bluuebunny/crossref_metadata_2025 huggingface dataset:
The structural basis for inhibition of ribosomal translocation by viomycin
Authors: Zhang Ling , Wang Ying-Hui , Zhang Xing , Lancaster Laura , Zhou Jie , Noller Harry F.
Published: April 2020

Viomycin, an antibiotic that has been used to fight tuberculosis infections, is believed to block the translocation step of protein synthesis by inhibiting ribosomal subunit dissociation and trapping the ribosome in an intermediate state of intersubunit rotation. The mechanism by which viomycin stabilizes this state remains unexplained. To address this, we have determined cryo-EM and X-ray crystal structures of
Escherichia coli
70S ribosome complexes trapped in a rotated state by viomycin. The 3.8-Å resolution cryo-EM structure reveals a ribosome trapped in the hybrid state with 8.6° intersubunit rotation and 5.3° rotation of the 30S subunit head domain, bearing a single P/E state transfer RNA (tRNA). We identify five different binding sites for viomycin, four of which have not been previously described. To resolve the details of their binding interactions, we solved the 3.1-Å crystal structure of a viomycin-bound ribosome complex, revealing that all five viomycins bind to ribosomal RNA. One of these (Vio1) corresponds to the single viomycin that was previously identified in a complex with a nonrotated classical-state ribosome. Three of the newly observed binding sites (Vio3, Vio4, and Vio5) are clustered at intersubunit bridges, consistent with the ability of viomycin to inhibit subunit dissociation. We propose that one or more of these same three viomycins induce intersubunit rotation by selectively binding the rotated state of the ribosome at dynamic elements of 16S and 23S rRNA, thus, blocking conformational changes associated with molecular movements that are required for translocation.
SuperPlots: Communicating reproducibility and variability in cell biology
Authors: Lord Samuel J. , Velle Katrina B. , Mullins R. Dyche , Fritz-Laylin Lillian K.
Published: April 2020

P values and error bars help readers infer whether a reported difference would likely recur, with the sample size n used for statistical tests representing biological replicates, independent measurements of the population from separate experiments. We provide examples and practical tutorials for creating figures that communicate both the cell-level variability and the experimental reproducibility.
Thickness-dependent magnetic order and phase transition in V5S8*
Authors: Zhang Rui-Zi , Zhang Yu-Yang , Du Shi-Xuan
Published: April 2020

V5S8 is an ideal candidate to explore the magnetism at the two-dimensional (2D) limit. A recent experiment has shown that the V5S8 thin films exhibit an antiferromagnetic (AFM) to ferromagnetic (FM) phase transition with reducing thickness. Here, for the first time, using density functional theory calculations, we report the antiferromagnetic order of bulk V5S8, which is consistent with the previous experiments. The specific antiferromagnetic order is reproduced when U
eff = 2 eV is applied on the intercalated vanadium atoms within LDA. We find that the origin of the magnetic ordering is from superexchange interaction. We also investigate the thickness-dependent magnetic order in V5S8 thin films. It is found that there is an antiferromagnetic to ferromagnetic phase transition when V5S8 is thinned down to 2.2 nm. The main magnetic moments of the antiferromagnetic and ferromagnetic states of the thin films are located on the interlayered vanadium atoms, which is the same as that in the bulk. Meanwhile, the strain in the thin films also influences the AFM–FM phase transition. Our results not only reveal the magnetic order and origin in bulk V5S8 and thin films, but also provide a set of parameters which can be used in future calculations.
Simple Woods-Saxon-type form for Ωα and Ξα interactions using folding model
Authors: Etminan Faisal , Firoozabadi Mohammad Mehdi
Published: April 2020

We derive a simple Woods-Saxon-type form for potentials between

, and

using a single-folding potential method, based on a separable Y-nucleon potential. The potentials

and

are accordingly obtained using the ESC08c Nijmegens

potential (in

channel) and HAL QCD collaboration

interactions (in lattice QCD), respectively. In deriving the potential between Y and

, the same potential between Y and N is employed. The binding energy, scattering length, and effective range of the Y particle on the alpha particle are approximated by the resulting potentials. The depths of the potentials in

and

systems are obtained at

MeV and

MeV, respectively. In the case of the

potential, a fairly good agreement is observed between the single-folding potential method and the phenomenological potential of the Dover-Gal model. These potentials can be used in 3-,4- and 5-body cluster structures of

and

hypernuclei.
Microscopic study of 7Li-nucleus potential *
Authors: Chen Wen-Di , Guo Hai-Rui , Sun Wei-Li , Ye Tao , Ying Yang-Jun , Han Yin-Lu , Shen Qing-Biao
Published: April 2020

A microscopic approach is employed to study the optical potential for the 7Li-nucleus interaction system without any free parameters. It is obtained by folding the microscopic optical potentials of the constituent nucleons of 7Li over their density distributions. We employ an isospin-dependent nucleon microscopic optical potential, which is based on the Skyrme nucleon-nucleon effective interaction and derived using the Green's function method, as the nucleon optical potential. The harmonic oscillator shell model is used to describe the internal wave function of 7Li and obtain the nucleon density distribution. The 7Li microscopic optical potential is used to predict the reaction cross-sections and elastic scattering angular distributions for the target range from 27Al to 208Pb and energy range below 450 MeV. Generally, the results can reproduce the measured data reasonably well. In addition, the microscopic optical potential is comparable to a global phenomenological optical potential by fitting the presently existing measured data.
The spin-isospin decomposition of the nuclear symmetry energy from low to high density *
Authors: Guo Wenmei , Colonna M. , Greco V. , Lombardo U. , Schulze H.-J.
Published: April 2020

