bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving access to and effectiveness of mental health care for personality disorders: the guideline-informed treatment for personality disorders (GIT-PD) initiative in the Netherlands
Authors: Hutsebaut Joost , Willemsen Ellen , Bachrach Nathan , Van Rien
Published: August 2020

Evidence-based treatment for patients suffering from personality disorders (PDs) is only available to a limited extend in the Netherlands. Consequently, most patients receive non-manualized, unspecialized care.

This manuscript describes the background, rationale and design of the Guideline-Informed Treatment for Personality Disorders (GIT-PD) initiative. GIT-PD aims to provide a simple, principle-driven, ‘common-factors’ framework for the treatment of PDs. The GIT-PD framework integrates scientific knowledge, professional expertise and patient experience to design a good-enough practice, based on common factors. It offers a basic framework including general principles, a structured clinical pathway, a basic professional stance, interventions focused on common factors, and team and organizational strategies, based on common features of evidence-based treatments and generic competences of professionals.

The GIT-PD initiative has had a large impact on the organization of treatment for PDs in the Netherlands. For countries with an interest in improving their health care system for PDs, it could serve as a template that requires only limited resources.
Management of medical emergencies in orthodontic practice
Authors: Amiri Bavandpour M. , Livas C. , Jonkman R. E. G.
Published: August 2020

Background

The aims of this study were to survey the occurrence of acute medical situations in Dutch orthodontic practice and to examine the self-perceived competence of orthodontists in managing acute medical emergencies.

Methods

A self-designed questionnaire was distributed among all 149 Dutch orthodontists attending the spring meeting of the Dutch Society for Orthodontists. The questionnaire was divided into three parts, addressing background information of the orthodontist, precautions against and experiences in acute medical situations, and self-perceived competence of nine common medical emergencies. The statistical analysis was performed using the chi-square test and a multiple logistic regression analysis.

Results

The response rate was 74.5% (105 out of 149). The male to female ratio in this population was 55:50. Mean age of all participants was 46.9 years (SD 10.4 years) with on average 16.7 years of working experience (SD 10.6 years). The most common medical emergency reported by Dutch orthodontists was vasovagal collapse (n = 219), followed by acute allergic reaction (n = 163) and hyperventilation (n = 83). On average, 75% (n = 79) of the orthodontists felt competent to handle any acute medical situation with an average occurrence of 0.36 acute medical emergencies per orthodontist per year. Male participants were more likely to send patients towards the emergency department (p = 0.049). Moreover, a statistically significant negative correlation was observed between self-perceived competence handling hypoglycemia and years of clinical experience. The longer orthodontists were clinically active, the less competent they felt when encountered with a hypoglycemia (p = 0.031).

Conclusions

Medical emergencies may be rare but challenging occurrences in the orthodontic practice. It is strongly recommended for all orthodontists and supporting staff to be trained regularly in the management of medical emergencies and to possess up-to-date evidence-based knowledge. Familiarity with and availability of appropriate drugs and equipment are deemed essential to the management of acute medical emergencies that may arise in the orthodontic practice.
The p48 MW flow modulation device for treatment of unruptured, saccular intracranial aneurysms: a single center experience from 77 consecutive aneurysms
Authors: AlMatter Muhammad , Henkes Elina , Sirakov Alexander , Aguilar Pérez Marta , Hellstern Victoria , Serna Candel Carmen , Ganslandt Oliver , Henkes Hans
Published: August 2020

Background

The p48 MW Flow Modulation Device (phenox, Bochum Germany) is a low profile flow diverter stent (FDS), designed for implantation into intracranial arteries with a diameter of less than 3.5 mm.

Objective

To evaluate the safety and efficacy of the p48 MW FDS in the treatment of unruptured aneurysms located at intracranial arteries with less than 3.5 mm diameter based on a retrospective analysis from a single tertiary neurovascular center.

Methods

A prospectively maintained database was retrospectively reviewed to identify all cases of intracranial saccular aneurysms treated electively with the p48 MW device. Records were made of basic demographics, aneurysmal characteristics, interventional procedures, adverse events, clinical outcomes and occlusion rates on angiographic follow-ups.

Results

A total of 77 aneurysms and 74 patients were included. The mean size of the treated aneurysms was 3.5 ± 2.4 mm and the mean aspect ratio was 1.3 ± 0.4. A total of 80 endovascular procedures were performed with a total of 12 (15%) adverse events leading to two (2.5%) permanent morbidities/mortalities. Technical issues were encountered in 3 (3.9%) cases. Adequate occlusion of the treated aneurysm was recorded in 55.6% and 63.9% on the first and latest available DSA follow-ups, respectively. There were no cases of side-branch occlusion.

Conclusions

The p48 MW is an easy-to-use implant with very good safety margins. Side branch occlusion and significant in-stent stenosis are infrequently encountered. The time from implantation to sufficient aneurysm occlusion takes longer than with FDS with lower porosity.
Sexually Dimorphic Crosstalk at the Maternal-Fetal Interface
Authors: Sun Tianyanxin , Gonzalez Tania L , Deng Nan , DiPentino Rosemarie , Clark Ekaterina L , Lee Bora , Tang Jie , Wang Yizhou , Stripp Barry R , Yao Changfu , Tseng Hsian-Rong , Karumanchi S Ananth , Koeppel Alexander F , Turner Stephen D , Farber Charles R , Rich Stephen S , Wang Erica T , Williams John , Pisarska Margareta D
Published: August 2020

Context

Crosstalk through receptor ligand interactions at the maternal-fetal interface is impacted by fetal sex. This affects placentation in the first trimester and differences in outcomes. Sexually dimorphic signaling at early stages of placentation are not defined.

