@article{Valen2020a,

title = {Molecular approach for identification of Asian seabass (Lates calcarifer Bloch 1790) based on COI gene sequence from Java, Indonesia},

author = {Lutfiatunnisa and Maheno Sri Widodo and Abdul Rahem Faqih and Ledi Diana Sari and Fitri Sil Valen },

url = {http://www.bioflux.com.ro/docs/2020.2445-2451.pdf},

issn = {1844-8143},

year  = {2020},

date = {2020-10-24},

journal = {AACL Bioflux},

volume = {13},

number = {5},

pages = {2828-2833},

abstract = {Asian seabass or barramundi in Australia, valid as Lates calcarifer (Bloch 1790) is one of the most  important  food  fishes  found  in  tropical  and  semi-tropical  regions  of  the  Indo-West Pacific. This species  has  been  utilized  in  aquaculture  for  the  past  several  decades  in  many  countries  including Indonesia.  In  order  to  support  the species success in aquaculture,  it  is  necessary  to  conduct  some research,  one  of  which  is  species  identification  for  the  initial  selection  of  parent  candidates  by  the molecular  approach  based  on  the  COI  gene  sequence  using  the  DNA  Barcoding  method.  The  two analyzed specimens  of  Asian  seabass  from  Java,  Indonesia  were  identical  to  the Lates  calcarifer from Australia, with a matching percentage of about 99.83-100% and with 0.000\textendash0.007 genetic distance.  },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wicaksono2020cb,

title = {Is COVID-19 impacting plant science, and is plant science impacting COVID-19?},

author = {Adhityo Wicaksono and Jaime A. Teixeira da Silva},

url = {https://www.notulaebiologicae.ro/index.php/nsb/article/view/10778},

doi = {DOI:10.15835/nsb12310778 },

issn = {2067-3264},

year  = {2020},

date = {2020-09-29},

journal = {Notulae Scientia Biologicae},

volume = {12},

number = {3},

pages = {769-772},

abstract = {COVID-19 changed 2020 massively after becoming a worldwide pandemic. Many countries affected by the disease witnessed disruptions in the agricultural, farming, industry, production and distribution sectors, causing a loss of crops due to reduced consumer demand. Sales of cut flowers, potted plants and seasonal crops that are sensitive to specific seasons or dates were affected, as were fertilizer and food security. Academics, including plant scientists, with limited work or research conditions during the pandemic, alleviated their work through alternative approaches, eg, in silico research, or made more time to writing research papers, while student education has largely been placed on hold or held online by lecturers. Most COVID-19 research has focused primarily on medical and social aspects while some plant science-related research has been conducted on the use of traditional medicinal plants as possible alleviating agents, but not cures, to COVID-19 patients. The integrity of science and publishing, including research related to plants, is being tested as cases of superficial research, lax or superficial peer review, and misinformation abound. COVID-19 has thus had limited impact on plant science, and vice versa, thus far, even though it is likely that most plant scientists were affected.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ramadani2020a,

title = {Diversity of Edible Flora and Biotourism Potential Development of Botany Adventure in Turgo, Mount Merapi National Park Yogyakarta},

author = {Aisyah Hadi Ramadani and Muhammad Badrut Tamam and Heri Santoso and Thobib Hasan Al Yamini},

url = {http://jurnal.radenfatah.ac.id/index.php/biota/article/view/5259},

year  = {2020},

date = {2020-09-24},

journal = {Jurnal Biota},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wendy2020gb,

title = {Cratoxylum cochinchinense (Hypericaceae): A New Record for Sulawesi, Indonesia},

author = {Wendy Achmmad Mustaqim and Dewi S. Amboupe},

url = {http://philjournalsci.dost.gov.ph/images/pdf/pjs_pdf/vol149no3/Cratoxylum_cochinchinense_.pdf},

isbn = {0031-7683},

year  = {2020},

date = {2020-09-14},

journal = {Philippine Journal of Science},

volume = {149},

number = {3},

pages = {675-678},

abstract = {Cratoxylum is a small genus of plants belonging to the Hypericaceae family with six species known at present. The first record for Cratoxylum cochinchinense, a mainland Southeast Asia and West Malesian tree species, is presented for Sulawesi. This record adds the number of Cratoxylum in Sulawesi to three species. A key to Cratoxylum in Sulawesi is also presented.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Saputra2020,

title = {Dendrobium sagin (Orchidaceae: Epidendroideae), a new species from the Bird’s Head Peninsula, West New Guinea},

