Biotechnology Commons^™

Performance Analysis Of Bacterial Genome Assemblers Using Illumina Next Generation Sequencing Data, Nur ‘ Ain Mohd Ishak

Student Works (2020-2029)

The advancement of next generation sequencing (NGS) technology has revolutionized the field of genomic and genetic studies. As compared to conventional methods, NGS generate comprehensive genomic data at a fraction of the cost with a higher percentage of accuracy. One of the processing and analyzing NGS data is genome assembly. De novo assembly is a process of assembling short reads into contiguous sections of sequence without a reference which is different with conventional mapping technique. De Bruijn graph is one of the assembly algorithms that are widely used for short reads sequences produced from NGS platforms. In this study, the …

Transcutaneous Energy Transmission: Can We Do It Now?, Yuriy Pya

The VAD Journal

The percutaneous driveline used in contemporary LVADs presents a continuous risk of infection for the duration of support. Minimizing infection in durable mechanical circulatory support systems requires total implantation of all components and energy transfer by means other than percutaneous drivelines. A novel coplanar energy transfer (CET) system, similar to the original transcutaneous energy transfer (TET) design, is unique by incorporating two large rings with coil-within-the-coil topology to ensure strong resonance power. The CET system consists of an internal integrated controller, a battery coupled with an internal thoracic coil ring, and the LVAD pump. External equipment includes a power transmission …

Herb-Layer Dynamics In An Old-Growth Forest: Vegetation–Environment Relationships And Response To Invasion-Related Perturbations, Taylor M. Buskey, Margaret E. Maloney, Julia I. Chapman, Ryan W. Mcewan

Biology Faculty Publications

Temperate forests of eastern North America are subject to multiple invasions from non-native species that have the potential to drive long-term dynamics in biodiversity. Garlic mustard (Alliaria petiolata (M. Bieb.) Cavara and Grande) is an invasive plant in many deciduous forests, and management efforts often focus on removing this species to initiate native species restoration. Agrilus planipennis Fairmaire (emerald ash borer; Coleoptera: Buprestidae) is a non-native insect pest that has caused substantial loss of ash trees (Fraxinus spp. L.) in North America. Our goal was to understand how the herbaceous layer in an old-growth forest responded to the removal of …

Changes In Lipid Profiles Of Epileptic Mouse Mode, Alicia Johnson, Ryan A. Grove, Deepak Madhavan, Cory H.T. Boone, Camila Pereira Braga, Hannah Kyllo, Kaeli K. Samson, Kristina A. Simeone, Timothy A. Simeone, Tomáš Helikar, Corrine K. Hanson, Jiri Adamec

Department of Biochemistry: Faculty Publications

Introduction Approximately 1% of the world’s population is impacted by epilepsy, a chronic neurological disorder characterized by seizures. One-third of epileptic patients are resistant to AEDs, or have medically refractory epilepsy (MRE). One non-invasive treatment that exists for MRE includes the ketogenic diet (KD), a high-fat, low-carbohydrate diet. Despite the KD’s success in seizure attenuation, it has a few risks and its mechanisms remain poorly understood. The KD has been shown to improve metabolism and mitochondrial function in epileptic phenotypes. Potassium channels have implications in epileptic conditions as they have dual roles as metabolic sensors and control neuronal excitation.

Objectives …

Optimization Of Building Configuration In Vertical Residential Housing Towards Outdoor Thermal Comfort: Case Study Of Tambora Flats, Jakarta, Indonesia, Rizqi Khairani Ayu, Prayitno Budi

ASEAN Journal on Science and Technology for Development

Population growth in Indonesia is not offset by the construction of urban facilities and infrastructure and the improvement of urban services. In densely populated urban areas with narrow residential conditions, the demand for shelter is higher, causing an increase in the price of land and housing. One of the efforts in responding to this problem in the Special Capital Region of Jakarta is to build vertical residential or flats. This study aimed to determine the level of outdoor thermal comfort of Tambora flats in Jakarta, which have air temperatures ranging 26–29°C and air humidity of 76–92%. Existing flats were simulated …

