Genomic analysis of Vibrio harveyi strain PH1009, a potential multi-drug resistant pathogen due to acquisition of toxin genes.

In has increasingly been observed that viral and bacterial coinfection frequently occurs among cultured shrimp and this coinfection could exacerbate the disease phenotype. Here, we describe a newly discovered bacterial strain, Vibrio harveyi PH1009 collected from Masbate Island, Philippines that was found to be co-infecting with the White Spot Syndrome virus in a sample of black tiger prawn, Penaeus monodon. The genome of V. harveyi PH1009 was sequenced, assembled, and annotated. Average Nucleotide identity calculation with Vibrio harveyi strains confirmed its taxonomic identity. It is a potential multi-drug and multi-heavy metal resistant strain based on the multiple antibiotic and heavy metal resistance determinants annotated on its genome. Two prophage regions were identified in its genome. One contained genes for Zona occludens toxin (Zot) and Accessory cholera toxin (Ace), essential toxins of toxigenic V. cholerae strains apart from CTX toxins. Pan-genome analysis of V. harveyi strains, including PH1009, revealed an "open" pan-genome for V. harveyi and a core genome mainly composed of genes necessary for growth and metabolism. Phylogenetic tree based on the core genome alignment revealed that PH1009 was closest to strains QT520, CAIM 1754, and 823tez1. Published virulence factors present on the strain QT520 suggest similar pathogenicity with PH1009. However, PH1009 Zot was not found on related strains but was present in strains HENC-01 and CAIM 148. Most unique genes found in the PH1009 strain were identified as hypothetical proteins. Further annotation showed that several of these hypothetical proteins were phage transposases, integrases, and transcription regulators, implying the role of bacteriophages in the distinct genomic features of the PH1009 genome. The PH1009 genome will serve as a valuable genomic resource for comparative genomic studies and in understanding the disease mechanism of the Vibrio harveyi species.

Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines.

The Omicron severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant led to a dramatic global epidemic wave following detection in South Africa in November 2021. The BA.1 Omicron lineage was dominant and responsible for most SARS-CoV-2 outbreaks in countries around the world during December 2021-January 2022, while other Omicron lineages, including BA.2, accounted for the minority of global isolates. Here, we describe the Omicron wave in the Philippines by analysing genomic data. Our results identify the presence of both BA.1 and BA.2 lineages in the Philippines in December 2021, before cases surged in January 2022. We infer that only the BA.2 lineage underwent sustained transmission in the country, with an estimated emergence around 18 November 2021 (95 per cent highest posterior density: 6-28 November), while despite multiple introductions, BA.1 transmission remained limited. These results suggest that the Philippines was one of the earliest areas affected by BA.2 and reiterate the importance of whole genome sequencing for monitoring outbreaks.

Detection and Genome Sequencing of SARS-CoV-2 Variants Belonging to the B.1.1.7 Lineage in the Philippines.

We report the sequencing and detection of 36 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples containing lineage-defining mutations specific to viruses belonging to the B.1.1.7 lineage in the Philippines.

The Green Revolution shaped the population structure of the rice pathogen Xanthomonas oryzae pv. oryzae.

The impact of modern agriculture on the evolutionary trajectory of plant pathogens is a central question for crop sustainability. The Green Revolution replaced traditional rice landraces with high-yielding varieties, creating a uniform selection pressure that allows measuring the effect of such intervention. In this study, we analyzed a unique historical pathogen record to assess the impact of a major resistance gene, Xa4, in the population structure of Xanthomonas oryzae pv. oryzae (Xoo) collected in the Philippines in a span of 40 years. After the deployment of Xa4 in the early 1960s, the emergence of virulent pathogen groups was associated with the increasing adoption of rice varieties carrying Xa4, which reached 80% of the total planted area. Whole genomes analysis of a representative sample suggested six major pathogen groups with distinctive signatures of selection in genes related to secretion system, cell-wall degradation, lipopolysaccharide production, and detoxification of host defense components. Association genetics also suggested that each population might evolve different mechanisms to adapt to Xa4. Interestingly, we found evidence of strong selective sweep affecting several populations in the mid-1980s, suggesting a major bottleneck that coincides with the peak of Xa4 deployment in the archipelago. Our study highlights how modern agricultural practices facilitate the adaptation of pathogens to overcome the effects of standard crop improvement efforts.

Draft Genome Sequence of Vibrio parahaemolyticus Strain PH1339, Which Causes Acute Hepatopancreatic Necrosis Disease in Shrimp in the Philippines.

We report the first draft genome sequence of an acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio parahaemolyticus strain isolated from a Penaeus vannamei sample from the Philippines. The strain carries the genes encoding the Pir-like toxin pair PirAvp and PirBvp.

