Journal Articles - UP - MSI
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- MPA-FishMApp – a citizen science app that simplifies monitoring of coral reef fish density and biomass in marine protected areasAbesamis, Rene; Balingit, Rodel; de Castro, Romulo; Aguila, Raphael Nelo; Cabiguin, Maryjune; Villagracia, Julius; Susmeña, Marynoll; Montemar, Mario Neil; Yocor, Antonio (National Fisheries Research and Development Institute, 2022-12)Monitoring changes in fish density and biomass inside marine protected areas (MPAs) through fish visual census (FVC) can determine if MPAs are achieving their goal of promoting fish population recovery. Simplified FVC methods have been developed for citizen scientists to enable them to monitor fish populations in MPAs. However, MPA monitoring programs led by local stakeholders remain rare and difficult to sustain due to technical barriers related to FVC data management. Here, we describe and evaluate a novel online app called MPA-FishMApp, which we developed to help stakeholders of MPAs that protect coral reefs in the Philippines efficiently store, analyze, and visualize FVC data. MPA-FishMApp is coupled to a simplified FVC method wherein the observer records only 21 reef fish species groups during surveys. The app provides a simple data entry interface, cloud storage, and algorithms to estimate fish density and biomass. Spatial and temporal trends in fish density and biomass can be instantaneously visualized in the app based on relative importance to fisheries. Field testing suggested that the MPA-FishMApp methodology (simplified FVC and app) is sensitive enough to detect qualitative patterns showing differences in density and biomass that may develop between MPAs and fished sites, especially in fishes that are highly important to fisheries. However, users must have sufficient training and experience in simplified FVC to produce reliable data. MPA-FishMApp may help reverse the lack of monitoring in MPAs across the Philippines and offers an accessible, transparent, and auditable venue for collaboration between citizen scientists and professional scientists.
- A conserved biosynthetic gene cluster is regulated by quorum sensing in a shipworm symbiontRobes, Jose Miguel D.; Altamia, Marvin A.; Murdock, Ethan G.; Concepcion, Gisela; Haygood, Margo G.; Puri, Aaron W. (American Society for Microbiology, 2022-06-14)Bacterial symbionts often provide critical functions for their hosts. For example, wood-boring bivalves called shipworms rely on cellulolytic endosymbionts for wood digestion. However, how the relationship between shipworms and their bacterial symbionts is formed and maintained remains unknown. Quorum sensing (QS) often plays an important role in regulating symbiotic relationships. We identified and characterized a QS system found in Teredinibacter sp. strain 2052S, a gill isolate of the wood-boring shipworm Bactronophorus cf. thoracites. We determined that 2052S produces the signal N-decanoyl-l-homoserine lactone (C10-HSL) and that this signal controls the activation of a biosynthetic gene cluster colocated in the symbiont genome that is conserved among all symbiotic Teredinibacter isolates. We subsequently identified extracellular metabolites associated with the QS regulon, including ones linked to the conserved biosynthetic gene cluster, using mass spectrometry-based molecular networking. Our results demonstrate that QS plays an important role in regulating secondary metabolism in this shipworm symbiont. This information provides a step toward deciphering the molecular details of the relationship between these symbionts and their hosts. Furthermore, because shipworm symbionts harbor vast yet underexplored biosynthetic potential, understanding how their secondary metabolism is regulated may aid future drug discovery efforts using these organisms.
- Somatostatin venom analogs evolved by fish-hunting cone snails: From prey capture behavior to identifying drug leadsRamiro, Iris Bea L.; Bjørn-Yoshimoto, Walden E.; Imperial, Julita S.; Gajewiak, Joanna; Salcedo, Paula Flórez; Watkins, Maren; Taylor, Dylan; Resager, William; Ueberheide, Beatrix; Bräuner-Osborne, Hans; Whitby, Frank G.; Hill, Christopher P.; Martin, Laurent F.; Patwardhan, Amol; Concepcion, Gisela; Olivera, Baldomero M.; Safavi-Hemami, Helena (American Association for the Advancement of Science, 2022-03-25)Somatostatin (SS) is a peptide hormone with diverse physiological roles. By investigating a deep-water clade of fish-hunting cone snails, we show that predator-prey evolution has generated a diverse set of SS analogs, each optimized to elicit specific systemic physiological effects in prey. The increased metabolic stability, distinct SS receptor activation profiles, and chemical diversity of the venom analogs make them suitable leads for therapeutic application, including pain, cancer, and endocrine disorders. Our findings not only establish the existence of SS-like peptides in animal venoms but also serve as a model for the synergy gained from combining molecular phylogenetics and behavioral observations to optimize the discovery of natural products with biomedical potential.
