bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variants in Homologous Recombination Genes EXO1 and RAD51 Related with Premature Ovarian Insufficiency
Authors: Luo Wei , Guo Ting , Li Guangyu , Liu Ran , Zhao Shidou , Song Meihui , Zhang Liangran , Wang Shunxin , Chen Zi-Jiang , Qin Yingying 
Published: August 2020

Abstract

Context
Premature ovarian insufficiency (POI) is characterized by cessation of menstruation before 40 years of age and elevated serum level of FSH (&gt;25 IU/L). Recent studies have found a few causative genes responsible for POI enriched in meiotic recombination and DNA damage repair pathways.

Objective
To investigate the role of variations in homologous recombination genes played in POI pathogenesis.

Methods
The whole exome sequencing was performed in 50 POI patients with primary amenorrhea. Functional characterizations of the novel variants were carried out in budding yeast and human cell line.

Results
We identified 8 missense variants in 7 homologous recombination genes, including EXO1, RAD51, RMI1, MSH5, MSH2, MSH6, and MLH1. The mutation p.Thr52Ser in EXO1 impaired the meiotic process of budding yeast and p.Glu68Gly in RAD51-altered protein localization in human cells, both of them impaired the efficiency of homologous recombination repair for DNA double-stranded breaks in human cells.

Conclusions
Our study first linked the variants of EXO1 and RAD51 with POI and further highlighted the role of DNA repair genes in ovarian dysgenesis.
Dipteran diversity and succession pattern on carcass of rabbits treated with opium dross: Implication in forensic medicine
Authors: Keshavarz Davood , Rassi Yavar , Oshaghi Mohamadali , AZIZI KOUROSH , RAFIZADEH SAYENA , SHAHRIARINAMADI MARZIEA 
Published: August 2020

Abstract. Keshavarz D, Rassi Y, Oshaghi MA, Azizi K, Rafizadeh S, Shahriarinamadi M. 2020. Dipteran diversity and succession pattern on carcass of rabbits treated with opium: Implication in forensic medicine. Biodiversitas 21: 3135-3141. The present study aimed to investigate the effect of opium on the succession pattern and diversity of Diptera on rabbit carcasses. In the present experimental study, dipteran species were collected from rabbit carcasses during the decay process. During this study, two replicates were performed, and four rabbits were used in each. Rabbits divided equally into two groups. In the first group, animals were received 25 mg opium dross orally via a gastric tube and then gradually increased the dose to 100 mg/case/day, while the second group were used as controls and received distilled water. The most frequent species on both carcass types were Chrysomya albiceps (26.2%), Lucilia sericata (15.9%), and Musca domestica (13.9%). Diversity analysis indicates high species richness on untreated carcasses (Shannon: 2.1; Margalef: 1.7). However, a significant difference was not detected for the Shannon index between the treated and untreated carcasses (P: 0.56). The taxa similarity values for sampling intervals ranged from 0.20-0.46 for both untreated and treated carcasses. Permutation analysis showed that successional patterns of dipteran species were similar between opium dross-treated and untreated carcasses. Therefore, in the case of opioid (opium) abused cadaver, this substance could not have an effect on the PMI estimation based on the pattern of succession. But it seems that the PMI should be corrected when the estimate is based on larval growth rate.
Prevalence and diversity of ectoparasites in scavenging chickens (Gallus domesticus) and their association to body weight
Authors: Riwidiharso Edy , Darsono Darsono , Setyowati Endang ariyani , Pratiknyo Hery , SUDIANA EMING , SANTOSO SLAMET , YANI EDY , Widhiono Imam 
Published: August 2020

Abstract. Riwidiharso E, Darsono, Setyowati EA, Pratiknyo H, Sudiana E, Santoso S, Yani E, Widhiono I. 2020. Prevalence and diversity of ectoparasites in scavenging chickens (Gallus domesticus) and their association to body weight. Biodiversitas 21: 3163-3169. Domestic chickens (Gallus domesticus) which are traditionally fed by scavenging on farms predispose them to ectoparasites infestation. In this study, a preliminary survey was conducted on the common ectoparasites on G. domesticus in the rural areas of Banyumas. The purposes of this study were to determine the diversity of ectoparasites, their prevalence, and their relationship to the chickens body weight. This research was conducted by the survey method from December 2019 to April 2020 in five villages around the city of Purwokerto, Banyumas District, Central Java, Indonesia viz., Kedungwuluh, Kedungwringin, Kutasari, Karangsalam, and Karanggintung. Data analysis was conducted by Shannon Wiener and Evenness indexes. Analysis of variance was used to calculate the difference in prevalence among sample locations. Regression correlation analysis was used to determine the relationship between prevalence and chicken body weight. The results showed that there were six ectoparasite species i.e., Menopon gallinae, Menacanthus cornutus, Lipeurus caponis, Dermanysus gallinae, Megninia ginglymura, and Haemaphysallis sp. parasitizing G. domesticus. The number of ectoparasite individuals among locations was significantly different (F 5.59 < 32.45; p <0.05). The most number of ectoparasite was found in Karangsalam (272 individuals). The most prevalent ectoparasite was M. cornutus (45%), followed by L. caponis (40%), and the lowest was M. synglineura (25%). Ectoparasite prevalence was associated with chicken weight loss (r = 0.98). The prevalence of ectoparasite of domestic chickens farm in the Banyumas Regency is classified as low but has the potential to influence body weight.
Comparison on seed germination and seedling growth between Indonesian local corn cultivars for decide the quality of seed
Authors: Wawo Albert Husein , Sumbogo Verina Gita , Lestari Peni 
Published: August 2020

