, there were 157,859 confirmed cases spread across 34 provinces and 415 districts / cities. The purpose of this study was to identify the impact the teachers, students and parents felt during the Covid 19 pandemic during the implementation of online learning. This study used a method descriptive analysis content. This method is used to describe some information about the impact of the Covid-19 pandemic on implementing online learning. The results of this study are the impact on teacher performance, that is, the loss of teacher motivation in teaching and there are teachers who do not understand use of electronic devices, the impact on the learning process is that students are not familiar with the distance learning process,Impact on parents as student guardians is issue between students and teachers and economic conditions can affect the learning process of the students. In the midst of this pandemic, parents are very influential in children's development, such as trying to create a supportive environment to motivate children in learning with these different situations, and the government is expected to participate in embracing the complaints and needs of children in learning, for example internet quotas. Hopefully with joint efforts, the pandemic will end quickly and we can return to building a pleasant situation better than before. ","PeriodicalId":8911,"journal":{"name":"Biogenesis: Jurnal Ilmiah Biologi","volume":"46 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85864916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3