The energy per particle BA
in nuclear matter is calculated up to high baryon density in the whole isospin asymmetry range from symmetric matter to pure neutron matter. The results, obtained in the framework of the Brueckner-Hartree-Fock approximation with two- and three-body forces, confirm the well-known parabolic dependence on the asymmetry parameter β = (N − Z)/A (β
2law) that is valid in a wide density range. To investigate the extent to which this behavior can be traced back to the properties of the underlying interaction, aside from the mean field approximation, the spin-isospin decomposition of BA
is performed. Theoretical indications suggest that the β
2law could be violated at higher densities as a consequence of the three-body forces. This raises the problem that the symmetry energy, calculated according to the β
2law as a difference between BA
in pure neutron matter and symmetric nuclear matter, cannot be applied to neutron stars. One should return to the proper definition of the nuclear symmetry energy as a response of the nuclear system to small isospin imbalance from the Z = N nuclei and pure neutron matter.
Possible scenarios of transition to the closed nuclear fuel cycle
Authors: Alekseev P N , Gurin A V , Subbotin S A , Zilberman B Ya , Kovalev N V
Published: April 2020

This work is devoted to the comparative analysis of various scenarios of transition to introduction of the closed nuclear fuel cycle and sodium fast reactors in nuclear power of Russia. The analysis of the permissible scale of introduction of water-water power reactors and fast sodium reactors into the Russian nuclear power system was carried out taking into account the estimated reserves of natural uranium, the expected volumes of spent nuclear fuel from both national and foreign nuclear power plants and the quantity of plutonium available for the introduction of fast sodium reactors. The rate of growth in the capacity of the nuclear power system is not yet high, the resources of natural uranium seem significant, the natural uranium mining facilities and the amount of depleted uranium have not yet been classified as encumbrances. In the current situation, the practical solution to the problems of closing the nuclear fuel cycle and transition to the trajectory of development of nuclear energy as a system that meets in the future the requirements of sustainable development and energy security can already be started with the use of mixed uranium-plutonium oxide fuel in combination with fuel from enriched regenerated uranium in existing water-water power reactors and in BN-800. This step is the most promising in terms of minimizing contradictions between the existing legal and institutional framework, allowing the development of closed fuel cycle technology and reducing the amount of spent nuclear fuel. Based on the assessment of the technical and economic characteristics of various scenarios for the long-term development of the two- component nuclear power system in Russia, several possibilities for reducing the cost of implementing the transition stage from open to closed nuclear fuel cycle.
Competitive ability of FNR NPPs: requirements and implementation in the Proryv Project Direction
Authors: Tolstoukhov D.A. , Panov S.A. , Presnyakov I.V.
Published: April 2020

A key condition for the advanced development of nuclear energy is to ensure the competitiveness of NPPs in comparison with alternative generation in solving system problems. Modern nuclear power technologies on Thermal Reactors, operating in open fuel cycle, can not guarantee long-term sustainable development of nuclear power, these technologies have almost exhausted the potential for increasing competitiveness. The report is considering the competitiveness of NPPs with thermal and fast reactors in comparison with power plants on organic fuels and renewable energy sources. The analysis performed on actual data of technical and economic indicators of competing generation types. The requirements of competitiveness for NPPs are considered, allowing to ensure development taking into account the possible improvement of technical and economic indicators of alternative generation. Determined the requirements to the criteria for competitiveness of NPPs with Fast Reactors and closed NFC. Also in the report are given facts on the evaluation of the achievement the required indicators for NPPs with BR and closed NFC on the basis of actual work in the Proryv Project.
Justification and optimization of FNR transition to the closed fuel cycle mode
Authors: Khomyakov Yu S , Rodina E A , Shmidt O V , Egorov A V , Makeeva I R , Popov I S , Sokolov V P
Published: April 2020

The «Proryv» project implies developing advanced nuclear technologies for next generation large-scale nuclear power based on fast neutron reactors (FRs) operating in a closed nuclear fuel cycle (NFC). All components of the closed NFC must be in agreement with the requirements for the product characteristics and optimized in accordance with the different stages of the fuel cycle. Different variants of the closed nuclear fuel cycle are being looked into with different types of FRs, fuel, and fuel cycle facility arrangement options (centralized or on-site). Many processes and technical solutions, which are being used to develop the fuel recycling technology, have never been applied on a commercial or laboratory scale. Successfully implementing this technology implies developing a system of codes within the «Proryv» project, which would allow researchers to model various closed NFC options using a hierarchical approach. Dedicated computer software is used for optimizing particular closed NFC modules (the reactor, fuel fabrication and reprocessing modules). Optimization criteria are selected based on the requirements for characteristics of the products (in relation to quality or production time), which are in turn obtained from calculating the system as a whole. The functional possibility of conducting correlated calculations for FR cores and back-end nuclear fuel cycle processes was developed, which enabled researchers to factor in the effect of variable reactor core arrangement, startup fuel characteristics, equilibrium state attainment strategies and SNF composition on technology components and closed nuclear fuel cycle management.
Next generation control rods for fast neutron nuclear reactors
Authors: Risovany V D , Zakharov A V
Published: April 2020