Abstract. Wawo AH, Sumbogo VG, Lestari P. 2020. Comparison on seed germination and seedling growth between Indonesian local corn cultivars for decide the quality of seed. Biodiversitas 21: 3189-3199. Each region in Indonesia has local corn cultivars (Zea mays L), for example, South Sulawesi has some Pulut Pangkajene cultivars and Purbalingga, Central Java has Entog and Senggani cultivars. Compared to hybrid corn, local corn has its advantages such as dry resistance, short life, and specific taste. The identification of seed germination and seedling growth for Pangkajene corn (South Sulawesi), Entog and Senggani corns (Purbalingga) has not been performed, thus, specific characteristics to differ those three corn cultivars have not been available. The study aims to establish the characteristics of local corn cultivars, comprise the seed germination, seedling growth, and determine the best local corn cultivars for supporting food sources. This research has Factorial patterned with a Completely Randomized Design and it was repeated 4 times. The main factor is the germination facility, namely germination chamber and nursery house. Meanwhile, the second factors are corn cultivars, namely Pangkajene, Entog, and Senggani. The result shows that the Pangkajene and Entog cultivars have higher germinability and germination value compared to Senggani corn cultivar. Pangkajene and Senggani cultivars have higher seedling growth than Entog cultivar seedlings characterized by high relative growth rate (R) values. The Pangkajene cultivar has higher quality compared to 2 local corn cultivars of Entog and Senggani from Purbalingga (Central Java). Further, Senggani cultivars have higher quality than Entog cultivars.
Metagenomic analysis and biodiversity of Lactic Acid Bacteria (LAB) on masin (fermented sauce) from Sumbawa, West Nusa Tenggara, Indonesia
Authors: Manguntungi Baso , Saputri Dinar , Mustopa Apon , Ekawati Nurlaili , Afgani Chairul , Sari Arlindah , Triratna Lita , Sukmarini Linda , FATIMAH Fatimah , Kusmiran Amirin , YANTI SAHRI , Irawan Shasmita , Prasetyo Muhammad , Fidien Khadijah ALLIYA 
Published: August 2020

Abstract. Manguntungi B, Saputri DS, Mustopa AZ, Ekawati N, Afgani CA, Sari AP, Triratna L, Sukmarini L, Fatimah, Kusmiran A, Yanti S, Irawan S, Prasetyo MD, Fidien KA. 2020. Metagenomic analysis and biodiversity of Lactic Acid Bacteria (LAB) on masin (fermented sauce) from Sumbawa, West Nusa Tenggara, Indonesia. Biodiversitas 21: 3287-3293. Masin is a spontaneously fermented sauce from Sumbawa, West Nusa Tenggara Indonesia that is made of shrimp paste, chili, turmeric flower, and herbs mixed with some spices. This study aims to isolate Lactic Acid Bacteria (LAB) and analyze the metagenomic and biodiversity of its bacteria. Genome isolation for metagenomic analysis was using ZymoBIOMICSTM DNA Miniprep Kit. Sequencing analysis to identify LAB strain form masin was using 16S rRNA universal primer. Metagenomic analysis showed that relative abundance bacteria in masin for order taxon was Lactobacillales, the family taxon was Enteroccocaceae, and the genus was Tetragenoccocus. Six different groups were obtained from the phylogenetic tree analysis of 40 isolates found in masin. The representatives of each group taken were isolates number 2, 17, 11, 34, 28, and 5. Based on the results of sequencing analysis, the 6 isolates found in masin are Staphylococcus piscifermentans strain CIP103958 (Isolate Code 2), S. piscifermentans strain BULST54 (Isolate Code 17), S. piscifermentans strain SK03 (Isolate Code 11), S. piscifermentans strain ATCC 51136 (Isolate Code 34), S. piscifermentans strain PCM 2409 (Isolate Code 28) and S. piscifermentans strain PU-87 (Isolate Code 5). Through this research, it has been described a whole diversity of bacteria contained in masin, one of them is Lactic acid bacteria. The six LAB isolates that have been identified can be developed as starter candidates for masin production.
Short Communication: Geometric morphometric analysis of leaf venation in four Shorea species for identification using Digital Image Processing
Authors: Ariawan Ishak , HERDIYENI YENI , SIREGAR ISKANDAR ZULKARNAEN 
Published: August 2020

