bluuebunny/crossref_metadata_2025 huggingface dataset:
Agronomic characteristics and genetic relationship of putative transgenic rice lines of cv. Fatmawati with the Glu-1Dx5 transgene
Authors: Carsono Nono , PRAYOGA GIGIH IBNU , SARI SANTIKA , RACHMADI MEDDY
Published: August 2022

Abstract. Carsono N, Prayoga GI, Sari S, Rachmadi M. 2021. Agronomic characteristics and genetic relationship of putative transgenic rice lines of cv. Fatmawati with the Glu-1Dx5 transgene. Biodiversitas 23: 291-298. Transgenic rice lines cv. Fatmawati with the Glu-1Dx5 transgene (encoding high molecular weight glutenin sub-unit Dx5 from bread wheat) has been produced in order to improve dough functionality of rice flour. These lines have reached T1 (transformant-1) dan T2 (transformant-2) generations. Some transgenic rice plants obtained from in vitro culture and transformation events frequently show phenotypic and genotypic variations from the original plants, thus evaluation of agronomic traits of these transgenic rice is highly important in order to obtain rice genotypes with the best agronomic traits that will be integrated into rice breeding program. Nine transgenic rice lines and two check lines, i.e. seed-derived and callus-derived rice lines, were used in this experiment. A comparison between transgenic rice traits with those of non-transgenic checks was done by student’s t-test and relationship among transgenic rice lines was evaluated by UPGMA (Unweighted Pair Group Method with Mean Arithmetic) method using NT Sys (Numerical Taxonomy and Multivariate Analysis System). Results indicated that agronomic traits of transgenic rice lines were similar to those of non-transgenic check except for number of productive tillers (T2-11, T2-12, T2-20), the maximum number of tillers (T2-7, T2-11, T2-12, T2-20), number of filled grains (T1-45) and days to maturity (all T2 lines). It suggests that somaclonal variations, gene insertional effect, genetic and epigenetic mutations might occur. Genetic relationship between putative transgenic and non-transgenic checks was closely related, although somaclonal variants were found. The selected transgenic rice lines will be incorporated into rice breeding programs.
Short communication: Amphidromous goby postlarvae (penja) migration seasons and fisheries in West Sulawesi, Indonesia
Authors: Nurjirana Nurjirana , Burhanuddin Andi I , Keith Philippe , Haris Abdul , Afrisal Muhammad
Published: August 2022

Abstract. Nurjirana, Burhanuddin AI, Keith P, Haris A, Afrisal M. 2021. Short communication: Amphidromous goby postlarvae (penja) migration seasons and fisheries in West Sulawesi, Indonesia. Biodiversitas 23: 375-380. Several gobioid species have amphidromous migration patterns; adult gobies spawn in their freshwater habitat, embryos are carried by river currents to reach the sea where they undergo a planktonic phase lasting several months before migrating to estuarine and then freshwater (predominantly riverine) environments to grow and breed. Around the island of Sulawesi in Indonesia, these migrating postlarvae have various local names; in West Sulawesi they are collectively known as penja, a popular fisheries commodity, but data on their migration patterns are limited. This study aimed to determine penja migration seasons and document some aspects of the penja fisheries in West Sulawesi. The research was conducted in the lower reaches of five rivers: the Mapilli, Mandar, Teppo, Palipi, and Lariang rivers. Penja samples were collected from fishermen's catches using several types of fishing gear such as seser (scoop nets), dariq or bunde (push nets), panesser (casting net) and other traditional or artisanal fishing equipment. Samples were also collected from traditional markets. The postlarvae were measured and grouped based on morphological characters. The results showed temporal differences in migration patterns between the five study sites, while external morphology indicated the presence of several species in migrating penja schools. During the rainy season, populations with a more diverse morphology were found than during the dry season.
Characteristics of physiology, phenology, and drought susceptibility index of two varieties of Job’s tears under water deficit stress
Authors: WICAKSONO FIKY YULIANTO , SINNIAH UMA RANI , RUMINTA RUMINTA , SUMADI SUMADI , NURMALA TATI
Published: August 2022

Abstract. Wicaksono FY, Sinniah UR, Ruminta, Sumadi, Nurmala T. 2021. Characteristics of physiology, phenology, and drought susceptibility index of two varieties of job’s tears under water deficit stress. Biodiversitas 23: 381-387. Job’s tears or hanjeli (Coix lacryma-jobi L.) is a functional food crop with less popularly cultivated and longer life cycle than paddy and maize, so that it is potentially exposed to drought stress in the dry season in tropical areas. This study aims to evaluate the physiology, phenology, and drought susceptibility index lack of both Job’s tears varieties under water deficit stress. The study was conducted in quantitative method, by using 2 populations of ma-yuen and stenocarpa varieties which were treated with two levels of watering treatment during the vegetative phase (6 to 12 weeks after sowing), i.e. every day watering and every three days watering. Observations were made on physiological traits, phenology, and drought susceptibility index. The results showed that water deficit decreased stomatal conductance and chlorophyll content, but it could increase electrolyte leakage and proline content. Increasing proline content had a significant correlation with crop yields improvement. Flowering time was prolonged as the effect of drought stress in both varieties. Based on drought susceptibility index, stenocarpa was more tolerant than ma-yuen. However, some farmers might still cultivate the ma-yuen due to the soft seed shell character, therefore, this study finding could be used as a basis for developing further plant irrigation techniques for sensitive variety amid a prolonged dry season.
Comparison of bioconcentration factor of heavy metals between endemic fish and aquacultured fish in Maninjau Lake, West Sumatra, Indonesia
Authors: Komala Puti Sri , Azhari Restu Maulida , Hapsari Febi Yulia , Edwin Tivany , Ihsan Taufiq , Zulkarnaini Zulkarnaini , Harefa Mustika
Published: August 2022