author = {Reza Saputra and Wendy Achmmad Mustaqim and Destario Metusala and Andr\'{e} Schuiteman},

url = {https://www.biotaxa.org/Phytotaxa/article/view/phytotaxa.459.2.9},

doi = {https://doi.org/10.11646/phytotaxa.459.2.9},

issn = {11793163},

year  = {2020},

date = {2020-09-11},

journal = {Phytotaxa},

volume = {459},

number = {2},

pages = {190\textendash196},

abstract = {With about a dozen species, Dendrobium section Fugacia Smith (1905: 343) is one of the smaller but also one of the more distinctive clades within the large genus Dendrobium Swartz (1799: 82) (Schuiteman 2014). The plants have unbranched, tufted, clavate and usually distinctly angular stems of several internodes, of which only two or three of the uppermost ones carry a non-sheathing leaf. The inflorescences are subsessile and one- or few-flowered and arise singly from the swollen upper internodes. Flowers are ephemeral, generally opening early in the morning, often before sunrise, and withering in the afternoon. Unusually in Dendrobium, the lip is mobile and delicately hinged to the short column-foot, a character-state more commonly found in the sister genus Bulbophyllum Thouars (1822: t. 3). The lip is often broader than long and can be broadly obreniform in outline.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Valen2020b,

title = {Growth analysis of Asian seabass (Lates calcarifer Bloch 1790) based on morphometrics in BPBAP},

author = {Ledi Diana Sari and Mohamad Fadjar and Maheno Sri Widodo and Lutfiatunnisa and Fitri Sil Valen },

url = {http://www.bioflux.com.ro/docs/2020.2445-2451.pdf},

issn = {1899-1905},

year  = {2020},

date = {2020-09-05},

journal = {AACL Bioflux},

volume = {13},

number = {5},

pages = {2445-2451},

abstract = {Asian seabass  (Lates  calcarifer)  is an important  food resource and  has  high economic value. This  species  has  been farmed in  aquaculture systems for  the  past  several  decades  in  many  countries including  Indonesia.  In  Indonesia, this  species  has been grown in numerous  farms, one farm  being  the one belonging  to the Association  of  Brackish  Water  Cultivated  Fishery  (BPBAP)  of  Situbondo. In  this study, we  examine  the  growth  patterns  of  Asian seabass juveniles based  on morphometrics  using  the truss morphometric method. Asian seabass juveniles are maintained at the following parameters: salinity 34 gr/L, dissolved oxygen 5.8 mg/L, temperature 31.2OC and pH 8.1. Asian seabass juveniles at the age of  60  days have  an  average  total  length of 54  mm, at  the  age  of  75  days  they  have an  average total length of 73 mm and at 148 days they have an average total length of 117 mm. The growth pattern of each specimen is negative allometric, with the resulting b value of b\<3. Thus, the growth rate of Asian seabass juveniles can be influenced by age and environmental factors in aquaculture. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Arif2020,

title = {In Silico and in Vitro Study of Trace Amines (TA) and Dopamine (DOP) Interaction with Human Alpha 1-Adrenergic Receptor and the Bacterial Adrenergic Receptor QseC},

author = {Arif Luqman and Viol Dhea Kharisma and Ruben Amian Ruiz and Friedrich G\"{o}tz},

url = {https://pubmed.ncbi.nlm.nih.gov/32930525/},

doi = {https://doi.org/10.33594/000000276},

issn = {14219778},

year  = {2020},

date = {2020-09-03},

journal = {Cellular Physiology and Biochemistry},

volume = {54},

number = {5},

pages = {888-898},

abstract = {Background/aims: Trace amines (TA) are small organic compounds that have neuromodulator activity due to their interaction with some neuron-related receptors, such as trace amine associated receptors (TAARs), α2-adrenergic receptor (α2-AR) and \ss-adrenergic receptor (\ss-AR). However, there is little information on whether TA and dopamine (DOP) can interact with other adrenergic receptors (ARs) such as the mammalian α1-AR and the bacterial counterpart QseC, which is involved in quorum sensing of some Gram-negative pathogens. The aim of this study was to investigate the interaction of TA and DOP with α1-AR and QseC.



Methods: We performed an in silico study using 3D structure from SWISS MODEL and analyzed the protein interaction via molecular docking using PyMol, PoseView and PyRX 8.0. For the in vitro study, we investigated the QseC kinase activity by measuring the remaining ATP in a reaction containing QseC-enriched membrane incubated together with purified QseB and EPI, TA, DOP, or PTL respectively. We also measured the intracellular Ca++ levels, which represents the α1-AR activation, in LNCAP (pancreatic cell line) cells treated with EPI, TA, DOP and PTL respectively using a fluorescence-based assay. The LNCAP cell proliferation was measured using an MTT-based assay.



