Teaching Python programming for bioinformatics with Jupyter notebook in the Post-COVID-19 era

The COVID-19 pandemic has forced the Bioinformatics course to switch from on-site teaching to remote learning. This shift has prompted a change in teaching methods and laboratory activities. Students need to have a basic understanding of DNA sequences and how to analyze them using custom scripts. To facilitate learning, we have modified the course to use Jupyter Notebook, which offers an alternative approach to writing custom scripts for basic DNA sequence analysis. This approach allows students to acquire the necessary skills while working remotely. It is a versatile and user-friendly platform that can be used to combine explanations, code, and results in a single document. This feature enables students to interact with the code and results, making the learning process more engaging and effective. Jupyter Notebook provides a hybrid approach to learning basic Python scripting and genomics that is effective for remote teaching and learning during the COVID-19 pandemic.

Optimization and application of loop-mediated isothermal amplification technique for sex identification in red-whiskered bulbul (Pycnonotus jocosus)

The red‐whiskered bulbul (Pycnonotus jocosus) is a popular avian species in Thailand and many other countries. The red‐whiskered bulbul has a high economic value, but breeding is challenging since sex identification is difficult. The PCR method is now used for sex identification. However, PCR amplification and post‐PCR analysis necessitate the use of a laboratory equipped with specialized scientific instruments, which is inconvenient for field operations. This research describes a method for amplification of DNA samples using the loop‐mediated isothermal amplification (LAMP) approach, which is a molecular biology methodology for isothermal amplification that is extremely sensitive, fast, and easy for post‐LAMP product visualization. Herein, total of 23 blood samples were collected and DNA was extracted. Two sets of LAMP primers were designed for CHD‐Z and CHD‐W genes. The colorimetric assay was used to investigate the best conditions for LAMP reactions and post‐LAMP product visualization. LAMP reactions for sex identification were compared to traditional PCR in terms of sensitivity and specificity. LAMP reactions were found to be 10‐fold more sensitive than PCR at 1 ng of DNA. When compared to electrophoresis analysis, the visualization with colorimetric assay using GelRed® and SYTO™ 9 was 100% accurate. The optimal LAMP condition tested simple DNA extracted from bird feathers using the HotSHOT technique. The result showed that the optimal condition could distinguish the sex of red‐whiskered bulbuls totally and accurately. A powerful method for red‐whiskered bulbul sex identification is demonstrated in this study, which can be used in field studies because it is quick and easy to perform, has high sensitivity, and does not require advanced scientific equipment.

The complete mitochondrial genome of giant cricket, Tarbinskiellus portentosus (Orthoptera: Gryllidae) and its curation

Tarbinskiellus portentosus, commonly known as giant cricket one of the important edible cricket species. However, the genetic information of these species is still limited. Therefore, we have assembled and annotated the first mitochondrial genome of T. portentosus. The mitogenome is 15710 bp long and has GC content of 27.19%. The nucleotide composition is similar with other insect mitogenomes (A 40.6%; T 32.2%; C 17.3%; G 9.9%). The gene organization in the mitogenome of T. portentosus is identical to the mitogenome of other cricket species. The complete mitogenome of T. portentosus consisted 37 genes including 13 protein coding genes, 22 tRNA genes, and two rRNA genes. The newly assembled mitogenome will help molecular biology research on edible crickets. Since mitogenome genes are traditionally used for DNA barcoding and phylogenetic analysis, comparative analysis of

T. portentosus mitogenome with other related cricket species will also aid researchers in developing universal primers for species identification toward food security. Apart from the main goal of providing full mitogenome of T. portentosus, paper also provides conceptual workflow based on de novo assembly and its correction for final mitogenome construction.