Abstract. Komala PS, Azhari RM, Hapsari FY, Edwin T, Ihsan T, Zulkarnaini, Harefa M. 2022. Comparison of bioconcentration factor of heavy metals between endemic fish and aquacultured fish in Maninjau Lake, West Sumatra, Indonesia. Biodiversitas 23: 4026-4032. Fish have a high risk of accumulating metals and poses a risk of entering human bodies through the food chain. This study aims to analyze the concentration of lead (Pb), mercury (Hg), and cadmium (Cd) spatially and temporally as well as the Bioconcentration Factor (BCF) in endemic fish (Rasbora argyrotaenia) and aquacultured fish (Oreochromis niloticus) in Maninjau Lake and its relationship to environmental parameters (pH, DO and temperature). Sampling was conducted at domestic, hydropower, fish cage, and endemic fisheries. Spatial and temporal distribution using one-way ANOVA with 95% significance, while parameter correlation using linear regression. Almost all heavy metals in both fish samples exceeded the permissible level except in endemic fisheries sites. Metal concentrations in both fish species spatially showed a significant difference, while temporally showed no significant difference. Rasbora argyrotaenia showed a slightly higher BCF value than O.niloticus. The BCF values were low accumulative with order Pb>Hg>Cd ??in R. argyrotaenia and Pb>Cd>Hg for O. niloticus. There is a strong and positive correlation between temperature and the BCF value of both fish species for the three different metals. Monitoring fish by keeping metal content within acceptable limits is necessary. Further research on risk analysis of fish consumption in humans is recommended.
Monitoring and analyzing tree diversity using i-Tree eco to strengthen urban forest management
Authors: MOSYAFTIANI AMARIZNI , WAHYU ADE , KASWANTO KASWANTO , WIYOGA HARITYAS , SYASITA NADA , SEPTA ARIE FAJAR , DJAUHARI DJAYUS
Published: August 2022

Abstract. Mosyaftiani A, Wahyu A, Kaswanto, Wiyoga H, Syasita N, Septa AF, Djauhari D. 2022. Monitoring and analyzing tree diversity using i-Tree eco to strengthen urban forest management. Biodiversitas 23: 4033-4039. Inadequate data on vegetation growth makes it difficult for managers to determine the additional measures necessary for effective urban forest management. The management of urban forests in Jakarta also raises this issue. Collaborative research with multiple stakeholders was conducted in five Jakarta urban forests to assess the diversity and structure of the vegetation as a basis for long-term monitoring and management. Using 49 plots, we carried out a field inventory to gather information on tree number, diameter at breast height, tree height, and crown size. The i-Tree Eco programme was used to examine the data and information gathered. The widely used i-Tree Eco analysis was conducted to make viable evidence-based evaluation feasible and to help stakeholders with data processing. The results showed that the five urban forests had a moderate level of diversity, with an index value ranging from 2.1 to 3.0. The five most common tree species—Swietenia macrophylla, Terminalia sp., Delonix regia, Ceiba pentandra, and Aleurites moluccanus—dominate urban forests, whereas three of them are exotic and most native species have substantially lower values. Increasing tree diversity by enriching native species is recommended to be a top priority for urban forest management in Jakarta. Additionally, this research shows that adopting advanced and user-friendly tools to regularly monitor and analyze vegetation helps stakeholders achieve better urban forest management.
Assessment of zygosity and nitrogen used efficacy in Mekongga transgenic rice
Authors: AINI MACHZANI QURAITUL , SUHARSONO SUHARSONO , APRIANA ANIVERSARI , SISHARMINI ATMITRI , SANTOSO TRI JOKO , TRIJATMIKO KURNIAWAN RUDI
Published: August 2022

Abstract. Aini MQ, Suharsono, Apriana A, Sisharmini A, Santoso TJ, Trijatmiko KR. 2022. Assessment of zygosity and nitrogen used efficacy in Mekongga transgenic rice. Biodiversitas 23: 4040-4046. Nitrogen (N) is a vital macronutrient that can be a limiting factor for rice plant growth. Nitrogen-efficient plants can be assembled by modifying nitrogen-related metabolic pathways to improve Nitrogen Use Efficiency (NUE) in plants. T0 generation of transgenic Mekongga rice plants containing the LeAlaAT gene was obtained. In transgenic plant research, zygosity test was desirable to ensure the integration and inheritance stability of transgene. This study aimed to assess zygosity and nitrogen use efficacy of two transgenic Mekongga rice lines, namely M41 and M50. This research involved three main activities, i.e. detection of flanking sequence for T0 generation by TAIL-PCR method, zygosity test for T1 generation, and efficacy test for T2 generation of Mekongga transgenic lines in response to different N fertilizer rates of 0, 60, 90, and 120 kg ha?1. Zygosity analysis showed that six out of 14 M41 and three of 13 M50 transgenic lines were homozygous for LeAlaAT transgene. The efficacy test showed that homozygous transgenic lines had higher tiller numbers, grain numbers, and biomass compared to non-transgenic ones under the same nitrogen level. The notable discrepancies of the transgenic plants can also be recognized in the absorption, agronomical, and grain NUE of the studied plants.
Traditional knowledge of land management in Maybrat District, West Papua Province, Indonesia: implication for agriculture development
Authors: SAGRIM MEKY
Published: August 2022