Results: Our in silico analysis revealed that TAs and DOP have high binding affinity to the human α1-AR and the bacterial adrenergic receptor (QseC), comparable to epinephrine (EPI). Both are membrane-bound kinases. Experimental studies with pancreatic cell line (LNCAP) showed that the TAs and DOP act as α1-AR antagonist by counteracting the effect of EPI. In the presence of EPI, TA and DOP trigger an increase of the intracellular Ca++ levels in the LNCAP cells leading to an inhibition of cell proliferation. Although in silico data suggest an interaction of TA and DOP with QseC, they do not inhibit the kinase activity of QseC, a histidine kinase receptor involved in quorum sensing which is also sensitive to EPI.



Conclusion: Our study showed that the TAs and DOP act as α1-AR antagonist but no effect was observed for QseC.



Keywords: Trace amines; Dopamine; QseC; α1-adrenergic receptor.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hasan2020b,

title = {The presence of Bull shark Carcharhinus leucas (Elasmobranchii: Carcharhinidae) in the fresh waters of Sumatra, Indonesia},

author = {Veryl Hasan and Maheno S. Widodo},

doi = {DOI: 10.13057/biodiv/d210962},

isbn = { 2085-4722 },

year  = {2020},

date = {2020-09-01},

journal = {Biodiversitas},

volume = {21},

number = {9},

pages = {4433-4439 },

abstract = {The presence of Bull shark Carcharhinus leucas (Elasmobranchii: Carcharhinidae) in the fresh waters of Sumatra, Indonesia. Biodiversitas 21: 4433-4439. A single subadult specimen of Bull shark Carcharhinus leucas was photographed and captured by local fisherman using casting net on June 2020 in the upper Indragiri River, Riau Province, Indonesia. Carcharhinus leucas are one of only a few species of elasmobranchs that live in both marine and freshwater environments. This species currently listed as a near-threatened species based on the IUCN Red List Status. Singel specimen identified as C. leucas by the coloration of fresh specimen: white belly and greyish back, first dorsal fin high, tip of second dorsal and caudal fins black. Meristic characters measurement results as follows: total length 102 cm; fork length 86.3 cm; preanal length 65.1 cm; pre pelvic length 51.9 cm; pre pectoral length 22.5 cm; pre-orbital length 8.3 cm; head length 25 cm; pre-first dorsal length 29.4 cm; pre-second dorsal length 56 cm, and pre-caudal length 78.1 cm. This photo is considered as the third record from freshwaters of Sumatra after in the Batang Hari River, Jambi Province in 1997, and in the Musi River, South Sumatra Province in 2019. The photographic records indicate that a single specimen of C. leucas was found in the upper Indragiri River recorded more than 150 km inland. These results enhanced the understanding of C. leucas distribution in Sumatra freshwaters. Monitoring is needed to assess the possibility of the importance of the upper Indragiri River as a migration route, nursery, and growth ground of C. leucas. Studying small scale habitat use of C. leucas is challenged by their preferred habitats in freshwaters environments with fast-changing environmental conditions. Water conditions in the upper Indragiri River, namely salinity 0‰, temperature 25-27°C, dissolved oxygen 3.9-11.1 mg/l, are ideal for A. leucas habitat.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wicaksono2020a,

title = {Lugol’s iodine test on Rafflesia patma\textendashTetrastigma leucostaphylum intersection tissue for preliminary starch visualization},

