Complete chloroplast genome data of Shorea macrophylla (Engkabang): Structural features, comparative and phylogenetic analysis.

Shorea macrophylla belongs to the Shorea genus under the Dipterocarpaceae family. It is a woody tree that grows in the rainforest in Southeast Asia. The complete chloroplast (cp) genome sequence of S. macrophylla is reported here. The genomic size of S. macrophylla is 150,778 bp and it possesses a circular structure with conserved constitute regions of large single copy (LSC, 83,681 bp) and small single copy (SSC, 19,813 bp) regions, as well as a pair of inverted repeats with a length of 23,642 bp. It has 112 unique genes, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The genome exhibits a similar GC content, gene order, structure, and codon usage when compared to previously reported chloroplast genomes from other plant species. The chloroplast genome of S. macrophylla contained 262 SSRs, the most prevalent of which was A/T, followed by AAT/ATT. Furthermore, the sequences contain 43 long repeat sequences, practically most of them are forward or palindrome type long repeats. The genome structure of S. macrophylla was compared to the genomic structures of closely related species from the same family, and eight mutational hotspots were discovered. The phylogenetic analysis demonstrated a close relationship between Shorea and Parashorea species, indicating that Shorea is not monophyletic. The complete chloroplast genome sequence analysis of S. macrophylla reported in this paper will contribute to further studies in molecular identification, genetic diversity, and phylogenetic research.

Genome-Wide Identification, Characterisation and Phylogenetic Analysis of 52 Striped Catfish (Pangasianodon hypophthalmus) ATP-Binding Cassette (ABC) Transporter Genes.

The Pangasianodon hypophthalmus (striped or tra catfish) is a Pangasiidae family member famous for its high unsaturated fatty acid content flesh. This riverine catfish can breathe in the air unlike the channel catfish. One of the most well-known ecotoxicological protein superfamily, the ATP-binding cassette (ABC) transporters, has been characterised in channel catfish through a genome-wide approach. Therefore, it is interesting to unearth these proteins within the striped catfish genome for a comprehensive comparison across all catfishes available. A total of 52 ABC transporters were discovered from the striped catfish genome. The motif analysis has unconcealed various unshared characteristics of some catfishes. The phylogenetic analysis has evidenced its effectiveness in the successful annotations of these transporter proteins. Duplicated genes such as ABCA1, ABCB3, ABCB6, ABCC5, ABCD3, ABCE1, ABCF2 as well as ABCG2 were uncovered within the striped and channel catfish genomes. This entire set of ABC transporters yields precious genomic data for future ecotoxicological, biochemical and physiological research in striped catfish.

Assessing the effect of the COVID-19 pandemic, shift to online learning, and social media use on the mental health of college students in the Philippines: A mixed-method study protocol.

INTRODUCTION: The COVID-19 pandemic declared by the WHO has affected many countries rendering everyday lives halted. In the Philippines, the lockdown quarantine protocols have shifted the traditional college classes to online. The abrupt transition to online classes may bring psychological effects to college students due to continuous isolation and lack of interaction with fellow students and teachers. Our study aims to assess Filipino college students' mental health status and to estimate the effect of the COVID-19 pandemic, the shift to online learning, and social media use on mental health. In addition, facilitators or stressors that modified the mental health status of the college students during the COVID-19 pandemic, quarantine, and subsequent shift to online learning will be investigated. METHODS AND ANALYSIS: Mixed-method study design will be used, which will involve: (1) an online survey to 2,100 college students across the Philippines; and (2) randomly selected 20-40 key informant interviews (KIIs). Online self-administered questionnaire (SAQ) including Depression, Anxiety, and Stress Scale (DASS-21) and Brief-COPE will be used. Moreover, socio-demographic factors, social media usage, shift to online learning factors, family history of mental health and COVID-19, and other factors that could affect mental health will also be included in the SAQ. KIIs will explore factors affecting the student's mental health, behaviors, coping mechanism, current stressors, and other emotional reactions to these stressors. Associations between mental health outcomes and possible risk factors will be estimated using generalized linear models, while a thematic approach will be made for the findings from the KIIs. Results of the study will then be triangulated and summarized. ETHICS AND DISSEMINATION: Our study has been approved by the University of the Philippines Manila Research Ethics Board (UPMREB 2021-099-01). The results will be actively disseminated through conference presentations, peer-reviewed journals, social media, print and broadcast media, and various stakeholder activities.