Bar-cas12a, a novel and rapid method for plant species authentication in case of Phyllanthus amarus Schumach. & Thonn

Rapid and accurate species diagnosis accelerates performance in numerous biological fields and associated areas. However, morphology-based species taxonomy/identification might hinder study and lead to ambiguous results. DNA barcodes (Bar) has been employed extensively for plant species identification. Recently, CRISPR-cas system can be applied for diagnostic tool to detect pathogen's DNA based on the collateral activity of cas12a or cas13. Here, we developed barcode-coupled with cas12a assay, "Bar-cas12a" for species authentication using Phyllanthus amarus as a model. The gRNAs were designed from trnL region, namely gRNA-A and gRNA-B. As a result, gRNA-A was highly specific to P. amarus amplified by RPA in contrast to gRNA-B even in contaminated condition. Apart from the large variation of gRNA-A binding in DNA target, cas12a- specific PAM's gRNA-A as TTTN can be found only in P. amarus. PAM site may be recognized one of the potential regions for increasing specificity to authenticate species. In addition, the sensitivity of Bar-cas12a using both gRNAs gave the same detection limit at 0.8 fg and it was 1,000 times more sensitive compared to agarose gel electrophoresis. This approach displayed the accuracy degree of 90% for species authentication. Overall, Bar-cas12a using trnL-designed gRNA offer a highly specific, sensitive, speed, and simple approach for plant species authentication. Therefore, the current method serves as a promising tool for species determination which is likely to be implemented for onsite testing.

The fast multi-frame X-ray diffraction detector at the Dynamic Compression Sector

A multi-frame, X-ray diffraction (XRD) detector system has been developed for use in time-resolved XRD measurements during single-event experiments at the Dynamic Compression Sector (DCS) at the Advanced Photon Source (APS). The system is capable of collecting four sequential XRD patterns separated by 153 ns, the period of the APS storage ring in the 24-bunch mode. This capability allows an examination of the temporal evolution of material dynamics in single-event experiments, such as plate impact experiments, explosive detonations, and split-Hopkinson pressure bar experiments. This system is available for all user experiments at the DCS. Here, the system description and measured performance parameters (detective quantum efficiency, spatial and temporal resolution, and dynamic range) are presented along with procedures for synchronization and image post-processing.

Short communication: Insect detection using a machine learning model

Abstract. Homchan S, Gupta YM. 2021. Short communication: Insect detection using a machine learning model. Nusantara Bioscience 13: 69-73. The key step in characterizing any organisms and their gender highly relies on correct identification of specimens. Here we aim to classify insect and their sex by supervised machine learning (ML) model. In the present preliminary study, we used a newly developed graphical user interface (GUI) based platform to create a machine learning model for classifying two economically important cricket species. This study aims to develop ML model for Acheta domesticus and Gryllus bimaculatus species classification and sexing. An experimental investigation was conducted to use Google teachable machine GTM for preliminary cricket species detection and sexing using pre-processed 2646 still images. An alternative method for image processing is used to extract still images from high-resolution video for optimum accuracy. Out of the 2646 images, 2247 were used for training ML model and 399 were used for testing the trained model. The prediction accuracy of trained model had 100 % accuracy to identify both species and their sex. The developed trained model can be integrated into the mobile application for cricket species classification and sexing. The present study may guide professionals in the field of life science to develop ML models based on image classification, and serve as an example for researchers and taxonomists to employ machine learning for species classification and sexing in the preliminary analysis. Apart from our main goals, the paper also intends to provide the possibility of ML models in biological studies and to conduct the preliminary assessment of biodiversity.

Crystal Structure and Melting of Fe Shock Compressed to 273 GPa: In Situ X-Ray Diffraction

Despite extensive shock wave and static compression experiments and corresponding theoretical work, consensus on the crystal structure and the melt boundary of Fe at Earth's core conditions is lacking. We present in situ x-ray diffraction measurements in laser-shock compressed Fe that establish the stability of the hexagonal-close-packed (hcp) structure along the Hugoniot through shock melting, which occurs between ∼242 to ∼247  GPa. Using previously reported hcp Fe Hugoniot temperatures, the melt temperature is estimated to be 5560(360) K at 242 GPa, consistent with several reported Fe melt curves. Extrapolation of this value suggests ∼6400  K melt temperature at Earth's inner core boundary pressure.