Abstract. Sagrim M. 2022. Traditional knowledge of land management in Maybrat District, West Papua Province, Indonesia: implication for agriculture development. Biodiversitas 23: 4145-4152. Traditional concepts of land management have been part of the local people in Maybrat, West Papua, Indonesia for generations. On the other hand, the governments, either at central, provincial, or local levels, promote agricultural development to enhance the well-being of the community in Maybrat and Papua in general. Thus, it is interesting to look at whether traditional knowledge and practices of land management in Maybrat can be aligned with development policies enacted by the governments. This research aimed to investigate the traditional knowledge of land management in Maybrat District to support agricultural development using an application of the socio-cultural approach. A semi-structured interview was applied for data collection representing communities of 24 sub-districts in Maybrat District. In total, 200 informants were selected purposively to obtain perceptual knowledge of the land-use system. The results showed that the local people benefit from natural resources in terms of social prominence, ecological prominence, economic prominence, medicinal prominence, energy prominence, and construction prominence. Agriculture is the main land use in Maybrat where it supports the livelihood of local people, especially in terms of economic benefit. Furthermore, the local people in Maybrat have been conducting their local wisdom to preserve the natural resource by using the traditional concepts where the local people have realized the function of vegetated land. Hence, development programs in the agricultural sector promoted by the regional or national governments could accommodate the local knowledge in land management. Yet, assessing the biophysical factors is necessary to monitor the dynamic of land management to achieve sustainability in socio-cultural, economic, and ecological aspects.
Secondary trait and index selection determination for maize genotype selection in acidic tidal swamp environment
Authors: SUWARTI SUWARTI , GHULAMAHDI MUNIF , SOPANDIE DIDY , TRIKOESOEMANINGTYAS TRIKOESOEMANINGTYAS , SULISTYONO EKO , AZRAI MUHAMMAD
Published: August 2022

Abstract. Suwarti, Ghulamahdi M, Sopandie D, Trikoesoemaningtyas, Sulistyono E, Azrai M. 2022. Secondary trait and index selection determination for maize genotype selection in acidic tidal swamp environment. Biodiversitas 23: 4169-4179. Determining secondary traits as complementary selection in maize genotypes for abiotic stress environment is compulsory since yield-based selection usually provides biased result. This study aimed to obtain secondary traits for maize selection in an abiotic multi-stresses of Fe, Al, and temporary flooding environments of acid sulfate tidal swamp land using multivariate analysis. A total of 150 (un-repeated) maize inbred lines and five check genotypes in five replicates were arranged in a randomized augmented plot design in three environments to generate 525 single plots. Three types of environments based on irrigation regimes were applied on acid soil tidal swamp land to study the agronomic characteristics of maize genotypes in each environment. Saturated Cultivation Technology (SSC) was considered the optimal environment. Dryland treatment was the condition to let the irrigation only depend on rainwater. Temporary flooding treatment was carried out at five stages of different growth periods. Several steps of analysis were applied in this study by taking variance, and heritability was used as the basis for selections. The characters affected by treatments with medium to high heritability were then analyzed with correlation and pathway analysis. Seven selection indexes, SSI, GMP, YSI, YI, TOL, STI, and MP, that have a high correlation to yield in both optimum and stress environments, were applied simultaneity with the selected trait characters to screen the genotypes utilizing PCA biplot analysis. Venn analysis was used to group the genotypes based on the result of the analysis. Indices of STI, MP, GMP, and traits of rows number per ear and the weight of 6 ears were selected as secondary characters for the maize genotypes selection in Saturated Soil culture with temporary flooding stress. Meanwhile, STI, MP, and ear stand height were the selected characters in the dryland of acid sulfate tidal swamp land. Based on the combination of all secondary character selection, genotypes were grouped into five types of stress tolerance in SSC+TF and DL environments. Eight genotypes were tolerant to both SSC+TF and DL stress, and two genotypes were susceptible to both environments.
Isolation and screening of lovastatin-producing endophytic fungi from lemongrass (Cymbopogon nardus)
Authors: RAHMI ZIKRINA , YURNALIZA YURNALIZA , HASTUTI LIANA DWI SRI
Published: August 2022

Abstract. Rahmi Z, Yurnaliza Y, Hastuti LDS. 2022. Isolation and screening of lovastatin-producing endophytic fungi from lemongrass (Cymbopogon nardus L.). Biodiversitas 23: 4189-4194. Fungi have long been studied for their cholesterol-lowering compounds, known as statins and the derivatives through fermentation in laboratory investigations. Therefore, this study aimed to isolate and screen endophytic fungal strains from lemongrass capable of producing lovastatin. Endophytic fungi were isolated from the stems and leaves of lemongrass (Cymbopogon nardus) and the selection of their ability to produce lovastatin was assayed using three approaches, namely negative test against Candida albicans, measurement based on absorbance at a wavelength (?) of 230 nm or colorimetric assay, and observation using thin layer chromatography (TLC). A total of 22 endophytic fungi, 15 from the leaves and 7 from the stems were isolated from lemongrass. The capability to produce lovastatin was confirmed using three approaches, resulting in three potential fungal strains, namely Trichoderma sp. CNB 2.5.3, unidentified fungus CND 2.5.4, and Nigrospora sp. CND 2.1.1. Based on the colorimetric assay, the potential strains produced a significant zone of inhibition against C. albicans, with greater lovastatin levels than the other isolates. The TLC analysis showed that the fungal ethanolic extracts contained crude lovastatin as indicated from the same retention factor (Rf) value as standard lovastatin. The presence of lovastatin-producing endophytic fungi can be investigated progressively for optimum production through fermentation and evaluation of its cholesterol-lowering activity in the future.
Anthocyanin content, phenolic content, antioxidant activity and yield in indigenous rice as affected by different fertilizers
Authors: PRAJUNTASAN RAPEEPUN , RATANANIKOM KHAKHANANG , PAYOUNGKIATTIKUN WISARUT
Published: August 2022