Objective

Investigate the impact of fetal sex on maternal-fetal crosstalk.

Design

Receptors/ligands at the maternal-fetal surface were identified from sexually dimorphic genes between fetal sexes in the first trimester placenta and defined in each cell type using single-cell RNA-Sequencing (scRNA-Seq).

Setting

Academic institution.

Samples

Late first trimester (~10-13 weeks) placenta (fetal) and decidua (maternal) from uncomplicated ongoing pregnancies.

Main outcome measures

Transcriptomic profiling at tissue and single-cell level; immunohistochemistry of select proteins.

Results

We identified 91 sexually dimorphic receptor-ligand pairs across the maternal-fetal interface. We examined fetal sex differences in 5 major cell types (trophoblasts, stromal cells, Hofbauer cells, antigen-presenting cells, and endothelial cells). Ligands from the CC family chemokine ligand (CCL) family were most highly representative in females, with their receptors present on the maternal surface. Sexually dimorphic trophoblast transcripts, Mucin-15 (MUC15) and notum, palmitoleoyl-protein carboxylesterase (NOTUM) were also most highly expressed in syncytiotrophoblasts and extra-villous trophoblasts respectively. Gene Ontology (GO) analysis using sexually dimorphic genes in individual cell types identified cytokine mediated signaling pathways to be most representative in female trophoblasts. Upstream analysis demonstrated TGFB1 and estradiol to affect all cell types, but dihydrotestosterone, produced by the male fetus, was an upstream regulator most significant for the trophoblast population.

Conclusions

Maternal-fetal crosstalk exhibits sexual dimorphism during placentation early in gestation.
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

Context

Premature ovarian insufficiency (POI) is characterized by cessation of menstruation before 40 years of age and elevated serum level of FSH (>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.
Short Communication: The lifecycle of Neocaridina denticulata and N. palmata in aquariums
Authors: HANAN HASSAN ALSHEIKH MAHMOUD  , MOH. HUSEIN SASTRANEGARA  , Kusmintarsih Endang Srimurni K
Published: August 2020

Abstract. Mahmoud HHA, Sastranegara MH, Kusmintarsih ES. 2020. Short Communication: The lifecycle of Neocaridina denticulata and N. palmata in aquariums. Biodiversitas 21: 2396-2402. The study on the life cycle of Neocaridina spp. is important because it plays a major role in the economy and trade between countries. However, there is a lack of sufficient studies on this particular topic. One of the factors that influence Neocaridina spp. life production is its life cycle and the associated water parameters. The objectives of this study were to conduct, observe, and record the life cycle of Neocaridina denticulata and N. palmata and the associated with water parameters (temperature, pH, ammonia, nitrite, and oxygen) in the aquarium. The results showed that there was no difference in the life cycle stages between the two shrimp species. Both species reached the first sexual maturity stage of the life cycle at 75 days, with the maximum body length of the mature shrimp ranging from 2.30-3.00 cm. The eggs became larvae in 15 days, larvae reached the juvenile stage after 60 days, and the juvenile became mature in 15 days. The number of eggs was influenced by the body size of the female shrimps; smaller females produced fewer eggs. Optimal water quality varies by species and must be monitored to ensure growth and survival. The temperature range in this study was 25-28°C and the pH was 6.5-8.0. The ammonia level was in the range between 1.21 and1.72 mg/L, the nitrate was between 0.06 and 7.91 mg/L, and the oxygen was around 5.5-7.9 mg/L. All of the water quality parameters in this study are within the acceptable range for Neocardina cultivation.
The liverwort family Lejeuneaceae (Marchantiophyta) of Mount Lubuk Raya, North Sumatra, Indonesia
Authors: Siregar Etti sartina , NURSAHARA PASARIBU  , KHAIRANI
Published: August 2020

Abstract. Siregar ES, Pasaribu N, Khairani. 2020. The liverwort family Lejeuneaceae (Marchantiophyta) of Mount Lubuk Raya, North Sumatra, Indonesia. Biodiversitas 21: 2767-2776. Lejeuneaceae is the largest family in the liverworts. Information on the species of Lejeuneaceae in North Sumatra is still less reported, especially in Mount Lubuk Raya has never been reported. Therefore, the aim of this study is to explore the diversity of Lejeuneaceae in Mount Lubuk Raya, North Sumatra. The study was done using survey method by exploring along the hiking tracks on the study site. All the samples found were collected and then identified in the laboratory-based on morphological characters used the existing literature of Lejeuneaceae. Thirty-seven species of Lejeuneaceae, belonging to 18 genera were identified from Mount Lubuk Raya. Eight species are proposed as new reported for Sumatra: Ceratolejeunea belangeriana, Colura vitiensis, Lejeunea curviloba, Lejeunea dipterota, Lepidolejeunea bidentula, Leptolejeunea maculata, Schiffneriolejeunea pulopenangensis, Spruceanthus planiusculus. Identification key of species and pictures of species newly recorded is provided in this paper.
Heavy metals accumulation in Hertia cheirifolia along the highway in Setif region, Algeria
Authors: Belguidoum Amina , Lograda Takia , Ramdani Messaoud
Published: August 2020

