Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue

Esophageal carcinoma (ESCA) is a leading cause of cancer-related death worldwide, and certain oral and intestinal pathogens have been associated with cancer development and progression. We asked if esophageal microbiomes had shared alterations that could provide novel biomarkers for ESCA risk. We extracted DNA from tumor and non-tumor tissue of 212 patients in the NCI-MD case control study and sequenced the 16S rRNA gene (V3-4), with TCGA ESCA RNA-seq (n = 172) and WGS (n = 123) non-human reads used as validation. We identified four taxa, Campylobacter, Prevotella, Streptococcus, and Fusobacterium as highly enriched in esophageal cancer across all cohorts. Using SparCC, we discovered that Fusobacterium and Prevotella were also co-enriched across all cohorts. We then analyzed immune cell infiltration to determine if these dysbiotic taxa were associated with immune signatures. Using xCell to obtain predicted immune infiltrates, we identified a depletion of megakaryocyte-erythroid progenitor (MEP) cells in tumors with presence of any of the four taxa, along with enrichment of platelets in tumors with Campylobactor or Fusobacterium. Taken together, our results suggest that intratumoral presence of these co-occurring bacterial genera may confer tumor promoting immune alterations that allow disease progression in esophageal cancer.

Breeding habitats, bionomics and phylogenetic analysis of Aedes aegypti and first detection of Culiseta longiareolata, and Ae. hirsutus in Somali Region, eastern Ethiopia

INTRODUCTION

Arboviral diseases, such as dengue, chikungunya, yellow fever, and Zika, are caused by viruses that are transmitted to humans through mosquito bites. However, the status of arbovirus vectors in eastern Ethiopia is unknown. The aim of this study was to investigate distribution, breeding habitat, bionomics and phylogenetic relationship of Aedes aegypti mosquito species in Somali Regional State, Eastern Ethiopia.

METHODS

Entomological surveys were conducted in four sites including Jigjiga, Degehabur, Kebridehar and Godey in 2018 (October to December) to study the distribution of Ae. aegypti and with a follow-up collection in 2020 (July-December). In addition, an investigation into the seasonality and bionomics of Ae. aegypti was conducted in 2021 (January-April) in Kebridehar town. Adult mosquitoes were collected from indoor and outdoor locations using CDC light traps (LTs), pyrethrum spray collection (PSCs), and aspirators. Larvae and pupae were also collected from a total of 169 water-holding containers using a dipper between October and November 2020 (rainy season) in Kebridehar town. The species identification of wild caught and reared adults was conducted using a taxonomic key. In addition, species identification using mitochondrial and nuclear genes maximum likelihood-based phylogenetic analysis was performed.

RESULTS

In the 2018 collection, Ae. aegypti was found in all study sites (Jigjiga, Degahabour, Kebridehar and Godey). In the 2020-2021 collection, a total of 470 (Female = 341, Male = 129) wild caught adult Ae. aegypti mosquitoes were collected, mostly during the rainy season with the highest frequency in November (n = 177) while the lowest abundance was in the dry season (n = 14) for both February and March. The majority of Ae. aegypt were caught using PSC (n = 365) followed by CDC LT (n = 102) and least were collected by aspirator from an animal shelter (n = 3). Aedes aegypti larval density was highest in tires (0.97 larvae per dip) followed by cemented cisterns (0.73 larvae per dip) and the Relative Breeding Index (RBI) was 0.87 and Container Index (CI) was 0.56. Genetic analysis of ITS2 and COI revealed one and 18 haplotypes, respectively and phylogenetic analysis confirmed species identification. The 2022 collection revealed no Ae. aegpti, but two previously uncharacterized species to that region. Phylogenetic analysis of these two species revealed their identities as Ae. hirsutus and Culiseta longiareolata.