Abstract. Prajuntasan R, Ratananikom K, Payoungkiattikun W. 2022. Anthocyanin content, phenolic content, antioxidant activity and yield in indigenous rice as affected by different fertilizers. Biodiversitas 23: 4195-4201. This study was to evaluate the effects of fertilizer management methods (organic and inorganic) on total anthocyanin content (TAC), total phenolic content (TPC), antioxidant activity, and yield in eight local rice varieties. A 2×8 factorial experiment in a randomized complete block design with three replications was setup on a farmer’s farm. Organic fertilizer management increased TAC, TPC and antioxidant activity, but significant increases were found for TAC,and antioxidant activity. The highest TAC was found in Luem Puew, and Kum Puen Baan had the highest TPC. The highest TAC and TPCvarietiesdid not necessarily havethe highest antioxidant activity. Sung Yod, Chaow Daeng, Kum Ka Dum and Kum Puen Baan were the highest for this parameter. Luem Puew + organic was the treatment combined with the highest TAC. Still, the result found the highest antioxidant activities in several treatment combinations associated with most local rice varieties except Nang Nuan and Mali Nga Chang.
Potential feeding plants of Javan Langur (Trachypithecus auratus) in the eastern slope of Biru Mountain, Batu City, East Java, Indonesia
Authors: Djamil Wardhana Harrys , MUTTAQIN TATAG , ARYANTI NIRMALA AYU , KURNIAWAN IWAN
Published: August 2022

Abstract. Wardhana HD, Muttaqin T, Aryanti N, Kurniawan I. 2022. Potential feeding plants of Javan Langur (Trachypithecus auratus) in the eastern slope of Biru Mountain, Batu City, East Java, Indonesia. Biodiversitas 23: 4216-4222. The Javan langur (Trachypithecus auratus) is an endemic animal in Indonesia and is located on the island of Java. Javan langur is an endemic primate and an officially endangered species. The purpose of this study was to determine the potential of forage plants in the area that will be used as a Javan langur release location so that it becomes one aspect of assessing whether or not it is appropriate for a Javan langur release. This research was conducted in Gunung Biru, Batu City, East Java, Indonesia. The method used is wandering quarter to determine the species composition. The analysis used is vegetation analysis, Morisita distribution index, Shannon-Wiener diversity index, Evenness index, Margalef wealth index, and Sorensen similarity index. The results of this study obtained 45 species of plants from the level of the pole and tree. Some of the dominant species are Homalanthus giganteus, Quercus sondaicus, Engelhardia spicata, and Trema orientalis. All types of plants found during the study were included in the Javan langur forage plants. The distribution index was clustered at the pole and tree level with a value of 0.081 at the pole and 0.106 at the tree. The diversity index was high at the pole level with a value of 3.272, while the moderate tree level with a value of 2.539. The species richness index showed high at the pole and tree level, with a value of 6.916 at the pole level and 4.461 at the tree level. The evenness of the pole-level vegetation is 0.874 and the tree-level vegetation is 0.789, so it includes a high evenness value. The similarity value between paths below 50% indicates that the similarity is low. Knowing that all species in the area are a source of forage for langurs, it can be said that the forage sources for Javan langurs are very abundant and it can be said that the area is very suitable for the release area of ??Javan langurs.
Morpho-anatomical characterization and DNA barcoding analysis of Pluchea indica (L.) Less.
Authors: WAHYUNI DWI KUSUMA , MUKARROMAH SITI RIZQIYATUL , RAKHMAD PUTUT , ILHAM MOCHAMMAD , RAKASHIWI GALUH AYU , INDRIATI DANI TRI , YOKU BRUNY FLARANDA , PURNOBASUKI HERY , JUNAIRIAH JUNAIRIAH , PRASONGSUK SEHANAT
Published: August 2022

Abstract. Wahyuni DK, Mukarromah SR, Rakhmad P, Ilham M, Rakashiwi GA, Indriati DT, Yoku BF, Purnobasuki H, Junairiah, Prasongsuk S. 2022. Morpho-anatomical characterizationand DNA barcoding analysisof Pluchea indica (L.) Less.. Biodiversitas 23: 4272-4282. Pluchea indica (L.) Less. is a member of the Asteraceae family and is popular as a medicinal plant. It is very important to authenticate plants using various markers to confirm the labeling of plants and to reveal the bioactive compounds for pharmaceutical research. This study aims to characterize the morpho-anatomical and DNA barcoding aspects of P. indica. Three samples obtained from Taman Husada Graha Famili, Surabaya, Indonesia were used in this study. Morphological studies were carried out descriptively, while the paraffin method was used for anatomical observations. DNA barcoding analysis was performed by amplifying and aligning the rbcLand matKgenes. Morphologically, P. indicahas organs like Asteraceae plants in general, with specific characteristics in leaves and flowers. P. indica has an anatomical organ similar to that of Asteraceae plants globally, only that there are specific histological features on its leaves, including anomocytic stomata, glandular cells, and multicellular glandular trichomes. Alignment and reconstruction of the phylogenetic tree showed that the sample plants were closely related to P. indica in the GenBank database. Based on morpho-anatomical characters and DNA barcodes, the plant under study was confirmed as P. indica L. (Less).
Construction of Saccharomyces cerevisiae KEX2-650 gene expression vector and its introduction into Escherichia coli DH5?
Authors: ADIBAH DENABELA IFTINA , FUAD ASRUL MUHAMAD , BUDIARTI SRI , PRATIWI RIYONA DESVY
Published: August 2022