Abstract. Belguidoum A, Lograda T, Ramdani M. 2020. Heavy metals accumulation in Hertia cheirifolia along the highway in Setif region, Algeria. Biodiversitas 21: 2786-2793. The aim of this work was to study the possibility of using Hertia cheirifoia spontaneous plant, generally present in uncultivated environments, as an indicator of pollution. The aerial parts of ten H. cheirifolia populations were collected along the East-West highway. Sampling is carried out in areas considered polluted or low contaminated in the region of Setif. Nine metallic trace elements concentrations (Pb, Zn, Cu, Fe, Mn, Cd, Ag, Bi, and Sb) were determined, for each population, by Atomic Absorption Spectrophotometry with Flame (AASF). Statistical analyzes were performed using mainly box and whisker diagrams, principal component analysis, and UPGMA. The concentrations detected for contaminants (MTE), in general, were very high, far exceeding international certified standards. The MTE concentrations in different populations were calculated for each metal and a positive correlation is observed. The order of MTE in the plant was found as follows: Fe > Zn > Mn > Pb > Sb > Cu > Bi > Ag > Cd. The Fe concentrations are very high in H. cheirifolia with an average of 3600 ± 1491.5 mg/kg. The populations of H. cheirifolia have shown a significant capacity to accumulate heavy metals. The presence of metal ions in the aerial parts of the plant designates that H. cheirifolia is a super accumulator of MTE and can be used as a bioindicator, which opens up prospects for its application to soils phytoremediation.
Antibacterial activity of CaO from blood cockle shells (Anadara granosa) calcination against Escherichia coli
Authors: AMANDA FIRZA RUSDARYANTI  , ULFAH AMALIA  , SLAMET SUHARTO
Published: August 2020

Abstract. Rusdaryanti AF, Amalia U, Suharto S. 2020. Antibacterial activity of CaO from blood cockle shells (Anadara granosa) calcination against Escherichia coli. Biodiversitas 21: 2826-2830. Calcium carbonate (CaCO3) in blood clamp shells (BCS) was able to be converted into calcium oxide (CaO) through a calcination process. Some research stated that CaO can be used in the food industries b, one of which is as an antibacterial agent. The purpose of this study was to determine the most optimal size of BCS's powder during calcination as an antibacterial agent and its effect on the activity of Escherichia coli. Data were analyzed using analysis of variance and Kruskal-Wallis test. The results showed that 200 mesh size of BCS’s powder produced the highest yield of CaO at about 98.68% compared to 120 and 230 mesh size. The best concentration of CaO powder as an antibacterial was 3.5% with a pH of 11.3 ± 0.17. CaO powder had antibacterial activity against E. coli with minimum inhibitory concentration’s value (MIC) of-0.115; a minimum bactericidal concentration’s value (MBC) of 0 CFU/mL; inhibition zone of 3.23 ± 0.2 mm. By the PCR method, DNA degradation has occurred in E. coli cells. The differences of CaO powder concentration had significant effect (P <0.05) on the inhibition zone of E. coli.
Soil properties and sulfur-oxidizing bacterial diversity in response to different planting patterns of shallot (Allium ascalonicum)
Authors: Juwanda Muhammad , SAKHIDIN  , SAPARSO  , KHARISUN
Published: August 2020

Abstract. Juwanda M, Sakhidin, Saparso, Kharisun. 2020. Soil properties and sulfur-oxidizing bacterial diversity in response to different planting patterns of shallot (Allium ascalonicum). Biodiversitas 21: 2832-2839. Sulfur is one of the primary elements required by plants for growth and development. Sulfur-oxidizing bacteria (SOB) can oxidize sulfur to sulfate, which is directly taken up by plant roots. This study aims to evaluate the soil properties and SOB diversity in various shallot planting patterns, i.e. PP1 (shallot-dry season-shallot-shallot), PP2 (shallot-dry season-shallot-rice), and PP3 (shallot-pulses-shallot-rice). Soil samples were collected from the rhizosphere of the shallot plant and analyzed for the soil properties based on the standard methods. Bacteria isolation was cultured on Starkey broth and Starkey agar. Bacteria isolate was identified based on the 16S rRNA gene sequence and compared to the GenBank database. The results showed that shallot planting patterns influence soil properties and SOB diversity. The highest content of sulfate (41.31 ppm), organic C (0.957 %), organic matter (1.650%), C/N ratio (9.57), and SOB diversity was obtained in PP3 planting pattern. Three bacterial strains have been successfully isolated i.e. A-3245D, B-3246F, and C-3247C with their closest related to Burkholderia cepacia, Klebsiella variicola, and Klebsiella aerogenes, respectively. The highest diversity and population density of SOB was in the PP3 planting patterns, i.e Burkholderia cepacia (7.45 x 105 CFU/mL); Klebsiella variicola (1.79 x 107 CFU/mL; Klebsiella aerogenes: 3.9 x 106 CFU/mL). K. variicola can be found in three planting patterns of shallot.
Genetic characterization based on the D-loop MtDNA and the TSPY genes of the Dwarf Siamang (Hylobates klossii) of Mentawai Island, Indonesia
Authors: Hasanah Rizka , UUS SAEPULOH  , DYAH PERWITASARI-FARAJALLAH  , WALBERTO SINAGA  , YOHANA TRI HASTUTI  , DONDIN SAJUTHI
Published: August 2020