Comprehensive Assessment On The Environmental Conditions Of Abandoned And Inactive Mines In The Philippines, Samaniego Jessie, Gibaga Cris Reven, Tanciongco Alexandria, Rastrullo Rasty, Mendoza Norman, Racadio Charles Darwin

ASEAN Journal on Science and Technology for Development

Most abandoned and inactive mines in the Philippines pose high risks to human health and the environment due to the disturbed and exposed heavy metal-laden soils and sediments and water-filled open pit mines. Establishing these mines’ environmental conditions remains a challenge as it requires time, effort, resources, and faces a lack of funding as the economic phase of the mine has already ceased. In order to contribute to the solution on the assessment of abandoned and inactive mines, integrated methods with combined essential testing, sampling, and analyses of different environmental media present in the mine site are suggested in this …

Dynamic Changes Analysis Of Land Resource Balance In North Maluku Province, Indonesia, Faroh Elya Pratiwi Isti, Puspaningrani Fatih Cinderaswari, Reinadova Gema, Akbar Muhammad Rais, Anggraeni Novanna Dwi Septyo, Wildiyanti Oki Silvie, Kafafa Utia, Putri Ratih Ratih

ASEAN Journal on Science and Technology for Development

Land resources are part of nature related to the availability of water, nutrients, and food that are dynamic and play an important role in the lives of living creatures, including humans. From time to time, land use experiences changes in response to human activities that benefit their lives. This research was conducted to determine trends in land use change in North Maluku Province, Indonesia, as well as to find out the land resource balance and land carrying capacity in the province. The methods comprised a simple descriptive and quantitative analysis along with spatial analysis using GIS. The results showed that …

Water Quality Assessment And Monitoring Of Closed Rearing System Of The Sea Cucumber Holothuria Scabra, Meirinawati Hanny, Prayitno Hanif Budi, Indriana Lisa Fajar, Firdaus Muhammad, Wahyudi A'An Johan

ASEAN Journal on Science and Technology for Development

Sea cucumbers are an essential fishery resource. Therefore, effective aquaculture methods should be developed to achieve their optimal production. Sea cucumbers are susceptible to various environmental factors, one of which is water quality. Monitoring water quality based on physical and chemical parameters should be useful to the rearing system in aquaculture. In practical use, farmers usually monitor only temperature, salinity, and pH, neglecting the essential role of chemical parameters. This review focuses on and urges the monitoring of physical and chemical parameters. We explored the water quality parameters that may be crucial to the sea cucumber rearing system, including temperature, …

Biofilm Forming Ability Of Bacteria Isolated From Dental Caries: With Reference To Streptococcus Species, Sonali Kaustubh Ambulkar, Vidya Tale, Abhijit Jadhav, Komal Kulkarni

Future Dental Journal

Dental caries is formed by the group of microorganisms attached to a tooth surface embedded in a matrix of polymers. Biofilm plays an important role in the development of dental caries, plaque and other periodontal diseases. The present study is aimed to isolate, identify and characterize bacteria from dental caries. The ability of biofilm formation of these isolates was confirmed by Congo red agar method, Tube method and Microtitre plate method. High biofilm-forming bacteria were identified by 16S rRNA sequencing. Streptococcus mutans, Streptococcus anginosus, Enterococcus faecalis and Rothia dentocariosa are the predominant biofilm forming bacteria associated with dental caries.

Letter To The Editor: The Invasive Caribbean Mytilopsis Sallei (Bivalvia: Dreissenidae): A Short Review, Marelli Dan

ASEAN Journal on Science and Technology for Development

This letter seeks to comment on the taxonomy of members of the genus Mytilopsis (Bivalvia: Dreissenidae) that are found as invasive species in many Asian estuarine systems.

Reply To Letter To The Editor: The Invasive Caribbean Mytilopsis Sallei (Bivalvia: Dreissenidae): A Short Review, Tan Koh Siang, Tay Teresa

ASEAN Journal on Science and Technology for Development

This letter provides a response to the letter concerning "The Invasive Caribbean Mytilopsis sallei (Bivalvia: Dreissenidae): a Short Review" by Tan and Tay in AJSTD 35(1–2): 133–139.