Boron carbide with different boron-10 isotope content is used in the control rods of liquid sodium-cooled fast neutron nuclear reactors as absorbing material. “Trap” type control rods with heterogeneous placement of absorbing (B4C or EU2O3) and moderating (ZrH2) materials were developed. These products did not become widely used due to the high activity of europium radioisotopes and the high damageability of boron carbide. This article examines the design of next-generation control rods with boron carbide in the form of large diameter rings, hafnium hydride (HfHx, where x = 1.0-1.5) and made from a mixture of europium oxide and cobalt (Eu2O3 + Co) for fast neutron reactors . The use of a closed cycle using boron-10 isotopes, as well as spent absorbing kernels from Eu2O3+Co as gamma-ray sources is examined. It also deals with the prospects for the use of control rods with dysprosium hafnate (nDy2O3mHfO2) for lead-cooled fast reactors type BREST-OD-300.
Hydrometallurgical and combined technologies fast reactor MNUP and MOX UNF reprocessing
Authors: Shadrin A Yu , Dvoeglazov K N , Mochalov Yu S , Vidanov V V , Kashcheev V A , Terentiev A G , Gerasimenko M N , Cheshuyakov S A
Published: April 2020

Russian Federation is developing the key technologies for closed nuclear fuel cycle with FR used mixed uranium-plutonium nitride or oxide (MOX) fuel within the framework of the project “Proryv”. This is a new integrated comprehensive product for nuclear power, which provides in the future

- no accumulation of spent nuclear fuel;

- radioactive waste management based on the principles of radiation-equivalent disposal;

- technological support for the non-proliferation treaty;

- competitiveness with other large-scale power technologies.

The experimental and demonstration energy complex is under construction now on the site of Siberian Chemical Combine for the industrial development of the closed nuclear fuel cycle. ODEC will include a fast reactor BREST-OD-300 with lead coolant, facility for fabricating/refabrication of nitride fuel and the spent nuclear fuel processing facility.

Up today, the key technology elements were demonstrated using macro quantities U, Pu, Np, irradiated mixed nitride fuel and real high-level waste. Within the framework of the project “Proryv” a prototype of the fuel cycle of fast reactors is developing.
CNFC process codes
Authors: Schmidt O V , Feigin A I , Makeeva I R , Liventsov S N
Published: April 2020

The following models and codes for technological stages of CNFC are being developed in the frames of “Proryv” project

• Mathematical models of technological processes describing physical and chemical, gas/hydrodynamic, kinetic and phase processes occurring in apparatus. The models are focused on reasoning the range of technical parameters under normal, transitional and abnormal modes and on reasoning and optimization of mass-dimensional characteristics of the equipment and calculation of separate units lifetime;

• KOD TP code is intended for real-time simulation of the operation of technological schemes in order to define the functionality, controllability and to optimize the technology including control systems and simulation of accidents;

• Kinematic model of processing lines is intended for virtual definition of commutated workability both separate processes, nodes and facilities and processing lines in all. Starting, transitional, stationary modes are considered as 4D-models taking into account kinematic and technological features and restrictions.

Developing models and codes are currently used when technologies for closing stages of CNFC are designed (preparing initial data for equipment design and construction). Calculation models allow to detect collisions on early stages and to correct technological, design and engineering documentation; to perform polyvariant calculations to define the efficiency of separate nodes and the scheme in whole; to reason technical and design solutions and to evaluate the fission and nuclear materials during all the stages of the technological process including the in-process one. Currently the integrated system of models and codes is being developed for consistent simulation of heterogeneous processes and phenomena that are required to consider under calculating maintaining and reasoning the safety of CNFC technologies. The integrated system includes the existing and newly developed models and codes intended to describe technologic processes and apparatus, nuclear and radiation safety, ignition criteria, combustion, construction and engineering system behavior under critical loading and so on. The use of modern computational systems allows to perform associate calculations with date exchange between different codes from simple engineering to CFD- codes and to provide the solution of the complex problem of CNFC technology simulation.
The relationship between frontotemporal effective connectivity and performance during auditory working memory task in noise
Authors: Othman E A , Yusoff A N , Mohamad M , Abdul Manan H
Published: April 2020

The present study examined the relationship between effective connectivity among frontotemporal brain regions and auditory working memory (AWM) performance. Twenty healthy participants performed a word-based backward recall task in four signal-to-noise ratio (SNR) conditions during functional magnetic resonance imaging scans. Functional data were pre-processed and analyzed using Statistical Parametric Mapping. Optimum connectivity model and strength of effective connectivity were analyzed using Dynamic Causal Modelling. Group results indicated significant brain activation in left superior temporal gyrus (STG) and left inferior frontal gyrus (IFG). Behavioral results showed that performance was enhanced in good SNR but worsened in low SNR. Bayesian model selection showed strong evidence of a bidirectional connection between left STG and left IFG. Correlation analyses showed a moderate positive linear relationship between effective connectivity from left STG to left IFG and behavioral performance. These findings suggest that the strength of effective connectivity from left STG and left IFG may underpin successful AWM performance.
Dosimetric comparison between different radiotherapy protocols for prostate cancer using Geant4 Monte Carlo simulation
Authors: Syahir M K , Fahmi M R , Hashikin N A A
Published: April 2020

