Modeling clinical states and metabolic rhythms in bioarcheology

Bioarcheology is cross disciplinary research encompassing the study of human remains. However, life’s activities have, up till now, eluded bioarcheological investigation. We hypothesized that growth lines in hair might archive the biologic rhythms, growth rate, and metabolism during life. Computational modeling predicted the physical appearance, derived from hair growth rate, biologic rhythms, and mental state for human remains from the Roman period. The width of repeat growth intervals (RI’s) on the hair, shown by confocal microscopy, allowed computation of time series of periodicities of the RI’s to model growth rates of the hairs. Our results are based on four hairs from controls yielding 212 data points and the RI’s of six cropped hairs from Zweeloo woman’s scalp yielding 504 data points. Hair growth was, ten times faster than normal consistent with hypertrichosis. Cantú syndrome consists of hypertrichosis, dyschondrosteosis, short stature, and cardiomegaly. Sympathetic activation and enhanced metabolic state suggesting arousal was also present. Two-photon microscopy visualized preserved portions of autonomic nerve fibers surrounding the hair bulb. Scanning electron microscopy found evidence that a knife was used to cut the hair three to five days before death. Thus computational modeling enabled the elucidation of life’s activities 2000 years after death in this individual with Cantu syndrome. This may have implications for archeology and forensic sciences

Evidence for Microbial Involvement in Pool Finger Precipitation, Hidden Cave, New Mexico

Although speleothems are usually considered inorganic precipitates, recent work has demonstrated hitherto unsuspected biogenic influence in some twilight areas. We have expanded this notion to the dark zone, examining pool fingers from Hidden Cave, New Mexico, to test for possible bacterial involvement. The pool fingers in Hidden Cave are pendant speleothems that formed subaqueously in paleo-pools. They are 1 to 4 cm in diameter and 5 to 50 cm long. A knobby, irregular external shape is underlaid by a layered interior on two scales, a 0.5 to 1.0 cm alternation between dense and porous layers and a mm-scale alternation between dark micritic calcite and clear dogtooth spar. The micrite is similar to microbialites identified in modern and ancient carbonates. Fossil bacteria were found in all layers. These include (1) calcified filaments 1 w m in diameter and 5–50 w m long and (2) micro-rods 0.1 w m by 1–2 w m. Most filaments are curved rods with a smooth surface but rare examples display a diamond crosshatch surface. The micro-rods occur as isolated crystals to dense meshes. We interpret the micro-rods as calcified bacilliform bacteria and the filaments as calcified filamentous bacteria. Carbon isotopic data are slightly more negative (by - 0.5 to - 1.0% in micritic layers than in dogtooth spar layers, suggesting a greater microbial influence in the micritic layers. Based on these similarities to known microbialites (e.g., petrographic fabrics, the presence of fossil bacteria, and the suggestive carbon isotopic data), we conclude that microbial activity was an intimate part of pool finger formation in Hidden Cave. The significance of such involvement goes beyond speleological contexts to wider questions of identification of biosignatures in rocks on earth and beyond

Activities and Ultrastructural Effects of Antifungal Combinations against Simulated Candida Endocardial Vegetations ▿

