Journal Articles - UP - MSI
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- Acetic acid pretreatment in agar extraction of Philippine Gelidiella acerosa (Forsskaal) Feldmann et Hamel (Rhodophyta, Gelidiales)Roleda, M. Y.; Montaño, N. E.; Ganzon-Fortes, E. T.; Villanueva, R. D. (Walter de Gruyter GmbH, 1997)Application of different pre-extraction treatments and extraction methods were used to isolate agar from Gelidiella acerosa. Acetic acid pretreatment entailed soaking the sample in 0.5% acetic acid for 1 hour at 16-20 °C. Alkali pretreatment entailed treatment with l N NaOH at 90°C for 1 hour and eutralization in weak acid for another hour at 16-20 °C. Native agar was extracted directly from air dried samples. One hour extraction using steam pressure at 15-2PSI and boiling at 100 °C in a water bath were applied respectively. Comparative analysis showed that the acetic acid pretreated and autoclaved sample gave the highest agar yield (29.8 ± 2.41%) and gel strength (676 ± 4 g cm"2) among the extraction methods applied. Other physico-chemical properties of acid-modified agar were measured. Relative viscosity of a 1.0% solution at 65 °C ranged from 5-70 cps. A melting temperature of 90-98 °C is comparable to that of the agars from most Gelidiales, while a gelling temperature of 42-47 °C is relatively high which is suspected to be associated with a number of chemical variables masking or altering the basic structural unit of agar. Temperature hysteresis (difference between gelling and melting temperatures) at 48—50 °C was comparable to that of Difco Bacto agar tested at 50 °C.
- Characterization of the hidden break in giant clam 28S ribosomal RNATan, Keana; Conaco, Cecilia (Oxford University Press, 2021-09)The molluscan 28S ribosomal RNA (rRNA) naturally cleaves into two fragments of similar size as 18S rRNA. This phenomenon, known as the hidden break, has been described in many other protostome species. Here, we characterize the 28S rRNA hidden break region in seven giant clam species, Tridacna gigas, T. derasa, T. maxima, T. noae, T. crocea, Hippopus hippopus and H. porcellanus. We confirm that the break consistently occurs in giant clams and is observed in all tissues and developmental stages. The region of the giant clam 28S rRNA break is located at a position homologous to the well-characterized 28S rRNA break in insects. High AU content and a stem–loop secondary structure in the region may contribute to fragmentation of the 28S rRNA molecule. An awareness of the existence of the hidden break in molluscs, such as the giant clams, which are emerging systems for understanding how environmental change affects life in the ocean, will facilitate progress of RNA sequencing-based analyses that currently rely on standard RNA profiles as a measure of sample integrity.The authors would like to thank Dr Ronnie Estrellada of the Semirara Marine Laboratory and Hatchery for generously providing giant clam samples, the Bolinao Marine Laboratory for providing access to the Silaqui Island Giant Clam Ocean Nursery and Niño Dan Posadas for sharing sponge RNA. This work was supported by a grant to C.C. from the Philippine Council for Agriculture, Aquaculture and Natural Resources Research and Development of the Department of Science and Technology (grant no. QMSR-MRRD-MEC-314-1545).