- Genomic and targeted approaches unveil the cell membrane as a major target of the antifungal cytotoxin amantelide AElsadek, Lobna A.; Matthews, James H.; Nishimura, Shinichi; Nakatani, Takahiro; Ito, Airi; Gu, Tongjun; Luo, Danmeng; Salvador-Reyes, Lilibeth A.; Paul, Valerie J.; Kakeya, Hideaki; Luesch, Hendrik (Wiley, 2021-03-23)Amantelide A, a polyhydroxylated macrolide isolated from a marine cyanobacterium, displays broad-spectrum activity against mammalian cells, bacterial pathogens, and marine fungi. We conducted comprehensive mechanistic studies to identify the molecular targets and pathways affected by amantelide A. Our investigations relied on chemical structure similarities with compounds of known mechanisms, yeast knockout mutants, yeast chemogenomic profiling, and direct biochemical and biophysical methods. We established that amantelide A exerts its antifungal action by binding to ergosterol-containing membranes followed by pore formation and cell death, a mechanism partially shared with polyene antifungals. Binding assays demonstrated that amantelide A also binds to membranes containing epicholesterol or mammalian cholesterol, thus suggesting that the cytotoxicity to mammalian cells might be due to its affinity to cholesterol-containing membranes. However, membrane interactions were not completely dependent on sterols. Yeast chemogenomic profiling suggested additional direct or indirect effects on actin. Accordingly, we performed actin polymerization assays, which suggested that amantelide A also promotes actin polymerization in cell-free systems. However, the C-33 acetoxy derivative amantelide B showed a similar effect on actin dynamics in vitro but no significant activity against yeast. Overall, these studies suggest that the membrane effects are the most functionally relevant for amantelide A mechanism of action.This research was supported by the National Institutes of Health (grant R01CA172310 to H.L.), the Debbie and Sylvia DeSantis Chair Professorship (H.L), and a Grant-in Aid for Scientific Research (no. 17H06401 to S.N. and H.K.) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. L.E. was supported by the NIH/NIGMS T32GM136583 “Chemistry-Biology Interface Training Program at the University of Florida”. We thank Dr. Yanping Zhang (University of Florida) from the UF ICBR NextGen DNA Sequencing core facility for carrying out the nextgeneration sequencing, Dr. Maya Schuldiner (Weizmann Institute of Science, Israel) for providing the triple yeast deletion library, Dr. Kaoru Takegawa (Kyushu University, Japan) for providing the ergosterol mutants, Dr. Charles Boone laboratory (University of Toronto, Canada) for providing the wild-type S. cerevisiae Y7092 and Dr. Kalina Atanasova (CNPD3, University of Florida) for assistance with the imaging.
- Geomorphological and sedimentological records of recent storms on a volcaniclastic coast in Bicol, PhilippinesSoria, Janneli Lea A.; Switzer, Adam D.; Pile, Jeremy; Siringan, Fernando P.; Brill, Dominik; Daag, Arturo (Elsevier, 2021-08-01)Typhoon Durian in November 2006 was most notable for a series of devastating lahars that buried communities at the base of Mayon volcano in Bicol, Philippines. Typhoon Durian delivered extreme rainfall that remobilized volcanic debris that caused more than ~1200 deaths and extensive property damage. Although not as deadly as the lahar, Typhoon Durian also generated a storm surge that caused localized dune breaching on Malinao barrier sand spit in Lagonoy Gulf. In the absence of instrumental data of the storm surge, we used the geomorphical and sedimentary imprints including erosion scarps, washover fans and terraces to infer the inundation heights on the barrier spit. The surface elevations of washover fans, terraces and relic dunes indicate inundation heights above 1.5 m but not exceeding 3 m. Typhoon Durian's overwash deposit is characterized by typical washover fan stratigraphy, and exhibits horizontal to sub-horizontal lamination on the front to mid-fan and foreset stratification near the fan terminus. Subsurface stratigraphy using shore-normal ground penetrating radar (GPR) imaging reveals at least two buried erosional surfaces farther inland from the erosional surface of Typhoon Durian. Similar to Durian, the older erosional surfaces were probably sustained from previous typhoons. We infer that episodic erosional events most likely have repeatedly disrupted the prograding development of the Malinao barrier spit. Typhoon Durian highlights the exposure of volcanic landscapes to multiple hazards from cyclone landfall.This work comprises Earth Observatory of Singapore contribution no. 169. This research is supported by the Singapore National Research Foundation fellowship scheme (Grant No: NRF-RF2010-04) and the Singapore Ministry of Education under the Research Centres of Excellence initiative. This paper is a contribution to IGCP Project 639 Sea-Level Changes from Minutes to Millennia. We thank German Gonzaga of the Malinao Local Government Unit who facilitated our access to the study site. We also appreciate Cabria family for being our hospitable host during the series of field campaigns. We thank Mr. Raul Capistrano on behalf of NAMRIA for providing tide gauge data, and the Mines and Geosciences Bureau for granting us permit to transport sediments. We are grateful to Joan Reotita, Ronald Lloren, Yo Muan, Lester Valle, Arlene Tengonciang, Mabelline Cahulogan, Ariel Malonda, Antonio Ceres and Elmer Cas for their generous help in collecting field data.