author = {Adhityo Wicaksono and Sofi Mursidawati},

url = {https://smujo.id/nb/article/view/6444},

doi = {DOI: 10.13057/nusbiosci/n120202},

isbn = {2087-3948},

year  = {2020},

date = {2020-09-01},

journal = {Nusantara Bioscience},

volume = {12},

number = {2},

pages = {91-96},

abstract = {As holoparasitic plant, Rafflesia has no recognizable plastid genome, but it has plastid-like organelle. Despite the fact that it obtains nutrients from host plant, it is unknown if Rafflesia stores primary metabolites, such as carbohydrates, from its host. A study was performed to visualize the starch in Rafflesia patma Blume proximal tissue which was intersected to its host root, Tetrastigma leucostaphylum (Dennst.) Alston, using modified Sachs’ test with Lugol’s iodine. The result revealed the absence of blackening in the R. patma tissue caused by starch reaction with the iodine, but occurred in the root cortical tissue of T. leucostaphylum. The absence of starch in R. patma tissue indicated that possibly the plastid-like organ has no similar function to amyloplast, and starch is not used for storage in the flower. It is likely that R. patma relies completely on the host’s photosynthate to maintain the flower metabolism during anthesis period. However, detailed histochemical analysis for starch or carbohydrate is needed for confirmation whether the starch is existing even in small quantity, and molecular genetic observation on sucrose intake and flowering (anthesis) regulatory genes will also be required to confirm if Rafflesia takes the photosynthate directly from its host and possibility if Rafflesia coordinates the formation of flower bud and anthesis between the endophytic tissues to prevent overexploitation of nutrients from its host.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hasan2020a,

title = {Presence of striped flying barb Esomus metallicus (teleostei, cyprinidae) from West Sumatra, Indonesia},

author = {Veryl Hasan and Maheno S. Widodo and Abdul R. Faqih and Gunanti Mahasri and Muhammad Arief and Fitri S. Valen and Muhammad Badrut Tamam and Danang Yonarta and Fajar S. Pratama and Ren Fitriadi},

url = {http://www.envirobiotechjournals.com/EEC/Vol26AugSuppl20/EEC-11.pdf},

isbn = {0971\textendash765X},

year  = {2020},

date = {2020-08-31},

journal = {Ecology, Environment and Conservation Paper},

volume = {26},

pages = {73-75},

abstract = {Striped flying Barb Esomus metallicus is native fish from Indochina and introduced to several countries in Southeast Asia. In Sumatra (Indonesia), it was previously known only from Siak River and Reteh River, Riau Province. This paper provide the first record of E. metallicus from Maninjau Lake in West Sumatra Province, thereby extending the distribution of the species approximately 270 and 350 km west from the previous records.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Valen2020,

title = {Contemporary records of sea urchin Tripneustes gratilla (Echinodermata: Echinoidea) in Timor Island, Indonesia},

author = {Aryok Nomleni and Maheno S. Widodo and Yuni Kilawati and Fitri S. Valen },

url = {http://www.bioflux.com.ro/docs/2020.1899-1905.pdf},

issn = {1844-8143 },

year  = {2020},

date = {2020-08-31},

journal = {AACL Bioflux},

volume = {13},

number = {4},

pages = {1899-1905},

abstract = {This study was conducted to determine the distribution of sea urchin Tripneustes gratilla in several locations on the island of Timor, Indonesia, from 10 April to 19 June 2018, using a random sampling method and description based on habitat and distribution. The results showed that T. gratilla was more found in coastal areas with sandy muddy substrate, overgrown with seagrass beds and with salinity between 30-450 /00. Samples had an average diameter from 60 to 80 mm, with a height of 50-60 mm and a weight of 5-7 grams},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Leo,

title = {Herpetofauna diversity in Zamrud National Park, Indonesia: baseline checklist for a Sumatra peat swamp forest ecosystem},

author = {Sandy Leo and Muhammad Suherman and Anggi Permatasari and Darwan Suganda and Zulamri and Nurul L. Winarni},

url = {http://amphibian-reptile-conservation.org/pdfs/Volume/Vol_14_no_2/ARC_14_2_[General_Section]_250-263_e249.pdf},

isbn = {1525-9153},

year  = {2020},

date = {2020-08-30},

journal = {Amphibian \& Reptile Conservation },

volume = {14},

number = {2},

pages = {250-263},

abstract = {\textemdashSumatra is an island that contains rich wildlife biodiversity and a variety of ecosystems, and is

categorized as one of the most threatened terrestrial ecoregions on earth. One of Sumatra’s ecosystems is

peat swamp forest, which has unusually extreme conditions, but otherwise can support diverse fora and fauna

with many endemic and endangered species, including herpetofauna. This survey was conducted in Zamrud

National Park (ZNP) with the goal of determining the herpetofaunal diversity and community. Visual encounter

survey and glue trap methods were used to sample and determine species diversity and distributions. The

survey identifed 33 herpetofauna species in ZNP, which included 12 amphibian and 21 reptile species.

