A few papers

i. The Living Dead: Bacterial Community Structure of a Cadaver at the Onset and End of the Bloat Stage of Decomposition. There are a lot of questions one might ask about how the world works. Incidentally I should note that when I die I really wouldn’t mind contributing to a study like this. Here’s the abstract, with a couple of links added to ease understanding:

“Human decomposition is a mosaic system with an intimate association between biotic and abiotic factors. Despite the integral role of bacteria in the decomposition process, few studies have catalogued bacterial biodiversity for terrestrial scenarios. To explore the microbiome of decomposition, two cadavers were placed at the Southeast Texas Applied Forensic Science facility and allowed to decompose under natural conditions. The bloat stage of decomposition, a stage easily identified in taphonomy and readily attributed to microbial physiology, was targeted. Each cadaver was sampled at two time points, at the onset and end of the bloat stage, from various body sites including internal locations. Bacterial samples were analyzed by pyrosequencing of the 16S rRNA gene. Our data show a shift from aerobic bacteria to anaerobic bacteria in all body sites sampled and demonstrate variation in community structure between bodies, between sample sites within a body, and between initial and end points of the bloat stage within a sample site. These data are best not viewed as points of comparison but rather additive data sets. While some species recovered are the same as those observed in culture-based studies, many are novel. Our results are preliminary and add to a larger emerging data set; a more comprehensive study is needed to further dissect the role of bacteria in human decomposition.”

The introduction contains a good description of how decomposition in humans proceed:

“A cadaver is far from dead when viewed as an ecosystem for a suite of bacteria, insects, and fungi, many of which are obligate and documented only in such a context. Decomposition is a mosaic system with an intimate association between biotic factors (i.e., the individuality of the cadaver, intrinsic and extrinsic bacteria and other microbes, and insects) and abiotic factors (i.e., weather, climate, and humidity) and therefore a function of a specific ecological scenario. Slight alteration of the ecosystem, such as exclusion of insects or burial, may lead to a unique trajectory for decomposition and potentially anomalous results; therefore, it is critical to forensics that the interplay of these factors be understood. Bacteria are often credited as a major driving force for the process of decomposition but few studies cataloging the microbiome of decomposition have been published […]

A body passes through several stages as decomposition progresses driven by dehydration and discernible by characteristic gross taphonomic changes. The early stages of decomposition are wet and marked by discoloration of the flesh and the onset and cessation of bacterially-induced bloat. During early decay, intrinsic bacteria begin to digest the intestines from the inside out, eventually digesting away the surrounding tissues [3]. Enzymes from within the dead cells of the cadaver also begin to break down tissues (autolysis). During putrefaction, bacteria undergo anaerobic respiration and produce gases as by-products such as hydrogen sulfide, methane, cadaverine, and putrescine [5]. The buildup of resulting gas creates pressure, inflating the cadaver, and eventually forcing fluids out [3]. This purging event marks the shift from early decomposition to late decomposition and may not be uniform; the head may purge before the trunk, for example. Purge may also last for some period of time in some parts of the body even as other parts of the body enter the most advanced stages of decomposition. In the trunk, purge is associated with an opening of the abdominal cavity to the environment [3]. At this point, the rate of decay is reported by several authors to greatly increase as larval flies remove large portions of tissues; however, mummification may also occur, thus serving to preserve tissues [6][9]. The final stages of decomposition last through to skeletonization and are the driest stages [7], [10][13].”

It’s really quite an interesting paper, but you probably don’t want to read this while you’re having dinner. A few other interesting observations and conclusions:

“Many factors can influence the bacteria detected in and on a cadaver, including the individual’s “starting” microbiome, differences in the decomposition environments of the two cadavers, and differences in the sites sampled at end-bloat. The integrity of organs at end-bloat varied between cadavers (as decomposition varied between cadavers) and did not allow for consistent sampling of sites across cadavers. Specifically, STAFS 2011-016 no longer had a sigmoidal colon at the end-bloat sample time.” […]

“With the exception of the fecal sample from STAFS 2011-006, which was the least rich sample in the study with only 26 unique OTUs [operational taxonomic units – US] detected, fecal samples were the richest of all body sites sampled, with an average of nearly 400 OTUs detected. The stomach sample was the second least rich sample, with small intestine and mouth samples slightly richer. The body cavity, transverse colon, and sigmoidal colon samples were much richer. Overall, these data show that as one moves from the upper gastrointestinal tract (mouth, stomach, and small intestine) to the lower gastrointestinal tract (colon and rectal/fecal), microbiome richness increases.” […]

“It is important to note that while difference in abundance seen in particular species between this study and the others noted above could be due to the discussed constraints of culturing bacteria, differences could also be due to a variety of factors such as individual variability between the cadaver microbiomes, seasonality, climate, and species of colonizing insects. Finally, abundance does not necessarily indicate metabolic significance for decomposition, a point of importance that our study cannot address.” […]

“Our data represent initial insights into the bacteria populating decomposing human cadavers and an early start to discovering successive changes through time. While our data support the findings of previous culture studies, they also demonstrate that bacteria not detected by culture-based methods comprise a large portion of the community. No definitive conclusion regarding a shift in community structure through time can be made with this data set.”

ii. Protein restriction for diabetic renal disease.