Application Of Biogasoline In A Four-Stroke Motorcycle Engine, Saputra Sutrisna, Wijaya Karna, Mudjijana

ASEAN Journal on Science and Technology for Development

The problems facing the world, in relation to the increasing consumption of petroleum and its limited sources, as well as pollution by fuel-related gases, such as CO, have sparked research on the application of biogasoline as an environmentally friendly alternative fuel. Our research aimed to determine engine performance through mixtures of biogasoline and gasoline to measure torque, power, and fuel consumption rate, and to determine the effect of the mixture on the level of air pollution. The biogasoline used was previously prepared from cooking oil through a Cr-zeolite-catalyzed process. The testing methods on the fuel mixture as a working substance …

Global Retrofitting Strategies For An Existing Three-Storied Rc School Building In Mandalay, Myanmar, Thwe Thiri, Thwin Nang Su Le′ Mya, Hein Ne Min

ASEAN Journal on Science and Technology for Development

Low to severe earthquakes occur around the world every year, damaging and causing structural failure in buildings. Consequently, seismic improvements are required for existing buildings that are vulnerable to damage by seismic forces. The objective of this study was to investigate retrofitting strategies in terms of their sustainability. Mandalay, Myanmar, was selected as the study area as it is located near the Sagaing fault, which itself is in a strong earthquake zone (seismic zone 4). A three-storied RC building with a non-seismic design was selected as a case study building. An investigation was carried out into the performance and vulnerability …

A Practical Guide To Mechanistic Systems Modeling In Biology Using A Logic-Based Approach, Anna Niarakis, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Mechanistic computational models enable the study of regulatory mechanisms implicated in various biological processes. These models provide a means to analyze the dynamics of the systems they describe, and to study and interrogate their properties, and provide insights about the emerging behavior of the system in the presence of single or combined perturbations. Aimed at those who are new to computational modeling, we present here a practical hands-on protocol breaking down the process of mechanistic modeling of biological systems in a succession of precise steps. The protocol provides a framework that includes defining the model scope, choosing validation criteria, selecting …

Cautionary Tale Of Using Tris(Alkyl)Phosphine Reducing Agents With Nad+-Dependent Enzymes, Sagar M. Patel, Thomas G. Smith, Martha Morton, Kyle M. Stiers, Javier Seravalli, Stephen J. Mayclin, Thomas E. Edwards, John J. Tanner, Donald F. Becker

Department of Biochemistry: Faculty Publications

Protein biochemistry protocols typically include disulfide bond reducing agents to guard against unwanted thiol oxidation and protein aggregation. Commonly used disulfide bond reducing agents include dithiothreitol, β-mercaptoethanol, glutathione, and the tris(alkyl)phosphine compounds tris(2-carboxyethyl)phosphine (TCEP) and tris(3-hydroxypropyl)phosphine (THPP). While studying the catalytic activity of the NAD(P)H-dependent enzyme Δ¹-pyrroline-5-carboxylate reductase, we unexpectedly observed a rapid non-enzymatic chemical reaction between NAD⁺ and the reducing agents TCEP and THPP. The product of the reaction exhibits a maximum ultraviolet absorbance peak at 334 nm and forms with an apparent association rate constant of 231–491 M⁻¹ s⁻¹. The reaction is …

A Catalyst Reusability Study In Palm Fatty Acid Distillate And Glycerol Esterification Using Multi-Criteria Decision Analysis And Reaction Kinetics Approach, Sudibyo Hanifrahmawan, Setyaningrum Febbie, Rochmadi, Fahrurrozi Mohammad

ASEAN Journal on Science and Technology for Development

As a byproduct of the physical refinement of crude palm oil, palm fatty acid distillate or PFAD has a potential to be transformed into monoglycerides by means of irreversible esterification with glycerol over a cation exchange resin catalyst. Irreversibility of the esterification can be assured by continuous azeotropic removal of water by adding xylene as an entrainer. Because PFAD-glycerol esterification demands high temperatures for fast conversion and high selectivity of monoglycerides, it is necessary to test catalyst reusability performance. In this research, evaluation of catalyst reusability performance was based on five parameters: free fatty acid conversion, the rate of free …