CONCLUSION

Data from our study indicate that, Ae. aegypti is present both during the wet and dry seasons due to the availability of breeding habitats, including water containers like cemented cisterns, tires, barrels, and plastic containers. This study emphasizes the necessity of establishing a national entomological surveillance program for Aedes in Somali region.

Identification of Mid-Polar and Polar AhR Agonists in Cetaceans from Korean Coastal Waters: Application of Effect-Directed Analysis with Full-Scan Screening

Major aryl hydrocarbon receptor (AhR) agonists were identified in extracts of blubber, liver, and muscle from six long-beaked common dolphins (Delphinus capensis) and one fin whale (Balaenoptera physalus) collected from Korean coastal waters using effect-directed analysis. Results of the H4IIE-luc bioassay indicated that the polar fractions of blubber and liver extracts from the fin whale exhibited relatively high AhR-mediated potencies. Based on full-scan screening with high-resolution mass spectrometry, 37 AhR agonist candidates, spanning four use categories: pharmaceuticals, pesticides, cosmetics, and natural products, were selected. Among these, five polar AhR agonists were newly identified through toxicological confirmation. Concentrations of polar AhR agonists in cetaceans were tissue-specific, with extracts of blubber and liver containing greater concentrations than muscle extracts. Polar AhR agonists with great log KOA values (>5) were found to biomagnify in the marine food chain potentially. Polar AhR agonists contributed 8.9% of the observed AhR-mediated potencies in blubber and 49% in liver. Rutaecarpine and alantolactone contributed significantly to the total AhR-mediated potencies of blubber, whereas hydrocortisone was a major AhR contributor in the liver of the fin whale. This study is the first to identify the tissue-specific accumulation of polar AhR agonists in blubber and liver extracts of cetaceans.

Activity, substrate preference and structure of the HsMCM8/9 helicase

The minichromosomal maintenance proteins, MCM8 and MCM9, are more recent evolutionary additions to the MCM family, only cooccurring in selected higher eukaryotes. Mutations in these genes are directly linked to ovarian insufficiency, infertility, and several cancers. MCM8/9 appears to have ancillary roles in fork progression and recombination of broken replication forks. However, the biochemical activity, specificities and structures have not been adequately illustrated, making mechanistic determination difficult. Here, we show that human MCM8/9 (HsMCM8/9) is an ATP dependent DNA helicase that unwinds fork DNA substrates with a 3'-5' polarity. High affinity ssDNA binding occurs in the presence of nucleoside triphosphates, while ATP hydrolysis weakens the interaction with DNA. The cryo-EM structure of the HsMCM8/9 heterohexamer was solved at 4.3 Å revealing a trimer of heterodimer configuration with two types of interfacial AAA+ nucleotide binding sites that become more organized upon binding ADP. Local refinements of the N or C-terminal domains (NTD or CTD) improved the resolution to 3.9 or 4.1 Å, respectively, and shows a large displacement in the CTD. Changes in AAA+ CTD upon nucleotide binding and a large swing between the NTD and CTD likely implies that MCM8/9 utilizes a sequential subunit translocation mechanism for DNA unwinding.

Fiber Orientation Quantification for Large Area Additively Manufactured Parts Using SEM Imaging

Polymer-based additively manufactured parts are increasing in popularity for industrial applications due to their ease of manufacturing and design form freedom, but their structural and thermal performances are often limited to those of the base polymer system. These limitations can be mitigated by the addition of carbon fiber reinforcements to the polymer matrix, which enhances both the structural performance and the dimensional stability during cooling. The local fiber orientation within the processed beads directly impacts the mechanical and thermal performances, and correlating the orientation to processing parameter variations would lead to better part quality. This study presents a novel approach for analyzing the spatially varying fiber orientation through the use of scanning electron microscopy (SEM). This paper presents the sample preparation procedure including SEM image acquisition and analysis methods to quantify the internal fiber orientation of additively manufactured carbon fiber-reinforced composites. Large area additively manufactured beads with 13% by weight large aspect ratio carbon fiber-reinforced acrylonitrile butadiene styrene (ABS) pellets are the feedstock used in this study. Fiber orientation is quantified using the method of ellipses (MoE), and the spatial change in fiber orientation across the deposited bead cross-section is studied as a function of process parameters including extrusion speed, raster height, and extrusion temperature zones. The results in the present paper show the results from the novel use of SEM to obtain the local fiber orientation, and results show the variation in alignment within the individual processed bead as well as an overall aligned orientation state along the direction of deposition.