Development of microsatellite markers for the house cricket, Acheta domesticus (Orthoptera: Gryllidae)

Abstract. Gupta YM, Tanasarnpaiboon S, Buddhachat K, Peyachoknagul S, Inthim P, Homchan S. 2020. Development of microsatellite markers for the house cricket, Acheta domesticus (Orthoptera: Gryllidae). Biodiversitas 21: 4094-4099. The house cricket, Acheta domesticus, is one of the species of crickets commonly found in Thailand. Insect breeders in Thailand prefer to breed house cricket as food due to its better taste and popularity among local people. Moreover, largescale breeding industries also breed house cricket to produce cricket-based edible products. Insect breeding industry is growing rapidly and requires primary precaution for sustainable production. To facilitate breeding system to maintain genetic variation in the captive population, we have sequenced the whole genome of A. domesticus to search for simple sequence repeats (SSRs) in order to develop polymorphic microsatellite markers for preliminary population genetic analysis. A total of 112,157 SSRs with primer pairs were identified in our analysis.  Of these, 91 were randomly selected to check for amplification of microsatellite polymorphisms. From these, nine microsatellites were used to check genetic variation in forty-five individuals of A. domesticus from the Phitsanulok population (Thailand).  These microsatellite markers also showed cross-amplification with other three species of edible crickets, specifically Gryllus bimaculatus, Gryllus testaceus, and Brachytrupes portentosus. The microsatellite markers presented herein will facilitate future population genetic analysis of A. domesticus populations. Moreover, the transferability of these makers would also enable researchers to conduct genetic studies for other closely related species.

What Determines the fcc-bcc Structural Transformation in Shock Compressed Noble Metals?

High pressure structural transformations are typically characterized by the thermodynamic state (pressure-volume-temperature) of the material. We present in situ x-ray diffraction measurements on laser-shock compressed silver and platinum to determine the role of deformation-induced lattice defects on high pressure phase transformations in noble metals. Results for shocked Ag show a copious increase in stacking faults (SFs) before transformation to the body-centered-cubic (bcc) structure at 144-158 GPa. In contrast, shock compressed Pt remains largely free of SFs and retains the fcc structure to over 380 GPa. These findings, along with recent results for shock compressed gold, show that SF formation promotes high pressure structural transformations in shocked noble metals that are not observed under static compression. Potential SF-related mechanisms for fcc-bcc transformations are discussed.

Structural Transformation and Melting in Gold Shock Compressed to 355 GPa

Gold is believed to retain its ambient crystal structure at very high pressures under static and shock compression, enabling its wide use as a pressure marker. Our in situ x-ray diffraction measurements on shock-compressed gold show that it transforms to the body-centered-cubic (bcc) phase, with an onset pressure between 150 and 176 GPa. A liquid-bcc coexistence was observed between 220 and 302 GPa and complete melting occurs by 355 GPa. Our observation of the lower coordination bcc structure in shocked gold is in marked contrast to theoretical predictions and the reported observation of the hexagonal-close-packed structure under static compression.

Nanosecond Melting and Recrystallization in Shock-Compressed Silicon

In situ, time-resolved, x-ray diffraction and simultaneous continuum measurements were used to examine structural changes in Si shock compressed to 54 GPa. Shock melting was unambiguously established above ∼31-33  GPa, through the vanishing of all sharp crystalline diffraction peaks and the emergence of a single broad diffraction ring. Reshock from the melt boundary results in rapid (nanosecond) recrystallization to the hexagonal-close-packed Si phase and further supports melting. Our results also provide new constraints on the high-temperature, high-pressure Si phase diagram.

Twinning and Dislocation Evolution during Shock Compression and Release of Single Crystals: Real-Time X-Ray Diffraction

Determining the temporal evolution of twinning and/or dislocation slip, in real-time (nanoseconds), in single crystals subjected to plane shock wave loading is a long-standing scientific need. Noncubic crystals pose special challenges because they have many competing slip and twinning systems. Here, we report on time-resolved, in situ, synchrotron Laue x-ray diffraction measurements during shock compression and release of magnesium single crystals that are subjected to compression along the c axis. Significant twinning was observed directly during stress release following shock compression; during compression, only dislocation slip was observed. Our measurements unambiguously distinguish between twinning and dislocation slip on nanosecond timescales in a shocked hexagonal-close-packed metal.