Does The Presence Of Multiple Β-Lactamases In Gram-Negative Bacilli Impact The Results Of Antimicrobial Susceptibility Tests And Extended-Spectrum Β-Lactamase And Carbapenemase Confirmation Methods?, Fred C. Tenover, Caitlin M. Dela Cruz, Scott Dewell, Victoria M. Le, Isabella A. Tickler

Biology Faculty Publications

Objectives: Many multidrug-resistant Gram-negative bacilli (MDR-GNB) harbour multiple β-lactamases. The aim of this study was to assess the impact of multiple β-lactamase carriage on the accuracy of susceptibility tests and extended-spectrum β-lactamase (ESBL) and carbapenemase confirmation methods.

Methods: A total of 50 MDR-GNB, of which 29 carried multiple β-lactamases, underwent broth microdilution (BMD) and disk diffusion (DD) testing as well as confirmation tests for ESBLs and carbapenemases. Whole-genome sequencing (WGS) was used for β-lactamase gene identification.

Results: Categorical agreement of BMD and DD testing results ranged from 86.5 to 97.7% for 10 β-lactam agents. BMD and DD algorithms for ESBL …

The Influence Of Riparian Invasion By The Terrestrial Shrub Lonicera Maackii On Aquatic Macroinvertebrates In Temperate Forest Headwater Streams, Michelle N. Little, Kevin W. Custer, Eric B. Borth, Julia I. Chapman, Mitchell J. Kukla, Corey Kuminecz, Margaret E. Maloney, Michaela J. Woods, Ryan Mcewan

Biology Faculty Publications

The ecology of headwater streams is tightly linked to the riparian zone through organic matter subsidies which are highly susceptible to alteration due to biological invasion. Lonicera maackii is a non-native shrub that is a highly successful invader of headwater stream riparian zones in the American Midwest. We assessed effects on benthic macroinvertebrates across a gradient of invasion intensity from references sites with minimal invasion to a site that had a very heavy invasion. Benthic macroinvertebrates were sampled throughout the year and compositional differences were assessed using Non-metric Multidimensional Scaling ordination, and by comparing the prevalence of sensitive (Ephemeroptera, Plectoptera, …

Conceptual Shield Design For Boron Neutron Capture Therapy Facility Using Monte Carlo N-Particle Extended Simulator With Kartini Research Reactor As Neutron Source, Tsurayya Afifah Hana, Iman Azzam Zukhrofani, Sari R. Yosi Aprian, Fauzi Arief, Wijaya Gede Sutresna

ASEAN Journal on Science and Technology for Development

The research aims to measure the radiation dose rate over the radiation shielding which is made of paraffin and aluminium and to determine the best shield material for the safety of radiation workers. The examination used MCNP (Monte Carlo N-Particle) simulator to model the BNCT neutron source and the shield. The shield should reduce radiation to less than the dose limit of 10.42 µSv/h, which is assumed to be the most conservative limit when the duration of workers is 1920 h. The first design resulted in a radiation dose rate which was still greater than the limit. Therefore, optimization was …

Discoveries In Aerosol Science: Characterization Of Nanoparticles Emitted From Metallic Coils In Electronic Cigarettes, Kaushal Prasad

The Journal of Purdue Undergraduate Research

Electronic (e-) cigarettes, also known as electronic nicotine delivery systems, are battery-operated devices that are growing in popularity worldwide. Although e-cigarettes are known to be safer than traditional cigarettes, their potential health risks have not been extensively reviewed yet. In this study, aerosol nanoparticles generated from e-cigarette heaters were characterized. Kanthal A1 (iron + chromium + aluminum) coils, without nicotine solution or a wick, were installed in an e-cigarette atomizer. The operating conditions were varied coil resistances (0.1–1.0 Ω), a set applied power (10 W), and a stable duty cycle (50%: 5 s on, 5 s off ). The size …