Cyrtodactylus majulah was the most common species that could be found in all transects. The 33 species, or

approximately 30.8% of all herpetofauna in Kampar Peninsular, were found in only 15 days of feldwork, and

included two high-risk species, i.e., Limnonectes malesianus (NT) and Cuora amboinensis (VU). Furthermore,

two endemic Sumatra species, Chalcorana parvaccola and Pulchrana rawa, were also recorded, along with

a new distribution record of a skink species for Sumatra and Indonesia. Further surveys and monitoring are

needed to continue the inventory and to monitor the current communities, as well as to document new fndings

in other areas of ZNP.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Silva2020,

title = {Shoot tip necrosis of in vitro plant cultures: a reappraisal of possible causes and solutions},

author = {Jaime A. Teixeira da Silva and Esmaeil Nezami‑Alanagh and Mar\'{i}a E. Barreal and Mafatlal M. Kher and Adhityo Wicaksono and Andrea Guly\'{a}s and Norbert Hidv\'{e}gi and Katalin Magyar‑T\'{a}bori and N\'{o}ra Mendler‑Drienyovszki

L\'{a}szl\'{o} M\'{a}rton2

 · Mariana Land\'{i}n7 · Pedro Pablo Gallego3 · John A. Driver8

 · Judit Dobr\'{a}nszki},

url = {https://link.springer.com/content/pdf/10.1007/s00425-020-03449-4.pdf},

doi = {https://doi.org/10.1007/s00425-020-03449-4},

issn = {0032-0935},

year  = {2020},

date = {2020-08-27},

journal = {Planta},

volume = {252},

number = {47},

pages = {1-35},

abstract = {Shoot tip necrosis is a physiological condition and disorder that can arise in plantlets or shoots in vitro that results in death of the shoot tip. This condition, which can spread basipetally and affect the emergence of axillary shoots from buds lower down the stem, is due to the cessation of apical dominance. STN can occur at both shoot multiplication and rooting stages. One of the most common factors that cause STN is nutrient deficiency or imbalance. Moreover, the presence or absence of plant growth regulators (auxins or cytokinins) at specific developmental stages may impact STN. The cytokinin to auxin ratio within an in vitro plant can be modified by varying the concentration of cytokinins used in the culture medium. The supply of nutrients to in vitro shoots or plantlets might also affect their hormonal balance, thus modifying the occurrence of STN. High relative humidity within culture vessels and hyperhydricity are associated with STN. An adequate supply of calcium as the divalent cation (Ca2+) can hinder STN by inhibiting the accumulation of phenolic compounds and thus programmed cell death. Moreover, the level of Ca2+ affects auxin transport and ethylene production, and higher ethylene production, which can occur as a result of high relative humidity in or poor ventilation of the in vitro culture vessel, induces STN. High relative humidity can decrease the mobility of Ca2+ within a plant, resulting in Ca2+ deficiency and STN. STN of in vitro shoots or plantlets can be halted or reversed by altering the basal medium, mainly the concentration of Ca2+, adjusting the levels of auxins or cytokinins, or modifying culture conditions. This review examines the literature related to STN, seeks to discover the associated factors and relations between them, proposes practical solutions, and attempts to better understand the mechanism(s) underlying this condition in vitro.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kharisma2020a,

title = {A Vaccine Candidate of ZIKA Virus (ZIKV) from Polyvalent Conserved B-Cell Epitope on Viral Glycoprotein: In Silico Approach},

author = {Viol Dhea Kharisma and Nashi Widodo and Arif Nur Muhammad Ansori and Alexander Patera Nugraha},

url = {https://www.researchgate.net/publication/343415333_A_Vaccine_Candidate_of_ZIKA_Virus_ZIKV_from_Polyvalent_Conserved_B-Cell_Epitope_on_Viral_Glycoprotein_In_Silico_Approach},

