Helen Brandenburg\u27s Letter

3 pages. Letter from Helen Brandenburg Carney to Tom W. Bryant, Pittsburg State University, April 28, 2003, regarding a donatio

Microbial Ecogenomics and Forensic Archaeology: New Methods for Investigating Clandestine Gravesites

In the mid-1990s, the crime scene toolkit was revolutionised by the introduction of DNA-based analyses such as the polymerase chain reaction, low copy number DNA analysis, short-tandem repeat typing, pulse-field gel electrophoresis and variable number tandem repeat. Since then, methodological advances in other disciplines, especially molecular microbial ecology, can now be adapted for cutting-edge applications in forensic contexts. Despite several studies and discussions, there is, however, currently very little evidence of these techniques’ adoption at the contemporary crime scene. Consequently, this article discusses some of the popular ‘omics’ and their current and potential exploitations in the ‘forensic ecogenomics’ of body decomposition in a crime scene. Thus, together with published supportive findings and discourse, knowledge gaps are identified. These then justify the need for more comprehensive, directed, concerted and global research towards state-of-the-art microecophysiology method application and/or adaptation for subsequent successful exploitations in this additional context of microbial forensics

Categorizing, Coding, and Manipulating Qualitative Data Using the WordPerfect® Word Processor

In this paper, we present a method of categorizing, coding, and sorting/manipulating qualitative (descriptive) data using the capabilities of a commonly-used word processor: WordPerfect®. We explain the process and its development in simple terms for the person who may be familiar with qualitative research and data, but not with computer and/or word processor manipulation of that data. Although we developed the process to suit our methods, it can easily be adapted/evolved to fit different research situations where a method of rapidly handling large amounts of descriptive data is desirable

Glycosaminoglycan Synthesis by Human Keratinocytes: Cell Growth and Medium Calcium Effects

The influences of cell density, differentiation, and medium calcium levels on glycosaminoglycan biosynthesis were evaluated in cultured human epidermal keratinocytes. Following metabolic labeling with [35S]-sulfate and [3H]-glucosamine under steady state conditions in “high” medium calcium (> 1.0 mMol), the majority of sulfated glycosaminoglycans remained associated with the cell layers, whereas hyaluronic acid, which was present in smaller amounts than the sulfated products, was about equally distributed between the medium and the cell layers. Of the sulfated glycosaminoglycans, heparan sulfate and chondroitin 4/6-sulfate were the major species and were present in roughly comparable amounts, whereas dermatan sulfate was quantitatively the lesser of the products. The effects of “low” medium calcium (0.3 and 0.025 mM) were complex, although a consistent decrease in the incorporation of the [3H]-glucosamine precursor was found at high cell density, probably reflecting a decrease in its intracellular specific activity. In “high” calcium cultures, there was a strong inverse correlation (r = -0.92) between keratinocyte cell number and cellular production of sulfated glycosaminoglycans, whereas no such relationship was evident in cultures grown in “low” calcium medium at comparable cell density. Because keratinocyte differentiation is inhibited in the low calcium conditions, the results suggest that the decrease in production of sulfated glycosaminoglycans by confluent keratinocytes may actually correlate with differentiation rather than with cell number

A Combined Application of Molecular Microbial Ecology and Elemental Analyses Can Advance the Understanding of Decomposition Dynamics

Introducing animal carbon-source to soil initiates biochemical and microbial processes that lead to its decomposition and recycling, which subsequently cause successional shifts in soil microbial community. To investigate the use of soil microbial community to inform criminal investigation, this study was designed to mimic clandestine graves. It compared the decomposition of stillborn piglets (Sus scrofa domesticus), as human analogues, to oak (Quercus robur) leaf litter and soil-only controls outdoors for 720 days. Environmental and edaphic parameters were monitored and showed soil microbial community alignment with temperature seasonality, which highlighted the importance of this abiotic factor. Denaturing gradient gel electrophoresis (DGGE) data were used to calculate Hill numbers and diversity indices of the bacterial 16S rRNA community did not distinguish mammalian- from plant-based decomposition consistently during the first or second year of the study. In contrast, the fungal 18S rRNA community allowed clear differentiation between different treatments (beta diversity) throughout the 720-day experiment and suggested the moment of the decomposing mammalian skin rupture. 16S rRNA-based NGS facilitated the identification of e.g., Pirellulaceae, Acidobacteria ii1-15_order and Candidatus xiphinematobacter as Year 2 bacterial markers of gravesoil at family, order and species taxonomic levels, respectively, and confirmed the similarity of the calculated Hill diversity metrics with those derived from DGGE profiling. Parallel soil elemental composition was measured by portable X-ray Fluorescence where calcium profiles for the piglet-associated soils were distinct from those without carrion. Also, soil calcium content and PMI correlated positively during the first year then negatively during the second. This study is one of the first to apply a multidisciplinary approach based on molecular and physicochemical analytical techniques to assess decomposition. It highlights the recognised potential of using soil microbial community in forensic investigations and provides a proof-of-concept for the application of a combined molecular and elemental approach to further understand the dynamics of decomposition. In addition, it sets the scene for further research in different conditions based on Hill numbers metrics instead of the classic ecological indices for soil necrobiome richness, diversity and evenness.</p