Abstract. Adibah DI, Fuad AM, Budiarti S, Pratiwi RD. 2022. Construction of Saccharomyces cerevisiae KEX2-650 gene expression vector and its introduction into Escherichia coli DH5?. Biodiversitas 23: 4289-4296. Kex2 (EC 3.4.21.61) is a serine protease that binds Ca2+ molecules and naturally found intracellularly as a transmembrane protein. Kex2 has a unique function, the conversion process of recombinant protein precursor into mature protein. Kex2 from Saccharomyces cerevisiae has similar functions also with furin in mammals (about 47% of sequence similarity). To gain advantage, extracellular Kex2 would be highly favorable for this process. This study aimed to construct recombinant Kex2 that could be produced extracellularly in Pichia pastoris host through pD902-KEX2-699 vector (synthetic) with FLAG-tag and 6 His-tag by removing most of C-terminal region, including transmembrane domain (TMD) from KEX2 gene sequence. Constructed KEX2 is the KEX2-650 variant with TMD deletion and cytoplasmic domain. The recombinant plasmid was constructed through site-directed mutagenesis using FP-Kex2-699 and RP-Kex2-650 primers, including the BamHI site for plasmid religation. PCR site-directed mutagenesis produces an amplicon DNA with an expected length of 5551 bp. After restriction (BamHI) and religation, the plasmid was reintroduced into Escherichia coli DH5? and obtained 16 colonies. Verification PCR target gene showed that clones number 9 produced an amplicon of expected length (646 bp). DNA sequencing analysis confirmed that TMD was removed from the gene construct to form the KEX2-650 construct.
Ethnomedicinal study, phytochemical characterization, and pharmacological confirmation of selected medicinal plant on the northern slope of Mount Wilis, East Java, Indonesia
Authors: BHAGAWAN WEKA SIDHA , SUPROBORINI ARUM , PUTRI DENTHA LORENZA PRASTYA , NURFATMA AISSYAH , PUTRA ROY TRI
Published: August 2022

Abstract. Bhagawan WS, Suproborini A, Putri DLP, Nurfatma A, Putra RT. 2022. Ethnomedicinal study, phytochemical characterization, and pharmacological confirmation of selected medicinal plant on the northern slope of Mount Wilis, East Java, Indonesia. Biodiversitas 23: 4303-4313. The traditional usage of plants in ethnomedicine is a valuable resource for human primary healthcare. The effectiveness of herbal medicines and the creation of new drugs are proven by pharmacological and phytochemical verification. This study documented the traditional ethnomedicine knowledge (TEK) on the northern slope of Mount Wilis community in utilizing medicinal plants and revealed the ethnopharmacology relevance of selected medicinal plants. Data on TEK and its practices were collected through in-depth and semi-structured interviews with informants who were selected using purposive sampling and snowball sampling techniques. The phytochemical compounds of the selected medicinal plant were identified using the UPLC-Qtof-MS/MS instrument, while their pharmacological activity was measured in antibacterial tests. The results showed that the community continued to apply TEK that had been passed down by the previous generation through a method called Gethok Tular. The medicinal plant species in the study area were diverse, 82 species from 39 families with various modes of preparation were used to treat seven disease categories. Tithonia diversivolia had the highest use value of 0.65 and it contained 23 phytochemical compounds. In addition, this plant has high pharmacological potential for antibacterial agents.
Physicochemical and microbiological fermented buffalo milk produced by probiotic Lactiplantibacillus pentosus HBUAS53657 and sweet orange juice (Citrus nobilis)
Authors: SUSMIATI SUSMIATI , MELIA SRI , PURWATI ENDANG , ALZAHRA HURRIYA
Published: August 2022

Abstract. Susmiati, Melia S, Purwati E, Alzahra H. 2022. Physicochemical and microbiological fermented buffalo milk produced by probiotic Lactiplantibacillus pentosus HBUAS53657 and sweet orange juice (Citrus nobilis). Biodiversitas 23: 4329-4335. Fermented milk is a type of dairy product that has been fermented with lactic acid bacteria. Changes in starter lactic acid bacteria and fruits can improve fermented dairy's physicochemical quality and total lactic acid bacteria (LAB) colonies. This study investigates how changes in the concentration of starter Lactiplantibacillus pentosus HBUAS53657 and sweet orange juice concentration affect protein, fat, moisture, total titratable acidity, pH value, and total lactic acid bacteria (LAB) colonies in buffalo fermented milk. This study used randomized block design (RBD) experiment, with factor A being starter L. pentosus strain HBUAS53657 4%, 5% and 6% (A1, A2 and A3) and factor B being sweet orange juice 10%, 15% and 20% (B1, B2 and B3) with three replications as a treatment. The data were statistically processed using analysis of variance, and the smallest significant difference test was p<0.05. The results showed that the protein content ranged from 5.81-6.33%, fat content 6.14-6.35%, water content 81.63- 85.78%, pH 3.57-4.23, TTA value 1.30-1.85 and total LAB colonies from 4.67×109 to 9.0×109 CFU/mL. Fermented milk products with 6% starter L. pentosus HBUAS53657 and 20% sweet orange juice produced the best results. This product is suitable for consumption as a probiotic beverage.
Two new species of Kaempferia subgenus Kaempferia (Zingiberaceae: Zingibereae) from Thailand
Authors: SAENSOUK PIYAPORN , SAENSOUK SURAPON , BOONMA THAWATPHONG
Published: August 2022