We aimed to evaluate absorbed doses received by organs at risk (OARs) following prostate treatment with external beam radiotherapy (EBRT), using different techniques (3D-CRT and box), number of fields (4 and 6 fields) and photon energies (6 and 10 MV). The MIRD5 adult male anthropomorphic phantom in GEANT4 package was used. However, the prostate, rectum and both femoral heads were not available, hence, were created within the phantom. A dose of 75 Gy was prescribed to the prostate, in all simulated treatments. Field size of 6.4 × 5.9 cm2 was used in all techniques. For 3D-CRT technique, beams with similar shape to the prostate were used, while for box technique, square-shaped beams were used. Absorbed doses to OARs (rectum, urinary bladder and both femoral heads) were then evaluated. The 3D-CRT technique resulted in lower dose to OARs compared to box technique. Also, the findings show an inverse relationship between number of fields and the OARs doses. There was no dose difference between the OARs with different beam energies. In conclusion, the 6-field 3D-CRT technique with 6 MV photon beam is an ideal treatment option for prostate cancer.
Identification of acute intracranial bleed on computed tomography using computer aided detection
Authors: Foo Y H , Wong J H D , Azman R R , Leong Y L , Tan L K
Published: April 2020

Intracranial haemorrhage can be life threatening. Timely detection of acute intracranial haemorrhage in an emergency room is essential so that the patient can be given medical attention without delay. This has led to the use of Computer Aided Detection (CAD) systems which can help to pick up and prioritize patients with high risk of bleeding. A CAD for identification of acute intracranial haemorrhage in Computed Tomography (CT) on a per patient basis was developed in this project. The CAD is aimed to be a triage tool which determines the priority of image being read by radiologists. It was developed and validated using 119 and 108 volumes of brain CT images respectively. The volumes were first registered to standard Montreal Neurological Institute (MNI) space. Slices close to the base and top of the skull that tend to contribute to false positives were omitted. Then, the volumes were analysed by a fully automated CAD program developed in MATLAB. The algorithm involved multiple thresholding and symmetry detection in 3D to detect acute intracranial haemorrhage. The evaluation took around 5s per volume. On a per patient basis, the CAD achieved sensitivity of 75.0%, specificity of 83.8%, and accuracy of 80.6% in the validation set.
Changes in divergent thinking strategy due to creativity training: Findings from dynamic causal modelling
Authors: Abdul Hamid K , Yusoff A N , Rahman S , Osman S S , Surat S , Marzuki Ahmad M , Azmi N H
Published: April 2020

Enhancing divergent thinking skills via creativity stimulation training has proven to increase performance in creativity, and caused changes in neuronal responses. However, the studies on effective connectivity between these regions has yet to be explored. This study aims to identify the most optimum connectivity model between left angular gyrus (AG), left precuneus (PCU) and medial prefrontal cortices (mPFC) during divergent thinking task in 36 healthy volunteers. All participants performed a behavioral alternative use test (AUT) and were divided into two groups, in which experimental group received creativity training, and control group were void of it. Both groups then underwent functional magnetic resonance imaging (fMRI) data acquisition, in which participants were instructed to alternative use test (AUT) of the common household object visually projected to them in the MRI bore. Post-fMRI AUT assessment was also done. Data were analysed using Statistical Parametric Mapping (SPM12) and Dynamic Causal Modelling (DCM12.5) software. Findings revealed full bidirectional connectivity between left AG, left PCU and mPFC during execution of alternative use generation. Creativity stimulation training has impacted in the change of input centre to be on left AG in the control group and mPFC in the experimental group, implying different divergent thinking strategies among participants who attended the creativity training.
Preliminary evaluation of Time-of-flight (ToF) imaging system for monitoring DIBH radiotherapy
Authors: Abubakar A , Imran S S , Karim N K A , Kassim M Z , Gokula K , Norhafizah I , Zin H M
Published: April 2020

The study focusses on evaluation of a Time-of-flight (ToF) camera for monitoring breath-hold (BH) level during voluntary deep inspiration breath-hold radiotherapy (vDIBH-RT). A commercial Argos 3D P330 ToF camera (Bluetechnix, Austria) was used to provide the distance of the patient imaged based on the light reflected from the illuminated surface. A volunteer was recruited in this study to preliminary evaluate the performance of the ToF camera for optical surface imaging. The vDIBH-RT was simulated by instructing the patient to perform DIBH for 15 seconds during ToF imaging. A small region was selected on the image of the patient’s chest surface, mid-way between the nipples. 200 consecutive ToF images of the selected area were captured during the DIBH. Imaging was repeated during free breathing (FB). These were performed for two times (representing fractions) to evaluate the inter-fraction variability. MATLAB (MathWork, Natick, MA) was used to calculate the average distance and standard deviation (SD) across each set of images acquired during a DIBH representing the BH level and BH stability, respectively. The inter-fraction variability defined as the difference between fraction-1 and fraction-2 was 4.5 mm ± 0.86. The BH stability for both sessions were within 1 mm. The distance measured during free breathing shows traces similar to the respiratory pattern obtained when using spirometry system. In conclusion, the ToF camera has potential in monitoring BH during DIBH-RT for breast cancer.
Quantitative imaging with commercial SPECT
Authors: Said M A , Masud M A , Razak H R Abdul
Published: April 2020