Long telomeres are associated with clonality in wild populations of the fissiparous starfish Coscinasterias tenuispina

elomeres usually shorten during an organism's lifespan and have thus been used as an aging and health marker. When telomeres become sufficiently short, senescence is induced. The most common method of restoring telomere length is via telomerase reverse transcriptase activity, highly expressed during embryogenesis. However, although asexual reproduction from adult tissues has an important role in the life cycles of certain species, its effect on the aging and fitness of wild populations, as well as its implications for the long-term survival of populations with limited genetic variation, is largely unknown. Here we compare relative telomere length of 58 individuals from four populations of the asexually reproducing starfish Coscinasterias tenuispina. Additionally, 12 individuals were used to compare telomere lengths in regenerating and non-regenerating arms, in two different tissues (tube feet and pyloric cecum). The level of clonality was assessed by genotyping the populations based on 12 specific microsatellite loci and relative telomere length was measured via quantitative PCR. The results revealed significantly longer telomeres in Mediterranean populations than Atlantic ones as demonstrated by the Kruskal-Wallis test (K=24.17, significant value: P-value<0.001), with the former also characterized by higher levels of clonality derived from asexual reproduction. Telomeres were furthermore significantly longer in regenerating arms than in non-regenerating arms within individuals (pyloric cecum tissue: Mann-Whitney test, V=299, P-value<10−6; and tube feet tissue Student's t=2.28, P-value=0.029). Our study suggests that one of the mechanisms responsible for the long-term somatic maintenance and persistence of clonal populations is telomere elongation

Food Security in the COVID-19 Era

Food insecurity is a national issue, one that affected 10.5% of households during some point of the year 2019. Those affected by food insecurity can have their access to food jeopardized due to financial hardship, eating patterns altered to prolong the food available, or various other adjustments including reliance on low-cost food, skipping meals, etc. The state of Vermont is not immune to food insecurity, with a rate of 11.3% of households in 2018. The Covid-19 pandemic created an unprecedented shift in daily life, with households having to rapidly adapt to meet newly imposed governmental regulations, including stay at home orders, while maintaining access to food essentials. This changed exacerbated food insecurity in already food-insecure households, while simultaneously creating food insecurity for those previously unaffected. A study focusing on food insecurity in Vermont from March to April 2020 found a 32.3% increase in food insecurity, with 35.5% of food-insecure households being previously food-secure. This change highlighted not only the growing incidence of food insecurity, but also acknowledged the demographic change seen by newly food insecure households. While this increase is dramatic and alarming, to our knowledge there is no research looking at the continuation of these trends regarding the impact of the Covid-19 pandemic on food insecurity in Vermont households. This lack of data indicates a need for continued follow up to best inform governmental agencies on both how Vermont households are being affected, and how regulations during summer & fall 2020 impacted the rise in food insecurity. These data will then provide guidance for future action to combat current and future food insecurity.https://scholarworks.uvm.edu/comphp_gallery/1304/thumbnail.jp

Evolutionary changes in the genome of Mycobacterium tuberculosis and the human genome from 9000 years BP until modern times

The demonstration of Mycobacterium tuberculosis DNA in ancient skeletons gives researchers an insight into its evolution. Findings of the last two decades sketched the biological relationships between the various species of tubercle bacilli, the time scale involved, their possible origin and dispersal. This paper includes the available evidence and on-going research. In the submerged Eastern Mediterranean Neolithic village of Atlit Yam (9000 BP), a human lineage of M. tuberculosis, defined by the TbD1 deletion in its genome, was demonstrated. An infected infant at the site provides an example of active tuberculosis in a human with a naïve immune system. Over 4000 years later tuberculosis was found in Jericho. Urbanization increases population density encouraging M. tuberculosis/human co-evolution. As susceptible humans die of tuberculosis, survivors develop genetic resistance to disease. Thus in 18th century Hungarian mummies from V ac, 65% were positive for tuberculosis yet a 95-year-old woman had clearly survived a childhood Ghon lesion. Whole genome studies are in progress, to detect changes over the millennia both in bacterial virulence and also host susceptibility/resistance genes that determine the NRAMP protein and Killer Cell Immunoglobulin-like Receptors (KIRs). This paper surveys present evidence and includes initial findings.The contribution made by our many collaborators, researchers and students is gratefully acknowledged. Special acknowledgement is due to Dr Angela Gernaey (deceased) who helped pioneer the early mycolic acid work on the bison bone