Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures

Coprolites are fossilized feces that can be used to provide information on the composition of the intestinal microbiota and, as we show, possibly on diet. We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement on Vieques Island, Puerto Rico. While more is known about the Saladoid culture, it is believed that both societies co-existed on this island approximately from 5 to 1170 AD. By extracting DNA from the coprolites, followed by metagenomic characterization, we show that both cultures can be distinguished from each other on the basis of their bacterial and fungal gut microbiomes. In addition, we show that parasite loads were heavy and also culturally distinct. Huecoid coprolites were characterized by maize and Basidiomycetes sequences, suggesting that these were important components of their diet. Saladoid coprolite samples harbored sequences associated with fish parasites, suggesting that raw fish was a substantial component of their diet. The present study shows that ancient DNA is not entirely degraded in humid, tropical environments, and that dietary and/or host genetic differences in ancient populations may be reflected in the composition of their gut microbiome. This further supports the hypothesis that the two ancient cultures studied were distinct, and that they retained distinct technological/cultural differences during an extended period of close proximity and peaceful co-existence. The two populations seemed to form the later-day Taínos, the Amerindians present at the point of Columbian contact. Importantly, our data suggest that paleomicrobiomics can be a powerful tool to assess cultural differences between ancient populations.     

Genome‐wide association study of word reading: Overlap with risk genes for neurodevelopmental disorders

Reading disabilities (RD) are the most common neurocognitive disorder, affecting 5% to 17% of children in North America. These children often have comorbid neurodevelopmental/psychiatric disorders, such as attention deficit/hyperactivity disorder (ADHD). The genetics of RD and their overlap with other disorders is incompletely understood. To contribute to this, we performed a genome‐wide association study (GWAS) for word reading. Then, using summary statistics from neurodevelopmental/psychiatric disorders, we computed polygenic risk scores (PRS) and used them to predict reading ability in our samples. This enabled us to test the shared aetiology between RD and other disorders. The GWAS consisted of 5.3 million single nucleotide polymorphisms (SNPs) and two samples; a family‐based sample recruited for reading difficulties in Toronto (n = 624) and a population‐based sample recruited in Philadelphia [Philadelphia Neurodevelopmental Cohort (PNC)] (n = 4430). The Toronto sample SNP‐based analysis identified suggestive SNPs (P ~ 5 × 10^?7) in the ARHGAP23 gene, which is implicated in neuronal migration/axon pathfinding. The PNC gene‐based analysis identified significant associations (P < 2.72 × 10^?6) for LINC00935 and CCNT1, located in the region of the KANSL2/CCNT1/LINC00935/SNORA2B/SNORA34/MIR4701/ADCY6 genes on chromosome 12q, with near significant SNP‐based analysis. PRS identified significant overlap between word reading and intelligence (R² = 0.18, P = 7.25 × 10^?181), word reading and educational attainment (R² = 0.07, P = 4.91 × 10^?48) and word reading and ADHD (R² = 0.02, P = 8.70 × 10^?6; threshold for significance = 7.14 × 10^?3). Overlap was also found between RD and autism spectrum disorder (ASD) as top‐ranked genes were previously implicated in autism by rare and copy number variant analyses. These findings support shared risk between word reading, cognitive measures, educational outcomes and neurodevelopmental disorders, including ASD.     

Effects of Phytic Acid and Exercise on Some Serum Analytes in Rats Orally Exposed to Diets Supplemented with Cadmium

Cadmium is an environmental pollutant of increasing worldwide concern. It has been reported to be high in the soil where food crops are grown in some parishes of Jamaica. Surprisingly, no adverse effect of cadmium has been reported among the Jamaican population. However, phytic acid has also been shown to be high in some food crops grown in Jamaica. In this study, we evaluated the effects of phytic acid (1 %) and exercise on the metabolism of cadmium (5 mg cadmium/kg body weight) in rats. Five groups of rats were fed as follows: rats fed control diet, control diet supplemented with cadmium and subjected to exercise, control diet supplemented with phytic acid plus cadmium and subjected to exercise, control diet supplemented with cadmium plus phytic acid, and control diet supplemented with cadmium only. The animals were fed for 4 weeks and then sacrificed. Blood samples were collected for some biochemical assays. Percentage weight loss (28.42 %) was greatest in the group that had cadmium supplement only. The group fed control diet supplemented with cadmium only displayed increased liver enzymes and electrolytes except for the significant decrease in bicarbonate compared to other test groups. Similarly, blood urea nitrogen and uric acid were increased in the group fed cadmium supplement only compared to other test groups. Total cholesterol trended downwards in the test groups compared to control. These observations suggest that consumption of diet high in phytic acid with relatively high physical activity may be protective against the adverse effects of cadmium.     

Design and synthesis of MMP inhibitors with appended fluorescent tags for imaging and visualization of matrix metalloproteinase enzymes

We describe the synthesis, MMP-2 and 9 potency, and in vitro evaluation of a series of α-sulfone hydroxmate MMP inhibitors conjugated to a series of dyes with different absorption/emission lamina maxima’s that can be used to visualize tumors.     

