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Local Fungal Endophytes as Rich Sources of Chitinase Genes

Zabrina Bernice L. Malto, Christine Jurene O. Bacal,
Mark Jeffrey S. Diaz, and Eizadora T. Yu*

Institute of Chemistry, College of Science, University of the Philippines
Diliman, Quezon City 1101 Philippines


*Corresponding Author: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

 

 

ABSTRACT

The ability of three fungal endophytes (JB10, JB11, and D12 isolates) to degrade chitin, and their potential as microbial sources of chitinases was investigated. Amplification and sequencing of the ITS regions revealed the identity of the fungal isolates: JB10 (Fomitopsis sp.), JB11 (Aspergillus tubingensis), and D12 (Daldinia eschscholzii). All three fungi were able to grow on minimal media with colloidal chitin as sole carbon source, albeit at different rates. Isolates JB11 and D12 are observed to have comparable or faster growth rates in chitin as compared to the simpler potato dextrose carbon source. Turbidimetric measurements show that the fungal cultures are able to degrade chitin with 3–5 d of incubation. While the crude, secreted proteins from these three fungi show comparable total chitinolytic activities (~0.35 U/mL), JB11 was found to have the highest exochitinase activity (~0.25 U/mL). Bioinformatic analysis of the chitinase (GH18) genes for A. tubingensis (JB11) and D. eschscholzii (D12) revealed variability in the GH18 chitinase sequences in terms of the amino acid sequences of the canonical DXXDXDXE catalytic motif as well as the presence of additional domain architectures, which make these fungi ideal sources for chitinases for both biotechnology applications and chitinase enzyme mechanistic studies.

 


INTRODUCTION

The processing of crustacean products generates a lot of shell waste as crustacean meat accounts for less than 50% of the animal’s body mass. Efforts to valorize and refine these crustacean shells for chemicals (e.g., amino acids, calcium carbonate, and N-acetyl glucosamine or NAG) are being explored to create a high-value supply chain for what is normally just discarded as waste (Yan and Chen 2015). While the complete breakdown of chitin to NAG is desirable, depolymerization to lower molecular weight chitin oligosaccharides (CTOS) can also yield high-value products with biomedical applications. Enzymes such as chitinases can degrade chitin into CTOS or NAG monomers by hydrolyzing the glycosidic bonds under physiological conditions. These chitin-degrading enzymes can be endochitinases, which cleave the polymer internally producing CTOS or exochitinases, which cleave the reducing end of the polymer producing NAG [for N-acetyl glucosaminidases (NAGase)] or (NAG)2 (for chitobiosidases) (Hamid 2013). These enzymes can, therefore, be used in the processing of crustacean waste to produce CTOS or NAG precursors. . . . read more

 


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Small Maar Lakes of Luzon Island, Philippines: Their Limnological Status and Implications on the Management of Tropical Lakes – A Review

Milette U. Mendoza1,6*, Jonathan Carlo A. Briones1,2,3,
Masayuki Itoh4, Karol Sophia Agape R. Padilla1, Jaydan I. Aguilar1,
Noboru Okuda5, and Rey Donne S. Papa1,2,3

1The Graduate School, University of Santo Tomas 1015 Philippines
2Department of Biological Sciences, University of Santo Tomas 1015 Philippines
3Research Center for the Natural and Applied Sciences, University of Santo Tomas 1015 Philippines
4School of Human Science and Environment, University of Hyogo,
1-1-12 Shinzaike-Honcho, Himeji 670-0092 Japan
5Research Institute for Humanity and Nature, 457-4 Motoyama,
Kamigamo, Kita-ku, Kyoto 603-8047 Japan
6Department of Environmental Science, School of Science
& Engineering, Ateneo de Manila University 1108 Philippines


*Corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

 