Abstract. Saensouk P, Saensouk S, Boonma T. 2022. Two new species of Kaempferia subgenus Kaempferia (Zingiberaceae: Zingibereae) from Thailand. Biodiversitas 23: 4343-4354. Two new species of Kaempferia L., namely Kaempferia napavarniae Saensouk, P. Saensouk & Boonma, and Kaempferia sakonensis Saensouk, P. Saensouk & Boonma, are discribed here. The production of terminal inflorescences, covered by leaf sheaths, makes both species fall into the subgenus Kaempferia. The first species were found only in Nakhon Sawan Province, Northern Thailand, and the second species were found only in Sakon Nakhon Province, Northeastern Thailand. Living specimens and spirit specimens of both new species were compared to the existing allied species, but they differed and were never reported in taxonomic treatment before. Thus, we claimed both of them as new species to science and named the first species to honor Associate Professor Dr. Napavarn Noparatnaraporn (Director of Center for Research-driven in Natural Resources and Environment towards Utilization) who is a specialist in Biodiversity in Thailand. And named the second species according to its locality by using the province name as the epithet name. The descriptions with their illustrations, ecology, etymology, distributions, and a revised key to species of Kaempferia subgenus Kaempferia in Thailand for facilitating identification are also prepared.
Growing together: displaced women’s resilience and growth in reciprocal relationship
Authors: Holmyard Lucy , Bellinger Avril , Smithson Janet , Karl Anke
Published: August 2022

This research set out to investigate displaced women’s resilience and growth relationally, including relationships between displaced women and their children and how growth might extend to those working with displaced women. A unique relational, narrative and ethnographic approach demonstrated how processes of ‘reciprocal growth’ were constructed. Moving beyond previous concepts such as vicarious post-traumatic growth and ‘reciprocal resilience’, the unique finding of the research was women’s and volunteers’ co-construction of resilience and growth interpersonally and intersubjectively. ‘Othering’ narratives were dismantled through shared story and reciprocal human relationships, which allowed for a growthful connection between intra-psychic meaning making and wider community: linking what’s ‘within’ (I) to what’s ‘between’ (we). Consciously paying attention to reciprocal growth processes has empowering connotations for displaced women, those in relationship with them and society itself.
Imaging of custom-made single scatterers with the confocal laser scanning microscope
Authors: Lohner Stefan A. , Brenner Thomas , Glöckler Felix , Hevisov David , Kienle Alwin
Published: August 2022

In this work, we investigate image formation in the confocal laser scanning microscope for different single scatterers, both theoretically and experimentally. For spherical scatterers, an effective and fast algorithm was implemented to calculate the confocal image for different diameters and wavelengths. Measurements on a polystyrene sphere (PS) with a diameter of 20 µm confirmed the expected effects, for example, the appearance of a central signal similar to the point spread function of the optical system. Custom single scatterers were produced using 3D-direct laser writing (DLW), including a sphere with dimensions comparable to the aforementioned PS sphere. Despite an inevitably lower surface quality and symmetry, only minor differences were observed in the confocal image of the 3D-DLW sphere compared to a near-perfect PS sphere. Having verified the experimental images of spheres with the computed theoretical data, confocal measurements of four platonic bodies produced by 3D-DLW were measured with the goal to contribute to the understanding of image formation involving more complex scattering geometries.
High-resolution depth imaging with a small-scale SPAD array based on the temporal-spatial filter and intensity image guidance
Authors: Kang Yan , Xue Ruikai , Wang Xiaofang , Zhang Tongyi , Meng Fanxing , Li Lifei , Zhao Wei
Published: August 2022

Currently single-photon avalanche diode (SPAD) arrays suffer from a small-scale pixel count, which makes it difficult to achieve high-resolution 3D imaging directly through themselves. We established a CCD camera-assisted SPAD array depth imaging system. Based on illumination laser lattice generated by a diffractive optical element (DOE), the registration of the low-resolution depth image gathered by SPAD and the high-resolution intensity image gathered by CCD is realized. The intensity information is used to guide the reconstruction of a resolution-enhanced depth image through a proposed method consisting of total generalized variation (TGV) regularization and temporal-spatial (T-S) filtering algorithm. Experimental results show that an increasement of 4 × 4 times for native depth image resolution is achieved and the depth imaging quality is also improved by applying the proposed method.
Nanoparticle manipulation using plasmonic optical tweezers based on particle sizes and refractive indices
Authors: Li Huaxin , Ren Yatao , Li Yang , He Mingjian , Gao Baohai , Qi Hong
Published: August 2022

As an effective tool for micro/nano-scale particle manipulation, plasmonic optical tweezers can be used to manipulate cells, DNA, and macromolecules. Related research is of great significance to the development of nanoscience. In this work, we investigated a sub-wavelength particle manipulation technique based on plasmonic optical tweezers. When the local plasmonic resonance is excited on the gold nanostructure arrays, the local electromagnetic field will be enhanced to generate a strong gradient force acting on nanoparticles, which could achieve particle sorting in sub-wavelength scale. On this basis, we explored the plasmonic enhancement effect of the sorting device and the corresponding optical force and optical potential well distributions. Additionally, the sorting effect of the sorting device was investigated in statistical methods, which showed that the sorting device could effectively sort particles of different diameters and refractive indices.
Wnt5a–Vangl1/2 signaling regulates the position and direction of lung branching through the cytoskeleton and focal adhesions
Authors: Zhang Kuan , Yao Erica , Chuang Ethan , Chen Biao , Chuang Evelyn Y. , Volk Regan F. , Hofmann Katherine L. , Zaro Balyn , Chuang Pao-Tien
Published: August 2022