- Assessing the viability of commercial media for the mass culture of Chaetoceros muelleriCabanayan-Soy, Rona; de Peralta, Glycinea; Juinio–Meñez, Marie Antonette (National Fisheries Research and Development Institute, 2021-12)The microalgae Chaetoceros muelleri is considered a highly nutritious feed for the cultured larvae of the tropical sea cucumber Holothuria scabra. Due to the cost of analytical grade culture media used in the production of C. muelleri, there is a need to evaluate cheap alternative commercial media to decrease the cost of producing quality live microalgal food. In this study, two different indoor batch culture systems (1 L glass bottles and 10 L plastic carboys) were used to evaluate the effectiveness of two conventional (modified F/2 and Walne’s) and one commercial (Epizyme AGP complete) microalgal culture media. Results of the 1 L glass bottle experiment showed that the peak cell density of C. muelleri in AGP (1,241 ± 116 x 104 cells ml-1) was not significantly different from the modified F/2 (1,584 ± 41 x 104 cells ml-1) and Walne’s medium (1,319 ± 162 x 104 cells ml-1) (Kruskal-Wallis test, p=0.78). Likewise, in the plastic carboy experiment, the maximum cell density of C. muelleri in Walne’s medium (750 ± 144 x 104 cells ml-1) and F/2 medium (653 ± 79 x 104 cells ml-1) were higher, but not significantly different from AGP (496 ± 184 x 104 cells ml-1) (Kruskal-Wallis test, p=0.43). The highest growth rate in the glass bottle cultures was the modified F/2 (0.38 div day-1), while AGP was the lowest (0.34 div. day-1). On the other hand, in carboy culture, AGP was higher (0.17 div.day-1) compared to modified F/2 (0.15 div. day-1) and Walne’s medium (0.13 div. day-1). The exponential growth phase was similar in the glass bottles, while in the carboy, the exponential phase was reached at a shorter time in the AGP treatment than those in the modified F/2 and Walne’s media. The findings showed that AGP medium is an adequate alternative to replace the conventional media (modified F/2 and Walne’s) during the secondary stock culture for C. muelleri. The viability of using cheaper and more readily available commercial AGP media for the indoor culture production of C. muelleri can contribute to cost-effective scaling-up of the hatchery production of quality H. scabra larvae and early juveniles.The authors would like to thank Dr. Rene Abesamis for his valuable comments and the two anonymous reviewers for their suggestions to improve the manuscript. We are also grateful for the guidance of Ms. Elsie Tech in improving the microalgal cultures and providing valuable inputs for this paper. We also thank the Sea Cucumber Research Team and the staff of the University of the Philippines - Marine Science Institute, Bolinao Marine Laboratory for their support and assistance during the conduct of the study. We would also like to acknowledge the Department of Science and Technology Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development (DOST-PCAARRDQSR-MR-CUC.02.02) and the Australian Centre for International Agricultural Research (ACIAR – FIS/2003/059) for the financial support in the conduct of this study.
- Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu SeaMendiola, Michael John R.; Ravago‐Gotanco, Rachel (Wiley, 2021-05-04)Connectivity of marine populations is shaped by complex interactions between biological and physical processes across the seascape. The influence of environmental features on the genetic structure of populations has key implications for the dynamics and persistence of populations, and an understanding of spatial scales and patterns of connectivity is crucial for management and conservation. This study employed a seascape genomics approach combining larval dispersal modeling and population genomic analysis using single nucleotide polymorphisms (SNPs) obtained from RADseq to examine environmental factors influencing patterns of genetic structure and connectivity for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea. Dispersal simulations reveal widespread but asymmetric larval dispersal influenced by persistent southward and westward surface circulation features in the Sulu Sea. Despite potential for widespread dispersal across the Sulu Sea, significant genetic differentiation was detected among eight populations based on 1,655 SNPs (FST = 0.0057, p < .001) and a subset of 1,643 putatively neutral SNP markers (FST = 0.0042, p < .001). Oceanography influences genetic structure, with redundancy analysis (RDA) indicating significant contribution of asymmetric ocean currents to neutral genetic variation (R2adj = 0.133, p = .035). Genetic structure may also reflect demographic factors, with divergent populations characterized by low effective population sizes (Ne < 50). Pronounced latitudinal genetic structure was recovered for loci putatively under selection (FST = 0.2390, p < .001), significantly correlated with sea surface temperature variabilities during peak spawning months for S. olivacea (R2adj = 0.692–0.763; p < .050), suggesting putative signatures of selection