In vitro pharmacodynamic model (PDM) simulation of serum antifungal concentrations may predict the value of combination antifungal regimens against Candida sp. endocarditis. We investigated the effects of combinations of flucytosine (5FC), micafungin (Mica), and voriconazole (Vor) against Candida-infected human platelet-fibrin clots, used as simulated endocardial vegetations (SEVs). Single clinical bloodstream isolates of Candida albicans, Candida glabrata, Candida parapsilosis, and Candida tropicalis were used. All four isolates were susceptible to 5FC, while C. glabrata was resistant to Vor and C. tropicalis had a paradoxical resistance phenotype to Mica. The SEVs were prepared with an initial inoculum of 1 × 106 CFU/g of SEV and added to a PDM, which utilized yeast nitrogen broth-2% glucose and incubation at 35°C and simulated antifungal pharmacokinetic profiles. Fungal densities in the SEVs were determined in quadruplicate over 72 h. Scanning electron microscopy (SEM) was used to evaluate treatment and control SEVs. Vor was the least active single agent against all Candida spp. except for C. parapsilosis, where it was comparable to Mica. In contrast, 5FC was the most active against all Candida spp. except for C. tropicalis, where it was comparable to Mica. The combination of 5FC plus Vor was superior to either agent alone against C. parapsilosis. The combination of Vor plus Mica was inferior to the use of Mica alone against C. tropicalis. The triple combination of 5FC plus Vor plus Mica was no better than single or dual agents against any of the Candida spp. The ultrastructural features of infected SEVs were unique for each Candida sp., with C. parapsilosis in particular manifesting friable biofilm clusters. In general, 5FC and Mica were superior in their rates and extents of fungal burden reduction compared to Vor against Candida-infected SEVs. Evaluation of 5FC and Mica in animal models of Candida endocarditis is warranted

Methods to analyze metastable and microparticulate hydrated and hydrous iron sulfate minerals

We evaluate analytical methods for characterizing hydrated and hydrous iron sulfate minerals (HHIS) that are typically metastable in air or vacuum, commonly form micrometer-sized particles, and contain multi-valent and light elements (Fe2+, Fe3+, OH-, and H2O) that may be challenging to quantify. We synthesized or obtained HHIS-szomolnokite, melanterite, rhomboclase, schwertmannite, ferricopiapite, paracoquimbite, and jarosite-as well as Fe-oxides. These nominally pure samples were characterized with X-ray diffraction (XRD), and then used to evaluate bulk analyses obtained from combined inductively coupled plasma, optical emission spectroscopy (ICP-OES), ion chromatography (IC), Mössbauer spectroscopy, and mass spectrometry. Integrated bulk analyses showed excellent agreement with the nominal formulas for the minerals. Because HHIS commonly form micro-sized particles-for example, HHIS found in acid mine drainage (AMD) environments and in martian meteorites-it is necessary to develop micro-analytical techniques. Microscopic mid-infrared spectroscopy allows the analyst to successfully discriminate among HHIS with minimal sample preparation on the small scale (̃40 × 40 μm). For chemical analysis, electron probe microanalysis (EPMA) is preferred for samples that can be mounted, polished, coated, and that are stable under high vacuum; however, few HHIS meet those criteria. To characterize HHIS compositions, we show that multiple low-vacuum scanning electron microscopy (SEM) analyses of the same uncoated, unpolished mineral are required. Analysis of each mineral shows linear trends on ternary diagrams of 5×Fe-SO4-O (where oxygen is in O, OH, and H2O) that may be used to narrow down the HHIS mineralogy. Low-vacuum SEM also provides invaluable information about the geochemical and textural context of the samples. Our study provides protocols for microanalysis of these challenging, fine-grained, and metastable HHIS that may also be applied to other mineral groups

Descubriendo la riqueza de las Cuevas: La Cueva de Villa Luz, en Tabasco

Sabías que…La Cueva de Villa Luz es famosa por su singular ambiente, rico en compuestos de azufre. Esta cueva se encuentra entre las más peligrosas para los humanos, ya que en su interior hay grandes concentraciones de gas sulfhídrico, muy tóxico, que le da a la cueva el típico olor a huevo podrido. La Villa Luz es el típico ejemplo de una cueva cuyo desarrollo y crecimiento se encuentran aún activos, debido a la acción del ácido sulfúrico. Este ácido es generado por el desecho metabólico de las colonias de bacterias, que obtienen sulfuro de hidrógeno de las rocas. El ácido sulfúrico es un elemento natural que interviene en varios procesos biogeoquímicos responsables de la formación de la cuev

Geomicrobiology of Cave Ferromanganese Deposits: A Field and Laboratory Investigation