ABSTRACT

In developing countries such as the Philippines, the inadequacy of even the most basic limnological datasets available has hindered planning and implementation of science-based management policies for inland waters. This situation is aggravated by overutilization of natural resources for ecosystem services such as water usage, aquaculture, fishing, and tourism. We reviewed published researches related to the Seven Maar Lakes (SMLs) in Luzon Is., Philippines to summarize information invaluable for the protection and sustainable use of these resources. Popular scientific search engines were utilized to gather peer-reviewed research articles and reports from both private institutions and government agencies. Literature and timeline from the 1930s to 2019 was classified into topics – namely socioeconomics, fisheries, biodiversity, and environment. Based on the literature survey, a variety of challenges, knowledge gaps, and promising research directions were identified, which are essential to the sustainable ecosystem management of the SMLs. Aquaculture practices impacting the lakes and its underestimated biodiversity were described. Measured vertical profiles of dissolved oxygen (DO), temperature, conductivity, pH, and salinity was supplemented by our preliminary limnological survey in the SMLs. Past and present monitoring data of selected physicochemical parameters were assessed from which the changing limnological status of the lakes was determined. We recommended measures motivated by strategic environmental assessments while still considering maintained economic yields. A sustained collaborative effort from different sectors is strongly suggested not only to manage the SMLs but also to address trade-offs among critical ecosystem services. Aside from the need for well-designed, long-term water quality monitoring, we also stress the synergistic interpretation of all available knowledge, which can contribute to the resolution of environmental issues at both local and global scales.

 

INTRODUCTION

Freshwater lakes are essential to humanity as they provide critical ecosystem services and serve as sentinels and integrators of a range of environmental processes (Williamson et al. 2008). Small lakes in the Philippines – defined here with surface area (SA) of ≤ 2,000,000 m2 (Brillo 2016a, b) – often receive less research and management attention compared to bigger lakes, even though they are equally important for conservation (Briones et al. 2016, Scheffer et al. 2006). Intensive and systematic limnological research is needed for a better understanding of the small lakes, as these ecosystems are more vulnerable than larger lakes to human activities in the catchment and are more sensitive to the resultant environmental changes (Brillo 2015a). Sixty-three percent of the Philippine lakes are classified as small (Brillo 2015b), suggesting its advantage since small aquatic ecosystems have great importance and global impact in nutrient spiraling and retention of important materials, as well as in biotic complexity and richness (Downing 2010). . . . read more

 


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STA. ANA JG, RIVERA AC, ENCARNACION BP, CABRERA RR, ALCANTARA FMB, DALISAY JS, NICOLAS JU, DE LA CRUZ AR, PASCUAL MST. 2005g. Water Quality Report on Sampaloc Lake 1996–2005. Quezon City, Philippines: Laguna Lake Development Authority. 31p.
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VICENTE IST, FONSECA-ALVES CE. 2013. Impact of introduced Nile Tilapia (Oreochromis niloticus) on non-native aquatic ecosystems. Pak J Biol Sci 16: 121–126.
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WILLIAMSON CE, DODDS W, KRATZ TK, PALMER MA. 2008. Lakes and streams as sentinels of environmental change in terrestrial and atmospheric processes. Front Ecol Environ 6: 247–254. doi: 10.1890/070140
ZAFARALLA MT. 2010. Plankton biodiversity, water quality and environmental status of Los Baños’ Crocodile Lake and San Pablo City’s seven lakes (Lakes Sampaloc and Pandin). International System for Agricultural Science and Technology. Retrieved from http://agris.fao.org/agris-search/search.do?recordID=PH2012000144
ZAFARALLA MT. 2014. Microalgae of the Seven Lakes of San Pablo City & Crocodile Lake of Los Baños. Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development. ISBN: 978-971-547-317-0.
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Letters to the Editor

 

 

Dear Editor,

As countries continue to compete in the global market for social and economic advantage, there is an increasing demand for higher education to provide work-ready graduates. To meet this demand, educators require innovative and manageable professional learning to keep up with current practices in their field. Morales and co-authors (2019) developed a self-rating tool to assess the proficiency of STEAM educators within the Philippines’ higher education sector. There is potential for such tools to inform the development of open-access professional learning programs for all educators in higher education. These programs can be developed in other specialist teaching areas as a pathway to broad use of micro-credentials.

Traditionally, universities placed emphasis on classic longitudinal knowledge learning over relatively long timeframes. In contrast, a micro-credentials system provides opportunities for individuals to achieve small and measurable qualifications with these new skills and accomplishments being immediately recognized. In the context of competitive and evolving workplace, these training modules provide a cost-effective way for individuals to remain agile and current (Fong et al. 2016).

With a view to a competency-based approach to professional learning, educators also have opportunities to focus on fostering valuable skills in adult education such as the ability to cooperate, communicate, and problem-solve (Kouwenhoven 2009).

However, despite being well-suited for faculty development in higher education, micro-credential systems are surprisingly rare for faculty in higher education.