Diabetic renal disease (diabetic nephropathy) is a leading cause of end-stage renal failure. Once the process has started, it cannot be reversed by glycaemic control, but progression might be slowed by control of blood pressure and protein restriction.


To assess the effects of dietary protein restriction on the pro gression of diabetic nephropathy in patients with diabetes .

Search methods

We searched The Cochrane Library , MEDLINE, EMBASE, ISI Proceedings, Science Citation Index Expanded and bibliographies of included studies.

Selection criteria

Randomised controlled trials (RCTs) and before and after studies of the effects of a modified or restricted protein diet on diabetic renal function in people with type 1 or type 2 diabetes following diet for at least four months were considered.

Data collection and analysis

Two reviewers performed data extraction and evaluation of quality independently. Pooling of results was done by means of random- effects model.

Main results

Twelve studies were included, nine RCTs and three before and after studies. Only one study explored all-cause mortality and end-stage renal disease (ESRD) as endpoints. The relative risk (RR) of ESRD or death was 0.23 (95% confidence interval (CI) 0.07 to 0.72) for patients assigned to a low protein diet (LPD). Pooling of the seven RCTs in patients with type 1 diabetes resulted in a non-significant reduction in the decline of glomerular filtration rate (GFR) of 0.1 ml/min/month (95% CI -0.1 to 0.3) in the LPD group. For type 2 diabetes, one trial showed a small insignificant improvement in the rate of decline of GFR in the protein-restricted group and a second found a similar decline in both the intervention and control groups. Actual protein intake in the intervention groups ranged from 0.7 to 1.1 g/kg/day. One study noted malnutrition in the LPD group. We found no data on the effects of LPDs on health-related quality of life and costs.

Authors’ conclusions

The results show that reducing protein intake appears to slightly slow progression to renal failure but not statistically significantly so. However, questions concerning the level of protein intake and compliance remain. Further longer-term research on large representative groups of patients with both type 1 and type 2 diabetes mellitus is necessary.”

The paper has a lot more. Do note that due to the link between kidney disease and dietary protein intake, at least one diabetic I know has actually considered the question of whether to adjust protein intake at an even earlier point in the disease process than the one comtemplated in these studies, i.e. before the lab tests show that the kidneys have started to fail – this is hardly an outrageous idea given evidence in related fields. I do think however that the evidence is much too inconclusive in the case of diabetic nephropathy for anything like this to make much sense at this point. Lowering salt intake seems to be far more likely to have positive effects. I’d be curious to know if the (very tentative..) finding that the type of dietary protein (‘chicken and fish vs red meat’) may matter for outcomes, and not just the amount of protein, holds; this seems very unclear at this point, but it’s potentially important as it also relates to the compliance/adherence problem.

iii. Direct evidence of 1,900 years of indigenous silver production in the Lake Titicaca Basin of Southern Peru:

“Archaeological excavations at a U-shaped pyramid in the northern Lake Titicaca Basin of Peru have documented a continuous 5-m-deep stratigraphic sequence of metalworking remains. The sequence begins in the first millennium AD and ends in the Spanish Colonial period ca. AD 1600. The earliest dates associated with silver production are 1960 ± 40 BP (2-sigma cal. 40 BC to AD 120) and 1870 ± 40 BP (2-sigma cal. AD 60 to 240) representing the oldest known silver smelting in South America. Scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) analysis of production debris indicate a complex, multistage, high temperature technology for producing silver throughout the archaeological sequence. These data hold significant theoretical implications including the following: (i) silver production occurred before the development of the first southern Andean state of Tiwanaku, (ii) the location and process of silverworking remained consistent for 1,500 years even though political control of the area cycled between expansionist states and smaller chiefly polities, and (iii) that U-shaped structures were the location of ceremonial, residential, and industrial activities.”

A little more from the paper:

“Our data establish an initial date for silverworking that is at least three centuries earlier than previous studies had indicated. […] Three independent lines of evidence establish the chronological integrity of the deposit: 1) a ceramic sequence in uninterrupted stratigraphic layers, 2) absolute radiocarbon dates, and 3) absolute ceramic thermoluminescence (TL) dates (1). […] the two absolute dating methods are internally consistent, and […] these match the relative sequence derived from analyzing the diagnostic pottery or ceramics. The unit excavated at Huajje represents a rare instance of an intact, well-demarcated stratigraphic deposit that allows us to precisely define the material changes through time in silver production. […] The steps required for silver extraction include mining, beneficiation (i.e., crushing of the ore and sorting of metal-bearing mineral), optional roasting to remove sulfur via oxidation, followed by smelting, and cupellation […] Archaeological or ethnographic evidence for most of these steps is extremely scarce, making this a very significant assemblage for our understanding of early silver production. A total of 3,457 (7,215.84 g) smelting-related artifacts were collected.”

November 1, 2013 - Posted by | archaeology, biology, diabetes, medicine, papers

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