Unusual ferromanganese deposits are found in several caves in New Mexico. The deposits are enriched in iron and manganese by as much as three orders of magnitude over the bedrock, differing significantly in mineralogy and chemistry from bedrock-derived insoluble residue. The deposits contain metabolically active microbial communities. Enrichment cultures inoculated from the ferromanganese deposits produced manganese oxides that were initially amorphous but developed into crystalline minerals over an 8-month period and beyond; no such progression occurred in killed controls. Phylogenetic analyses of sequences from clone libraries constructed from culture DNA identified two genera known to oxidize manganese, but most clones represent previously unknown manganese oxidizers. We suggest that this community is breaking down the bedrock and accumulating iron and manganese oxides in an oligotrophic environment

Bridgman Growth of Laser-Cooling-Grade LiLuF 4 :Yb 3+ Single Crystals

The first demonstration of solid-state laser cooling in fluoride grown by the Bridgman method is reported. We present advances in the Bridgman crystal growth of Yb3+-doped LiLuF4 (LLF:Yb) single crystals in a radio-frequencyheated furnace. COMSOL Multiphysics numerical simulations are used to investigate the thermal gradients within the crucible during the crystal growth. Optical spectroscopy and laser-cooling efficiency measurements of three LLF:Yb crystals as well as laser cooling of a LLF:5%Yb crystal in a double-pass geometry from room temperature to 195 K are reported. Solid-state laser cooling is only possible in materials having extremely high chemical purity and crystal quality. The vertical Bridgman method is well suited for the growth of high-quality crystals on the few gram scale, a quantity that is compatible with purification techniques that aim to exceed the 99.999−99.9999% purity that is typical of commercial precursor materials. The results demonstrate that the small-scale Bridgman growth of LLF:Yb in glassy-carbon crucibles is able to produce laser-coolinggrade crystals, opening a new route to produce high-performance materials for solid-state optical refrigerators and radiation-balanced lasers

Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves

Lechuguilla Cave is an ancient, deep, oligotrophic subterranean environment that contains an abundance of low‐density ferromanganese deposits, the origin of which is uncertain. To assess the possibility that biotic factors may be involved in the production of these deposits and to investigate the nature of the microbial community in these materials, we carried out culture‐independent, small subunit ribosomal RNA (SSU rRNA) sequence‐based studies from two sites and from manganese and iron enrichment cultures inoculated with ferromanganese deposits from Lechuguilla and Spider Caves. Sequence analysis showed the presence of some organisms whose closest relatives are known iron‐ and manganese‐oxidizing/reducing bacteria, including Hyphomicrobium, Pedomicrobium, Leptospirillum, Stenotrophomonas and Pantoea. The dominant clone types in one site grouped with mesophilic Archaea in both the Crenarchaeota and Euryarchaeota. The second site was dominated almost entirely by lactobacilli. Other clone sequences were most closely related to those of nitrite‐oxidizing bacteria, nitrogen‐fixing bacteria, actinomycetes and β‐ and γ‐Proteobacteria. Geochemical analyses showed a fourfold enrichment of oxidized iron and manganese from bedrock to darkest ferromanganese deposits. These data support our hypothesis that microorganisms may contribute to the formation of manganese and iron oxide‐rich deposits and a diverse microbial community is present in these unusual secondary mineral formations

Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA

<div><p>Subsurface habitats harbor novel diversity that has received little attention until recently. Accessible subsurface habitats include lava caves around the world that often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. To investigate these differences, we analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soil overlying each cave. The same phyla were represented in both surface soils and cave microbial mats, but the overlap in shared OTUs (operational taxonomic unit) was only 11.2%. Number of entrances per cave and temperature contributed to observed differences in diversity. In terms of species richness, diversity by mat color differed, but not significantly. <i>Actinobacteria</i> dominated in all cave samples, with 39% from caves and 21% from surface soils. <i>Proteobacteria</i> made up 30% of phyla from caves and 36% from surface soil. Other major phyla in caves were <i>Nitrospirae</i> (7%) followed by minor phyla (7%), compared to surface soils with <i>Bacteroidetes</i> (8%) and minor phyla (8%). Many of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. This study is the first comprehensive comparison of bacterial communities in lava caves with the overlying soil community.</p></div