Biology Commons^™

Impacts Of Hiv Cure Interventions On Viral Reservoirs In Tissues, Paul W. Denton, Ole S. Søgaard, Martin Tolstrup

Paul W. Denton

HIV reservoirs persist in infected individuals despite combination antiretroviral therapy and can be identified in secondary lymphoid tissues, in intestinal tissues, in the central nervous system as well as in blood. Clinical trials have begun to explore effects of small molecule interventions to perturb the latent viral infection, but only limited information is available regarding the impacts of HIV cure-related clinical interventions on viral reservoirs found in tissues. Of the 14 HIV cure-related clinical trials since 2012 that have evaluated the effects of small molecule interventions in vivo, four trials have examined the impacts of the interventions in peripheral …

The Efficacy Of Whole Human Genome Capture On Ancient Dental Calculus And Dentin, Kirsten A. Ziesemer, Jazmin Ramos-Madrigal, Allison E. Mann, Bernd W. Brandt, Krithivasan Sankaranarayanan, Andrew T. Ozga, Menno Hoogland, Courtney A. Hofman, Domingo C. Salazar-Garcia, Bruno Frohlich, George R. Miller, Anne C. Stone, Mark Aldenderfer, Cecil M. Lewis Jr., Corinne L. Hofman, Christina Warinner, Hannes Schroeder

Andrew Ozga

Objectives

Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques.

Materials and methods

Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in‐solution hybridization capture and high‐throughput sequencing.

Results

Total DNA from calculus exceeded that of dentin in all cases, …

Successful Enrichment And Recovery Of Whole Mitochondrial Genomes From Ancient Human Dental Calculus, Andrew T. Ozga, Maria A. Nieves-Colon, Tanvi P. Honap, Krithivasan Sankaranarayanan, Courtney A. Hofman, George R. Milner, Cecil M. Lewis Jr., Anne C. Stone, Christina Warinner

Andrew Ozga

Objectives

Archaeological dental calculus is a rich source of host‐associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis.

Materials and …

Subsistence Strategies In Traditional Societies Distinguish Gut Microbiomes, Alexandra J. Obregon-Tito, Raul Y. Tito, Jessica Metcalf, Krithivasan Sankaranarayanan, Jose C. Clemente, Luke K. Ursell, Zhenjiang Zech Xu, Will Van Treuren, Rob Knight, Patrick M. Gaffney, Paul Spicer, Paul Lawson, Luis Marin-Reyes, Omar Trujillo-Villarroel, Morris Foster, Emilio Guija-Poma, Luzmila Troncoso-Corzo, Christina Warinner, Andrew T. Ozga, Cecil M. Lewis Jr.

Andrew Ozga

Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26–513) and functional …

Intrinsic Challenges In Ancient Microbiome Reconstruction Using 16s Rrna Gene Amplification, Kirsten Ziesemer, Allison Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-Garcia, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. Macdonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis Jr., Corinne Hofman, Christina Warinner

Andrew Ozga

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon …

Origins Of An Unmarked Georgia Cemetery Using Ancient Dna Analysis, Andrew T. Ozga, Raul Y. Tito, Brian M. Kemp, Hugh Matternes, Alexandra J. Obregon-Tito, Leslie Neal, Cecil M. Lewis Jr.

Andrew Ozga

Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and, in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we used ancient DNA extraction methods in well-preserved skeletal fragments from 20 individuals buried in Avondale Burial Place to investigate the origins of the …

Comparison Of Two Ancient Dna Extraction Protocols For Skeletal Remains From Tropical Environments, Maria A. Nieves-Colon, Andrew T. Ozga, William J. Pestle, Andrea Cucina, Vera Tiesler, Travis W. Stanton, Anne C. Stone

Andrew Ozga

Objectives

The tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semi‐tropical sites in Tanzania, Mexico, and Puerto Rico (N = 12).

Materials and Methods

All samples were extracted twice, built into double‐stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for …

Differential Preservation Of Endogenous Human And Microbial Dna In Dental Calculus And Dentin, Allison E. Mann, Susanna Sabin, Kirsten Ziesemer, Ashild J. Vagene, Hannes Schroeder, Andrew T. Ozga, Krithivasan Sankaranarayanan, Courtney A. Hofman, James A. Fellows Yates, Domingo C. Salazar-Garcia, Bruno Frohlich, Mark Aldenderfer, Menno Hoogland, Christopher Read, George R. Milner, Anne C. Stone, Cecil M. Lewis Jr., Johannes Krause, Corinne Hofman, Kirsten I. Bos, Christina Warinner