Real-Time Examination of Atomistic Mechanisms during Shock-Induced Structural Transformation in Silicon

The experimental determination of atomistic mechanisms linking crystal structures during a compression-driven solid-solid phase transformation is a long-standing and challenging scientific objective. Using new capabilities at the Dynamic Compression Sector at the Advanced Photon Source, the structure of shocked Si at 19 GPa was identified as simple hexagonal, and the lattice orientations between ambient cubic diamond and simple hexagonal structures were related. The approach is general and provides a powerful new method for examining atomistic mechanisms during stress-induced structural changes.

Real-time, high-resolution x-ray diffraction measurements on shocked crystals at a synchrotron facility

The Advanced Photon Source (APS) at Argonne National Laboratory was used to obtain real-time, high-resolution x-ray diffraction measurements to determine the microscopic response of shock-compressed single crystals. Disk shaped samples were subjected to plane shock wave compression by impacting them with half-inch diameter, flat-faced projectiles. The projectiles were accelerated to velocities ranging between 300 and 1200 m/s using a compact powder gun designed specifically for use at a synchrotron facility. The experiments were designed to keep the sample probed volume under uniaxial strain and constant stress for a duration longer than the 153.4 ns spacing between x-ray bunches. X-rays from a single pulse (<100 ps duration) out of the periodic x-ray pulses emitted by the synchrotron were used for the diffraction measurements. A synchronization and x-ray detection technique was developed to ensure that the measured signal was obtained unambiguously from the desired x-ray pulse incident on the sample while the sample was in a constant uniaxial strain state. The synchronization and x-ray detection techniques described can be used for a variety of x-ray measurements on shock compressed solids and liquids at the APS. Detailed procedures for applying the Bragg-Brentano parafocusing approach to single crystals at the APS are presented. Analytic developments to determine the effects of crystal substructure and non-ideal geometry on the diffraction pattern position and shape are presented. Representative real-time x-ray diffraction data, indicating shock-induced microstructural changes, are presented for a shock-compressed Al(111) sample. The experimental developments presented here provided, in part, the impetus for the Dynamic Compression Sector (DCS) currently under development at the APS. Both the synchronization∕x-ray detection methods and the analysis equations for high-resolution single crystal x-ray diffraction can be used at the DCS.

High spectral resolution, real-time, Raman spectroscopy in shock compression experiments

The use of Raman measurements to examine molecular changes associated with shock-induced structural and chemical changes in condensed materials often poses two challenging requirements: high spectral resolution and significantly reduced background light. Here, we describe an experimental method that addresses these requirements and provides better quality data than the time resolved approach used previously. Representative measurements are presented for shock compression of two energetic crystals: pentaerythritol tetranitrate and cyclotrimethylene trinitramine. The high spectral resolution data have provided insight into molecular changes that could not be obtained from lower-resolution, time-resolved methods.

Experimental determination of third-order elastic constants of diamond

To determine the nonlinear elastic response of diamond, single crystals were shock compressed along the [100], [110], and [111] orientations to 120 GPa peak elastic stresses. Particle velocity histories and elastic wave velocities were measured by using laser interferometry. The measured elastic wave profiles were used, in combination with published acoustic measurements, to determine the complete set of third-order elastic constants. These constants represent the first experimental determination, and several differ significantly from those calculated by using theoretical models.

Raman and X-ray scattering studies of high-pressure phases of urea

Single-crystal and polycrystalline urea samples were compressed to 12 GPa in a diamond-anvil cell. Raman-scattering measurements indicate a sequence of four structural phases occurring over this pressure range at room temperature. The transitions to the high-pressure phases take place at pressures near 0.5 GPa (phase I --> II), 5.0 GPa (II --> III), and 8.0 GPa (III --> IV). Lattice parameters in phase I (tetragonal, with 2 molecules per unit cell, space group P42(1)m (D3(2d))) and phase II (orthorhombic, 4 molecules per unit cell, space group P2(1)2(1)2(1) (D2(4))) were determined using angle-dispersive X-ray diffraction experiments. For phases III and IV, the combined Raman and diffraction data indicate that the unit cells are likely orthorhombic with four molecules per unit cell. Spatially resolved Raman measurements on single-crystal samples in phases III and IV reveal the coexistence of two domains with distinct spectral features. Physical origins of the spatial domains in phases III and IV are examined and discussed.