and local adaptation to thermal clines. While oceanography and dispersal ability likely shape patterns of gene flow and genetic structure of S. olivacea across the Sulu Sea, the impacts of genetic drift and natural selection influenced by sea surface temperature also appear as likely drivers of population genetic structure. This study contributes to the growing body of literature documenting population genetic structure and local adaptation for highly dispersive marine species, and provides information useful for spatial management of the fishery resource.This project was funded by the Department of Science and Technology—Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development (DOST-PCAARRD project no. QSR-IA-MCR.05.01), and implemented by the University of the Philippines—Marine Science Institute (UP-MSI). MJM acknowledges support provided by the DOST-Accelerated Science and Technology Human Resource Development Program (ASTHRDP; Thesis Grant) and the UP-MSI (Thesis Writing Grant). We are deeply thankful to Dr. Evangeline Magdaong, Jeniffer De Maligaya, and Benedict Castro of the Physical Oceanography Laboratory, UP-MSI headed by Dr. Cesar Villanoy for the larval dispersal biophysical modeling, Angela Camille Aguila and Simon Alcantara for laboratory assistance, Bhenjamin Ona for the remote sensing data, Dr. Din Matias for analysis recommendations, Von Yip for QGIS assistance, and Dr. Richard Mualil and Yunadzmal Ong of Mindanao State University (MSU Tawi-Tawi) for sample collection. We also thank Sharon Magnuson and Chris Bird (Genomics Core Lab, Texas A&M University, Corpus Christi) for performing the RAD sequencing. We thank the reviewers whose comments and insights greatly improved the manuscript. This is MSI contribution number 483.
- Variability and potential of seaweeds as ingredients of ruminant diets: An in vitro studyde la Moneda, Ana; Carro, Maria Dolores; Weisbjerg, Martin R.; Roleda, Michael Y.; Lind, Vibeke; Novoa-Garrido, Margarita; Molina-Alcaide, Eduarda (MDPI AG, 2019-10-22)This study was designed to analyze the chemical composition and in vitro rumen fermentation of eight seaweed species (Brown: Alaria esculenta, Laminaria digitata, Pelvetia canaliculata, Saccharina latissima; Red: Mastocarpus stellatus, Palmaria palmata and Porphyra sp.; Green: Cladophora rupestris) collected in Norway during spring and autumn. Moreover, the in vitro ruminal fermentation of seventeen diets composed of 1:1 oat hay: concentrate, without (control diet) or including seaweeds was studied. The ash and N contents were greater (p < 0.001) in seaweeds collected during spring than in autumn, but autumn-seaweeds had greater total extractable polyphenols. Nitrogen in red and green seaweeds was greater than 2.20 and in brown seaweeds, it was lower than 1.92 g/kg DM. Degradability after 24 h of fermentation was greater in spring seaweeds than in autumn, with Palmaria palmata showing the greatest value and Pelvetia canaliculata the lowest. Seaweeds differed in their fermentation pattern, and autumn Alaria esculenta, Laminaria digitata, Saccharina latissima and Palmaria palmata were similar to high-starch feeds. The inclusion of seaweeds in the concentrate of a diet up to 200 g/kg concentrate produced only subtle effects on in vitro ruminal fermentation.
- 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.
- Transcriptome analysis of growth variation in early juvenile stage sandfish Holothuria scabraOrdoñez, June Feliciano F.; Galindez, Gihanna Gaye S.T.; Gulay, Karina Therese; Ravago-Gotanco, Rachel (Elsevier, 2021-12)The sandfish Holothuria scabra is a high-value tropical sea cucumber species representing a major mariculture prospect across the Indo-Pacific. Advancements in culture technology, rearing, and processing present options for augmenting capture production, stock restoration, and sustainable livelihood activities from hatchery-produced sandfish. Further improvements in mariculture production may be gained from the application of genomic technologies to improve performance traits such as growth. In this study, we performed de novo transcriptome assembly and characterization of fast- and slow-growing juvenile H. scabra from three Philippine populations. Analyses revealed 66 unigenes that were consistently differentially regulated in fast-growing sandfish and found to be associated with immune response and metabolism. Further, we identified microsatellite and single nucleotide polymorphism markers potentially associated with fast growth. These findings provide insight on potential genomic determinants underlying growth regulation in early juvenile sandfish which will be useful for further functional studies.The authors are grateful to the following individuals and institutions for providing samples and facilitating their collection: D. Ticao of (Finfish Hatcheries, Inc.); Dr. M.A. Juinio-Menez, ˜ J.R. Gorospe, C. Edullantes, B. Rodriguez, A. Rioja, T. Catbagan, and G. Peralta of Bolinao Marine Laboratory, University of the Philippines Marine Science Institute; and E. Tech (Palawan Aquaculture Corp.).