First high-quality genome assembly data of sago palm (Metroxylon sagu Rottboll).

The sago palm (Metroxylon sagu Rottboll) is a tropical halophytic starch-producing, economically important crop palm mainly located in Southeast Asian countries. Recently, a genome survey was conducted on this palm using the Illumina sequencing platform, with a very low (21.5%) BUSCO genome completeness score, and most of them (∼78%) are either fragmented or missing. Thus, in this study, the sago palm genome completeness was further improved with the utilization of the Nanopore sequencing platform that produced longer reads. A hybrid genome assembly was conducted, and the outcome was a much complete sago palm genome with BUSCO completeness achieved at as high as 97.9%, with only ∼2% of them either fragmented or missing. The estimated genome size of the sago palm is 509,812,790 bp in this study. A sum of 33,242 protein-coding genes was revealed from the sago palm genome and around 96.39% of them had been functionally annotated. An investigation on the carbohydrate metabolism KEGG pathways also unearthed that starch synthesis was one of the major sago palm activities. The genome data obtained from this work is indispensable for future molecular evolutionary and genome-wide association studies on the economically important sago palm.

The first transcriptome sequencing and data analysis of the Javan mahseer (Tor tambra).

The Javan mahseer (Tor tambra) is one of the most valuable freshwater fish found in Tor species. To date, other than mitogenomic data (BioProject: PRJNA422829), genomic and transcriptomic resources for this species are still lacking which is crucial to understand the molecular mechanisms associated with important traits such as growth, immune response, reproduction and sex determination. For the first time, we sequenced the transcriptome from a whole juvenile fish using Illumina NovaSEQ6000 generating raw paired-end reads. De novo transcriptome assembly generated a draft transcriptome (BUSCO5 completeness of 91.2% [Actinopterygii_odb10 database]) consisting of 259,403 putative transcripts with a total and N50 length of 333,881,215 bp and 2283 bp, respectively. A total count of 77,503 non-redundant protein coding sequences were predicted from the transcripts and used for functional annotation. We mapped the predicted proteins to 304 known KEGG pathways with signal transduction cluster having the highest representation followed by immune system and endocrine system. In addition, transcripts exhibiting significant similarity to previously published growth-and immune-related genes were identified which will facilitate future molecular breeding of Tor tambra.

Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers.

The true mahseer (Tor spp.) is one of the highest valued fish in the world due to its high nutritional value and great unique taste. Nevertheless, its morphological characterization and single mitochondrial gene phylogeny in the past had yet to resolve the ambiguity in its taxonomical classification. In this study, we sequenced and assembled 11 complete mahseer mitogenomes collected from Java of Indonesia, Pahang and Terengganu of Peninsular Malaysia as well as Sarawak of East Malaysia. The mitogenome evolutionary relationships among closely related Tor spp. samples were investigated based on maximum likelihood phylogenetic tree construction. Compared to the commonly used COX1 gene fragment, the complete COX1, Cytb, ND2, ND4 and ND5 genes appear to be better phylogenetic markers for genetic differentiation at the population level. In addition, a total of six population-specific mitolineage haplotypes were identified among the mahseer samples analyzed, which this offers hints towards its taxonomical landscape.

Sequencing and characterisation of complete mitogenome DNA for Rasbora sarawakensis (Cypriniformes: Cyprinidae: Rasbora) with phylogenetic consideration.

