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Articles 1 - 26 of 26

Full-Text Articles in Structural Biology

Morphological Characteristics Of The Mediophyceae Diatom Lampriscus Cf. Shadboltianus Var. Crenulatus Collected From Gili Meno, Indonesia, Arief Rachman, Riani Widiarti, Setiarti Sukotjo, Mark Wells Mar 2026

Morphological Characteristics Of The Mediophyceae Diatom Lampriscus Cf. Shadboltianus Var. Crenulatus Collected From Gili Meno, Indonesia, Arief Rachman, Riani Widiarti, Setiarti Sukotjo, Mark Wells

Makara Journal of Science

Diatoms are the most common and abundant microalgae group in seawater, with an estimated 200 genera and 200,000 species categorized into three distinct taxonomic classes: Mediophyceae, Bacillariophyceae, and Coscinodiscophyceae. This study describes the morphological characteristics of Lampriscus GM052022, a diatom belonging to the Mediophyceae family, which was collected from Gili Matra, Lombok, Indonesia. Analysis using light microscopy (LM) and electron microscopy (EM) showed that the morphological characteristics of the Lampriscus GM052022 specimen are similar to those of Lampriscus shadboltianus var. crenulatus due to the distinct crenulation lines on the frustule, which differentiate this variation from Lampriscus shadboltianus. However, the …


Potency Dependent Angiogenic Effect Of Bellis Perennis On In Ovo Chick Chorioallantoic Membrane Assay, Jayanthdevan V, Winston Vargheese V, Anish Fathima K, Lohita S Dec 2025

Potency Dependent Angiogenic Effect Of Bellis Perennis On In Ovo Chick Chorioallantoic Membrane Assay, Jayanthdevan V, Winston Vargheese V, Anish Fathima K, Lohita S

Indian Journal of Research in Homoeopathy

Background: Hormesis is the biological response of an organism for a particular dosage of a substance. The lower dose stimulates and higher dose inhibits. J Compton Burnett, an eminent homeopath, prescribed Bellis perennis for breast and uterine tumours, which suggests it could be due to the antiangiogenic property or angiogenic inhibiting property and clinically also it is used for healing of fractured bone and wound healing which may be due to angiogenic promoting property. This experiment deals with the dose dependent effect of Bellis perennis on In Ovo Chick Chorioallantoic Membrane Assay. Objective: To evaluate the Hormesis effect of Bellis …


Design And Evaluation Of An Innovative Biomimetic Coral Transport Container, John-Christopher L. Calulo, Wilfredo Y. Licuanan, Leah D. Madrazo, Dana Isabelle P. Villano, Angel Nicole B. Villanueva Jun 2025

Design And Evaluation Of An Innovative Biomimetic Coral Transport Container, John-Christopher L. Calulo, Wilfredo Y. Licuanan, Leah D. Madrazo, Dana Isabelle P. Villano, Angel Nicole B. Villanueva

Sinaya: A Philippine Journal for Senior High School Teachers and Students

Coral reefs are vulnerable to disruptive human activities such as pollution, overfishing, and coastal development—degrading water quality and reef structures. Active reef restoration entails temporarily relocating several corals to aquaculture facilities to achieve successful rehabilitation; however, current coral transport methods pose certain risks, such as stress-induced mortality, which can result from physical damage during transportation. Existing studies on coral transport have explored various techniques for collecting, shipping, and maintaining live coral specimens. The design consists of petal-shaped areas where the waves gather, akin to a coral reef’s grooves, separated by wedges—the spurs—that cause waves to divide. The different design modifications …


Toward Ar Visualization Of The Fluid-Mosaic Model Of The Cell Membrane, Yoonwoo Lee, Allison Ost, Junghyuk Lee, Krisztina Z. Bencze Apr 2025

Toward Ar Visualization Of The Fluid-Mosaic Model Of The Cell Membrane, Yoonwoo Lee, Allison Ost, Junghyuk Lee, Krisztina Z. Bencze