With the introduction of the Computed Tomography (CT) into the SPECT technology, SPECT-CT is now capable to quantify the uptake to the organ by the introduction of Activity Calibration Factor (ACF). We implemented three different phantoms geometry to obtain the ACF. First acquisition done with uniform cylinder phantom from Data Spectrum, followed with uniform NEMA IEC Body and uniform glass bottle allows the simulation of different type of clinical imaging study. Acquisitions were performed on a Brightview XCT (Philip) gamma camera. All acquisition and reconstruction protocol according to the clinical practice setting with different voxel volume sizes of 0.811 cm3, 0.104 cm3 and 0.012 cm3 to demonstrate the different values of ACFs. The ACFs for Tc-99m, I-131 and Lu-177 calculated from 3D segmentation of SPECT-CT images for scaling three different matrix sizes. The results obtained in this study demonstrated that SPECT-CT is able to quantify uptake at the organ, and it has high possibility to be used as quantitative SPECT in clinical practice in the future.
Metabolic monitoring via on-line analysis of 13C-enriched carbon dioxide in exhaled mouse breath using substrate-integrated hollow waveguide infrared spectroscopy and luminescence sensing combined with Bayesian sampling
Authors: Seichter Felicia , Vogt Josef , Tütüncü Erhan , Hagemann Leila Tamina , Wachter Ulrich , Gröger Michael , Kress Sandra , Radermacher Peter , Mizaikoff Boris
Published: April 2020

In studies that target specific functions or organs, the response is often overlaid by indirect effects of the intervention on global metabolism. The metabolic side of these interactions can be assessed based on total energy expenditure (TEE) and the contributions of the principal energy sources, carbohydrates, proteins and fat to whole body CO2 production. These parameters can be identified from indirect calorimetry using respiratory oxygen intake and CO2 dioxide production data that are combined with the response of the 13CO2 release in the expired air and the glucose tracer enrichment in plasma following a 13C glucose stable isotope infusion. This concept is applied to a mouse protocol involving anesthesia, mechanical respiration, a disease model, like hemorrhage and therapeutic intervention. It faces challenges caused by a small sample size for both breath and plasma as well as changes in metabolic parameters caused by disease and intervention. Key parameters are derived from multiple measurements, all afflicted with errors that may accumulate leading to unrealistic values. To cope with these challenges, a sensitive on-line breath analysis system based on substrate-integrated hollow waveguide infrared spectroscopy and luminescence (iHWG-IR-LS) was used to monitor gas exchange values. A Bayesian statistical model is developed that uses established equations for indirect calorimetry to predict values for respiratory gas exchange and tracer data that are consistent with the corresponding measurements and also provides statistical error bands for these parameters. With this new methodology, it was possible to estimate important metabolic parameters (respiratory quotient (RQ), relative contribution of carbohydrate, protein and fat oxidation fcarb, ffat
and fprot
, total energy expenditure TEE) in a resolution never available before for a minimal invasive protocol of mice under anesthesia.
New pest record of emerald stem borer, Agrilus sp. (Coleoptera: Buprestidae) on clove in South Bolaang Mongondow district, North Sulawesi, Indonesia
Authors: Watung J F , Tulung M , Salaki C L
Published: April 2020

The attack of emerald stem borer, Agrilus sp. on clove plant was first detected in 2007 by plant census officers at the plantation of P.T. Kawanua Kahuripan Pantera (KKP) in Bolaang Mongondow Selatan District. The surveys of clove pests at the end of 2016 to early 2017 in several clove plantations in South Bolaang Mongondow District, clove trees were found to have died from the attacks of the emerald stem borer. The attack occurred on the young clove tree about 5 to 20-yr-old plant, at a location with a height elevation of about 400 m above sea level (asl) on Lungkap village plantation up to 900 m asl on Tonsili plantation. As a result, the attack can cause the death of clove trees because the larvae bore around the tissue under the bark (cambium, xylem and phloem) so that it interferes with nutrient transport. In clove tree can be found in 1 to 4 larvae. Attack symptoms is in the form of zig-zag grooves. The average attack rate ranged from 17%, 26%, and 25% in each of the plantation resorts observed, namely: Lombuguwon resort, Tapamayondi and Tamonok. Distribution pattern in type fields are clustered with range I values (index of relationship variance and mean) greater than 1 (2,68, 3,03, 2,71); Iδ (Morisita index) greater than 1 (5,88, 3,99, 3,92); and k (negative binomial distribution index) smaller 2 (0,60, 0,49, 0,59). Agrilus sp. is categorized as a new pest in clove plant in Indonesia because it has never been reported before.
Simple method for mass-trapping of Chalcosoma atlas (Coleoptera: Scarabaeidae) in oil palm plantation
Authors: Pradana M G , Prasetyo A E , Sitompul P , Daulay A S , Pasaribu H
Published: April 2020