Abstract. Hasanah R, Saepuloh U, Perwitasari-Farajallah D, Sinaga W, Hastuti Y, Sajuthi D. 2020. Genetic characterization based on the D-loop MtDNA and the TSPY genes of the Dwarf Siamang (Hylobates klossii) of Mentawai Island, Indonesia. Biodiversitas 21: 2854-2861. Hylobates klossii is an endemic primate on the Mentawai Island, Indonesia that categorized as endangered species due to fragmentation, illegal hunting, and habitat loss. This study aimed to analyze the genetic characterization of H. klossii based on maternal and paternal lineages. The samples were collected from TSI (Bogor, Indonesia) cage consist of two males and two females (blood and fecal of four individuals) and Siberut Island, Mentawai, West Sumatra, Indonesia from one unknown gender (one individual fecal sample). PCR amplification was carried out on DNA and cDNA samples using specific primers for D-loop MtDNA and TSPY genes. The amplicon was analyzed with MEGA-7. The dimensional structure model of the TSPY protein was determined using I-TASSER and visualized with PyMol. The maternal analysis showed five samples consisted of four haplotypes revealed that Nam-nam and April were identic with 0% genetic distance. It’s revealed that Nam-nam and April were mother and son. The paternal analysis of two H. klossii males revealed that April was the closest relative to H. muelleri (99.56% identity) and Gou-gou to H. klossii (100% identity). Characterization of partial TSPY gene (990 bp) of April and Gou-Gou indicated four amino acids mutation, causing the shift in-amino acid structure position. The results assumed that April was a cross-breeding between H. klossii female and H. muelleri male. This genetic characterization is expected to support the conservation efforts through recommendations for good management in H. klossii preservation.
Trophic level and position of Pterygoplichthys pardalis in Ciliwung River (Jakarta, Indonesia) ecosystem based on the gut content analysis
Authors: Elfidasari Dewi , Wijayanti Fahma , Afifatus Sholihah
Published: August 2020

Abstract. Elfidasari D, Wijayanti F, Sholihah A. 2020. Trophic level and Position of Pterygoplichthys pardalis in Ciliwung River (Jakarta, Indonesia) ecosystem based on the gut content analysis. Biodiversitas 21: 2862-2870. The trophic level of an organism describes its sequence of natural diet visible to the food chain along with its ecosystem. This is also related to the type of diet composition and food fraction obtained by analyzing its gut content. The Pterygoplichthys pardalis from Ciliwung River show the diversity of the natural diet. The aims of this study is to determine the trophic level and position of P. pardalis in the Ciliwung River ecosystem based on gut content analysis using the purposive sampling method. Data were obtained from a total of 30 fishes from the Kalibata and Cawang areas through observations. The fishes were dissected, and gut contents were observed using a light microscope, with observations repeated 5 times of each sample. Data analysis includes relative length of gut, Index of Preponderance, area of the diet niche, niche area, niche overlap, and trophic level of an organism. The results showed that P. pardalis in Ciliwung River is at trophic level II, and included as herbivores (2.00 < troph < 2.90) that consist of Bacillariophyta (82.03%), Chlorophyta (12.7%), Cyanophyta (3.74%), Euglenophyta (1.19%), Amoebozoa (0.28%), and Dinoflagellata (0.68%).
Floristic composition and vegetation community analysis of Gesha and Sayilem Forest in Kaffa Zone south western Ethiopia
Authors: Addi Admassu , Soromessa Teshome , Bareke Tura
Published: August 2020

Abstract. Addi A, Soromessa T, Bareke T. 2020. Plant diversity and community analysis of Gesha and Sayilem Forest in Kaffa Zone, southwestern Ethiopia. Biodiversitas 21: 2878-2888. The study was conducted at Gesha and Sayilem districts of the Kaffa Zone with the objective of identifying the floristic compositions, plant community types, and associated environmental factors of the forest. Stratified random sampling technique was used. A total of 90 plots were used to collect vegetation data. The plant community classification was performed using agglomerative Hierarchical cluster analysis Ward’s linkage method was applied in R-software. Species diversity and evenness were evaluated using the Shannon diversity and evenness indices respectively. The study revealed that the study area composed of 300 species that belong to 239 genera in 96 families. Asteraceae was the most abundant family followed by Fabaceae, Acanthaceae, Poaceae, Rubiaceae, and Euphorbiaceae accounting 37%, 15%, 14%, 13%, 12%, and 9% respectively. Five plant community types were identified and these were Ilex mitis-Syzygium guineense, Pouteria adolfi-friedericii-Schefflera abyssinica, Millettia ferruginea-Sapium ellipticum, Arundinaria alpina and Schefflera volkensii-Masea-lanceolata community types. Among the community types, Pouteria adolfi-friedericii-Syzygium guineense community was the most diverse whereas Arundinaria alpina community was the least diverse community. Canonical Correspondence of vegetation data analysis indicated that altitude, disturbance, slope, phosphorus, and the electrical conductivity were the environmental factors that significantly influence the plant communities. The high dependency of local communities on the forest resources is affecting the plant biodiversity. Thus, conservation of the forest through the introduction of sustainable forest management interventions including participatory forest management seems an appropriate action.
Detection of virulence and specific genes of Salmonella sp. indigenous from Jember, Indonesia
Authors: Yulian Ria , Narulita Erlia , IQBAL MOCHAMMAD , SARI DESY ROCHMIYAH , SURYANINGSIH IRMA , NINGRUM DIAN EKA APRILIA FITRIA
Published: August 2020

Abstract. Yulian R, Narulita E, Iqbal M, Rochmiyah D, Suryaningsih I, Ningrum DEAF. 2020. Detection of virulence and specific genes of Salmonella sp. indigenous from Jember, Indonesia. Biodiversitas 21: 2889-2892. The bacterium Salmonella sp. is the most common cause of foodborne infection in humans. It has the ability to invAde the host, Salmonellosis is highly influenced by the combination of chromosome and plasmid in which Salmonella Pathogenisitas Islands (SPIs) are the biggest gene in the chromosome that are responsible to build specific interaction between Salmonella and the host. This research performed detection on virulence and specific genes in the SPIs area using PCR method for two Salmonella spp. bacterial isolates originated from Jember which were KP2 and P21D. Seven pairs of primers including stn, fimA, spvR (virulence genes), invA, ivaB, spvC, and fliC-d (specific genes) were used. The result revealed that P21D bacteria containing 3 virulence genes i.e. stn, fimA, and spvR. Meanwhile, only two virulent genes stn, and spvR were present in KP2 bacteria. For the detection of specific genes, three genes invA, ivaB, and spvC were present while fliC-d genes were not detected. Only two, invA, and ivaB genes were detected in P21D bacteria, while spvC, and fliC-d were not detected.
Ultrastructure characters and partial mtDNA-COI haplotypes of Asian corn borer, Ostrinia furnacalis (Guenée) (Lepidoptera: Crambidae) from Indonesia
Authors: Arminudin Ahmad Taufiq , Suputa  , Wijonarko Arman , Trisyono Y. Andi
Published: August 2020