Draft Genome Sequence of Multidrug-Resistant Vibrio parahaemolyticus Strain PH698, Infecting Penaeid Shrimp in the Philippines.

The emergence of multidrug-resistant bacterial strains in diverse settings has been reported globally. In the Philippine shrimp aquaculture industry, antibiotics are used for the treatment of bacterial diseases during the production cycle. We report the draft genome of Vibrio parahaemolyticus PH698, a multidrug-resistant strain isolated from a Philippine shrimp farm.

Non-additive effects of ACVR2A in preeclampsia in a Philippine population.

BACKGROUND: Multiple interrelated pathways contribute to the pathogenesis of preeclampsia, and variants in susceptibility genes may play a role among Filipinos, an ethnically distinct group with high prevalence of the disease. The objective of this study was to examine the association between variants in maternal candidate genes and the development of preeclampsia in a Philippine population. METHODS: A case-control study involving 29 single nucleotide polymorphisms (SNPs) in 21 candidate genes was conducted in 150 patients with preeclampsia (cases) and 175 women with uncomplicated normal pregnancies (controls). Genotyping for the GRK4 and DRD1 gene variants was carried out using the TaqMan Assay, and all other variants were assayed using the Sequenom MassARRAY Iplex Platform. PLINK was used for SNP association testing. Multilocus association analysis was performed using multifactor dimensionality reduction (MDR) analysis. RESULTS: Among the clinical factors, older age (P <  1 × 10-4), higher BMI (P <  1 × 10-4), having a new partner (P = 0.006), and increased time interval from previous pregnancy (P = 0.018) associated with preeclampsia. The MDR algorithm identified the genetic variant ACVR2A rs1014064 as interacting with age and BMI in association with preeclampsia among Filipino women. CONCLUSIONS: The MDR algorithm identified an interaction between age, BMI and ACVR2A rs1014064, indicating that context among genetic variants and demographic/clinical factors may be crucial to understanding the pathogenesis of preeclampsia among Filipino women.

Targeted next generation sequencing of the entire vitamin D receptor gene reveals polymorphisms correlated with vitamin D deficiency among older Filipino women with and without fragility fracture.

This study aimed to discover genetic variants in the entire 101 kB vitamin D receptor (VDR) gene for vitamin D deficiency in a group of postmenopausal Filipino women using targeted next generation sequencing (TNGS) approach in a case-control study design. A total of 50 women with and without osteoporotic fracture seen at the Philippine Orthopedic Center were included. Blood samples were collected for determination of serum vitamin D, calcium, phosphorus, glucose, blood urea nitrogen, creatinine, aspartate aminotransferase, alanine aminotransferase and as primary source for targeted VDR gene sequencing using the Ion Torrent Personal Genome Machine. The variant calling was based on the GATK best practice workflow and annotated using Annovar tool. A total of 1496 unique variants in the whole 101-kb VDR gene were identified. Novel sequence variations not registered in the dbSNP database were found among cases and controls at a rate of 23.1% and 16.6% of total discovered variants, respectively. One disease-associated enhancer showed statistically significant association to low serum 25-hydroxy vitamin D levels (Pearson chi-square P-value=0.009). The transcription factor binding site prediction program PROMO predicted the disruption of three transcription factor binding sites in this enhancer region. These findings show the power of TNGS in identifying sequence variations in a very large gene and the surprising results obtained in this study greatly expand the catalog of known VDR sequence variants that may represent an important clue in the emergence of vitamin D deficiency. Such information will also provide the additional guidance necessary toward a personalized nutritional advice to reach sufficient vitamin D status.

VEGF-A and VEGFR1 SNPs associate with preeclampsia in a Philippine population.

The vascular endothelial growth factor (VEGF) family is important for establishing normal pregnancy, and related single nucleotide polymorphisms (SNPs) are implicated in abnormal placentation and preeclampsia. We evaluated the association between preeclampsia and several VEGF SNPs among Filipinos, an ethnically distinct group with high prevalence of preeclampsia. The genotypes and allelic variants were determined in a case-control study (191 controls and 165 preeclampsia patients) through SNP analysis of VEGF-A (rs2010963, rs3025039) and VEGF-C (rs7664413) and their corresponding receptors VEGFR1 (rs722503, rs12584067, rs7335588) and VEGFR3 (rs307826) from venous blood DNA. VEGF-A rs3025039 C allele has been shown to associate with preeclampsia (odds ratio of 1.648 (1.03-2.62)), while the T allele bestowed an additive effect for the maintenance of normal, uncomplicated pregnancy and against the development of preeclampsia (odds ratio of 0.62 (0.39-0.98)). VEGFR1 rs722503 is associated with preeclampsia occurring at or after the age of 40 years. The results showed that genetic variability of VEGF-A and VEGFR1 are important in the etiology of preeclampsia among Filipinos.