Next Generation Aryl Hydantoins As Antischistosomal Agents, Derek A. Leas

Theses & Dissertations

Schistosomiasis, also known as “snail fever,” is both an acute and chronic disease spread by trematode flukes from the tropical parasitic worm genus Schistosoma. The flukes are spread via diseased freshwater snails, which release the parasites into the water column where they find a new human host. According to the World Health Organization (WHO), 99 million people were treated for schistosomiasis in 2017. The primary treatment used to combat schistosomiasis is the drug praziquantel (PZQ), but due to high drug pressure and widespread administration, its effectiveness has eroded because of rising drug resistance. Furthermore, PZQ is active against adult but …

Respons Dua Mutan Tomat Terhadap Cekaman Kekeringan, Ayu Ratna Ningrum, Anne Nuraini, Erni Suminar, Syariful Mubarok

Jurnal Kultivasi

Kondisi cekaman kekeringan pada tanaman tomat dapat menyebabkan pertumbuhan dan produksi tanaman tomat menurun. Salah satu upaya yang dapat dilakukan untuk mengatasi masalah tersebut adalah dengan perakitan varietas tanaman baru yang tahan terhadap cekaman kekeringan. Beberapa hasil mutasi gen IAA pada tomat mutan Micro-Tom mampu menghasilkan tanaman yang toleran terhadap kondisi stress secara abiotik, yaitu pada galur iaa9-3 dan iaa9-5. Penelitian ini dilakukan untuk mengetahui respons pertumbuhan vegetatif pada iaa9-3 dan iaa9-5 dalam kondisi cekaman kekeringan dengan metode in vitro. Penelitian dilaksanakan di Laboratorium Kultur Jaringan dan Teknologi Benih Fakultas Pertanian Universitas Padjadjaran pada bulan September sampai Desember 2019. Rancangan …

Functional Characterization Of Petiolule-Like Pulvinus (Plp) Gene In Abscission Zone Development In Medicago Truncatula And Its Application To Genetic Improvement Of Alfalfa, Juan Du, Shaoyun Lu, Maofeng Chai, Chuanen Zhou, Liang Sun, Yuhong Tang, Jin Nakashima, Jaydeep Kolape, Zhaozhu Wen, Marjan Behzadirad, Tianxiu Zhong, Juan Sun, Yunwei Zhang, Zeng-Yu Wang

Nebraska Center for Biotechnology: Faculty and Staff Publications

Alfalfa (Medicago sativa L.) is one of the most important forage crops throughout the world. Maximizing leaf retention during the haymaking process is critical for achieving superior hay quality and maintaining biomass yield. Leaf abscission process affects leaf retention. Previous studies have largely focused on the molecular mechanisms of floral organ, pedicel and seed abscission but scarcely touched on leaf and petiole abscission. This study focuses on leaf and petiole abscission in the model legume Medicago truncatula and its closely related commercial species alfalfa. By analysing the petiolule-like pulvinus (plp) mutant in M. truncatula at phenotypic level …

Longitudinal Clonal Lineage Dynamics And Functional Characterization Of Pancreatic Cancer Chemo-Resistance And Metastasization, Chieh-Yuan Li

Dissertations and Theses (Open Access)

In recent years, technological advancements, such as next-generation sequencing and single-cell interrogation techniques, have enriched our understanding in tumor heterogeneity. By dissecting tumors and characterizing clonal lineages, we are better understanding the intricacies of tumor evolution. Tumors are represented by the presence of and dynamic interactions amongst clonal lineages. Each lineage and each cell contributes to tumor dynamics through intrinsic and extrinsic mechanisms, and the variable responses of clones to perturbations in the environment, especially therapeutics, underlie disease progression and relapse. Thus, there exists a pressing need to understand the molecular mechanisms that determine the functional heterogeneity of tumor sub-clones …

Non-Invasive Tests For The Detection Of Nasopharyngeal Carcinoma, Mohan Sivanesan Vijaya

Student Works (2020-2029)

Nasopharyngeal carcinoma (NPC) is a malignancy that arises in the epithelium of the nasopharynx. Diagnosis is often delayed due to inaccessibility of primary tumour site which leads to inaccurate biopsy. The pathogenesis of NPC is linked to the Epstein-Barr virus (EBV) and studies have shown the employability of plasma EBV DNA for the detection and monitoring of NPC. MicroRNAs (miRNA) are a class of small non-coding RNA that are dysregulated in various cancers and have been extensively studied as biomarker due to their stability in various biospecimens. The aim of this project is to evaluate the load of EBV DNA …