Lung branching morphogenesis requires reciprocal interactions between the epithelium and mesenchyme. How the lung branches are generated at a defined location and projected toward a specific direction remains a major unresolved issue. In this study, we investigated the function of Wnt signaling in lung branching in mice. We discovered that Wnt5a in both the epithelium and the mesenchyme plays an essential role in controlling the position and direction of lung branching. The Wnt5a signal is mediated by Vangl1/2 to trigger a cascade of noncanonical or planar cell polarity (PCP) signaling. In response to noncanonical Wnt signaling, lung cells undergo cytoskeletal reorganization and change focal adhesions. Perturbed focal adhesions in lung explants are associated with defective branching. Moreover, we observed changes in the shape and orientation of the epithelial sheet and the underlying mesenchymal layer in regions of defective branching in the mutant lungs. Thus, PCP signaling helps define the position and orientation of the lung branches. We propose that mechanical force induced by noncanonical Wnt signaling mediates a coordinated alteration in the shape and orientation of a group of epithelial and mesenchymal cells. These results provide a new framework for understanding the molecular mechanisms by which a stereotypic branching pattern is generated.
Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification
Authors: Lundgren Erik , Romero-Severson Ethan , Albert Jan , Leitner Thomas
Published: August 2022

To identify and stop active HIV transmission chains new epidemiological techniques are needed. Here, we describe the development of a multi-biomarker augmentation to phylogenetic inference of the underlying transmission history in a local population. HIV biomarkers are measurable biological quantities that have some relationship to the amount of time someone has been infected with HIV. To train our model, we used five biomarkers based on real data from serological assays, HIV sequence data, and target cell counts in longitudinally followed, untreated patients with known infection times. The biomarkers were modeled with a mixed effects framework to allow for patient specific variation and general trends, and fit to patient data using Markov Chain Monte Carlo (MCMC) methods. Subsequently, the density of the unobserved infection time conditional on observed biomarkers were obtained by integrating out the random effects from the model fit. This probabilistic information about infection times was incorporated into the likelihood function for the transmission history and phylogenetic tree reconstruction, informed by the HIV sequence data. To critically test our methodology, we developed a coalescent-based simulation framework that generates phylogenies and biomarkers given a specific or general transmission history. Testing on many epidemiological scenarios showed that biomarker augmented phylogenetics can reach 90% accuracy under idealized situations. Under realistic within-host HIV-1 evolution, involving substantial within-host diversification and frequent transmission of multiple lineages, the average accuracy was at about 50% in transmission clusters involving 5–50 hosts. Realistic biomarker data added on average 16 percentage points over using the phylogeny alone. Using more biomarkers improved the performance. Shorter temporal spacing between transmission events and increased transmission heterogeneity reduced reconstruction accuracy, but larger clusters were not harder to get right. More sequence data per infected host also improved accuracy. We show that the method is robust to incomplete sampling and that adding biomarkers improves reconstructions of real HIV-1 transmission histories. The technology presented here could allow for better prevention programs by providing data for locally informed and tailored strategies.
Integrative experimental/computational approach establishes active cellular protrusion as the primary driving force of phagocytic spreading by immune cells
Authors: Francis Emmet A. , Heinrich Volkmar
Published: August 2022

The dynamic interplay between cell adhesion and protrusion is a critical determinant of many forms of cell motility. When modeling cell spreading on adhesive surfaces, traditional mathematical treatments often consider passive cell adhesion as the primary, if not exclusive, mechanistic driving force of this cellular motion. To better assess the contribution of active cytoskeletal protrusion to immune-cell spreading during phagocytosis, we here develop a computational framework that allows us to optionally investigate both purely adhesive spreading (“Brownian zipper hypothesis”) as well as protrusion-dominated spreading (“protrusive zipper hypothesis”). We model the cell as an axisymmetric body of highly viscous fluid surrounded by a cortex with uniform surface tension and incorporate as potential driving forces of cell spreading an attractive stress due to receptor-ligand binding and an outward normal stress representing cytoskeletal protrusion, both acting on the cell boundary. We leverage various model predictions against the results of a directly related experimental companion study of human neutrophil phagocytic spreading on substrates coated with different densities of antibodies. We find that the concept of adhesion-driven spreading is incompatible with experimental results such as the independence of the cell-spreading speed on the density of immobilized antibodies. In contrast, the protrusive zipper model agrees well with experimental findings and, when adapted to simulate cell spreading on discrete adhesion sites, it also reproduces the observed positive correlation between antibody density and maximum cell-substrate contact area. Together, our integrative experimental/computational approach shows that phagocytic spreading is driven by cellular protrusion, and that the extent of spreading is limited by the density of adhesion sites.
Seasonal variation in SARS-CoV-2 transmission in temperate climates: A Bayesian modelling study in 143 European regions
Authors: Gavenčiak Tomáš , Monrad Joshua Teperowski , Leech Gavin , Sharma Mrinank , Mindermann Sören , Bhatt Samir , Brauner Jan , Kulveit Jan
Published: August 2022