The Blueline Rasbora (Rasbora sarawakensis) is a small ray-finned fish categorized under the genus Rasbora in the Cyprinidae family. In this study, the complete mitogenome sequence of R. sarawakensis was sequenced using four primers targeting overlapping regions. The mitogenome is 16,709 bp in size, accommodating 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organisation was detected between this species and other genus counterparts. The heavy strand houses 28 genes while the light strand stores the other nine genes. Most protein-coding genes employ ATG as start codon, excluding COI gene, which utilizes GTG instead. The central conserved sequence blocks (CSB-F, CSB-E and CSB-D), variable sequence blocks (CSB-3, CSB-2 and CSB-1) as well as the terminal associated sequence (TAS) are conserved in the control region. The maximum likelihood phylogenetic tree revealed the divergence of R. sarawakensis from the basal region of the Rasbora clade, where its evolutionary relationships with R. maculatus and R. pauciperforata are poorly resolved as indicated by the low bootstrap values. This work acts as steppingstone towards further molecular evolution and population genetics studies of Rasbora genus in future.

Sequencing and Characterisation of Complete Mitochondrial DNA Genome for Trigonopoma pauciperforatum (Cypriniformes: Cyprinidae: Danioninae) with Phylogenetic Consideration.

The Trigonopoma pauciperforatum or the redstripe rasbora is a cyprinid commonly found in marshes and swampy areas with slight acidic tannin-stained water in the tropics. In this study, the complete mitogenome sequence of T. pauciperforatum was first amplified in two parts using two pairs of overlapping primers and then sequenced. The size of the mitogenome is 16,707 bp, encompassing 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organisation was detected between this species and other family members. The heavy strand accommodates 28 genes while the light strand houses the remaining nine genes. Most protein-coding genes utilise ATG as start codon except for COI gene which uses GTG instead. The terminal associated sequence (TAS), central conserved sequence block (CSB-F, CSB-D and CSB-E) as well as variable sequence block (CSB-1, CSB-2 and CSB-3) are conserved in the control region. The maximum likelihood phylogenetic tree revealed the divergence of T. pauciperforatum from the basal region of the major clade, where its evolutionary relationships with Boraras maculatus, Rasbora cephalotaenia and R. daniconius are poorly resolved as suggested by the low bootstrap values. This work contributes towards the genetic resource enrichment for peat swamp conservation and comprehensive in-depth comparisons across other phylogenetic researches done on the Rasbora-related genus.

A mixture of sewage sludge and red gypsum as an alternative material for temporary landfill cover.

This study proposed the recycling of sewage sludge (SS) and red gypsum (RG) as potential temporary landfill cover materials. Mixtures with different SS and RG compositions were prepared and tested in determining the most suitable design mix based on the resulting physical, mechanical, and geotechnical properties, namely the hydraulic conductivity, compressive strength, and plasticity. A maximum compressive strength of 524 kPa was achieved for the optimum SS:RG composition of 1:1, corresponding to Ca:Si composition of 2.5:1, which was appropriate to form the calcium silicate hydrate (CSH) gel. The SS and RG compositions did not affect the hydraulic conductivity, which was in the order 10-5 cm/s for all mixtures. Mixtures with RG greater than SS in composition exhibited plastic behaviour due to the Fe content in the RG, which helped minimize the risk of cracking. The optimum mixture had compressive strength greater than the specified minimum of 345 kPa, medium hydraulic conductivity, and moderate plasticity, thus appropriate for application as an alternative material for the temporary landfill cover in the tropics.

Sequencing and characterization of complete mitogenome DNA of Rasbora tornieri (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance.

The yellowtail rasbora (Rasbora tornieri) is a miniature ray-finned fish categorized under the genus Rasbora in the family of Cyprinidae. In this study, a complete mitogenome sequence of R. tornieri was sequenced using four primers targeting two halves of the mitogenome with overlapping flanking regions. The size of mitogenome was 16,573 bp, housing 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organization was detected between this species and other members of Rasbora genus. The heavy strand encompassed 28 genes while the light strand accommodated the other nine genes. Most protein-coding genes execute ATG as start codon, excluding COI and ND3 genes, which utilized GTG instead. The central conserved sequence blocks (CSB-E, CSB-F and CSB-D), variable sequence blocks (CSB-1, CSB-3 and CSB-2) as well as the terminal associated sequence (TAS) were conserved within the control region. The maximum likelihood phylogenetic family tree revealed the divergence of R. tornieri from the basal region of the Rasbora clade, where its evolutionary relationships with other Rasbora members are poorly resolved as indicated by the low bootstrap values. This work acts as window for further population genetics and molecular evolution studies of Rasbora genus in future.