Abstract. Ariawan I, Herdiyeni Y, Siregar IZ. 2020. Short Communication: Geometric morphometric analysis of leaves venation in Shorea spp. for identification using Digital Image Processing. Biodiversitas 21: 3303-3309. Shorea is one of the genera of the Dipterocarpaceae family which consists of more than 190 species. Massive exploitation of forests has threatened the sustainability of Shorea in nature. A total of 156 species has been listed on the IUCN (International Union for Conservation of Nature) red list. From the 156 species, 59.6% are in the critically endangered category, so urgent conservation is needed. However, during collection of Shorea at the seedling phase for conservation purposes, it is often difficult to distinguish among them that can cause errors in their collection process. To avoid these errors, identification needs to be done, usually based on plant leaf and flower morphology. Leaves are easier because they have the main features that distinguish each plant species, one of which is the venation structure. Geometric morphometric techniques are a modern approach recognized as useful for the identification of species in many plants. Geometric morphometrics analyzes the position of the venation point using coordinate geometry values. This research was aimed to extract venation features of Shorea leaves using a geometric morphometric approach. The extraction process result in some features, such as straightness, different angle, length ratio, scale projection, and secondary nerves. On extracted features, an analysis was then performed to find out the best features in classifying species of Shorea spp. The results of this study indicated that the geometric morphometric approach could extract the value of the features of straightness, different angle, length ratio, scale projection, and secondary nerves. The secondary nerve feature is the best feature because it can distinguish between fourcommonly planted species of Shorea spp. (S. acuminata, S. leprosula, S. ovalis, and S. selanica). By using the support vector machine classification technique to identify species of Shorea spp., the classification results obtained an average accuracy of 84.46%.
Morphometric and DNA Barcoding of endemic Halmaheran walking shark (Hemiscyllium halmahera, Allen, 2013) in North Maluku, Indonesia
Authors: MADDUPPA Hawis , PUTRI ARINI S. P. , WICAKSONO RIDHO Z. , SUBHAN BEGINER , AKBAR NEBUCHADNEZZAR , ISMAIL FIRDAUT , ARAFAT DONDY , PRABUNING DERTA , MUKSIN L.M. IQBAL , SRIMARIANA ENDANG S. , BAKSIR ABDURRACHMAN , BENGEN DIETRIECH G. 
Published: August 2020

Abstract. Madduppa H, Putri ASP, Wicaksono RZ, Subhan B, Akbar N, Ismail F, Arafat D, Prabuning D, Sani LMI, Srimariana ES, Baksir A, Bengen DG. 2020. Morphometric and DNA Barcoding of endemic Halmaheran walking shark (Hemiscyllium halmahera, Allen, 2013) in North Maluku, Indonesia. Biodiversitas 21: 3331-3343. The walking shark (Hemiscyllium halmahera) commonly referred to as bamboo shark, is a shark species that belongs to the Hemiscyllidae family which is endemic in North Maluku, and Indonesian waters. These Hemiscyllium species are generally confined to the Australian-New Guinea region, save a specie which originates from Halmahera, an Indonesian island. Ever since its discovery, sufficient information on its existence has been largely unavailable. Hence, the purpose of this study is (1) to assess the morphology, using meristic measurements and length-weight relationship, and (2) to determine the molecular characteristics through DNA barcoding, phylogenetic reconstruction, and genetic diversity. The samples used in this research were obtained from Halmahera Archipelago, North Maluku, including Halmahera, Tidore, Ternate, Maitara, and Guraici in several expeditions between March 2017 and January 2018. 36 individuals in total were measured for morphometric parameters including Total Length (TL), Standard Length (SL), Head Length (HL), Body Circumference (BC), and Body Weight (BW). Out of a total of 36 sharks, tissue samples were obtained from 32 individuals for molecular identification. After the required measurements were obtained, all individuals sharks were released back to their habitat safely. Equations of linear regression were used to analyze the relationship between length and weight. Morphometric measurements indicated that the average total length of the walking shark samples obtained, were not more than 75± cm for both male and female specimens. The length-weight analysis revealed a positive allometric growth pattern in H. halmahera species, where weight was gained faster than an increase in length. The results of the DNA fragment length analysis from all samples were 793-bp. All 32 tissue samples identified as H. halmahera consisted of 3 samples from Ternate Island, 14 samples from Maitara Island, 9 samples from Guraici Island (South Halmahera), 10 samples from Central Halmahera, and 2 samples from Tidore Island. These results confirmed that DNA subsequence analysis indicates that H. halmahera is different from those sequences extracted from Genbank in the Australia-New Guinea region. This study successfully identified H. halmahera based on their morphological and molecular characters, and has therefore contributed to international genetic database (Barcoding Of Life Database-BOLD) for further studies.
Body weight, body measurements and slaughter characteristics of Madura cattle raised in Pamekasan District, East Java Province, Indonesia
Authors: PRIHANDINI PENI WAHYU , MAHARANI DYAH , Sumadi Sumadi 
Published: August 2020