doi = {10.35124/bca.2020.20.S1.2785},

isbn = {0972-5075},

year  = {2020},

date = {2020-08-09},

journal = {Biochemical and Cellular Archives},

volume = {20},

pages = {2785-2793},

abstract = {Zika virus (ZIKV) is a member of the Flaviviridae family. This virus is spread and carried by mosquitoes (Aedes aegypti and Aedes albopictus). ZIKV belongs to the Flavivirus genus, enveloped, and positive-sense RNA that encodes structural (E) and non-structural (NS) proteins. the envelope glycoprotein of ZIKV interact with the Axl receptor to fuse the host cells. Thus, the glycoprotein molecule is an important target for the design of antiviral and vaccine candidates. Up until today, the ZIKV vaccine has not been found, so it is necessary to develop a vaccine. In silico studies such as the ZIKV vaccine design have previously been carried out, based on the conserved regions, but have not explained how many peptides are used. Moreover, researchers have not explained the possibility of peptides being recognized by B-cell receptors (BCR) as epitopes and have antigenicity to trigger direct immune responses. Thus, this study aims to develop a method for selecting candidate vaccine peptides through of polyvalent conserved regions in ZIKV glycoprotein, prediction of B cell immunogenicity, and molecular simulation of peptide interactions with BCR, biological pathways prediction of immune responses mediated by these receptors. The results showed that there were five conserved region domains in ZIKV glycoprotein as antigens. Interestingly, from the five domains, vaccine candidate peptides were obtained which could potentially be recognized by Fab/BCR. There is a functional amino acid residue position in BCR which is predicted to possibly interacting with vaccine candidate peptides, specifically Asp152 and Ser153, which have played in the activity of these receptors thus triggering protein interactions that have a role in the regulation of immune response.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ansori2020c,

title = {Phylogenetic and Pathotypic Characterization of Avian Paramyxovirus Serotype 1 (APMV-1) in Indonesia},

author = {Arif Nur Muhammad Ansori and Viol Dhea Kharisma and Alexander Patera Nugraha },

url = {https://www.researchgate.net/publication/343426183_Phylogenetic_and_Pathotypic_Characterization_of_Avian_Paramyxovirus_Serotype_1_APMV-1_in_Indonesia},

doi = { 10.35124/bca.2020.20.S1.3023},

isbn = {0972-5075},

year  = {2020},

date = {2020-08-09},

journal = {Biochemical and Cellular Archives},

volume = {20},

pages = {3023-3027},

abstract = {Newcastle disease (ND) is recognized as one of the highly contagious and lethal infectious diseases of poultry industry globally. ND is caused by avian paramyxovirus type-1 (APMV-1) or Newcastle disease virus (Paramyxoviridae: Avulavirus). ND outbreaks have occurred in many parts of the world including Indonesia, it brought an implication on a large economic loss due to the mortality and a trade embargo on poultry in the outbreak area. This study was to characterize 58 isolates of Newcastle disease virus (NDV) collected from GenBank ® (National Center for Biotechnology Information, USA) from 1976 to 2020. Interestingly, we revealed the data of pathotype and phylogenetic analysis of the circulating NDV isolated from Indonesia based on the fusion protein gene. In sum, the results from the current study suggested that the data of pathotype and phylogenetic analysis can be used as a reference for vaccine design in Indonesia.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kharisma2020b,

title = {Molecular Simulation: The Potency of Conserved Region on E6 HPV-16 as a Binding Target of Black Tea Compounds Against Cervical Cancer},

author = {Viol Dhea Kharisma and Arif Nur Muhammad Ansoria and Muhammad Hermawan Widyananda and Santika Lusia Utami and Alexander PateraNugraha},

url = {https://www.researchgate.net/profile/Viol_Kharisma/publication/343415589_Molecular_Simulation_The_Potency_of_Conserved_Region_on_E6_HPV-16_as_a_Binding_Target_of_Black_Tea_Compounds_Against_Cervical_Cancer/links/5f28f474a6fdcccc43a89e06/Molecular-Simulation-The-Potency-of-Conserved-Region-on-E6-HPV-16-as-a-Binding-Target-of-Black-Tea-Compounds-Against-Cervical-Cancer.pdf},

doi = { 10.35124/bca.2020.20.S1.2795},

isbn = { 0972-5075},

year  = {2020},

date = {2020-08-09},

journal = {Biochemical and Cellular Archives},

volume = {20},

pages = {2795-2802},

abstract = {Cervical cancer ranks fourth as the deadliest cancer in women in this part of the world, around 0.5 million women and close to 0.25 million people infected with cervical cancer, some of which is caused by infection with infectious agents such as human papillomavirus (HPV). HPV consists of 2 types of genes late (L) for structural protein and early (E) for functional. E protein, which plays a crucial role in normal cell transformation called E6. E6 affects p53 activity in cells by forming the E6-p53 complex, thus directing the complex to the mechanism of degradation through the proteasome pathway. E6 has a specific binding on the conserved region, it interacts with p53, therefore the potency of E6 HPV-16 conserved region is the focus of this study. Previous research explained, the black tea compounds were identified as inhibitor effects on various types of viral infections in vitro, but the molecular mechanism was still unknown. Therefore, this study aims to identify the functional conserved region in E6 HPV-16 from all strains and chemical compounds of black tea that have the potential to become inhibitors through in silico studies, to obtain drug candidates that prevent cervical cancer. The analytical method used in this research is in silico consisting of identification of conserved region E6 HPV-16, protein modeling, docking, and molecular interaction. The results showed that all chemical compounds contained in black tea were able to act as E6 HPV-16 inhibitors by binding directly to the conserved functional region used to interact with p53. The binding of these complex compounds can affect in a biological activity of E6, so it is predicted that p53 will not be degraded because the binding domain of E6 on p53 is inhibited by black tea compounds, and has the potential to prevent cervical cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kharisma2020c,