As an example, at our institution eight core teaching competencies have been identified, these form the basis of professional learning modules. Educators in our program are required to keep an ePortfolio with a record of professional practice linked to an individual teaching inquiry. Within each teaching competency, educators are guided to select their own proficiency level. If educators demonstrate that they are highly capable in an area, and they are able to provide evidence of their practice, they can receive credit for the module. When the educator self-identifies a gap, they are provided with a series of guided workshops and modules to provide the necessary skills.


These modules are organized around the concept of micro-credentials, but – similar to other institutes of higher education – we have not implemented a formal micro-credential system.
A new approach is required to motivate and document faculty professional development. The system introduced by Morales et al. (2019) could be applied to other professions and inform an assessment model for modularized micro-credentials in higher education. Educators are reminded that there is no one size fits all theory of adult learning and that this assessment tool could provide a simple approach to meeting an identified need in the professional development of faculty at institutes of higher education worldwide.
Lee-Anne Turton
Unitec Institute of Technology, Auckland,
New Zealand
This email address is being protected from spambots. You need JavaScript enabled to view it.

 


REFERENCES

FONG J. JANZOW P, PECK DK. 2016. Demographic shifts in educational demand and the rise of alternative credentials. Retrieved from https://upcea.edu/wpcontent/uploads/2017/05/Demographic-Shifts-in-Educational-Demand-and-the-Rise-ofAlternative-Credentials.pdf
KOUWENHOVEN W. 2009. Competence-based Curriculum Development in Higher Education: a Globalised Concept? In: Technology, Education and Development. Lazinica A, Calafate C ed. IntechOpen, p. 1–22.
MORALES MPE. ANITO JC. AVILLA RA. ABULON ELR, PALISOC CP. 2019. Proficiency Indicators for Philippine STEAM (Science, Technology, Engineering, Agri/fisheries, Mathematics) Educators. Philipp J Sci 148 (2): 265–281.

 


Dear Editor,

We would like to thank you for the opportunity to respond to the issues raised in Dr. Turton’s letter to the Editor. We attest and extend our appreciation for the ingenuity of the idea of how to extend the self-rating proficiency tool to reach the topography of professional learning and micro-credentialing.

In her letter to the editor, she expounds on the potential of the tool to propel open-access professional learning programs for educators at higher education, which may be developed in other specialist teaching area as a pathway to broad use of micro-credentialing. We appreciate and agree with the concept of assessing the professional educators’ proficiency for micro-credentialing purposes. In fact, we also believe that micro-credentialing is an outstanding idea as a future of the proficiency indicator tool. This concept matches our vision of utilizing the tool to initiate up-skilling and reskilling strategies for the Philippine human resource for them to attain the required skill set of Teacher 4.0. Micro-credentialing as a professional learning system works on the principles of the personalized and self-directed system – focused on the needs, competency-based, and job-embedded system (Ryerse 2017) – which makes it practical aside from being in the short track compared to the long traditional macro-credentialing to earn a degree. In fact, most first world countries – specifically the United States – pursue the micro-credentialing track grounding on the belief that this system can expand choices for educators and administrators as they shape their formal professional development. The Digital Promise company, for example, successfully partnered with the Center for Teacher Quality and has been hosting the micro-credentialing system of nine states in its digital platform (DP 2017). The State University of New York (SUNY) initiated the same processes of skilling their entire populace clustering the micro-credentialing process as university-based, non-profit partnership with higher education, and for profit-offering for those in the industry (SUNY 2018).

As per Dr. Turton’s claim, her institution has an informal micro-credentialing system. It maintains an ePortfolio with a record of professional practice linked to an individual teaching inquiry. Within each teaching competency, educators are guided to select their own proficiency levels. If high and with evidence, they receive credit for the module. If low, they identify the gap and are provided the necessary skills through modules organized around micro-credentialing principles. Relatively, many institutions of higher and advanced learning are already using micro-credentialing and issuances of digital badges for specific skills (e.g., Arizona State University and the University of Wisconsin- Milwaukee thru Digital Promise). In the realm of the fourth industrial revolution era, digital badging flourished to reward achievement or acquisition of competencies fit for targeted 21st Century skills. In the graduate school of the National Center for Teacher Education, we engage our graduate students with the concept of certification, which basically resembles micro-credentialing. However, we follow a structure of completion of several courses for a graduate student to earn certification (e.g., on pedagogy, assessment, curriculum) – which may not exactly mimic the goals of micro-credentialing as performance-based in nature. This system may need to have a surrogate framework to emphasize an authentic assessment of performance of teachers in the graduate school for micro-credentialing or certification purposes, in which the principle of self-assessment using a highly structured proficiency tool may come as an integral component of a micro-credentialing framework in teacher education, and even in teacher professional development programs. We envision such a system to highly improve teacher education graduates’ skills towards the expert level, and bring in-service teachers to leap from one career stage to another until they seat on being distinguished teachers. The framework may also work its way to professional learning, and continuing professional development in other fields.