SACAD: Scholarly Activities

Background: During the first semester of biochemistry experience, students focus on learning the structure and function of biomolecules: carbohydrates, lipids, proteins, and nucleic acids. Visualizing these structures and understanding interactions between molecules helps students better understand biological function. A variety 3D visualization tools are available, ex. PyMol, Chimera, Avogadro, Blender. Within the past decade, Augmented Reality (AR) and Virtual Reality (VR) applications gained more popularity. VR with its immersive visual experience is more sought-after, but the higher cost and the need for headset creates limitations in the classroom. AR visualizations are cheaper and more accessible, several publications report successful implementation …


Ivy Proteins As Guardians Of Bacterial Cell Wall Integrity: Regulation Of Lytic Transglycosylases Explored, Aamna Aijaz, Trinity E. Alamutu, Vy T. Dao, Nathaniel R. Davis, Michael D. Landers, Nykolas K. Mackevicius, Liliana Ortiz, Irina F. Padilla-Montoya, Kacy J. Smith, Maria L. Snyder, Anthony J. Stefanie, Blaise M. Williams, Thomas C. Leeper Feb 2025

Ivy Proteins As Guardians Of Bacterial Cell Wall Integrity: Regulation Of Lytic Transglycosylases Explored, Aamna Aijaz, Trinity E. Alamutu, Vy T. Dao, Nathaniel R. Davis, Michael D. Landers, Nykolas K. Mackevicius, Liliana Ortiz, Irina F. Padilla-Montoya, Kacy J. Smith, Maria L. Snyder, Anthony J. Stefanie, Blaise M. Williams, Thomas C. Leeper

The Kennesaw Journal of Undergraduate Research

Lytic transglycosylases (LTs) are bacterial enzymes involved in biosynthesis and maintenance of the peptidoglycan cell wall. LTs are reported to be regulated by two paralogs of Inhibitor of Vertebrate Lysozymes: Ivyp1 and Ivyp2. This study investigated the regulatory dynamics between the soluble LT (SltB1), and Ivy paralogs as putative regulators in Pseudomonas aeruginosa (PA). The secondary objective was to delineate the critical roles played by a glutamic acid at position 135 in SltB1 and a histidine at position 62 in Ivyp1 in governing their molecular interaction through site directed mutagenesis. Isolated SltB1 shows no lytic activity in our assay, in …


Using Artificial (Ai) To Predict A Structure Of Protein Complex, Yiqing Zang Apr 2024

Using Artificial (Ai) To Predict A Structure Of Protein Complex, Yiqing Zang

SACAD: Scholarly Activities

Proteins play pivotal roles in essential life processes and elucidating their three-dimensional (3D) structures is crucial for understanding their functions. AlphaFold2, an advanced artificial intelligence-based method developed by Google DeepMind, has emerged as a promising tool for predicting protein structures. In this study, we evaluated the predictive capabilities of AlphaFold2. Our findings highlight AlphaFold2's efficacy in providing valuable insights into protein structure prediction, albeit with certain limitations. While AlphaFold2 represents a significant advancement in the field, its utility is best realized when integrated with complementary experimental approaches. Consequently, combining the strengths of AlphaFold2 with experimental validation remains essential for achieving …


Identification Of Regulatory Elements In The Untranslated Regions Of Streptolysin S Associated Gene A Messenger Rna From Group A Streptococcus, Cameron R. Carroll, Sara G. Nibar, Alexis S. Brown, Lauren R. Angello, Gabriela C. Pérez-Alvarado, Brian M. Lee Jan 2024

Identification Of Regulatory Elements In The Untranslated Regions Of Streptolysin S Associated Gene A Messenger Rna From Group A Streptococcus, Cameron R. Carroll, Sara G. Nibar, Alexis S. Brown, Lauren R. Angello, Gabriela C. Pérez-Alvarado, Brian M. Lee