title = {Computational Study of Ginger (Zingiber Officinale) as E6 Inhibitor in Human Papillomavirus Type 16 (HPV-16) Infection},

author = {Viol Dhea Kharisma and Arif Nur Muhammad Ansori and Alexander Patera Nugraha},

url = {https://www.researchgate.net/publication/343426817_Computational_Study_of_Ginger_Zingiber_Officinale_as_E6_Inhibitor_in_Human_Papillomavirus_Type_16_HPV-16_Infection},

doi = {10.35124/bca.2020.20.S1.3155},

issn = {10.35124/bca.2020.20.S1.3155},

year  = {2020},

date = {2020-08-09},

journal = {Biochemical and Cellular Archives},

volume = {20},

pages = {3155-3159,},

abstract = {Cervical cancer caused by a high-risk type of HPV-16 infection, causing death for a woman due to not being treated early. However, some problems such as the high cost of chemotherapy trigger a new perspective on alternative treatments through natural ingredients. The chemical compound of Zingiber officinale has potential as an antiviral agent, but its specific molecular mechanism is unknown. This study will predict the molecular mechanism of chemical compounds from Zingiber officinale as an antiviral candidate for HPV-16 infection, through the in silico approach. Chemical compounds from Zingiber officinale in this study were obtained from the database, then molecular docking simulations, protein-ligand interaction analysis, and 3D molecular visualization were performed. We demonstrated that 6-gingerol in Zingiber officinale was predicted as a drug candidate because it has the lowest binding energy. The antiviral activity of HPV-16 from Zingiber officinale is very possible, through inhibiting the mechanism of E6 protein by 6-gingerol. We recommend these results of computational simulations in this study, can be used as a reference for drug design through in vitro and in vivo analysis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ansori2020d,

title = {Therapeutic Potential of Avian Paramyxovirus Serotype 1 for Cancer Therapy},

author = {Arif Nur Muhammad Ansori and Amaq Fadholly and Viol Dhea Kharisma and Alexander Patera Nugraha},

url = {https://www.researchgate.net/publication/343415933_Therapeutic_Potential_of_Avian_Paramyxovirus_Serotype_1_for_Cancer_Therapy},

doi = {10.35124/bca.2020.20.S1.2827},

isbn = {0972-5075},

year  = {2020},

date = {2020-08-09},

journal = {Biochemical and Cellular Archives},

volume = {20},

pages = {2827-2832},

abstract = {Newcastle disease virus (NDV) or avian paramyxovirus serotype-1 (APMV-1) (Paramyxoviridae: Avulavirus) is recognized as one of the highly contagious and lethal virus of poultry industry globally. On the other hand, every year, morbidity and mortality caused by cancer are increasing globally. In 2014, the WHO stated that 103,100 men and 92,200 women died from cancer in Indonesia. WHO predicted that in 2030 there will be a surge in cancer patients in Indonesia up to seven times. However, the most dominant cancers are the lung, liver and colorectum in men and the breast, cervical, and lung cancers in women.In addition, development of cancer therapy with high effectiveness and selectivity towards cancer cells, as well as minimal side effects on normal cells is needed. Furthermore, NDV is a promising oncolytic virus that especially infects and kills human cancer cells.This virus, known as an oncolytic virus, can kill cancer cells without damaging healthy cells. In this review article, we demonstratedthe current update of NDV virotherapy against various human cancers.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rukmana2020,

title = {Molecular Identification of Trichoderma Isolates from Sugarcane Bagasse Based on Internal Transcribed Spacer (ITS) rDNA},

author = {Siti Rukmana and Arif Nur Muhammad Ansori and Muhammad K. J. Kusala and Ulfah Utami and Didik Wahyudi and Andita A. Mandasari},

url = {https://rjptonline.org/HTMLPaper.aspx?Journal=Research%20Journal%20of%20Pharmacy%20and%20Technology;PID=2020-13-7-45},