- Utility of low-cost recreational-grade echosounders in imaging and characterizing bubbly coastal submarine groundwater dischargeGabuyo, Mary Rose P.; Siringan, Fernando P. (Elsevier, 2022-01)Despite the growing knowledge on the significance of submarine groundwater discharge (SGD), mapping its occurrence is a continuing challenge. This study explores the capability and applicability of low-cost, off-the-shelf, recreational-grade echosounders (RGESs) to image different types and locate point sources of bubbly coastal SGD. Standard and systematic methodologies for efficient imaging and processing were established. The use of RGES was validated using a research-grade side scan sonar (RGSSS), continuous resistivity profiling, conductivity-temperature-depth casting, and MantaCam and SCUBA diving surveys. Lower frequencies (77/83 kHz) of RGESs showed more distinct acoustic signatures of bubbly SGD, as these were nearly the same as the effective resonance frequency of the bubbles. The clusters of bubbly discharges have higher backscatter strength than the water column noise, resulting in the definitive and convenient manual detection of SGD features. Hence, showing more accurate point sources of SGD. Three types of known SGD occurrence were identified and characterized based on acoustic behavior and spatial distribution: 1) sparse, discrete and sporadic discharge over wide area, 2) curtain, high and continuous bubble concentrations from widespread discharge, and 3) spring, direct bubble discharge from intense seafloor degassing at a single point source. These results showed that RGES provides a good alternative for more efficient and cost-effective preliminary coastal SGD works. Additional research on areas with water-dominated discharge but no bubbling is recommended.
- Chemical characteristics and gelling properties of agar from two Philippine Gracilaria spp. (Gracilariales, Rhodophyta)Montaño, Nemesio E.; Villanueva, Ronald D.; Romero, Jumelita B. (Springer, 1999)The chemical structure of agars extracted from Philippine Gracilaria arcuata and G. tenuistipitata were determined by NMR and infrared spectroscopy. Agar with alternating 3-linked 6-O-methyl-β-D-galactopyranosyl and 4-linked 3,6-anhydro-2- O-methyl-α-L-galactopyranosyl units was isolated from G. arcuata, while the agar from G. tenuistipitata possesses the regular agarobiose repeating unit with partial methylation at the 6-position of the D-galactosyl residues. Both agars exhibit sulphate substitution at varying positions in the polymer. Chemical analyses reveal higher 3,6-anhydrogalactose and lower sulphate contents in alkali-modified than in native agar from both samples. Also, alkali modification enhanced agar gel strength and syneresis. Native G. arcuata agar produces a viscous solution (2000 cP at 75 °C) with a high gelling point (>60 °C) that forms a soft gel even after alkali modification (gel strength: <300 g cm−2). On the other hand, the agar from G. tenuistipitata exhibits gel qualities typical of most Gracilaria agars.