Abstract. Prihandini PW, Maharani D, Sumadi. 2020. Body weight, body measurements, and slaughter characteristics of Madura cattle raised in Pamekasan District, East Java Province, Indonesia. Biodiversitas 21: 3415-3421. This study was designed to analyze the body weight, body measurements and slaughter characteristics of Madura cattle raised in Pamekasan district, East Java province, Indonesia. A total of 2,373 records on live body weight and body measurements (body length, height at withers and chest girth), and 69 records on slaughter traits (slaughter, carcass, and meat weight, as well as carcass and meat percentage) from both sexes were used. Sampled animals were divided into three groups based on age (calf: 0- to10-month-old; young: 11- to 24-month-old; adult: >24-month-old). The data were analyzed using independent sample t-test to assess significant differences between sex groups and subjected to multiple linear regression analyses to obtain prediction equations of body weight from body measurements, carcass weight from slaughter weight, and meat weight from slaughter- and carcass-weight. Results showed that body weight, height at withers, and chest girth between male and female cattle in all age groups were significantly different (P<0.05). Male cattle showed higher slaughter weight, carcass weight and carcass percentage mean values than female cattle. Body measurements showed high correlation with body weight (r ≥0.80). Height at withers, body length, and chest girth represented good body measurements to predict body weight (R2 = from 0.65 to 0.83). Moreover, as observed, high correlations between slaughter weight and carcass- (r = 0.94; R2 = 0.89) and meat-weight (r = 0.99; R2 = 0.98) would imply that meat weight could be predicted accurately from slaughter- and carcass-weight.
Screening of Burkholderia spp. from oil palm plantation with antagonistic properties against Ganoderma boninense
Authors: YURNALIZA YURNALIZA , RAMBE DITA ISNAINI , SARIMUNGGU LISTRA , PURBA MEYLISA , NURWAHYUNI ISNAINI , LENNY SOVIA , LUTFIA ANISA , HARTANTO ADRIAN 
Published: August 2020

Abstract. Yurnaliza. Rambe DI, Sarimunggu L, Purba M, Nurwahyuni I, Lenny S, Lutfia A, Hartanto A. 2020. Screening of Burkholderia spp. from oil palm plantation with antagonistic properties against Ganoderma boninense. Biodiversitas 21: 3431-3437. Burkholderia spp. are ubiquitous diazotrophic bacteria within β-Proteobacteria group, known for its occurrence in variety of niches from aquatic to terrestrial habitats and as endophytes. Beneficial strains of Burkholderia have been reported as plant growth-promoting rhizobacteria or as antagonistic bacteria against phytopathogenic fungi. This study evaluated the potential of multiple strains of Burkholderia spp. recovered from three ecological niches, such as rhizosphere, humus soil, and root endophytes of oil palm plantations in North Sumatra to suppress the growth of basal stem rot causative agent in oil palm (Elaeis guineensis Jacq.) by Ganoderma boninense Pat. The antagonistic isolates were identified on the basis of molecular identification using 16S rDNA sequence (27F–1462R), revealing twelve isolates (48%) as members of Burkholderia cepacia complex (Bcc), with other minor genera, such as Chitinophaga, Klebsiella, Mycobacterium, Paenibacillus, Rhizobium, Serratia, Stenotrophomonas, and Xanthomonas. The antagonistic activities as expressed in the percentage inhibition of radial growth (PIRG) against G. boninense were considerably potential with the highest percentage of 55%. In comparison, the crude extract (MeOH, EtOAc) was also tested against G. boninense colonies showing PIRG from 0 to 38%. Majority of isolates did not show any visible chitinolytic activity based on plate assay, in exception to B. contaminans RC02 while most of them were producers of glucanase. The collection of indigenous Burkholderia spp. originating from North Sumatran oil palm plantations, i.e. B. cepacia, B. contaminans, B. metallica, and B. stagnalis may then be considered as potential biocontrol agents against G. boninense based on their antagonistic activities, antifungal properties, and hydrolytic enzyme activities.
Characterization and identification of three thermophilic Bacillus strain isolated from Domas Crater, Mt. Tangkuban Perahu, Indonesia
Authors: SAFITRI RATU , KUSUMAWARDHANI DELICIA PUTRI , ANNISA ANNISA , Partasasmita Ruhyat , ASHARINA SINTA , MASKOEN ANI MELANI 
Published: August 2020