Andrew Ozga

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is …

Janani Subramaniam Thesis.Pdf, Janani Subramaniam

Janani Subramaniam

Life Is In The Blood, Alan L. Gillen, Jason Conrad

Alan L. Gillen

It takes about 60 seconds for all the blood in your body to complete its journey. It travels from your heart to your extremities and returns, there and back again. Blood moves with the rapid current of the great arterial rivers and through the smallest capillary creeks. William Harvey first noticed circulation (1628) through the heart into arteries and veins; however, he could not see how they connected since he did not have a microscope. The man who first described this was Anton van Leeuwenhoek about 46 years later (1674). Then, J. J. Lister and Thomas Hodgkin described the rouleaux …

Trpm4 Ion Channels In Pre-Bo¨Tzinger Complex Interneurons Are Essential For Breathing Motor Pattern But Not Rhythm, Marina Cristina D. Picardo, Yae K. Sugimura, Kaitlyn E. Dorst, Prajkta S. Kallurkar, Victoria T. Akins, Xingru Ma, Ryoichi Teruyama, Romaine Guinamard, Kaiwen Kam, Margaret Saha, Christopher A. Del Negro

Christopher Del Negro

Inspiratory breathing movements depend on pre-Bötzinger complex (preBötC) interneurons that express calcium (Ca2+)-activated nonselective cationic current (ICAN) to generate robust neural bursts. Hypothesized to be rhythmogenic, reducing ICAN is predicted to slow down or stop breathing; its contributions to motor pattern would be reflected in the magnitude of movements (output). We tested the role(s) of ICAN using reverse genetic techniques to diminish its putative ion channels Trpm4 or Trpc3 in preBötC neurons in vivo. Adult mice transduced with Trpm4-targeted short hairpin RNA (shRNA) progressively decreased the tidal volume of breaths yet surprisingly increased breathing frequency, often followed by gasping and …

The Origin Of Bubonic Plague, Alan L. Gillen, Frank Sherwin

Alan L. Gillen

Although some forms of the bacterium Yersinia are harmless, other forms have devastated human populations, causing a plague of biblical proportions (Psalm 91:3-7, Psalm 91:9-10,). Bubonic plague, also known as the ‘Black Death’ that killed one fourth of Europe’s population in the 1300s, appeared as a great pestilence several times in the Old Testament, including in Psalm 91 and in 2 Samuel 24:14-25. Perhaps the clearest example of such a plague is recorded in 1 Samuel 6:4-19, where there is a specific reference to the tumors on people (bubos = the tumors of lymph glands) …

Data Files Column Key: Effects Of Amur Honeysuckle (Lonicera Maackii) On Headwater Streams, Julia I. Chapman, Eric B. Borth, Ryan W. Mcewan

Ryan McEwan

Document provides a description for each column heading used in the data files contained in the collection "Effects of Amur Honeysuckle (Lonicera maackii) on Headwater Streams."

File is in comma-separated values (.csv) format; to view the file in Excel (.xlsx), see the supplemental file.

Decadal Effects Of Thinning On Understory Light Environments And Plant Community Structure In A Subtropical Forest, Ho-Chen Tsai, Jyh-Min Chiang, Ryan Mcewan, Teng-Chiu Lin

Ryan McEwan

Canopy-opening disturbance such as thinning has immediate and substantive effects on understory microclimate and therefore the establishment and growth of understory plants. A large number of studies have reported the effects of thinning on tree growth, but few studies have examined long-term effects of thinning on understory light environments and species and functional diversity of understory plants. Even less is known whether the change in understory plant community structure observed following canopy disturbance is short-lived and would diminish as the canopy closes or a long lasting due to legacy effects. We examined the effects of an experimental removal of 25% …

The Genesis Of Malaria: The Origin Of Mosquitoes And Their Protistan Cargo, Plasmodium Falciparum, Alan L. Gillen, Frank Sherwin

Alan L. Gillen

Malaria is caused by the parasite belonging to the genus Plasmodium; however, creation biologists maintain this organism was not always parasitic. Plasmodium is probably a degenerate form of algae. Mosquitoes, the vector of Plasmodium, were probably designed to be pollinators, not parasite vectors. In this article, we present both the evolutionary and creation explanation for the origin of malaria with a mention to its vector, the mosquito.

The purpose of this article is to provide a reasonable explanation for the genesis of malaria. Microbiology and parasitology research based on the creation paradigm appears to provide some answers to these puzzling …

The Genesis Of Pathogenic E. Coli, Alan L. Gillen, Douglas Oliver

Alan L. Gillen

Even though some strains are pathogenic, most E. coli strains still show evidence of being one of God’s “very good” creations.

Fig. 1. E. coli Gram stain (Wiki commons image). E. coli are Gram-negative bacteria, thus red or pink colored. The red color is due to a counterstain, called safranin.