Nanosecond freezing of water under multiple shock wave compression: continuum modeling and wave profile measurements

Using real time optical transmission and imaging measurements in multiple shock wave compression experiments, water was shown to solidify on nanosecond time scales [D. H. Dolan and Y. M. Gupta, J. Chem. Phys. 121, 9050 (2004)]. Continuum modeling and wave profile measurements, presented here, provide a complementary approach to examine the freezing of shocked water. The water model consisted of thermodynamically consistent descriptions of liquid and solid (ice VII) water, relationships for phase coexistence, and a time-dependent transition description to simulate freezing dynamics. Continuum calculations using the water model demonstrate that, unlike single shock compression, multiple shock compression results in pressure-temperature conditions where the ice VIII phase is thermodynamically favored over the liquid phase. Wave profile measurements, using laser interferometry, were obtained with quartz and sapphire windows at a peak pressure of 5 GPa. For water confined between sapphire windows, numerical simulations corresponding to a purely liquid response are in excellent agreement with the measured wave profile. For water confined between quartz windows (to provide a nucleating surface), wave profile measurements demonstrate a pure liquid response for an incubation time of approximately 100 ns followed by a time-dependent transformation. Analysis of the wave profiles after the onset of transformation suggests that water changes from a metastable liquid to a denser phase, consistent with the formation of a high-pressure ice phase. Continuum analyses and simulations underscore the need for multiple time scales to model the freezing transition. Findings from the present continuum work are extremely consistent with optical results reported previously. These studies constitute the first comprehensive investigation reported for freezing of a liquid at very short time scales.

Nanosecond freezing of water under multiple shock wave compression: optical transmission and imaging measurements

Water samples were subjected to multiple shock wave compressions, generating peak pressures of 1-5 GPa on nanosecond time scales. This loading process approximates isentropic compression and leads to temperatures where the ice VII phase is more stable than the liquid phase above 2 GPa. Time resolved optical transmission and imaging measurements were performed to determine the solidification rate under such conditions. Freezing occurred faster at higher pressures as water was compressed further into the ice VII phase, in agreement with classical micleation theory. Water consistently froze when in contact with a silica window, whereas no solidification occurred in the presence of sapphire windows. The transition was determined to be a surface initiated process--freezing began via heterogeneous nucleation at the water/window interface and propagated over thicknesses greater than 0.01 mm. The first optical images of freezing on nanosecond time scales were obtained. These images demonstrate heterogeneous nucleation and irregular solid growth over 0.01-0.10 mm lateral length scales and are consistent with latent heat emission during the transformation. The combination of optical transmission and imaging measurements presented here provide the first consistent evidence for freezing on short time scales.

Raman Spectra of Shock Compressed Pentaerythritol Tetranitrate Single Crystals: Anisotropic Response

To gain insight into the anisotropic sensitivity of shocked pentaerythritol tetranitrate (PETN) single crystals, single-pulse Raman spectroscopy was used to examine the response of crystals shocked along the [100] (insensitive) and [110] (sensitive) orientations. High-resolution Raman spectra revealed several orientation-dependent features under shock compression: (i) substantially different stress dependence of the Raman shift for the CH(2) and NO(2) stretching modes for the two orientations, (ii) discontinuity in the stress dependence of the Raman shift for the CH(2) stretching modes above 4 GPa for the [110] orientation, and (iii) large broadening for the CH(2) and NO(2) asymmetric stretching modes for stresses above 4 GPa for the [110] orientation. The present data in combination with previous static pressure results provide support for conformational changes in PETN molecules for shock compression along the [110] (sensitive) orientation. Implications of the present results for the anisotropic sensitivity of shocked PETN are discussed.

Real-time X-Ray diffraction measurements of the phase transition in KCl shocked along

X-ray diffraction measurements and analyses were developed and used to examine the phase transition in KCl shocked to 7 GPa. Diffraction data were obtained below and above the transition stress, and related quantitatively to macroscopic compression in the two phases. Interplanar spacing measurements revealed isotropic compression of the unit cell. Above the transition stress, a diffraction peak from the (110) planes in phase II was observed consistently and the orientation of the transformed crystal structure was determined with respect to the phase I structure. This determination provides a mechanism for the atomic rearrangement from the rocksalt to the cesium chloride structure in KCl shocked along [100].