Abstract. Arminudin AT, Suputa, Wijonarko A, Trisyono YA. 2020. Ultrastructure characters and partial mtDNA-COI haplotypes of Asian corn borer, Ostrinia furnacalis (Guenée) (Lepidoptera: Crambidae) from Indonesia. Biodiversitas 21: 2914-2922. In addition to the confirmation of the species of corn borer, we analyzed the relationship of Ostrinia furnacalis in Indonesia with that in other countries. Moths of O. furnacalis were collected from several areas in Java and Sumatra islands of Indonesia. Forewing and labial palpi scales were investigated under Scanning Electron Microscopy observation. A 658 bp of O. furnacalis partial COI gene sequences of 1480-2138 nucleotides were downloaded from GenBank and BOLD system databases. The ridge lamellae and window characters as unique ultrastructure characters of scale were further supported by the COI gene analysis. High similarity was observed between the Java and the Philippines specimens, but they were a different haplotype compared with Sumatra’s specimen. The results could provide the baseline data on the genetic variation of O. furnacalis in Indonesia.
Evaluation of in vitro antagonistic activity of fungi from peatlands against Ganoderma species under acidic condition
Authors: SUPRIYANTO  , PURWANTO  , S.H. POROMARTO  , SUPYANI
Published: August 2020

Abstract. Supriyanto, Purwanto, Poromarto SH, Supyani. 2020. Evaluation of in vitro antagonistic activity of fungi from peatlands against Ganoderma species under acidic conditions. Biodiversitas 21: 2935-2945. The use of peatlands is a significant contributor to the world’s palm oil production. A serious problem of oil palm plantations in peatlands is the high incidence of basal stem rot (BSR) disease caused by Ganoderma, which has a higher attack rate than on mineral soils. There is no effective way to control Ganoderma in peatlands. At present, the effort for the same focuses on environment-friendly biological methods; however, this is constrained by the unavailability of appropriate biological agents for peatlands. The development of biological control agents for peatlands is hampered by limited data on biological control of Ganoderma in peatlands. This research was conducted to evaluate the in vitro antagonistic activity of fungi isolated from a peatland in acidic pH conditions. Twenty-seven Ganoderma-antagonistic fungi from peatland were evaluated for their activity and their ability to antagonism in vitro within a pH range of 2-7. The results show that most antagonistic fungi from peatland, based on biomass weight, the sporulation ability, and germination of conidium, were able to grow optimally at pH 3.0-4.0, indicating that most of the Ganoderma-antagonistic fungi from peatland can be used as biological control agents for BSR on oil palms in peatlands.
Habitat preference and spatial distribution model of threatened species Saurauia microphylla in Mt. Slamet, Central Java, Indonesia
Authors: Helmanto Hendra , NISYAWATI  , IYAN ROBIANSYAH  , RIZMOON NURUL ZULKARNAEN  , NABELA FIKRIYYA
Published: August 2020

Abstract. Helmanto H, Nisyawati, Robiansyah I, Zulkarnaen RN, Fikriyya N. 2020. Habitat preference and spatial distribution model of threatened species Saurauia microphylla in Mt. Slamet, Central Java, Indonesia. Biodiversitas 21: 2946-2954. Saurauia microphylla de Vriese has the potentials for medicinal uses, yet it is listed in the IUCN Red List under Vulnerable status. The natural population of this species is only found in highlands one of which is in Mount Slamet, Central Java, Indonesia. This study aims to determine the population structure, habitat preference and predicted spatial distribution of S. microphylla in the Mount Slamet area. The method used was purposive sampling by establishing 103 observation plots with size of 20x20 m2 for each plot. The research parameters recorded were abiotic variables and biotic associations. Data were analyzed using Principal Component Analysis (PCA) to determine the most influencing environmental factors on the presence of S. microphylla. Species association of S. microphylla was analyzed using the Jaccard index equation. Spatial distribution model was analyzed using Maxent (Maximum Entropy) software. The results showed that S. microphylla populations were found in highland forest areas with elevations of 1689-2265 m above sea level, slope of 3-40°, temperature of 16°-26°C, air humidity of 49.3-90%, soil pH 5.8-7, soil moisture 5-70% and canopy cover of 0-92%. Our analyses revealed that elevation is the most influential factor in the presence of S. microphylla. There are 20 tree species which found around S. microphylla habitat with 4 species have significant association with the species. The spatial distribution model showed that S. microphylla spread across all the slopes of Mount Slamet with the southwestern slope was predicted had the most extensive habitat suitability for the species and become smaller to the north, east, and south slopes.
Exploring entomopathogenic fungi from South Sumatra (Indonesia) soil and their pathogenicity against a new invasive maize pest, Spodoptera frugiperda
Authors: Herlinda Siti , Noni OCTARIATI , Suwandi Suwandi , Hasbi Hasbi
Published: August 2020