Seemingly, Dr. Turton foresees our proficiency tool as a new approach to inform the assessment framework of other teacher education and teacher professional development programs towards developing their unique micro-credentialing system in higher education. The tool is foreseen to provide a much simpler approach to meeting an identified need in the professional development of faculty at higher education institutes. In fact, the tool provides the ground and base of micro-credentialing as visualized by Dr. Turton. Needs assessment using a structured self-rating tool may play the prelude to micro-credentialing main processes of providing evidence to claimed skills. The tool may likewise serve as a validation system of the evidence presented in the micro-credentialing system. Finally, the tool may offer a framework of assessment and feedback mechanism. This means that a highly structured micro-credentialing framework may be sourced from the developed proficiency tool – to aim at and emphasize reskilling and up-skilling of our human resource to meet the required skills of the fourth industrial revolution era for confidence building. Ultimately, we agree with Dr. Turton that the tool may serve as a framework of a highly structured micro-credentialing system in all professional learning and in continuing professional development in all fields advocating quality through equity of skills and resources.


Marie Paz E. Morales
Publication Office, Philippine Normal University, Manila 1000 Philippines
This email address is being protected from spambots. You need JavaScript enabled to view it.

Ruel A. Avilla
Faculty of Science, Technology and Mathematics
Philippine Normal University, Manila 1000 Philippines

Jovito C. Anito
Jose Rizal University, Mandaluyong 1552 Philippines

Caesar P. Palisoc
College of Graduate Studies and Teacher Education Research
Philippine Normal University, Manila 1000 Philippines

 

REFERENCES

[DP] Digital Promise. 2017. Powerful Learning. Retrieved from http://digitalpromise.org/wp-content/uploads/2018/08/2017-Digital-Promise-Annual-Report.pdf
RYERSE M. 2017. Competency-Based Micro-Credentials are Transforming Professional Learning. Retrieved from https://www.gettingsmart.com/2017/11/micro-credentials-transforming-professional-learning/
[SUNY] The State University of New York. 2018. Micro-Credentials at SUNY. Retrieved from https://system.suny.edu/academic-affairs/microcredentials/

Structural Stability Analysis of Models of Dopamine Synthesis and D1 Receptor Trafficking in RPT Cells using CRNT

John Justine S. Villar1*, Patrick Vincent N. Lubenia2, Eduardo R. Mendoza3,4,5,6, and Carlene P.C. Pilar-Arceo2

1Department of Computer Science, University of the Philippines Diliman, Quezon City, Philippines
2Institute of Mathematics, University of the Philippines Diliman, Quezon City, Philippines
3Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, Laguna, Philippines
4Mathematics & Statistics Department, De La Salle University, Manila, Philippines
5Physics Department, Ludwig Maximilians University, Munich, Germany
6Max Planck Institute of Biochemistry, Munich, Germany


Corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

 

ABSTRACT

Dopamine plays an important role in different physiological and metabolic functions, including the control of sodium excretion in the kidney. Studies have shown that there is a positive correlation between a defect in dopamine synthesis and/or dopamine receptor function, and a defect in renal sodium excretion – which may lead to the development of essential hypertension. Specific receptors for dopamine, such as the D1 receptor, have been identified in the various regions within the kidney. It is observed that errors regarding dopamine receptor-G protein coupling and changes in the signaling components may be responsible for the failure of dopamine to increase sodium excretion in hypertensive subjects. In this paper, two symbolic kinetic models of dopamine synthesis and one of dopamine D1 receptor trafficking are presented. The three models are chemical reaction networks constructed and analyzed using Chemical Reaction Network Theory (CRNT), a framework that provides different insights on the static properties of a chemical reaction network regarding the existence of steady states, their multiplicity, and structural stability. It is found that all three networks do not support multiple steady states.