Journal of the South Carolina Academy of Science

Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a human pathogen associated with a variety of diseases such as strep throat, scarlet fever, toxic shock syndrome, and necrotizing fasciitis. One of the virulence factors released by GAS during an invasive infection is a cytotoxic peptide, streptolysin S (SLS), which inhibits the immune response to necrotizing fasciitis. The streptolysin S associated gene A product, SagA, is modified to produce SLS. Thesag operon includes sagA and the genes required for enzyme-mediated post-translational modifications of SagA and the export of SLS. The sagA gene is contained within the pleiotropic …


Comparative Histological Study On The Algerian Thymus Ciliatus At Different Phenological Stages, Nina Sadou, Ratiba Seridi, Hamdi Bendif Dec 2023

Comparative Histological Study On The Algerian Thymus Ciliatus At Different Phenological Stages, Nina Sadou, Ratiba Seridi, Hamdi Bendif

Journal of Bioresource Management

The aim of the current study was to compare the histological observations of stems, leaves, and different secretory structures of Thymus ciliatus at three phenological stages. The anatomical observations of stems, leaves, and glandular trichomes were carried out by light microscopy. The results showed that phenological stages do not affect significantly the anatomical, whereas there was a significant increase in secretory trichomes. The glandular trichomes are distributed on the surface of the stems and the leaves. There are only two distinct types of secretory trichomes, Peltate consisting of a basal cell, a stalk cell, and an 8-celled head type, which …


Using In Silico Tools To Analyze The 5ʹ Untranslated Regions Of The Alcohol Dehydrogenase Gene From Arabidopsis Thaliana And Omega Sequence, Reza Mohammadhassan, Tina Asadishad Dec 2023

Using In Silico Tools To Analyze The 5ʹ Untranslated Regions Of The Alcohol Dehydrogenase Gene From Arabidopsis Thaliana And Omega Sequence, Reza Mohammadhassan, Tina Asadishad

Makara Journal of Science

The 5ʹ ends of protein-encoding genes contain 5ʹ untranslated regions (5ʹUTRs), which can effectively participate in regulating gene expression. The 5ʹUTRs of Arabidospis thaliana–derived alcohol dehydrogenase gene (AtADH) and omega (Ω) sequence from tobacco mosaic virus (TMV) are the most effective enhancers in biotechnology. In this study, bioinformatics techniques were employed to analyze the characteristics of the above sequences. After 5ʹUTR sequence collection, the inner ribosome entrance sites; small RNA (sRNA) target sequences; nucleotide contents; and upstream start and stop codons, ORFs, and coding DNA sequences of the Ω sequence and AtADH 5ʹUTR were identified. Moreover, the …


Identification Of A Small Regulatory Rna Usps Associated With The Universal Stress Protein In Lactobacillus Species, Zarah M. Fowler, Sasha S. Bronovitskiy, Finn K. Rose, Brian M. Lee Aug 2023

Identification Of A Small Regulatory Rna Usps Associated With The Universal Stress Protein In Lactobacillus Species, Zarah M. Fowler, Sasha S. Bronovitskiy, Finn K. Rose, Brian M. Lee

Journal of the South Carolina Academy of Science

The gut microbiome is a complex habitat with many bacterial species, each playing crucial roles in regulating various physiological processes in the body. As the use of probiotics to combat human disease continues to increase, it is important to understand the mechanisms by which probiotic bacteria regulate their interactions with other bacteria and their host. Our exploration of the physiological functions of probiotic bacteria hopes to elucidate the role of small regulatory RNA (sRNA) in regulating gene expression within the microbiome. The goal of this project was to characterize the structure and function of the sRNA, UspS, which is found …


Potential Use Of Proteolytic Bacteria Paenibacillus Dendritiformis (Bt7) Isolated From Batu Tannery Effluents For The Detergent Industry, Chandran Masi, Degafneh Tadesse, Abate Ayele Nov 2022

Potential Use Of Proteolytic Bacteria Paenibacillus Dendritiformis (Bt7) Isolated From Batu Tannery Effluents For The Detergent Industry, Chandran Masi, Degafneh Tadesse, Abate Ayele