Abstract. Herlinda S, Octariati N, Suwandi S, Hasbi. 2020. Exploring entomopathogenic fungi from South Sumatra (Indonesia) soil and their pathogenicity against a new invasive maize pest, Spodoptera frugiperda. Biodiversitas 21: 2955-2965. Fall armyworm (Spodoptera frugiperda) is a new invasive maize pest in Indonesia that can cause maize yield losses of 18 million tons/year. To overcome the pest, local-specific entomopathogenic fungi are needed. This study aimed to explore entomopathogenic fungi from soil in South Sumatra and to determine their pathogenicity against S. frugiperda larvae. The fungi exploration was carried out in the lowlands and highlands of South Sumatra and the pathogenicity of obtained isolates were tested against the third instar larvae. The entomopathogenic fungi found were Metarhizium spp. and were successfully isolated as many as 14 isolates. All of the isolates were pathogenic to S. frugiperda larvae (70.67−78.67% mortality), the most pathogenic caused 78.67% mortality and significantly suppressed the emergence of adults up to 81.2%. Unhealthy larvae had a dry, shrunken, shrinking, odorless body, and its integument was covered in mycelia and conidia like yellowish-white powdery mixed with dark green. The unhealthy pupae and adults were in the abnormal and malformation shape. The abnormal pupae were shorter in size, bent, the to-be wings got wrinkled, and darker color, while the unhealthy adults had folded wings and were unable to fly. The two most pathogenic isolates were found from the lowland (PirOI) and highland (CasPsPGA) soil of South Sumatra. In conclusion, both of these isolates had the potential to be developed into local-specific mycoinsecticides to control pest insects in the highlands and/or lowlands in Indonesia.
Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle
Authors: Jakaria Jakaria Jakaria , MOKHAMAD FAKHRUL ULUM  , DEWI LESTARI  , SAMUEL AKWILA  , DIAN ERMA WARU TIDOLF SIHITE  , RUDY PRIYANTO  , MULADNO  , CECE SUMANTRI
Published: August 2020

Abstract. Jakaria, Ulum MF, Lestari D, Akwila S, Sihite DEWT, Priyanto R, Muladno, Sumantri C. 2020. Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle. Biodiversitas 21: 2971-2976. The present investigation aims to explore specific SNPs of Bali cattle, focusing mainly on CAST, CAPN, and SCD genes in 5'UTR. DNA of Bali cattle (25 individuals) from Breeding Centre of Bali cattle in Bali Province, Indonesia, were extracted according to the protocol of GenAID. Amplification of the CAST, CAPN, and SCD genes were designed using the Primer3 program based on reference sequences (access numbers AH014526.2, AH009246.3, and AY241932). Furthermore, the PCR product was sequenced through forward primer sequencing. The data sequence results were analyzed using the Bioedit, MEGA7, Popgen 3.2, and DnaSP6 V6 programs. The results showed that SNPs were detected at g.921C>T and g.922T>G in 5'UTR for the CAST gene between the reference of GenBank AH014526.2 and Bali cattle, but it was monomorphic within the population. The high polymorphism of SNPs was found in g.232G>T for the CAPN gene and g.134A>del for the SCD gene. However, the SNP g.246C>del SCD gene was detected as monomorphic in this region. Moreover, this result shows that low nucleotide diversities (Pi) for CAST, CAPN, and SCD genes in 5'UTR of Bali cattle were 0.00422, 0.00632, and 0.00449, respectively. This finding was important for developing marker-assisted selection (MAS) to improve the meat quality of Bali cattle.
Genome evaluation of banana cultivars based on morphological character and Inter-Simple Sequence Repeat (ISSR) molecular marker
Authors: Wahyudi Didik , Uslan  , KHAFIDHOTUR RIFLIYAH
Published: August 2020

Abstract. Wahyudi D, Rifliyah K, Uslan. 2020. Genome evaluation of banana cultivars based on morphological character and Inter-Simple Sequence Repeat (ISSR) molecular marker. Biodiversitas 21: 2982-2990. This study aims to evaluate the genome group and to investigate the genetic variability of banana cultivar using morphological character and ISSR molecular marker. Fourteen banana cultivars with genomic group AA, AAA, AAB, ABB, and BB was used. All samples were Identified morphologically based on minimal descriptors for bananas issued by the International Plant Genetic Resources Institute (IPGRI). Total genomic DNA was extracted using DNA Isolation Kit Promega Wizard®. ISSR primer was used in this study, including UBC834, UBC835, UBC843, UBC848, and UBC855. Clustering analysis was used to evaluate genome grouping of the banana cultivar. Clustering analysis of morphological character was performed using the unweighted pair group method with arithmetic mean (UPGMA) algorithm and Bray-Curtis coefficient similarity using Paleontological Statistics (PAST) software. Morphological and ISSR was successfully differentiate banana cultivars and relatively similar to previous genome grouping. However, pisang Triolin (AAB) must be evaluated since it belongs to AAA group. The identification of cultivars and classification of their genome groups based on morphological characteristics and proved by molecular markers will strengthen the establishment of Musa improvement strategy especially in Indonesia and ease the breeder to identify desirable traits of progenitor to be included in the breeding program.
Variation in morphological traits of a selection of Indonesian winged bean accessions (Psophocarpus tetragonolobus) and its analysis to assess genetic diversity among accessions
Authors: Yulianah Izmi , Waluyo Budi , Ashari Sumeru , Kuswanto
Published: August 2020