- The harmful raphidophyte Chattonella (Raphidophyceae) in Western Pacific: Its red tides and associated fisheries damage over the past 50 years (1969–2019)Lum, Wai Mun; Benico, Garry; Doan-Nhu, Hai; Furio, Elsa; Leaw, Chui Pin; Leong, Sandric Chee Yew; Lim, Po Teen; Lim, Weol Ae; Lirdwitayaprasit, Thaithaworn; Lu, Songhui; Nguyen, Nguyen Van; Orlova, Tatiana Yu.; Rachman, Arief; Sakamoto, Setsuko; Takahashi, Kazuya; Teng, Sing Tung; Thoha, Hikmah; Wang, Pengbin; Yñiguez, Aletta T.; Wakita, Kazumi; Iwataki, Mitsunori (Elsevier, 2021-07)Red tides and associated fisheries damage caused by the harmful raphidophyte Chattonella were reassessed based on the documented local records for 50 years to understand the distribution and economic impacts of the harmful species in the Western Pacific. Blooms of Chattonella with fisheries damage have been recorded in East Asia since 1969, whereas they have been only recorded in Southeast Asia since the 1980s. Occurrences of Chattonella have been documented from six Southeast Asian countries, Indonesia, Malaysia, Philippines, Singapore, Thailand and Viet Nam, with mass mortalities mainly of farmed shrimp in 1980–1990s, and farmed fish in 2000–2010s. These occurrences have been reported with the names of C. antiqua, C. marina, C. ovata, C. subsalsa and Chattonella sp., owing to the difficulty of microscopic species identification, and many were not supported with molecular data. To determine the distribution of C. marina complex and C. subsalsa in Southeast Asia, molecular phylogeny and microscopic observation were also carried out for cultures obtained from Indonesia, Malaysia, Japan, Philippines, Russia, Singapore and Thailand. The results revealed that only the genotype of C. marina complex has been detected from East Asia (China, Japan, Korea and Russia), whereas both C. marina complex (Indonesia and Malaysia) and C. subsalsa (Philippines, Singapore and Thailand) were found in Southeast Asia. Ejection of mucocysts has been recognized as a diagnostic character of C. subsalsa, but it was also observed in our cultures of C. marina isolated from Indonesia, Malaysia, Japan, and Russia. Meanwhile, the co-occurrences of the two harmful Chattonella species in Southeast Asia, which are difficult to distinguish solely based on their morphology, suggest the importance of molecular identification of Chattonella genotypes for further understanding of their distribution and negative impacts.We thank Drs Yuuki Kosaka, Winnie Lik Sing Lau, Ing Kuo Law and Toh Hii Tan for their sampling assistances. We thank Dr. Sadaaki Yoshimatsu for providing a culture strain TAI-93, and Drs Mineo Yamaguchi and Haruo Yamaguchi for support on maintenance and rDNA analysis of the culture. This work was carried out under international collaboration of the IOC/WESTPAC-HAB project and Core-to-Core Program (B. Asia-Africa Science Platforms) of the Japan Society for the Promotion of Science (JSPS). This work was partially supported by Japanese JSPS Kakenhi 19H03027 and 19KK0160 (MI), Malaysian MOHE HICOE IOES and FRGS (PTL), Vietnamese VAST NVCC17.02/21-21 (HD-N), and the Japanese Fund-in-Trust (MEXT).
- 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.