doi = {10.5958/0974-360X.2020.00585.5 },

issn = {0974-3618},

year  = {2020},

date = {2020-07-10},

journal = {Research J. Pharm. and Tech.},

volume = {13},

number = {7},

pages = {3300-3304},

abstract = {This study aimed to identify Trichoderma from sugarcane bagasse based on iinternal transcribed spacer (ITS) rDNA. The sample used was pure isolate of Trichoderma from sugarcane bagasse. DNA samples were isolated using the modified CTAB method. DNA was amplified using the primers ITS1 and ITS4. Interestingly, the results showed that Trichoderma genomic DNA has a concentration of 92.56 mg with a purity of 1.91. The amplicon of Trichoderma DNA is about 600 bp, whereas phylogenetic analysis shows that the sample of Trichoderma from sugarcane bagasse is one group with Trichoderma harzianum, Trichoderma piluliferum, Trichoderma sp. SQR339, Hypocrea nigricans, and Trichoderma sp. NFML CH12 BB. 15, Trichoderma aureoviride, Hypocrea lixii, and Trichoderma BAB-4585.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ansori2020b,

title = {Immunobioinformatics analysis and phylogenetic tree construction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Indonesia:spike glycoprotein gene},

author = {Arif Nur Muhammad Ansori and Viol Dhea Kharisma and Yulanda Antonius and Martia Rani Tacharina and Fedik Abdul Rantam},

url = {https://www.teknolabjournal.com/index.php/Jtl/article/view/221/110},

doi = {https://doi.org/10.29238/teknolabjournal.v9i1.221},

issn = {2580-0191},

year  = {2020},

date = {2020-06-11},

journal = {Jurnal Teknologi Laboratorium},

volume = {9},

number = {1},

pages = {13-20},

abstract = {The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread worldwide and as a result, the World Health Organization (WHO) declared it a pandemic. At present, there are no approved vaccines against SARS-CoV-2. Therefore, the aim of this study was to predict epitope-based vaccines using bioinformatics approaches and phylogenetic tree construction of SARS-CoV-2 against the backdrop of the COVID-19 pandemic. In this study, we employed 27 isolates of SARS-CoV-2 spike glycoprotein genes retrieved from GenBank® (National Center for Biotechnology Information, USA) and the GISAID EpiCoV™ Database (Germany). We analyzed the candidate epitopes using the Immune Epitope Database and Analysis Resource. Furthermore, we performed a protective antigen prediction with VaxiJen 2.0. Data for B-cell epitope prediction, protective antigen prediction, and the underlying phylogenetic tree of SARS-CoV-2 were obtained in this research. Therefore, these data could be used to design an epitope-based vaccine against SARS-CoV-2. However, the advanced study is recommended for confirmation (in vitro and in vivo).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wicaksono2020b,

title = {Rafflesia patma Blume flower organs: histology of the epidermis and vascular structures, and a search for stomata},

author = {Sofi Mursidawati and Adhityo Wicaksono and Jaime A {Teixeira da Silva}},

url = {https://link.springer.com/article/10.1007/s00425-020-03402-5},

doi = {https://doi.org/10.1007/s00425-020-03402-5},

issn = {0032-0935},

year  = {2020},

date = {2020-06-03},

journal = {Planta},

volume = {251},

number = {112},

pages = {1-10},

abstract = {Rafflesia is an endophytic holoparasitic plant that infects Tetrastigma. In a previous study, we characterized the shape of the strands of an endophyte (Rafflesia patma Blume) and hypothesized their distribution. In this study, we deepened our analysis by assessing parts of flower tissue sampled during anthesis, performed surface casting of the abaxial and adaxial sides of the perigone lobe to profile their surface features, and histologically characterized the perigone lobe, perigone tube, and central column base, including the anther and cupula region. The objective of these observations was to compare tissues from different organs and the distribution of cells staining positive for tannin, suberin, and lignin. Observable features in this study were vascular and epidermal tissue. We also observed reduced vascular tissue with xylem and vascular parenchyma in multiple organs. The adaxial epidermis found in the perigone lobes and tube had papillate cells, and their function might be to assist with the emission of odor through chemical evaporation. The abaxial epidermis, also found in perigone lobes and tube, had flattened cells. These, combined with the nearby flattened parenchyma cells, especially in the outermost, early perigone lobe, might provide a tougher (stiffer) outer protective barrier for the flower. The accumulation of tannin in perigone lobes might offer protection to the flower from herbivores prior to anthesis. Although a previous observation indicated the possibility of stomata on the surface of Rafflesia flowers, no stomata were found in this study.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}