Karbala International Journal of Modern Science

This research was aimed at identifying a bacterium that can produce alkaline proteases. As a result, bacteria that produce proteases were isolated from Batu tannery effluents, tested for protease synthesis on skim milk agar plates, and validated with a protease assay. Microscopic and molecular phylogenetic analyses identified Paenibacillus dendritiformis (BT7) as the bacterial isolate with the highest alkaline protease production. The isolate's maximum enzyme production was obtained by 2% inoculum size, 40°C temperature, 9.0 pH, and a 48-hour incubation time with production media components such as glucose, casein, MgCl2, and 2% NaCl. The maximal enzyme activity was 270 U/mL under …


Plants Used By Nyamwezi Traditional Health Practitioners To Remedy Sexually Transmitted Infections In Sikonge, Tanzania, David S. Kacholi, Halima Amir Mar 2022

Plants Used By Nyamwezi Traditional Health Practitioners To Remedy Sexually Transmitted Infections In Sikonge, Tanzania, David S. Kacholi, Halima Amir

Journal of Humanities and Social Sciences

This study aims to document medicinal plants used by Nyamwezi traditional health practitioners (NTHPs) in managing sexually transmitted infections (STIs) in Sikonge District. The data on medicinal plants were collected using a semi-structured questionnaire. A total of 23 NTHPs were interviewed. The findings revealed that 28 medicinal plants, belonging to 16 families and 25 genera, are used for the management of STIs in Sikonge. Most species belonged to family Fabaceae (17.9%), Apocynaceae, Combretaceae and Euphorbiaceae (10.7% each), and Olacaceae and Rutaceae (7.1% each). Out of the recorded plants, 45.7% are used to manage gonorrhoea, 25.7% syphilis, 17.1% vaginal candidiasis, 8.6% …


A Nosy Neighbor: Purification And Functional Characterization Of Lpg2149, Ashley M. Holahan Oct 2021

A Nosy Neighbor: Purification And Functional Characterization Of Lpg2149, Ashley M. Holahan

The Journal of Purdue Undergraduate Research

Ubiquitination is a process that marks proteins for various cell-signaling pathways, namely protein degradation and other processes. Th ese pathways are essential in a wide array of cellular processes, including defense mechanisms against invading pathogens. Th e ubiquitination process is universally found in all eukaryotic organisms, including plants and animals, and thus plays a vital role in cellular homeostasis. Recently, more discoveries have been made on prokaryotic effector proteins that hijack the ubiquitination system even when they do not possess a ubiquitin system of their own. MavC, also known as lpg2147 (Gan, Nakayasu, Hollenbeck, & Luo, 2019; Puvar et al., …


Covid-19 In Silico Drug With Zingiber Officinale Natural Product Compound Library Targeting The Mpro Protein, Renadya Maulani Wijaya, Muhammad Aldino Hafidzhah, Viol Dhea Kharisma, Arif Nur Muhammad Ansori, Arli Aditya Parikesit Sep 2021

Covid-19 In Silico Drug With Zingiber Officinale Natural Product Compound Library Targeting The Mpro Protein, Renadya Maulani Wijaya, Muhammad Aldino Hafidzhah, Viol Dhea Kharisma, Arif Nur Muhammad Ansori, Arli Aditya Parikesit

Makara Journal of Science

Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a worldwide pandemic. Ginger (Zingiber officinale) is a rhizome, which is commonly used for culinary and medicinal purposes. In Indonesia, ginger is taken as traditional medicine by processing it into a drink known as jamu. The present study aimed to assess and evaluate the bioactive compounds in ginger that can be used in drug design for treating COVID-19. The crystal structure of the SARS-CoV-2 main protease (Mpro) was generated from a protein sequence database, i.e., Protein Data Bank, …


Investigating Photosynthetic Stability: Relation Between Thylakoid Lipid Content And The Stability Of The Cytochrome B6f Complex, Marina Mehling Aug 2020