Differentiation Propensity, Safety, And Therapeutic Potential Of Mesenchymal Stem Cells Of Dental Origin, Musa Sabri

Student Works (2020-2029)

Introduction: A new area in medical research has emerged with the discovery of mesenchymal stem cells (MSCs) and their ability to differentiate into other cell types. Specifically, these cells are found in various tissues and have been utilized in the field of regenerative medicine to support tissue repair as well as in cell replacement. Lately, MSCs of dental origin have been the main players used for regenerative purposes although subtle differences based on their tissue source separate them. Objectives: This study aims to determine the differential propensity, safety, and potential therapeutic applications of dental-derived MSCs. This involves examining various aspects …

Modeling, Fabrication And Characterization Of Coated Calcium Phosphate Scaffolds Produced By 3d-Printing For Tissue Engineering Application, Touri Maria

Student Works (2020-2029)

A fully interconnected 3-dimensional scaffold with pre-determined dimensions and porosity can be attained by design-dependent rapid prototyping techniques which possess precise control over the internal and external architecture of the scaffolds thus they can overcome the problems associated with the process-dependent classical approaches. Interruption of vascular flow with fracture or surgical osteotomy results in a transient hypoxic gradient within the wound and subsequent tissue necrosis. Tissue engineering scaffolds with oxygen generating elements have shown to be able to increase the level of oxygen and cell survivability. In this study, biphasic calcium phosphate (BCP) scaffolds with the composition of 60% hydroxyapatite …

Marine Biofouling Communities Of Manila South Harbor, Philippines, Nacorda Hildie M.E., Austero Nero M., Pagdilao Cesar R., Tan Koh Siang, Azanza Rhodora V.

ASEAN Journal on Science and Technology for Development

An immersion experiment was conducted in the Manila South Harbor to document the development of sessile biofouling communities. Test panels were submerged below the sea surface in April 2012 for short- (one and three months) and long-term (one year) exposures in seawater, then foauling types and occurrences were scored based on digital images of panel surfaces. The short-term immersed panels were found with significant cover of soft fouling (undet.), slime, and the invasive Balanus (=Amphibalanus) amphitrite. These also filled the long-term immersed panels, although some fell off due to mortality from crude oil smothering. Perna viridis, native but also invasive, …

Boron Neutron Capture Therapy For Cancer: Future Prospects In Indonesia, Poedjomartono Bagaswoto, Afkari Hanif, Meiyanto Edy, Bangun Alan, Sardjono Yohanes

ASEAN Journal on Science and Technology for Development

Boron neutron capture therapy (BNCT) is a form of cancer therapy based on the interaction of low-energy thermal neutrons and boron-10 (10-B) to produce alpha radiation from He-4 and Li-7 with a high linear energy transfer. A beam of neutrons irradiates a boron drug injected into the tumor, resulting in the boron-injected cancer cells receiving a lethal dose of radiation with the surrounding, healthy cells being minimally affected. Two boron drugs have been used clinically in BNCT, boron sodium captate (BSH) and borophenylalanine (BPA), while a third, pentagamaboronon-0 (PGB-0), is currently under development in the Faculty of Pharmacy of Universitas …

Characteristics Of Paraffin Shielding Of Kartini Reactor, Yogyakarta, Khanifah Lana, Widodo Susilo, Widarto, Putra Ngurah Made Dharma, Satrio Argo

ASEAN Journal on Science and Technology for Development

The National Nuclear Energy Agency (BATAN) Yogyakarta uses two kinds of paraffin for shielding radiation of Kartini reactor. For developing BNCT research, the radiation attenuation capability of paraffin has been analyzed to find out the coefficient attenuation, density, and composition of both kinds of paraffin. The components of the paraffin were analyzed using Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), and energy dispersive X-ray (EDX) spectroscopy characterization. Paraffin P1 has a density of 0.689 gr/mL and paraffin P2 is 0.578 gr/mL. Paraffin samples P1 and P2 were the sample content of functional group CH, CH2, and OH when …