Although seasonal variation has a known influence on the transmission of several respiratory viral infections, its role in SARS-CoV-2 transmission remains unclear. While there is a sizable and growing literature on environmental drivers of COVID-19 transmission, recent reviews have highlighted conflicting and inconclusive findings. This indeterminacy partly owes to the fact that seasonal variation relates to viral transmission by a complicated web of causal pathways, including many interacting biological and behavioural factors. Since analyses of specific factors cannot determine the aggregate strength of seasonal forcing, we sidestep the challenge of disentangling various possible causal paths in favor of a holistic approach. We model seasonality as a sinusoidal variation in transmission and infer a single Bayesian estimate of the overall seasonal effect. By extending two state-of-the-art models of non-pharmaceutical intervention (NPI) effects and their datasets covering 143 regions in temperate Europe, we are able to adjust our estimates for the role of both NPIs and mobility patterns in reducing transmission. We find strong seasonal patterns, consistent with a reduction in the time-varying reproduction number R(t) (the expected number of new infections generated by an infectious individual at time t) of 42.1% (95% CI: 24.7%—53.4%) from the peak of winter to the peak of summer. These results imply that the seasonality of SARS-CoV-2 transmission is comparable in magnitude to the most effective individual NPIs but less than the combined effect of multiple interventions.
Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria
Authors: Ikhimiukor Odion O. , Oaikhena Anderson O. , Afolayan Ayorinde O. , Fadeyi Abayomi , Kehinde Aderemi , Ogunleye Veronica O. , Aboderin Aaron O. , Oduyebo Oyinlola O. , Elikwu Charles J. , Odih Erkison Ewomazino , Komolafe Ifeoluwa , Argimón Silvia , Egwuenu Abiodun , Adebiyi Ini , Sadare Oluwadamilola A. , Okwor Tochi , Kekre Mihir , Underwood Anthony , Ihekweazu Chikwe , Aanensen David M. , Okeke Iruka N.
Published: August 2022

Background

Salmonellosis causes significant morbidity and mortality in Africa. Information on lineages of invasive Salmonella circulating in Nigeria is sparse.

Methods

Salmonella enterica isolated from blood (n = 60) and cerebrospinal fluid (CSF, n = 3) between 2016 and 2020 from five tertiary hospitals in southwest Nigeria were antimicrobial susceptibility-tested and Illumina-sequenced. Genomes were analysed using publicly-available bioinformatic tools.

Results

Isolates and sequence types (STs) from blood were S. Typhi [ST1, n = 1 and ST2, n = 43] and invasive non-typhoidal Salmonella (iNTS) (S. Enteritidis [ST11, n = 7], S. Durham [ST10, n = 2], S. Rissen [ST8756, n = 2], S. Chester [ST2063, n = 1], S. Dublin [ST10, n = 1], S. Infantis [ST603, n = 1], S. Telelkebir [ST8757, n = 1] and S. Typhimurium [ST313, n = 1]). S. Typhi ST2 (n = 2) and S. Adabraka ST8757 (n = 1) were recovered from CSF. Most S. Typhi belonged to genotype 3.1.1 (n = 44), carried an IncY plasmid, had several antibiotic resistance genes (ARGs) including blaTEM-1 (n = 38), aph(6)-Id (n = 32), tet(A) (n = 33), sul2 (n = 32), dfrA14 (n = 30) as well as quinolone resistance-conferring gyrA_S83Y single-nucleotide polymorphisms (n = 37). All S. Enteritidis harboured aph(3”)-Ib, blaTEM-1, catA1, dfrA7, sul1, sul2, tet(B) genes, and a single ARG, qnrB19, was detected in S. Telelkebir. Typhoidal toxins cdtB, pltA and pltB were detected in S. Typhi, Rissen, Chester, and Telelkebir.

Conclusion

Most invasive salmonelloses in southwest Nigeria are vaccine-preventable infections due to multidrug-resistant, West African dominant S. Typhi lineage 3.1.1. Invasive NTS serovars, including some harbouring typhoidal toxin or resistance genes, represented a third of the isolates emphasizing the need for better diagnosis and surveillance.
Host induced gene silencing of the Sclerotinia sclerotiorum ABHYDROLASE-3 gene reduces disease severity in Brassica napus
Authors: Wytinck Nick , Ziegler Dylan J. , Walker Philip L. , Sullivan Daniel S. , Biggar Kirsten T. , Khan Deirdre , Sakariyahu Solihu K. , Wilkins Olivia , Whyard Steve , Belmonte Mark F.
Published: August 2022

Sclerotinia sclerotiorumis a pathogenic fungus that infects hundreds of crop species, causing extensive yield loss every year. Chemical fungicides are used to control this phytopathogen, but with concerns about increasing resistance and impacts on non-target species, there is a need to develop alternative control measures. In the present study, we engineeredBrassica napusto constitutively express a hairpin (hp)RNA molecule to silenceABHYRDOLASE-3inS.sclerotiorum. We demonstrate the potential for Host Induced Gene Silencing (HIGS) to protectB.napusfromS.sclerotiorumusing leaf, stem and whole plant infection assays. The interaction between the transgenic host plant and invading pathogen was further characterized at the molecular level using dual-RNA sequencing and at the anatomical level through microscopy to understand the processes and possible mechanisms leading to increased tolerance to this damaging necrotroph. We observed significant shifts in the expression of genes relating to plant defense as well as cellular differences in the form of structural barriers around the site of infection in the HIGS-protected plants. Our results provide proof-of-concept that HIGS is an effective means of limiting damage caused byS.sclerotiorumto the plant and demonstrates the utility of this biotechnology in the development of resistance against fungal pathogens.