Atlas beetle is identified as one of minor pest in oil palm plantation. It feeds on oil palm fronds and some cases on the fruits. The beetle mass trapping has been conducted at an immature oil palm plantation in the peatland area located in Indragiri Hulu Region, Riau Province, Indonesia. In a total 2,963.89 ha area, the 10 dm3 dimension trap installed in the block boundaries every 100 m. The trap developed by 100 g of pineapple pieces which placed into a hanging container. The result showed from daily observation for 6 mo (June-Nov 2017), the trap caught 650,691 individuals. The highest catch number in the July-September period with total 39.96 individu/trap/day then decreased until the end of November with a total of 6.30 individu/trap/day.The result showed that the sex ratio trapped beetle is 1:1. The damage rate of atlas beetle decreased from 23.08% to 10.14% during trap application.
Rapid methods for screening sugarcane clones resistance against smut disease (Sporisorium scitamineum Syd.)
Authors: Khairani H S , Sinaga M S
Published: April 2020

The Indonesian government has a program to increase sugarcane productivity for domestic and export purposes. One constraint to sugarcane production is smut disease caused by Sporisorium scitamineum Syd. New resistant clones should be released since this disease already spreads to sugarcane varieties that are widely grown by farmers. Sugarcane clones are actually available, unfortunately the standard procedures for screening of clones resistance requires up to 5 mo. This experiment was conducted to develop a rapid screening method for smut resistance. The method was based on injecting 2 mL of S. scitamineum spores (106 spores/mL) on 4-mo-old plants. Injection was carried out on stem, 15 cm from the ground to avoid contamination; a maximum humidity of 72 hr in the inoculation area was maintained by sterile water droplets. Incidence of dried leaves and occurrence of smut spores at the leaves was observed as indication of plant responses to smut infection. With this method, plant responses can be obtained in less than 3 mo. This rapid screening method can be used as an alternative to shorten the testing period of sugarcane resistance to sugarcane smut.
Sensitivity of serological and polymerase chain reaction methods for detection of viruses in Allium spp.
Authors: Putri C A , Hidayat S H
Published: April 2020

Infection of Onion yellow dwarf virus (OYDV), Shallot yellow stripe virus (SYSV), and Garlic common latent virus (GCLV) has been reported on Allium spp. in Indonesia. Serology methods using enzyme-linked immunosorbent assay (ELISA), and dot immunobinding assay (DIBA) is a common method to detect viruses, while polymerase chain reaction (PCR) is popular as a molecular method to detect plant viruses nowadays. This research was conducted to assess the sensitivity of 3 detection methods, i.e. ELISA, DIBA and PCR for detecting viruses in Allium spp. Sensitivity level of each method was evaluated by diluting plant extract and antibody for ELISA and DIBA, and cDNA template for PCR. Result of this research showed that DIBA was able to detect OYDV, GCLV, and SYSV with plant extract dilution in the range of 10−1 to 10−2, and antibody dilution from 1:300 to 1:1000. ELISA seems to be more sensitive than DIBA because it was able to detect the same virus with plant extract dilution in the range of 10−1, 10−3, and 10−5, and antibody dilution from 1:300 to 1:1000. RT-PCR method was the most sensitive method compared to ELISA and DIBA because it has the highest accuracy, specification and sensitivity level. Specific DNA fragment was amplified using universal primers for Potyvirus and Carlavirus up to 10−3 and 10−4 dilution factor of cDNA respectively. Moreover, amplification using specific primers of OYDV, SYSV, and GCLV is more sensitive than using universal primers, because up to 10−5 dilution factor of cDNA was able to amplify virus target.
Shelf-life of Bacillus subtilis B298 inclusion in biopesticide microencapsule formula and its efficacy in suppressing anthracnose disease on chili
Authors: Prihatiningsih N , Erminawati  , Djatmiko H A
Published: April 2020

Bacillus subtilis B298 is an antagonistic bacterium isolated from the rhizosphere of potatoes. It is capable in controlling diseases both caused by fungi and bacteria. Inclusion of B. subtilis B298 in biopesticide microencapsule formula (BMF) is an effort to extend its shelf life, which maintain its stability and relatively more resistant to environmental change conditions. This study aimed to determine the shelf life of B. subtilis B298 in BMF, and its effectiveness in BMF to suppress chili anthracnose disease. Application of B. subtilis B298 in BMF was conducted by chili seed coating for 24 hr, after seed sowing the biopesticide was applied again by watering the roots of plants, i.e. 10, 20 and 30 d after planting. The experiment was arranged in a completely randomized block design with 4 treatments (control, B. subtilis B298 BMF, fungicide and combination of B. subtilis B298 BMF and fungicide), each treatment was repeated 6 times. Variables observed were; B. subtilis B298 population in the BMF, the disease intensity and infection rate by Colletotrichum sp. The study showed that B. subtilis B298 in BMF was capable to survive for 5 wk with a population of 14.4 107 cfu/g and suppressed chili anthracnose by 53.71%.
Characterization of soil microbes in an indicated fusarium wilt-suppressive and -conducive soils in banana plantation at Sukabumi, West Java
Authors: Effendi Y , Khalish A , Pambudi A
Published: April 2020