Abstract. Yulianah I, Waluyo B, Ashari S, Kuswanto. 2020. Variation in morphological traits of a selection of Indonesian winged bean accessions (Psophocarpus tetragonolobus) and its analysis to assess genetic diversity among accessions. Biodiversitas 21: 2991-3000. In Indonesia, winged bean (Psophocarpus tetragonolobus (L.) DC.) is a traditional vegetable crop grown mainly for its edible green pods. Plant breeding programs aim to produce cultivars with high production and good nutritional qualities. The objective of this present study was to assess genetic diversity among 21 selected Indonesian winged bean lines based on observation of morphological characters. This was the first step in determining an appropriate breeding program for the development of improved vegetable cultivars. Twelve qualitative characters and eight quantitative variables were assessed for each of the 21 lines. Categorical differences among lines were observed in characters such as leaflet, pod and seed shape, pod surface texture, anthocyanin pigmentation of stem, flowers and pods. Several of these characters are useful as genetic markers, and cluster analysis of the 21 lines on the basis of qualitative characters enabled two distinct groupings to be identified. Quantitative variation across line means was also high for several of the quantitative variables (a coefficient of variation > 25% for pod length, number of pods per plant, and total pod weight per plant). Principal component analysis applied to the eight variables accounted for 86% of the total variation in just three components with eigenvalues > 1. On Component 1, the characters number of days to first open flower, pod length and pod weight were closely aligned with total weight of pods per plant. Number of pods per plant was not closely aligned with weight of pods per plant. This study has enabled broad differences between groups of lines to be categorized and has identified particular lines with characteristics that recommend them for inclusion as parents in inheritance studies designed to elucidate the contribution that individual characters make to overall productivity, attractiveness, and nutrition of this useful, high protein, vegetable species.
Screening for probiotic of lactic acid bacteria isolated from the digestive tract of a native Aceh duck (Anas platyrhynchos)
Authors: Risa Yayuk Kurnia , Harimurti Sri , Wihandoyo  , Widodo Widodo
Published: August 2020

Abstract. Risna YK, Harimurti S, Wihandoyo, Widodo. 2020. Screening for Probiotic of lactic acid bacteria isolated from the digestive tract of a native Aceh duck (Anas platyrhynchos). Biodiversitas 21: 3001-3007. The lactic acid bacteria (LAB) isolated from the digestive tract of a native Aceh duck has emerged as a potential probiotic supplement for duck feed. In this study, we isolated the LAB from the digestive tract of an Aceh duck (Anas platyrhynchos) and identified the species and bacterial characteristics. Additionally, we isolated the LAB used in this study from the crop, proventriculus, ventriculus, duodenum, jejunum, ileum, and cecum of the native Aceh duck. Identification included the examination of morphology and physiology, followed by molecular identification by using 16S rRNA and sequence similarity tests for the bile salt hydrolase (bsh) gene. Bacterial isolation from the digestive tract of this duck resulted in 19 isolates with gram-positive, negative catalase, and non-motile characteristics. Of the 19 isolates, 11 isolates exhibited the ability to grow at 15°C, 37°C, and 45°C, with optimum growth at 37°C. From 11 isolates, only 6 were identified by using 16S rRNA primers and 5 were identified by using BSH primers. The identified LAB included Lactobacillus plantarum, Lactobacillus fermentum, and Pediococcus acidilactici. Hence, we conclude that Lactobacillus sp and Pediococcus sp. are potential probiotics that can be isolated and administered for duck feed.
Vegetation structure and floristic composition of tree species in the habitat of Scaphium macropodum in Gunung Leuser National Park, Sumatra, Indonesia
Authors: SUSILOWATI ARIDA , ELFIATI DENI , RACHMAT HENTI HENDALSTUTI , YULITA KUSUMADEWI SRI , HADI ADI NURUL , KUSUMA YOSIE SYADZA , BATU SRI ANJELI LUMBAN
Published: August 2020

Abstract. Susilowati A, Elfiati D, Rachmat HH, Yulita KS, Hadi AN, Kusuma YS, Batu SAL. 2020. Vegetation structure and floristic composition of tree species in the habitat of Scaphium macropodum in Gunung Leuser National Park, Sumatra, Indonesia. Biodiversitas 21: 3025-3033. Scaphium macropodum (Miq.) Beumee Ex K Heyne is a member of Malvaceae tree species and globally recognized as malva nut and locally known as ‘kembang semangkok’, ‘tempayang’, ‘merpayang’ or ‘kepayang’. The nut of S. macropodum has many benefits for medicinal purposes, yet destructive extraction of this tree species has led them to extinction. Among its natural distribution in Indonesia, North Sumatra Province, Indonesia is known as its original range, but there is limited information about the existence of this species. This study aimed to determine the vegetation structure of some tree species in the habitat of S. macropodum in Sikundur, Gunung Leuser National Park, Sumatra, Indonesia. Purposive sampling technique was employed by creating line transect at some forest areas where the population of S. macropodum is known to grow naturally. Four line transects with each transect consisting of five plots with nested plots within were established to record data at four growth stages, resulting in 80 plots in total. The results showed that the Important Value Index (IVI) of S. macropodum within the floristic community at the studied area was 21.98, 13.85, 27.30, and 39.60 for tree, pole, sapling, and seedlings stages, respectively. The Shannon-Wiener Diversity Index (H) were 3.80, 3.70, 3.06 and 2.45, Index of evenness (E) are 0.94, 0.92, 0.86, 0.77 and the Index of Richness (R) are 11.76, 10.73, 6.59, 4.10 for tree, pole, sapling, and seedlings stages. This result suggests that the natural population of S. macropodum in Sikundur forest was still in good condition at all stages from tree to seedling.
Characterization and expression of Cm-AAT1 gene encoding alcohol acyl-transferase in melon fruit (Cucumis melo L.) ‘Hikapel’
Authors: WIBOWO WIKO ARIF , FATKHUROHMAN MUHAMMAD IMAM , DARYONO BUDI SETIADI
Published: August 2020