A survey of recently emerged genome-wide computational enhancer predictor tools.

The race for the discovery of enhancers at a genome-wide scale has been on since the commencement of next generation sequencing decades after the discovery of the first enhancer, SV40. A few enhancer-predicting features such as chromatin feature, histone modifications and sequence feature had been implemented with varying success rates. However, to date, there is no consensus yet on the single enhancer marker that can be employed to ultimately distinguish and uncover enhancers from the enormous genomic regions. Many supervised, unsupervised and semi-supervised computational approaches had emerged to complement and facilitate experimental approaches in enhancer discovery. In this review, we placed our focus on the recently emerged enhancer predictor tools that work on general enhancer features such as sequences, chromatin states and histone modifications, eRNA and of multiple feature approach. Comparisons of their prediction methods and outcomes were done across their functionally similar counterparts. We provide some recommendations and insights for future development of more comprehensive and robust tools.

Cough syncope.

Loss of consciousness following cough was first described in 1876 as "laryngeal vertigo" Since then, several hundred cases of what is now most commonly termed cough syncope have been reported, often in association with various medical conditions. Some early authors assumed this entity to be a form of epilepsy, but by the mid-20th century, general consensus reflected that post-tussive syncope was a consequence of markedly elevated intrathoracic pressures induced by coughing. A typical profile of the cough syncope patient emerging from the literature is that of a middle-aged, large-framed or overweight male with obstructive airways disease. Presumably, such an individual would be more likely to generate the extremely high intrathoracic pressures associated with cough-induced fainting. The precise mechanism of cough syncope remains a matter of debate. Theories proposed include various consequences of the marked elevation of intrathoracic pressures induced by coughing: diminished cardiac output causing decreased systemic blood pressure and, consequently, cerebral hypoperfusion; increased cerebrospinal fluid (CSF) pressure causing increased extravascular pressure around cranial vessels, resulting in diminished brain perfusion; or, a cerebral concussion-like effect from a rapid rise in CSF pressure. More recent mechanistic studies suggest a neurally mediated reflex vasodepressor-bradycardia response to cough. Since loss of consciousness is a direct and immediate result of cough, elimination of cough will eliminate the resultant syncopal episodes. Thus, the approach to the patient with cough syncope requires thorough evaluation and treatment of potential underlying causes of cough, as summarized in several recently published cough management guidelines.

Interatrial block in patients with obstructive sleep apnea.

BACKGROUND: Obstructive sleep apnea (OSA) is a common disorder that affects 5% of the adult North American population. It is associated with atrial arrhythmias and stroke. The mechanisms of this association remain unclear. The aim to the study was to identify the factors associated with interatrial block (IAB) among patients with OSA. METHODS: Patients referred for polysomnography were studied. Sleep apnea severity (apnea-hypopnea index [AHI]) was measured in each subject. 12-lead ECGs were scanned and amplified (× 10); P-wave duration and dispersion were measured using a semi-automatic caliper. IAB was defined as a P-wave duration ≥ 120 ms. RESULTS: Data from 180 consecutive patients was examined. Moderate-severe OSA (mean AHI = 56.2 ± 27.9) was present in 144 (OSA group). The remaining 36 had mild or no OSA (mean AHI = 5.6 ± 3.6) and were used as controls. Age distribution between the groups did not differ and there were more males in the OSA group (69.4% vs 47.2%, p = 0.01). Obesity (78.5% vs 39.4%, p < 0.001) and hypertension (51.4% vs 27.8%, p < 0.01) were more prevalent in the OSA group. IAB was more prevalent in patients with moderate-severe OSA (34.7% OSA vs 0% controls, p < 0.001). In linear regression, age and AHI > 30 were independent predictors of maximum P-wave duration (p = 0.001 and p < 0.001, respectively). P-wave dispersion was significantly higher in the severe OSA group (14.6 ± 7.5 for OSA, 8.9 ± 3.1 controls, p < 0.001). CONCLUSIONS: Older age and moderate-severe OSA are predictors of IAB. P-wave dispersion is increased in patients with moderate-severe OSA. This may partly explain the high prevalence of atrial arrhythmias in patients with OSA.