Banana plants (Musa acuminata L.) on PT Perkebunan Nusantara (PTPN) VIII, Parakansalak, Sukabumi West Java plantation were indicated infected by panama wilt. This disease was caused by Fusarium oxysporum f.sp. cubense (Foc) resulting the decreases fruit production and quality. However, healthy plants were found on the same areas. This condition may be caused by the differences of soil microbiomes that creates Foc-suppressive or -conducive soils. In this study, bacteria in suppressive (BH) and conducive (BS) soil samples were isolated, and characterized through several tests. The tests consisted of nitrogen fixation, hydrogen cyanide (HCN) production, and Indole Acetic Acid (IAA) production. Sequencing of 16S rRNA gene was done for identification of 26 bacterial isolates. Based on the sequences the bacteria were identified as Bacillus, Staphylococcus, Enterobacter and Lysinibacillus genus. Several isolates showed their potential as biological agents for Foc, i.e. Bacillus cereus (BH 1), B. cereus (BH 2), B. velezensis (BH 4), B. cereus (BH 7), B. cereus (BS 12), B. megaterium (BS 13), B.cereus (BS 15), B. thuringiensis (BS 18), B. vallismortis (BS 19), B. bingmayongensis (BS 20), B. toyonensis (BS 22) and B. pseudomycoides (BS 25).
Epidemiology of bacterial wilt disease on Eucalyptus pellita F. Muell. in Indonesia
Authors: Siregar B A , Giyanto  , Hidayat S H , Siregar I Z , Tjahjono B
Published: April 2020

Productivity of forest plantation such as Eucalyptus pellita in Indonesia is strongly decreased by bacterial wilt disease (Ralstonia solanacearum Smith). However, studies of bacterial wilt disease on E. pellita in Indonesia is still inadequate, so several comprehensive research are required. This research was aimed to analyse the dominant silviculture factors and soil properties which can contribute to disease epidemiology. Observation on disease incidence was conducted by the transect method on 40 observation plots selected by the purposive random sampling in 4 provinces in Indonesia. Nine silviculture factors were collected by tracking the identity and the history of plot maintenance, while soil properties were analysed from soil samples. The correlation among disease incidence to silviculture factors and soil properties was carried out by chi-square and multiple regression analysis, respectively. Planting age, Eucalyptus clones, and root malformation were the top 3 of silviculture factors which has shown significant correlation to disease incidence. Early growth of Eucalyptus sp. plant was a critical period of the disease epidemic, especially in the susceptible clone. On the other hand, soil texture (percentage of sand, clay, and silt) were the dominant variables of soil properties which strongly affected the disease incidence.
Effect of secondary metabolites of Trichoderma spp. in inhibiting Phytophthora palmivora growth in cacao (Theobroma cacao L.)
Authors: Harni R , Amaria W , Mahsunah A H
Published: April 2020

Secondary metabolites are organic compounds produced by microorganisms or plants which are not directly involved to development and reproduction. The secondary metabolites produced by Trichoderma spp. are antibiotic compounds, enzymes, toxins, and hormones that inhibit the growth of plant pathogens. Phytophthora palmivora is a pathogen that causes black pod, leaf blight, and stem canker in cacao, which potentially reduce production up to 40%. This study was aimed to determine the inhibitory effect of Trichoderma spp. secondary metabolites against P. palmivora. Isolates of Trichoderma spp., i.e. T. virens LP1, T. hamatum LP2, T. amazonicum LP3, T. atroviride JB2, and T. viride PRD were cultured on vegetative and generative medium, then their secondary metabolites was extracted using butanol and ethyl acetate. Analysis of the extracts of secondary metabolite was performed using HPLC to determine their chromatogram profile. The secondary metabolites obtained were tested against P. palmivora using poisoned-medium method and cacao seedlings. In vitro inhibition activity, disease severity, and growth of cacao seedlings were observed. The results showed that extraction of the secondary metabolite using butanol produces more metabolites than those using ethyl acetate. Secondary metabolites of T. virens LP1 and T. amazonicum LP3, significantly inhibited P. palmivora growth up to 90.98%. In general, secondary metabolites of Trichoderma spp. can suppress P. palmivora infection (60.02%–70.00%) in cacao seedlings.
Stable inheritance of RF2a transgene integration in transgenic IR64 rice plants and evaluation of their tolerance against Rice tungro virus
Authors: Estiati A , Astuti D , Widyajayantie D , Nugroho S
Published: April 2020

Rice tungro disease (RTD) is one of the devastating diseases in Asia, caused by simultaneous infection of Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). The spread of these viruses is difficult to control especially in areas with intensive rice planting. RF2a is a rice transcription vector, regulate the expression of RTBV promoter and is also important for rice development. The overexpression of RF2a in transgenic rice plants has been reported can reduce virus accumulation and leads to tolerance against tungro virus. Transformation of RF2a transgene into a commercial susceptible cultivar, IR64 had been conducted. Four trangenic rice lines at T1 and T2 generations have been obtained. Stable inheritance and expression of RF2a transgene in successive generations are an indication of the successful development of tungro-tolerant cultivars. Therefore, PCR analysis for RF2a transgene and bioassay on transgenic plants at T2 and T3 generations against tungro virus had been done. PCR analysis showed that the RF2a transgene which is indicated by the presence of hpt was stably inherited and several transgenic rice plants harboring the overexpressed RF2a are gaining tolerance to an Indonesian tungro Purwakarta isolate compared to the IR64 wild type under greenhouse conditions.
Effect of combination of biofertilizer and nanobiopesticide citronella against mosaic disease on patchouli plant
Authors: Noveriza R , Mardiningsih T L , Trisilawati O , Rahma H , Zulkarnaen
Published: April 2020