Abstract. Wibowo WA, Fatkhurohman MI, Daryono BS. 2020. Characterization and expression of Cm-AAT1 gene encoding alcohol acyl-transferase in melon fruit (Cucumis melo L.) ‘Hikapel’. Biodiversitas 21: 3041-3046. Melon (Cucumis melo L.) is one of the horticulture commodities that have high economic value and its needs increase continuously. Many new melon cultivars have been assembled to produce a higher quality melon. Melon 'Hikapel' developed by the Laboratory of Genetics and Breeding, Faculty of Biology UGM has distinctive character in the form of a strong aroma. This aroma is a complex mixture of various kinds of volatile compound. One of the main determinant compounds is a volatile ester, synthesized by the alcohol acyl-transferase enzyme encoded by the Cm-AAT1 gene. Characterization of Cm-AAT1 began with isolation of melon rinds to get total RNAs. Synthesis cDNA was conducted with oligo-dT primer, followed by detection of Cm-AAT1 using specific primers. A specific band was sequenced to perform phylogenetic tree. Gene expression from 4 melon cultivars, ‘Hikapel’, ‘Hikadi’, ‘Sun Lady’, and ‘Luna’ analysis was performed using relative quantitative Real-Time PCR. The results of this study showed that Cm-AAT1 owned not only by aromatic cultivars ‘Hikapel’ and ‘Hikadi’, but also owned by non-aromatic cultivars ‘Sun Lady’ and ‘Luna’. Phylogenetic analysis shows a high similarity between Cm-AAT1 on 'Hikapel' and 'Hikadi'. Gene expression analysis on 'Hikapel' increases as the process of fruit ripening during the storage period and it is in contrast to 'Hikadi' at decrease when the fruit began to enter the decay process on day 7th. Expression of Cm-AAT1 on ‘Hikapel’ was higher than ‘Hikadi’ at the peak of fruit maturity.
Aquatic insect assemblages in four urban lakes of Bogor, West Java, Indonesia
Authors: Wakhid Wakhid , Rauf Aunu , Krisanti Majariana , Sumertajaya I Made , Maryana Nina
Published: August 2020

Abstract. Wakhid, Rauf A, Krisanti M, Sumertajaya IM, Maryana N. 2020. Aquatic insect assemblages in four urban lakes of Bogor, West Java, Indonesia. Biodiversitas 21: 3047-3056. Urban lakes represent important habitats for some freshwater organisms and support a high diversity of insect fauna. Study was conducted with the objectives to determine and compare aquatic insect assemblages in four urban lakes of Bogor, West Java, Indonesia. Insects were collected in the littoral zone using D-net at a certain interval along the perimeter of each lake. Sampling was carried out monthly during March, April, and May 2017. A total of 6,686 individuals representing 82 species/morphospecies, 28 families, and seven orders were recorded. Estimation of species richness by Chao1 suggested that sampling completeness for Situ Babakan, Situ Burung, Situ Gede, and Situ Tonjong were 88.71%, 75.86%, 82.17%, and 95.23%, respectively. Rarefaction curves indicated that more sampling would record a higher species richness. The least species richness and diversity of aquatic insect assemblages occurred in Situ Babakan characterized by high organic pollution due to fish farming. Canonical correspondence analysis showed that certain environmental factors were related to some species. Chironomus sp. (Diptera: Chironomidae), Micronecta ludibunda (Hemiptera: Micronectidae), and Anisops bouvieri (Hemiptera: Notonectidae) were associated with organically polluted water. Odonates such as Pseudagrion sp.1 (Coenagrionidae), Rhinocypha sp. (Chlorocyphidae), Acisoma panorpoides, Orthetrum sabina (Libellulidae), and Crocothemis servilia (Libellulidae) were associated with conditions of a high density of macrophytes. Our study provides baseline data for future monitoring and conservation management of these lakes.
Short Communication: Identification and phylogenetic analysis of Corynebacterium diphtheriae isolates from Jakarta, Indonesia based on partial rpoB gene
Authors: Yasmon Andi , ROSANA YEVA , USMAN DONI , INTA PRILANDARI LUH , HARTONO TEGUH SARRY
Published: August 2020

Abstract. Yasmon A, Rosana Y, Usman D, Prilandari LI, Hartono TS. 2020. Short Communication: Identification and phylogenetic analysis of Corynebacterium diphtheriae isolates from Jakarta, Indonesia based on partial rpoB gene. Biodiversitas 21: 3070-3075. Indonesia is a developing country with the greatest potential of diphtheria, so accurate identification is needed to detect C. diphtheriae. The genetic relationship analysis is important to be determined so that this transmittable disease can be prevented. In this study, we reported the identification and phylogenetic analysis of C. diphtheriae based on partial rpoB gene. Twelve samples from throat swabs of diphtheria suspected patients from 2018 to 2019 were used in this study. The result of VITEK 2 ANC-Automated Testing identified that all isolates were C. diphtheriae. However, the identification based on partial rpoB gene analysis showed that only 10 out of 12 isolates were C. diphtheriae, while 2 other isolates were C. argentoratense. Of 10 C. diphtheriae strains/isolates, 2 strains were unique for Indonesia. Thus, it is needed to evaluate the accuracy of VITEK 2 ANC-Automated Testing and to conduct further comprehensive studies on the genetic relationships of C. diphtheriae strains based on multiple virulence genes, multilocus sequence typing and/or whole-genome analysis.