Variable body and tissue weight reporting in preclinical cachexia literature may alter study outcomes and interpretation

Cancer cachexia is a multifactorial syndrome of body weight loss, muscle wasting, and progressive functional decline affecting many advanced cancer patients and leading to worsened clinical outcomes. Despite inherent limitations of many preclinical cachexia models, including large tumor burden, rapid tumor growth, and young age of animals, these animal models are widely used and imperative for the study of cachexia mechanisms and experimental therapeutics. However, there are currently no guidelines for reporting and representation of data in preclinical cachexia literature. We examined the current state of data reporting in publications using the colon-26 adenocarcinoma (C26) model of cachexia and compared statistical differences in reporting mechanisms using animals from our laboratory. We show that data reporting and representation in C26 preclinical cachexia literature is diverse, making comparison of study outcomes difficult. Further, different expression of body and tissue weights in our animals led to differential statistical significance, which could significantly alter data interpretation. This study highlights a need for consistent data reporting in preclinical cancer cachexia literature to effectively compare outcomes between studies and increase translatability to the human condition.

Mild Divergent Semireductive Transformations of Secondary and Tertiary Amides via Zirconocene Hydride Catalysis

The mild catalytic partial reduction of amides to imines has proven to be a challenging synthetic transformation, with many transition metals directly reducing these substrates to amines. Herein, we report a mild, catalytic method for the semireduction of both secondary and tertiary amides via zirconocene hydride catalysis. Utilizing just 5 mol % of Cp2ZrCl2, the reductive deoxygenation of secondary amides is demonstrated to furnish a diverse array of imines in up to 94% yield with excellent chemoselectivity and without the need for glovebox handling. Moreover, a novel reductive transamination of tertiary amides is also achievable when the catalytic protocol is carried out in the presence of a primary amine at room temperature, providing access to an expanded assortment of imines in up to 98% yield. Through slight procedural tuning, the single-flask conversion of amides to imines, aldehydes, amines or enamines is feasible, including multicomponent syntheses.

Comparative Analysis of RNA-Extraction Approaches and Associated Influences on RT-qPCR of the SARS-CoV-2 RNA in a University Residence Hall and Quarantine Location

Wastewater-based epidemiology (WBE) provides an early warning and trend analysis approach for determining the presence of COVID-19 in a community and complements clinical testing in assessing the population level, even as viral loads fluctuate. Here, we evaluate combinations of two wastewater concentration methods (i.e., ultrafiltration and composite supernatant-solid), four pre-RNA extraction modifications, and three nucleic acid extraction kits using two different wastewater sampling locations. These consisted of a quarantine facility containing clinically confirmed COVID-19-positive inhabitants and a university residence hall. Of the combinations examined, composite supernatant-solid with pre-RNA extraction consisting of water concentration and RNA/DNA shield performed the best in terms of speed and sensitivity. Further, of the three nucleic acid extraction kits examined, the most variability was associated with the Qiagen kit. Focusing on the quarantine facility, viral concentrations measured in wastewater were generally significantly related to positive clinical cases, with the relationship dependent on method, modification, kit, target, and normalization, although results were variable-dependent on individual time points (Kendall's Tau-b (τ) = 0.17 to 0.6) or cumulatively (Kendall's Tau-b (τ) = -0.048 to 1). These observations can support laboratories establishing protocols to perform wastewater surveillance and monitoring efforts for COVID-19.