Nanobiopesticide citronella (Nano-BC) at 1% concentration was effectively reduced the intensity of mosaic disease and yield loss ranging from 23 to 43%. The mixed formulation ofSerratia marsescensAR1 andPseudomonas fluorescensLPK1-9 with cow manure (15 kg/tree) and 0.1% nanobiopesticide citronella were able to reduce 20 to 25% the intensity of vascular streak dieback disease (VSD). The combination between biofertilizer and Nano-BC is assumed to be able to reduce the intensity of patchouli mosaic virus and its insect vector and increase the resistance of patchouli plants to the disease. The objective of this study was to obtain a dose of biofertilizer (0, 100, 200, 300 g) and 1% Nano-BC that effectively controlling patchouli mosaic disease and their vectors in the field. Research was conducted on patchouli var Sidikalang at Laing Experimental Garden, Solok from January to December 2018. Application of 1% Nano-BC and 300 g biofertilizer per plant showed as the best combination to reduce the incidence and intensity of patchouli mosaic disease in the field. In addition, the highest content of P2O5was 39.00 ppm available in the soil, in which the efficacy rate ranged from 9.37 to 12.47%.
Fungi associated with Falcataria moluccana (L.) seed
Authors: Istikorini Y , Wulandari A S , Sari O Y
Published: April 2020

Seeds are the most important input of any tree cultivation. Qualified seed is defined as one pure variety with high germination rate and free from pathogens. Qualified seed ensures good germination, rapid emergence, and vigorous growth. Sengon (Falcataria moluccana) is one of the major forest trees in Indonesia, particularly in West Java. This study aimed to detect and identify fungi of F. moluccana seeds and to determine the pathogenicity of the isolates. The method of fungi isolation was blotter test with 7-8 d of incubation period. As much as 7 fungi isolates were obtained based on the method. The isolates were Alternaria sp., Aspergillus flavus, Aspergillus niger, Botryodiplodia sp., Chaetomium globosum, Penicillium sp. and S5 isolate. A. flavus, A. niger and Penicillium sp. were found on sengon seeds in both treatments,with and without surface sterilization. Pathogenicity test showed that fungi within or on F. moluccana seeds had potential to be pathogens on seeds.
Are butterfly species useful indicators of ecosystem health in Bali Barat National Park?
Authors: Winarni N L , Afifah Z , Nuruliawati
Published: April 2020

In 2015, Bali Barat National Park was chosen for a Rainforest Standard (RFS) demonstration project. As part of the requirement for the Protected Area Credit of the RFS, species or a group of species that can act as indicators of ecosystem health in Bali Barat National Park (BBNP) have to be identified. Butterflies was one of the taxa assessed for this purpose. A biological survey was conducted in Bali Barat National Park during August-September 2015. Butterfly species were surveyed using a modification of Pollard walk methods by recording species while walking along transects. A total of 82 butterfly species were recoded representing the families Papilionidae, Nymphalidae, Pieridae, Lycaenidae and Riodinidae. Forty-one species, 50 %, were from the family Nymphalidae and 21, 25 % from Pieridae. Nymphalidae and Pieridae was found to be correlated to vegetation structures. The selection process for indicator species was based on Indicator Value (IV) developed by Dufrene and Legendre (1997). Indicator Value uses both abundance and frequency to identify species that may be effective as indicators of ecosystem health. Most of the species with high IV values were associated with savanna vegetation, which is more open and often disturbed. The only Lycaenidae found with a high IV was Tarucus waterstradti, which may be considered as a potential indicator species. However, caution is needed in assessing the potential for butterflies to be used as indicator species because they are small and may be difficult to identify and there is a lack of trained observers in many parts of the tropics.
Borneo Orangutan Pongo pygmaeus pygmaeus habitat sustainability and its challenges
Authors: Siregar P G , Supriatna J , Koestoer R H , Harmantyo D
Published: April 2020

This study aims to evaluate the current condition of landscape sustainability and its challenges in Orangutan Pongo pygmaeus pygmaeus habitat in West Kalimantan, Indonesia. The results of such a study assist researchers, planners and policymakers to formulate direction of regional development policy with mainstream the concept of sustainability into development practice. For evaluating landscape sustainability, this study deployed assessment through sustainable landscape index that has six assessment indicators, which are expected to reflect economic, social and environmental sustainability. The indicators are land use benefit and regional economy as the representation of economic indicators, fairness of land utilization and poverty conditions as the representation of social indicators as well as environmental service protection and biodiversity conservation as the representation of environmental indicators. The study shows the sustainability in landscape level appears to be balanced among the six indicators of evaluation, but in further detail, it shows the unfair use of land utilization and gaps between sub-landscapes. There is high dominated land ownership by private groups in the landscape. The utilization gap is also found where in coastal and middle sub-landscapes are utilized more economic-oriented. Contrarily, the upstream is dominated by protection utilization. The paper recommends that government should be seriously considers the carrying capacity concept in land allocation and initiate payment for environmental services or other incentive mechanisms for upstream districts to conserve and protect the remaining forests.