Hydraulic performance of a proposed in situ photocatalytic reactor for degradation of MTBE in water.

Methyl tert-butyl ether (MTBE) groundwater remediation projects often require a combination of technologies resulting in increasing the project costs. A cost-effective in situ photocatalytic reactor design, Honeycomb II, is proposed and tested for its efficiency in MTBE degradation at various flows. This study is an intermediate phase of the research in developing an in situ photocatalytic reactor for groundwater remediation. It examines the effect of the operating variables: air and water flow and double passages through Honeycomb II, on the MTBE removal. MTBE vaporisation is affected by not only temperature, Henry's law constant and air flow to volume ratio but also reactor geometry. The column reactor achieved more than 84% MTBE removal after 8 h at flows equivalent to horizontal groundwater velocities slower than 21.2 cm d⁻¹. Despite the contrasting properties between a photocatalytic indicator methylene blue and MTBE, the reactor efficiency in degrading both compounds showed similar responses towards flow (equivalent groundwater velocity and hydraulic residence time (HRT)). The critical HRT for both compounds was approximately 1 d, which corresponded to a velocity of 21.2 cm d⁻¹. A double pass through both new and used catalysts achieved more than 95% MTBE removal after two passes in 48 h. It also verified that the removal efficiency can be estimated via the sequential order of the removal efficiency of one pass obtained in the laboratory. This study reinforces the potential of this reactor design for in situ groundwater remediation.

Effect of tip size on force measurement in atomic force microscopy.

An atomic force microscope (AFM) has been used to study solvation forces at the solid-liquid interface between highly oriented pyrolytic graphite (HOPG) and the liquids octamethylcyclotetrasiloxane (OMCTS), n-hexadecane (n-C16H34), and n-dodecanol (n-C11H23CH2OH). Oscillatory solvation forces (F) are observed for various measured tip radii (Rtip=15-100 nm). It is found that the normalized force data, F/Rtip, differ between AFM tips with a clear trend of decreasing F/Rtip with increasing Rtip.

Adaptation of an amphibian mucociliary clearance model to evaluate early effects of tobacco smoke exposure.

RATIONALE: Inhaled side-stream tobacco smoke brings in all of its harmful components impairing mechanisms that protect the airways and lungs. Chronic respiratory health consequences are a complex multi-step silent process. By the time clinical manifestations require medical attention, several structural and functional changes have already occurred. The respiratory system has to undergo an iterative process of injury, healing and remodeling with every exposure. METHODS: To have a better understanding of the initial changes that take place when first exposed to environmental tobacco smoke, we have developed an exposure model, using the frog palate that closely represents the features of obstructive airways where ciliary dysfunction and mucus hypersecretion occur. RESULTS: Mucus transport was significantly reduced, even after exposure to the smoke of one cigarette (p < 0.05) and even further with 4-cigarettes exposure (p < 0.001). Morphometric and ultrastructural studies by SEM show extensive areas of tissue disruption. Gelatinase zymography shows activation of MMP9 in mucus from palates exposed to tobacco smoke. CONCLUSIONS: The clearance of mucus on the frog palate is significantly reduced after exposure to environmental tobacco smoke. Cilia and the extracellular matrix are anatomically disrupted. Tobacco smoke triggers an increased activity of matrix metalloproteinases associated with a substantial defoliation of ciliated epithelium. These studies enhance the knowledge of the changes in the mucociliary apparatus that occur initially after exposure to environmental tobacco smoke, with the goal of understanding how these changes relate to the genesis of chronic airway pathologies in humans.