Escherichia coli is frequently in the news (Fig. 1). E. coli often gets “bad press” for contaminating drinking water or causing a food-borne infection (via hamburgers, apple juice, spinach, or other foods). Recently a new strain (E. coli O145) has been implicated in contaminating lettuce in the U.S., while …

Robert Koch, Creation, And The Specificity Of Germs, Alan L. Gillen, Douglas Oliver, Frank Sherwin

Alan L. Gillen

Microbiology is dominated by evolution today. Just look at any text, journal article, or the topics presented at professional scientific meetings. Darwin is dominant.

Microbiology is dominated by evolution today. Just look at any text, journal article, or the topics presented at professional scientific meetings. Darwin is dominant. Many argue that “nothing in biology makes sense except in the light of evolution” (Dobzhansky 1973). But it was not always this way. In fact, a review of the major founders of microbiology has shown that they were creationists.1 We would argue that a better idea thanevolution and one of much …

Biblical Leprosy: Shedding Light On The Disease That Shuns, Alan L. Gillen

Alan L. Gillen

Leprosy has terrified humanity since ancient times and was reported as early as 600 BC in India, China, and Egypt. Hansen’s disease is still a major health problem.

Disease is a constant reminder of just how much things have changed since God pronounced a curse on the earth. At first, everything was “very good,” but Adam’s sin brought death and decay into the world.

Microbes And The Days Of Creation, Alan L. Gillen

Alan L. Gillen

The world of germs and microbes has received much attention in recent years. But where do microbes fit into the creation account? Were they created along with the rest of the plants and animals in the first week of creation, or were they created later, after the Fall? These are some questions that creation microbiologists have been asking in recent years. Ongoing research, based on the creation paradigm, appears to provide some answers to these puzzling questions. The answers to these questions are not explicit in Scripture, so the answers cannot be dogmatic. However, a reasonable extrapolation from biological data …

Darwin At The Drugstore? Testing The Biological Fitness Of Antibiotic Resistant Bacteria, Alan L. Gillen, Sarah Anderson

Alan L. Gillen

The issue of antibiotic resistance in bacteria is growing. For example, methicillin-resistant Staphylococcus aureus (MRSA) is a leading human pathogen. New strains of MRSA are resistant to methicillin and numerous other antibiotics, placing the patient in significant danger. Indeed, the Centers for Disease Control revealed in 2007 that the number of deaths due to MRSA exceeded that of AIDS in the United States. It is no wonder that antibiotic resistance is one of the most significant and important health care issues. The ability of bacterial pathogens to evade traditional antibiotics is faster than the drug makers’ ability to make new …

Our Impressive Immune System: More Than A Defense, Alan L. Gillen, Jason Conrad

Alan L. Gillen

Most likely the immune system was put into place in the original human body design. We know from Exodus 20:11 and other verses that God completed His work of creation in six days. Therefore, the human body and its functional parts, including the components of the immune system, must have been part of the original creation. God said that all He had made was very good (Genesis 1:31). Since there were no pathogens (germs), parasites, or diseases prior the Edenic Fall and subsequent Curse, the immune system may have functioned differently in that world unmarred by sin and death.

The …

Staph Bacteria From First Breath The Interweaving Of The Nasal Microbiome With The Intricate And Complex Nose, Alan L. Gillen

Alan L. Gillen

Many microbes live in a mutualistic relationship with the human body, make up the human microbiome, and play a role in our health by stimulating and modulating the immune system. Man’s body is “covered” both inside and outside with millions of microbes that play a role in maintaining normal bodily functions and sustaining life in our changing world. The inner nose in the human body is colonized by millions of microbes during the first week of life. This internal colonization of the upper respiratory system is termed our nasal microbiome. Though we cannot see it, this microbiome is important for …

The Design Of The Mosquito And Its Dangers, Alan L. Gillen, Frank Sherwin

Alan L. Gillen

Mosquitoes (Family Culicidae) have been the scourge of mankind since the Fall. Although seemingly designed to inflict suffering and pain via rapid reproduction and formidable mouthparts, evidence mounts that this creature was not always the deadly vector it is today. Mosquitoes are currently and have always been pollinators. The majority of their lives they feed on plants, nectar, pollen, and microbes even in today's world. The Zika virus is but the latest of a significant list of pathogens spread by “the world’s most dangerous animal.” In the past, Christians have been involved in key discoveries linking mosquitoes to diseases.