Investigating Photosynthetic Stability: Relation Between Thylakoid Lipid Content And The Stability Of The Cytochrome B6f Complex, Marina Mehling

The Journal of Purdue Undergraduate Research

The cytochrome b6f complex is an enzyme found in plants, cyanobacteria, and green algae that catalyzes the transport of electrons in the rate-limiting step of oxygenic photosynthesis. This dimeric complex has an extensive lipid architecture that is primarily composed of five distinct lipid classes: monogalactosyl diacylglycerol (MGDG), digalactosyl diacylglycerol (DGDG), phosphatidyl glycerol (PG), monoglucosyl diacylglycerol (GlcDG), and sulfoquinovosyl diacylglycerol (SQDG). While these lipid classes have been identified, their precise role in the function of the cytochrome complex are only beginning to be understood. Mechanisms describing the relation between thylakoid lipid content on the stability of the b6 …


Killi-Data News (Winter), Tyrone Genade Mar 2018

Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

Valued readers, it is with a heavy heart that I inform you that this is the last issue of Killi-Data News. The good news is that we will be back as Killifish Research Review. The dissolution of Killi-Data International created a prob- lem: how can the newsletter of a defunct organization live on without that organization? But other additional problems were building in the background. The first issue numbered 15 pages. The previous issue was 28 pages. The number of killifish related papers is increasing while time on our end (the editorial team) is running out. It takes a lot …


Killi-Data News (Fall), Tyrone Genade Mar 2018

Killi-Data News (Fall), Tyrone Genade

Killifish Research Review

Many interesting papers have been published over the last three months. The large volume of papers coupled with the start of the new college semester (and the workload it brings) delayed this issue of Killi-Data News. But better late than never—or so I hope! In this issue Richard van der Laan provides an insightful review of the recent Aphanius papers as to their taxonomic implications and questions. The systematic issues he raises show the importance of the Molecular project: we need to get more samples of the various cyprinodontiforme families to resolve unsettled systematic and taxonomic issues. In the Next …


Killi-Data News (Summer), Tyrone Genade Mar 2018

Killi-Data News (Summer), Tyrone Genade

Killifish Research Review

Over the last three months several interesting and exciting pa- pers have been published. By now most of you have heard the Nothobranchius fish poo news emanating from the Valenzano lab. That paper is reviewed and certainly has repercussions for the health of our captive fish. Polaçik et al have published interesting data with ramifications as to how we breed and incubate annual killifish. The big news in this issue is the paper from the Reznick lab which Jean Huber reviews. The contents of that paper goes to the heart of the question of just what a killifish is. The …


Killi-Data News (Spring), Tyrone Genade Mar 2018

Killi-Data News (Spring), Tyrone Genade

Killifish Research Review

This is the start of Killi-Data News’ second year. In this first issue of the year we have the usual review of research pub- lications as well as input from Martin Reichard on his lab’s Nothobranchius research. Martin is responding to my reviews of his lab’s work in the previous edition. I am serious about making sure the content in this newsletter is reliable but I erred in the previous edition and Martin has written extensively to correct my mistake in the section “Erratum”. This reply is welcomed and owed to readers. I must confess that I don’t know everything …


Killi-Data News (Winter), Tyrone Genade Mar 2018

Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

This is the fourth edition, and concluding issue of the first volume, of Killi-Data News and I am happy that it has been well received by readers. At 25 pages this issue is a bit thin- ner than the last but this is because we agreed to make the cut-off for submissions the 1 st of December so we could get this edition out by the New Year. This is an exciting edition full of new species descrip- tions and analyses that will keep taxonomists busy for years to come. Costa has given us two molecular phylogenies on Melanorivulus as …