 


INTRODUCTION

Essential hypertension is a common human disorder characterized by an increase in systemic blood pressure caused by high levels of sodium in the bloodstream. This happens when sodium reabsorption increases in the renal proximal tubule (RPT) cells in the kidney, which in turn occurs when more than the usual amount of sodium is returned to the bloodstream from the glomerular filtrate. Dopamine, an important catecholamine, has been identified to control primary physiological and metabolic processes in the human body – such as locomotion, hormone secretion, behavior– as well as various gastrointestinal, renal, and cardiovascular functions. In the kidney, dopamine is seen as an important regulator of blood pressure, sodium balance, and other metabolic functions. . . . . read more

 


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LUBENIA PVN. 2012. A Mathematical Model of Dopamine Synthesis in Renal Proximal Tubule Cells [Master's thesis]. Quezon City: University of the Philippines Diliman.
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Reoptimization of the Consensus Pattern Problem under Pattern Length Modification

Jhoirene B. Clemente1*, Proceso L. Fernandez Jr.2, Richelle Ann B. Juayong1,
Jasmine A. Malinao1, Ivy D. Ordanel1, and Henry N. Adorna1

1Department of Computer Science, University of the Philippines Diliman,
Quezon City, NCR 1101 Philippines
2Department of Information Systems and Computer Science, Ateneo de Manila University,
Quezon City, NCR 1108 Philippines

*Corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

 


ABSTRACT

In Bioinformatics, finding conserved regions in genomic sequences remains to be a challenge not just because of the increasing size of genomic data collected but because of the hardness of the combinatorial model of the problem. One problem formulation is called the Consensus Pattern Problem (CPP). Given a set of t n-length strings S = {S1,..., St} defined over some constant size alphabet Σ and an integer l, where l ≤ n, the objective of CPP is to find an l-length string v and a set of l-length substrings si of each Si in S such that the total sum of d(si, v) is minimized for all 1 ≤ i ≤ t. Here d(x, y) denotes the Hamming distance between the two strings x and y. It is known that CPP is NP-hard i.e., unless P = NP, there is no polynomial-time algorithm that produces an optimal solution for CPP. In this study, we investigate a combinatorial setting called reoptimization in finding an approximate solution for this problem. We seek to identify whether a specific additional information can help in solving CPP. Specifically, we deal with the following reoptimization scenario. Suppose we have an optimal l-length consensus substring of a given set of sequences S. How can this information be beneficial in obtaining an (l + k)-length and (l – k)-length consensus for S? In this paper, we show that the reoptimization variant of the problem is still computationally hard even with k = 1. In response, we present four algorithms that make use of the given optimal solution – we prove that the first three algorithms produce solutions with quality that is bounded from above by an additive error that grows as the parameter k increases, while the fourth algorithm achieves a guaranteed approximation ratio. It has been shown that there is no efficient polynomial-time approximation scheme for CPP (Boucher 2015). In this paper, we show that we can save 𝒕(𝒏−(𝒍+𝒌)+𝟏)(𝒕(𝒍+𝟐𝒌)𝒓) steps in computation from the original running time of the known polynomial-time approximation scheme for CPP.

 

 

INTRODUCTION

Transcription factor binding sites in genomic sequences are conserved segments in the DNA that are known to regulate the expression of one or more genes. Identifying these conserved segments is modelled as a substring selection problem in Computer Science. One formulation of the problem is called the Consensus Pattern Problem, abbreviated as CPP. Formally – given a set of t n-length strings S = {S1,..., St} defined over some constant size alphabet Σ and an integer l, where l ≤ n – the objective of CPP is to find an l-length string v and a set of l-length substrings si of each Si in S such that the total sum of d(si, v) is minimized for all 1 ≤ i ≤ t. Here d(x, y) denotes the Hamming distance between the two strings x and y. Algorithms for CPP have been applied to a variety of pattern identification – ranging from biological sequences to text mining. The general formulation of the problem can be applied to other discrete structures such as graphs and time-series datasets. . . . . read more

 

 

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BILÒ D. 2018.  New algorithms for Steiner tree reoptimization. ICALP 19: 1 – 19: 14.
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BÖCKENHAUER HJ, FREIRMUTH K, HROMKOVIČ J, MÖMKE T, SPROCK A, STEFFEN B. 2012. Steiner Tree Reoptimization in Graphs with Sharpened Triangle Inequality. Journal of Discrete Algorithms 11(1): 73–86. ISSN 15708667.
BORIA N, PASCHOS VT. 2010. Fast Reoptimization for the Minimum Spanning Tree Problem. Journal of Discrete Algorithms 8(3): 296–310. https://doi.org/10.1016/j.jda.2009.07.002
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