Acute hepatopancreatic necrosis disease (AHPND) outbreaks in Penaeus vannamei and P. monodon cultured in the Philippines.

Acute hepatopancreatic necrosis disease (AHPND) has recently emerged as a serious disease of cultured shrimp. It has also been described as early mortality syndrome (EMS) due to mass mortalities occurring within 20 to 30 d after stocking of ponds with postlarvae. Here, Penaeus vannamei and Penaeus monodon from shrimp farms in the Philippines were examined for the toxin-producing strain of Vibrio parahaemolyticus due to AHPND-like symptoms occurring in marketable size shrimp. In the P. vannamei, histology revealed typical AHPND pathology, such as sloughing of undifferentiated cells in the hepatopancreatic tubule epithelium. Analysis using the IQ2000 AHPND/EMS Toxin 1 PCR test generated 218 bp and 432 bp amplicons confirmative of the toxin-producing strain of V. parahaemolyticus among shrimp sampled from 8 of 9 ponds. In the P. monodon, histology revealed massive sloughing of undifferentiated cells of the hepatopancreatic tubule epithelium in the absence of basophilic bacterial cells. PCR testing generated the 2 amplicons confirmatory for AHPND among shrimp sampled from 5 of 7 ponds. This study confirms the presence of AHPND in P. vannamei and P. monodon farmed in the Philippines and suggests that the disease can also impact late-stage juvenile shrimp.

Prior individual training and self-organized queuing during group emergency escape of mice from water pool.

We study the impact of prior individual training during group emergency evacuation using mice that escape from an enclosed water pool to a dry platform via any of two possible exits. Experimenting with mice avoids serious ethical and legal issues that arise when dealing with unwitting human participants while minimizing concerns regarding the reliability of results obtained from simulated experiments using 'actors'. First, mice were trained separately and their individual escape times measured over several trials. Mice learned quickly to swim towards an exit-they achieved their fastest escape times within the first four trials. The trained mice were then placed together in the pool and allowed to escape. No two mice were permitted in the pool beforehand and only one could pass through an exit opening at any given time. At first trial, groups of trained mice escaped seven and five times faster than their corresponding control groups of untrained mice at pool occupancy rate ρ of 11.9% and 4%, respectively. Faster evacuation happened because trained mice: (a) had better recognition of the available pool space and took shorter escape routes to an exit, (b) were less likely to form arches that blocked an exit opening, and (c) utilized the two exits efficiently without preference. Trained groups achieved continuous egress without an apparent leader-coordinator (self-organized queuing)-a collective behavior not experienced during individual training. Queuing was unobserved in untrained groups where mice were prone to wall seeking, aimless swimming and/or blind copying that produced circuitous escape routes, biased exit use and clogging. The experiments also reveal that faster and less costly group training at ρ = 4%, yielded an average individual escape time that is comparable with individualized training. However, group training in a more crowded pool (ρ = 11.9%) produced a longer average individual escape time.

A bioinformatics survey for conotoxin-like sequences in three turrid snail venom duct transcriptomes.

The repertoire of venom peptides produced by Conoidean snails has shown to be useful for therapeutic and neuropharmacologic applications. Despite their dominance in terms of species number, the Family Turridae is the least studied among their other Conoidean counterparts. They provide a vast resource of pharmacological material only hindered by the inaccessibility of their deep water habitat for sample collection and their small size that allows only a limited amount of material from their venom duct amenable for analysis. Using high-throughput transcriptome sequencing, toxin transcripts can be extracted bioinformatically to fast-track toxin discovery. This approach was utilized on the venom duct transcriptomes of three species of turrids: Unedogemmula bisaya, Crassispira cerithina, and Gemmula speciosa and resulted in the discovery of 41, 22, and 74 putative turrid toxin genes, respectively. Comparisons among these turrid toxin genes to conotoxins show (i) similar superfamily precursors between conotoxins and turrid toxins for the classes D, I2, L, M, O1, O2, and P, (ii) a wider range of peptide lengths of up to 190 amino acids long for mature turritoxin, and (iii) nondisulfide-rich turritoxins with the B2 signal sequence. Novel superfamilies and cysteine frameworks including a novel 14-cysteine residue framework were also obtained.

Superantigen involvement and susceptibility factors in Kawasaki disease: profiles of TCR Vß2+ T cells and HLA-DRB1, TNF-α and ITPKC genes among Filipino patients.