Killi-Data News (Spring), Tyrone Genade Mar 2018

Killi-Data News (Spring), Tyrone Genade

Killifish Research Review

This is the start of Killi-Data News’ second year. In this first issue of the year we have the usual review of research pub- lications as well as input from Martin Reichard on his lab’s Nothobranchius research. Martin is responding to my reviews of his lab’s work in the previous edition. I am serious about making sure the content in this newsletter is reliable but I erred in the previous edition and Martin has written extensively to correct my mistake in the section “Erratum”. This reply is welcomed and owed to readers. I must confess that I don’t know everything …


Microstructure Of Attachment Mechanisms Of Newly Hatched Larvae Of Four Cyprinid Species With Comments On Terminology, George E. Maurakis, Eugene G. Maurakis Oct 2017

Microstructure Of Attachment Mechanisms Of Newly Hatched Larvae Of Four Cyprinid Species With Comments On Terminology, George E. Maurakis, Eugene G. Maurakis

Virginia Journal of Science

An adhesive organ is a prominent, protruding mucus secreting gland that is used by newly hatched tadpoles and larvae of some fishes to attach to aquatic vegetation.  The objective of this research is to test the hypothesis that newly hatched cyprinid larvae of Hybognathus hankinsoni, Notemigonus crysoleucas, Cyprinus carpio and Gila atraria contain cephalic adhesive organs.  Newly hatched larvae of Semotilus atromaculatus, which do not attach to submerged aquatic vegetation, were used as the control.  SEM examination of newly hatched larvae indicate there were no adhesive organs on the control species (S. atromaculatus) or test species …


Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager Aug 2016

Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager

Spora: A Journal of Biomathematics

The development of an embryo from a fertilised egg to a multicellular organism proceeds through numerous steps, with the formation of the three germ layers (endoderm, mesoderm, ectoderm) being one of the first. In this paper we study the mesendoderm (the tissue that collectively gives rise to both mesoderm and endoderm) gene regulatory network for two species, \textit{Xenopus laevis} and the axolotl (\textit{Ambystoma mexicanum}) using Boolean networks. We find that previously-established bistability found in these networks can be reproduced using this Boolean framework, provided that some assumptions used in previously-published differential equations models are relaxed. We conclude by discussing our …


3d Picture Of The Syk-Vav1 Protein Complex: Tracking The B-Cell Signal One Complex At A Time, Dan I. Piraner Jul 2011

3d Picture Of The Syk-Vav1 Protein Complex: Tracking The B-Cell Signal One Complex At A Time, Dan I. Piraner

The Journal of Purdue Undergraduate Research

Protein signaling is the key method by which cells recognize a stimulus from their environment and convert it into a response. Signaling occurs in many forms: hormones, growth factors, and even proteins may act as signals from the environment. The response to their detection must be carried from the cell surface, where the signal is detected, to the nucleus, where the cell alters its DNA expression. This study analyzes one component in the signaling pathway of Spleen Tyrosine Kinase (Syk). The Syk protein receives a signal from B-cell receptors and amplifies it, resulting in an adaptive immune response and the …


Letter From The Dean, Lalit Verma Jan 2009

Letter From The Dean, Lalit Verma

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.


Conformational And Circular Dichroism Studies On N-Acetyl-L-Prolyl-D-Alanyl-Methylamide, S. Ramaprasad Jan 1990

Conformational And Circular Dichroism Studies On N-Acetyl-L-Prolyl-D-Alanyl-Methylamide, S. Ramaprasad

Journal of the Arkansas Academy of Science

The compact ordered conformations of the molecule N-Acteyl-L-Prolyl-D-Alanyl-Methylamide have been studied by semiempirical energy calculations in vacuum and circular dichroism (CD) in solution. The presence of ordered structure has been observed in hydrogen bond promoting solvents like trifluoroethanol by CD studies. In hydrogen bond breaking solvents, like trifluoroacetic acid (TFA), significant fraction of the ordered conformers probably assume extended conformation without intramolecular hydrogen bonds and perhaps are in equilibrium with the fraction of compact ordered structures. The trend observed in going from nonpolar to polar solvent is also compatible with the previous NMR studies in solution. The semiempirical energy calculations …