Abstract. Safitri R, Kusumawardhani PD, Annisa, Partasasmita R, Asharina S, Maskoen AM. 2020. Characterization and identification of three thermophilic Bacillus strains isolated from Domas Crater, Mt. Tangkuban Perahu, Indonesia. Biodiversitas 21: 3444-3453. A community of thermophiles within the hot spring of Domas Crater, Mount Tangkuban West Java, has been cultivated and identified based on the 16S ribosomal RNA gene sequence. The hot spring has a temperature of 45°C-76 °C, pH 1-2, the isolate has been cultivated in Thermus medium at a temperature of 70 and pH 6. The three isolated strains were L61A, TS61A, and D41A identified based on the 16S ribosomal RNA gene sequence refer to the GenBank database and all of them belong to the Phylum Firmicutes, which are clustered within the taxonomic groups of Bacillus, the Bacillus, and Geobacillus genera. Nucleotide sequences were compared for homology with BLASTN search at the NCBI Web-site revealed that strains (L61A) had 99.93% similarity with Geobacillus uzenensis. TS61A strain has a 99.24% similarity with Bacillus wiedmannii. Whereas D41A has 99.79% similarity with Bacillus paramycoides. The characterization also includes the phenotypic and biochemical of strains. The bacillus genera were known as a source of thermostable enzymes, plant growth-promoting, probiotics, decomposers of various polysaccharide materials, and bioremediation.
The characteristics of Shorea macrophylla’s habitat in Tane’ Olen, Malinau District, North Kalimantan Province, Indonesia
Authors: Fajri Muhammad , PRATIWI Pratiwi , Ruslim Yosep 
Published: August 2020

Abstract. Fajri M, Pratiwi, Ruslim Y. 2020. The characteristics of Shorea macrophylla’s habitat in Tane’ Olen, Malinau District, North Kalimantan Province, Indonesia. Biodiversitas 21: 3454-3462. Shorea macrophylla is a tree species in Tane' Olen forest area. This study analyzed the soil’s physical and chemical properties, topography, and microclimate of S. macrophylla’s habitat. A purposive method was used to select a sampling plot and to place the subplots. Soil was analyzed to determine the physical properties, i.e., texture, bulk density, porosity, and water content, and the chemical properties, i.e., pH, CEC, total N, organic C, C/N ratio, P, K , and Al saturation. Importance value index was determined for each tree species to know the species composition in the study site. Only the dominant species were presented. The soil at the study site had bulk density of 0.60-1.31 gram cm³-1, porosity 50.60%-77.35%, water content 34.88%-95.37%, and soil texture sandy clay. The chemical properties of the soil were as follows: pH was 3.6-4.8, N 0.05%-0.19%, organic C 1.40%-3.65%, P 0.41-1.22 mg 100 gr-1, K 58.68-232.55 mg 100 gr-1, and Cation Exchange Capacity (CEC) 5.35-10.81 meg 100gr -1. Slope ranged between 0 and 25%. The microclimate characteristics were as follows: temperature was 24-26.5°C, relative humidity 76-87%, and light intensity 145-750 Lm. Trees species with an IVI ≥ 10% were S. macrophylla, Madhuca spectabilis, Myristica villosa Warb, Scorodocarpus borneensis, Eugenia spp., Palaquium spp., Macaranga triloba, Syzygium inophyllum and Shorea sp. Positive associations were observed between S. macropylla and S. borneensis, Eugenia spp., Palaquium spp.. and M. triloba, and negative associations were observed between S. macropylla and M. spectabilis, M. villosa Warb, S. inophyllum, and Shorea sp. S. macrophylla grows on riversides with flat and gentle topography, acidic soil, and lower fertility but with suitable microclimate. This species can be recommended to be planted in degraded tropical forest areas but the microclimate and soil properties should be taken into account.