The Origin Of Fleas And The Genesis Of Plague, Alan L. Gillen

Alan L. Gillen

Human history has been riddled by diseases spread by flea vectors including the bubonic plague. Recently, Madagascar has documented more than 100 cases. Fleas were part of God’s “very good” (Genesis 1:31) creation that transformed to an ectoparasitic condition after the Curse. Creation biologists continue to synthesize a working model of this conversion from environmental recyclers to parasites as a secondary state. Morphological design of the flea combined with its unique feeding ability has resulted in it being an exceptional vector for Yersinia pestis, the causative bacterium of the plague.

The Wonderfully Made Design Of The Skin And Its Microbiome, Alan L. Gillen

Alan L. Gillen

Many microbes live in a mutualistic relationship with the human body, make up the human microbiome, and play a role in our health by modulating the immune system. Man is “covered” inside and outside his body with millions of microbes to maintain normal bodily functions and sustain life in our changing world. The skin is the largest organ in the human body and is colonized by millions of microbes. This external colonization of the integumentary system is termed our skin microbiome. Man cannot see it (except with a microscope), but we need it for normal functioning, certainly in a pathogenic …

The Signature Of God In Medicine And Microbiology An Apologetic Argument For Declarative Design In The Discoveries Of Alexander Fleming, Alan L. Gillen, Michael Cargill

Alan L. Gillen

In logic and reasoning, a signature indicates the presence of an author; likewise, the characteristics of staphylococci indicate the presence of a Creator. Staphylococci and its “kind” are common bacteria, particularly in colonized people.1 Staphylococcus aureus has a complex molecular mechanism of assembling its golden pigment, staphyloxanthin. The biosynthesis of staphyloxanthin is a stellar example of irreducible complexity. Similar to staphylococci, the life and works of Alexander Fleming show the fingerprints of Providence. The so-called “serendipitous” achievements of Fleming have contributed to modern medicine, convincing Fleming and others that God was at work in his life. Fleming recognized that …

Super Staph In The Community: Is It Evolving?, Alan L. Gillen, Rachel Walters

Alan L. Gillen

Staphylococcus aureus infections are a common cause of disease, particularly in colonized people. They frequently cause staph infections and are often dubbed “Super Staph” because they are virulent and multidrug resistant. Recently, a series of published articles have reported that community-acquired methicillin-resistant S. aureus (CA-MRSA) strains are evolving and becoming more prevalent in households. In contrast, health care acquired MRSA (HA-MRSA) is declining in the United States. The changing “Superbugs” have often been used as an example of “evolution in action.” Although MRSA infections have become more prevalent in the community, studies of college students carrying S. aureus and MRSA …

The Coliform Kind: E. Coli And Its “Cousins” The Good, The Bad, And The Deadly, Alan L. Gillen, Matthew Augusta

Alan L. Gillen

Even though some intestinal bacteria strains are pathogenic and even deadly, most coliforms strains still show evidence of being one of God’s “very good” creations. In fact, bacteria serve an intrinsic role in the colon of the human body. These bacteria aid in the early development of the immune system and stimulate up to 80% of immune cells in adults. In addition, digestive enzymes, Vitamins K and B12, are produced byEscherichia coli and other coliforms. E. coli is the best-known bacteria that is classified as coliforms. The term “coliform” name was historically attributed due to the “Bacillus coli …

The Genesis Of The “Brain-Eating” Amoeba, Alan L. Gillen, Jonathan Augusta, Kurt Schneckenburger

Alan L. Gillen

The Creator made all creatures, including amoebas, with variation and plasticity in their genome for global differences of climate, terrain, and environment. God made all creatures to multiply and fill the earth. Diversification and speciation from the original kind would be normal even in a perfect world. Naegleria fowleri is a global amoeba pathogen that is the causative agent of primary amoebic meningoencephalitis (PAM), thus termed “brain-eating.” Many people are evidently exposed, based upon antibody levels, to this amoeba while swimming in warm waters. Only a small percentage succumb to the germ, but once invasion happens, only about 1% survive. …

Serratia Marcescens, The “Flame” Strain: The Genesis Of A New Variant A Newly Described Strain With Prolific Pigment Produced At High Temperature, Alan L. Gillen, Mandy Morgante, Matthew Augusta, Ryan Mackay

Alan L. Gillen

Serratia marcescens, a Gram-negative, rod-shaped, facultative anaerobe (Fig. 1), is ubiquitous in water, soil, and natural settings. It is easily grown in the lab and may serve as an ideal model for adaptation studies because of the natural color variation of S. marcescens (Gillen 2008). In this paper, we describe a new variant with prolific pigment (prodigiosin) production at high temperatures. In the wild and in buildings, S. marcescens is noted for the production of a bright red pigment called prodigiosin (Williams 1973). We have found a new strain that appears to have adapted to a relatively new pond …