- Seafloor structures and static stress changes associated with two recent earthquakes in offshore southern Batangas, PhilippinesSarmiento, Keanu Jershon S.; Aurelio, Mario A.; Flores, Paul Caesar M.; Carrillo, Anne Drew V.; Marfito, Bryan J.; Abigania, Maria Isabel T.; Daag, Arturo S.; Siringan, Fernando P. (Frontiers Media SA, 2022-02-02)The 1994 Mw 7.1 Mindoro Earthquake and the 2017 Mw 5.9 Batangas Earthquake Sequence both occurred in offshore southern Batangas and devastated southern Luzon and Mindoro. These earthquakes exhibited NW-striking right-lateral slip in an area presumably defined by a WNW-striking left-lateral fault, therefore implying the existence of previously unmapped offshore faults. High resolution multibeam bathymetry grid and subbottom profiles revealed a conjugate strike-slip fault system under an approximately EW-directed extension. NW-striking right-lateral faults (F1 Faults: Central Mindoro Fault, Aglubang River Fault, and Batangas Bay Fault System) bound the western part of the study area. On the other hand, a series of almost parallel NE-trending left-lateral and normal faults (F2 Faults: Macolod Corridor, North Verde Fault System, Central Verde Fault System, South Verde Fault, and Northeast Mindoro Fault System) approach the F1 faults from the northeast. The distribution of the 1994 and 2017 earthquakes suggests that the possible rupture areas for these events are the Aglubang River Fault and the southwest Batangas Bay Fault System, respectively. These two traces appear to be connected and a restraining bend is suggested to have acted as a rupture barrier between the two events. Coulomb stress transfer modeling showed that the 1994 earthquake promoted the failure of the 2017 earthquake. Furthermore, results from the stress transfer models showed stress increase on the F1 faults (Batangas Bay Fault System and Central Mindoro Fault) and the northern F2 faults (North Verde Fault System and Central Verde Fault System). The newly recognized faults redefine the knowledge of the neotectonic structure of the area but are still consistent with the ongoing east-west extension in southern Luzon and the overall extension in northern Central Philippines. These faults pose seismic hazards, and more studies are needed to determine their seismogenic potential.The authors would like to thank the National Mapping and Resource Information Authority (NAMRIA) for generously providing the multibeam bathymetry data and the Department of Science and Technology - Philippine Institute of Volcanology and Seismology for providing the earthquake catalog. The research party and the ship crew of M/Y Panata of the University of the Philippines Marine Science Institute is also thanked for their assistance in data collection during the research cruise in Verde Island Passage last July 2019. The authors are very much grateful to editor GR and reviewers YL and WF for providing valuable comments that greatly improved this manuscript. Topography data is from JAXA ALOS World 3D–30 m (AW3D30) DEM (https://www.eorc.jaxa.jp/ALOS/en/aw3d30/index.htm) while global bathymetry is from the GEBCO_2020 grid (https://www.gebco.net/data_and_products/gridded_bathymetry_data/). Focal mechanism solutions were obtained from Harvard GCMT (https://www.globalcmt.org/).
- Cryptic haploid stages in the life cycle of Leathesia marina (Chordariaceae, Phaeophyceae) under in vitro culturePoza, Ailen M.; Santiañez, Wilfred John E.; Croce, M. Emilia; Gauna, M. Cecilia; Kogame, Kazuhiro; Parodi,Elisa R. (2020-05-28)We evaluated the life cycle of Leathesia marina through molecular analyses, culture studies, morphological observations, and ploidy measurements. Macroscopic sporophytes were collected from two localities in Atlantic Patagonia and were cultured under long-day (LD) and short-day (SD) conditions. Molecular identification of the microscopic and macroscopic phases was performed through the cox3 and rbcL genes and the phylogeny was assessed on the basis of single gene and concatenated datasets. Nuclear ploidy of each phase was estimated from the DNA contents of individual nuclei through epifluorescence microscopy and flow cytometry. Molecular results confirmed the identity of the Argentinian specimens as L. marina and revealed their conspecificity with L. marina from New Zealand, Germany, and Japan. The sporophytic macrothalli (2n) released mitospores from plurilocular sporangia, which developed into globular microthalli (2n), morphologically similar to the sporophytes but not in size, constituting a generation of small diploid thalli, with a mean fluorescent nuclei cross-sectional area of 3.21 ± 0.7 μm2. The unilocular sporangia released meiospores that developed two morphologically different types of microthalli: erect branched microthalli (n) with a nuclear area of 1.48 ± 0.07 µm2 that reproduces asexually, and prostrate branched microthalli (n) with a nuclear area of 1.24 ± 0.10 µm2 that reproduces sexually. The prostrate microthalli released gametes in LD conditions, which merged and produced macroscopic thalli with a nuclear cross-sectional area of 3.45 ± 0.09 µm2. Flow cytometry confirmed that the erect and prostrate microthalli were haploid and that the globular microthalli and macrothalli were diploid.
- Karyology and agar analysis of the agarophyte Gelidiella acerosa (Forsskål) Feldmannet Hamel from the PhilippinesKapraun, Donald F.; Ganzon-Fortes, Edna; Bird, Kimon T.; Trono, Gavino; Breden, Chris (Springer, 1994-12)Microspectrophotometry with the DNA-localizing fluorochrome DAPI demonstrated ploidy level differences in tetrasporophytic and presumptive gametophytic phases of Gelidiella acerosa from the Philippines. Comparison of mean nuclear DNA (I f ) values to chicken erythrocytes (RBC) resulted in an estimate of 0.32 pg/2 C genome. Karyological studies with aceto-orcein revealed a chromosome complement of six bivalents during diakinesis of tetrasporocytes. The agar yield ranges from 13–24% dry weight, depending on the method of extraction. Agar extraction in 1 N NaOH resulted in an increased gel strength of 189 g cm−2 at 1.5% concentration. Infrared spectroscopy indicated a relatively high sulfate content in native agar. The low (61 °) melting temperature is indicative of high sulfation and small molecular size.