Superantigens and genetic factors may play roles in the etiology and susceptibility to Kawasaki disease (KD). To investigate these roles, percentages of TCR-Vß2+ T cells were compared by flow cytometry using anti-Vß2 monoclonal antibodies and genotyping was done on HLA-DRB1 exon 2, the -308 site of the TNF-α promoter region, and ITPKC SNP rs28493229 by polymerase chain reaction followed by direct sequencing. There were higher percentages of Vß2+ T-cells in KD patients (9.5 ± 2.15%) compared to healthy controls (7.25 ± 1.48%) (P<0.05, Student's t-test, n=6-8/group). However, no polymorphisms were observed in exon 2 of HLA-DRB1 and in the -308 region of the TNF-α promoter. The ITPKC SNP rs28493229 G/C polymorphism was observed in 1 KD patient and 4 healthy controls. This study suggests that KD etiology may be associated with a superantigen and that HLA-DRB1 exon2, TNF-α -308 region and ITPKC SNP rs28493229 may not be associated with KD. This is the first study investigating Vß2+ T cells and candidate genes involvement among Filipino KD patients.

Sorting nexin 1 loss results in D5 dopamine receptor dysfunction in human renal proximal tubule cells and hypertension in mice.

The peripheral dopaminergic system plays a crucial role in blood pressure regulation through its actions on renal hemodynamics and epithelial ion transport. The dopamine D5 receptor (D(5)R) interacts with sorting nexin 1 (SNX1), a protein involved in receptor retrieval from the trans-Golgi network. In this report, we elucidated the spatial, temporal, and functional significance of this interaction in human renal proximal tubule cells and HEK293 cells stably expressing human D(5)R and in mice. Silencing of SNX1 expression via RNAi resulted in the failure of D(5)R to internalize and bind GTP, blunting of the agonist-induced increase in cAMP production and decrease in sodium transport, and up-regulation of angiotensin II receptor expression, of which expression was previously shown to be negatively regulated by D(5)R. Moreover, siRNA-mediated depletion of renal SNX1 in C57BL/6J and BALB/cJ mice resulted in increased blood pressure and blunted natriuretic response to agonist in salt-loaded BALB/cJ mice. These data demonstrate a crucial role for SNX1 in D(5)R trafficking and that SNX1 depletion results in D(5)R dysfunction and thus may represent a novel mechanism for the pathogenesis of essential hypertension.

G protein-coupled receptor kinase 4 (GRK4) regulates the phosphorylation and function of the dopamine D3 receptor.

During conditions of moderate sodium excess, the dopaminergic system regulates blood pressure and water and electrolyte balance by engendering natriuresis. Dopamine exerts its effects on dopamine receptors, including the dopamine D(3) receptor. G protein-coupled receptor kinase 4 (GRK4), whose gene locus (4p16.3) is linked to essential hypertension, desensitizes the D(1) receptor, another dopamine receptor. This study evaluated the role of GRK4 on D(3) receptor function in human proximal tubule cells. D(3) receptor co-segregated in lipid rafts and co-immunoprecipitated and co-localized in human proximal tubule cells and in proximal and distal tubules and glomeruli of kidneys of Wistar Kyoto rats. Bimolecular fluorescence complementation and confocal microscopy revealed that agonist activation of the receptor initiated the interaction between D(3) receptor and GRK4 at the cell membrane and promoted it intracellularly, presumably en route to endosomal trafficking. Of the four GRK4 splice variants, GRK4-gamma and GRK4-alpha mediated a 3- and 2-fold increase in the phosphorylation of agonist-activated D(3) receptor, respectively. Inhibition of GRK activity with heparin or knockdown of GRK4 expression via RNA interference completely abolished p44/42 phosphorylation and mitogenesis induced by D(3) receptor stimulation. These data demonstrate that GRK4, specifically the GRK4-gamma and GRK4-alpha isoforms, phosphorylates the D(3) receptor and is crucial for its signaling in human proximal tubule cells.

Self-organized queuing and scale-free behavior in real escape panic.

Numerical investigations of escape panic of confined pedestrians have revealed interesting dynamical features such as pedestrian arch formation around an exit, disruptive interference, self-organized queuing, and scale-free behavior. However, these predictions have remained unverified because escape panic experiments with real systems are difficult to perform. For mice escaping out of a water pool, we found that for a critical sampling rate the escape behavior exhibits the predicted features even at short observation times. The mice escaped via an exit in bursts of different sizes that obey exponential and (truncated) power-law distributions depending on exit width. Oversampling or undersampling the mouse escape rate prevents the observation of the predicted features. Real systems are normally subject to unavoidable constraints arising from occupancy rate, pedestrian exhaustion, and nonrigidity of pedestrian bodies. The effect of these constraints on the dynamics of real escape panic is also studied.