Chronic Collection of Cerebrospinal Fluid from Rhesus Macaques (Macaca mulatta) with Cisterna Magna Ports: Update on Refinements

More than 20 y ago, we developed an animal model for chronic and continuous collection of cerebrospinal fluid (CSF) from conscious rhesus macaques. Since our previous publication in 2003, we have successfully implanted 168 rhesus macaques using this approach. Our experience enables us to provide up-to-date information regarding the model, including refinements to our implant design, reductions in maintenance, and new procedures for dealing with contamination. The results of our experiences have reduced the number of surgeries required and helped to increase the longevity of the implant, with some functioning for more than 18 y. Building on our success in rhesus macaques, we attempted to develop similar animal models in the African green monkeys and dogs but have been unable to develop reliable chronic models for CSF collection in these species.Abbreviation: CMP, cisterna magna port; CSF, cerebrospinal fluid

Cerebrospinal (CSF) biomarkers and pharmacokinetics are reliable tools for monitoring the therapeutic effect of compounds used for the treatment of various neurodegenerative diseases. CSF can be collected by using several methods, including lumbar and cisterna magna punctures or implanted devices.^{3,6,8,9,11-13} Each method has its own specific challenges but no matter which technique is used, performing CSF collections safely is imperative to avoiding risks to the animals and to providing the best CSF samples for analysis.¹ To support our research focus on neurocognitive disorders (including Alzheimer disease, Parkinson disease, and sleep disorders), we developed an NHP model of chronic CSF collection (the cisterna magna port [CMP] model) more than 20 y ago.⁴ This model allows safe, repeatable and reliable collections of CSF samples from the cisterna magna in conscious rhesus macaques (Macaca mulatta). The information summarized herein updates this animal model since its introduction in 2003 and reflects our 18 additional years of experience with it. We also provide information regarding our attempts to develop CMP models in African green monkeys and dogs. We recommend that readers review the 2003 article for further information and understanding of the CMP model.⁴     

Being Sticker Rich: Numerical Context Influences Children’s Sharing Behavior

Young children spontaneously share resources with anonymous recipients, but little is known about the specific circumstances that promote or hinder these prosocial tendencies. Children (ages 3–11) received a small (12) or large (30) number of stickers, and were then given the opportunity to share their windfall with either one or multiple anonymous recipients (Dictator Game). Whether a child chose to share or not varied as a function of age, but was uninfluenced by numerical context. Moreover, children’s giving was consistent with a proportion-based account, such that children typically donated a similar proportion (but different absolute number) of the resources given to them, regardless of whether they originally received a small or large windfall. The proportion of resources donated, however, did vary based on the number of recipients with whom they were allowed to share, such that on average, children shared more when there were more recipients available, particularly when they had more resources, suggesting they take others into consideration when making prosocial decisions. Finally, results indicated that a child’s gender also predicted sharing behavior, with males generally sharing more resources than females. Together, findings suggest that the numerical contexts under which children are asked to share, as well as the quantity of resources that they have to share, may interact to promote (or hinder) altruistic behaviors throughout childhood.     

Gut Microbiome of an 11th Century A.D. Pre-Columbian Andean Mummy

The process of natural mummification is a rare and unique process from which little is known about the resulting microbial community structure. In the present study, we characterized the microbiome of paleofeces, and ascending, transverse and descending colon of an 11^th century A.D. pre-Columbian Andean mummy by 16S rRNA gene high-throughput sequencing and metagenomics. Firmicutes were the most abundant bacterial group, with Clostridium spp. comprising up to 96.2% of the mummified gut, while Turicibacter spp. represented 89.2% of the bacteria identified in the paleofeces. Microbiome profile of the paleofeces was unique when compared to previously characterized coprolites that did not undergo natural mummification. We identified DNA sequences homologous to Clostridium botulinum, Trypanosoma cruzi and human papillomaviruses (HPVs). Unexpectedly, putative antibiotic-resistance genes including beta-lactamases, penicillin-binding proteins, resistance to fosfomycin, chloramphenicol, aminoglycosides, macrolides, sulfa, quinolones, tetracycline and vancomycin, and multi-drug transporters, were also identified. The presence of putative antibiotic-resistance genes suggests that resistance may not necessarily be associated with a selective pressure of antibiotics or contact with European cultures. Identification of pathogens and antibiotic-resistance genes in ancient human specimens will aid in the understanding of the evolution of pathogens as a way to treat and prevent diseases caused by bacteria, microbial eukaryotes and viruses.     

Entering adolescence: resistance to peer influence, risky behavior, and neural changes in emotion reactivity

Adolescence is often described as a period of heightened reactivity to emotions paired with reduced regulatory capacities, a combination suggested to contribute to risk-taking and susceptibility to peer influence during puberty. However, no longitudinal research has definitively linked these behavioral changes to underlying neural development. Here, 38 neurotypical participants underwent two fMRI sessions across the transition from late childhood (10 years) to early adolescence (13 years). Responses to affective facial displays exhibited a combination of general and emotion-specific changes in ventral striatum (VS), ventromedial PFC, amygdala, and temporal pole. Furthermore, VS activity increases correlated with decreases in susceptibility to peer influence and risky behavior. VS and amygdala responses were also significantly more negatively coupled in early adolescence than in late childhood while processing sad and happy versus neutral faces. Together, these results suggest that VS responses to viewing emotions may play a regulatory role that is critical to adolescent interpersonal functioning.     

Molecular investigations of a locally acquired case of melioidosis in Southern AZ, USA

Melioidosis is caused by Burkholderia pseudomallei, a Gram-negative bacillus, primarily found in soils in Southeast Asia and northern Australia. A recent case of melioidosis in non-endemic Arizona was determined to be the result of locally acquired infection, as the patient had no travel history to endemic regions and no previous history of disease. Diagnosis of the case was confirmed through multiple microbiologic and molecular techniques. To enhance the epidemiological analysis, we conducted several molecular genotyping procedures, including multi-locus sequence typing, SNP-profiling, and whole genome sequence typing. Each technique has different molecular epidemiologic advantages, all of which provided evidence that the infecting strain was most similar to those found in Southeast Asia, possibly originating in, or around, Malaysia. Advancements in new typing technologies provide genotyping resolution not previously available to public health investigators, allowing for more accurate source identification.