Total Syntheses of (+)-Ineleganolide and (-)-Sinulochmodin C

Described herein are the first total syntheses of the nor-furanocembranoid natural products (+)-ineleganolide (1) and (-)-sinulochmodin C (2). The synthetic strategy is predicated on a transannular Michael reaction that provides both natural products from a common macrocyclic intermediate and leverages a diastereoselective radical cyclization to furnish a key bicyclic lactone. The latter is further advanced to a macrocyclic precursor via a Nozaki-Hiyama-Kishi cyclization and a one-pot furan oxidation/oxa-Michael cascade. Unexpected stereochemical nuances that guided the evolution and eventual completion of the total synthesis are discussed.

Sex-specific epigenetic development in the mouse hypothalamic arcuate nucleus pinpoints human genomic regions associated with body mass index

Recent genome-wide association studies corroborate classical research on developmental programming indicating that obesity is primarily a neurodevelopmental disease strongly influenced by nutrition during critical ontogenic windows. Epigenetic mechanisms regulate neurodevelopment; however, little is known about their role in establishing and maintaining the brain's energy balance circuitry. We generated neuron and glia methylomes and transcriptomes from male and female mouse hypothalamic arcuate nucleus, a key site for energy balance regulation, at time points spanning the closure of an established critical window for developmental programming of obesity risk. We find that postnatal epigenetic maturation is markedly cell type and sex specific and occurs in genomic regions enriched for heritability of body mass index in humans. Our results offer a potential explanation for both the limited ontogenic windows for and sex differences in sensitivity to developmental programming of obesity and provide a rich resource for epigenetic analyses of developmental programming of energy balance.

Wolbachia 16S rRNA haplotypes detected in wild Anopheles stephensi in eastern Ethiopia

BACKGROUND

About two out of three Ethiopians are at risk of malaria, a disease caused by the parasites Plasmodium falciparum and Plasmodium vivax. Anopheles stephensi, an invasive vector typically found in South Asia and the Middle East, was recently found to be distributed across eastern and central Ethiopia and is capable of transmitting both P. falciparum and P. vivax. The detection of this vector in the Horn of Africa (HOA) coupled with widespread insecticide resistance requires that new methods of vector control be investigated in order to control the spread of malaria. Wolbachia, a naturally occurring endosymbiotic bacterium of mosquitoes, has been identified as a potential vector control tool that can be explored for the control of malaria transmission. Wolbachia could be used to control the mosquito population through suppression or potentially decrease malaria transmission through population replacement. However, the presence of Wolbachia in wild An. stephensi in eastern Ethiopia is unknown. This study aimed to identify the presence and diversity of Wolbachia in An. stephensi across eastern Ethiopia.

METHODS

DNA was extracted from An. stephensi collected from eastern Ethiopia in 2018 and screened for Wolbachia using a 16S targeted PCR assay, as well as multilocus strain typing (MLST) PCR assays. Haplotype and phylogenetic analysis of the sequenced 16S amplicons were conducted to compare with Wolbachia from countries across Africa and Asia.

RESULTS

Twenty out of the 184 mosquitoes screened were positive for Wolbachia, with multiple haplotypes detected. In addition, phylogenetic analysis revealed two superclades, representing Wolbachia supergroups A and B (bootstrap values of 81 and 72, respectively) with no significant grouping of geographic location or species. A subclade with a bootstrap value of 89 separates the Ethiopian haplotype 2 from other sequences in that superclade.

CONCLUSIONS

These findings provide the first evidence of natural Wolbachia populations in wild An. stephensi in the HOA. They also identify the need for further research to confirm the endosymbiotic relationship between Wolbachia and An. stephensi and to investigate its utility for malaria control in the HOA.

Genetic diversity of Anopheles stephensi in Ethiopia provides insight into patterns of spread

BACKGROUND

The recent detection of the South Asian malaria vector Anopheles stephensi in the Horn of Africa (HOA) raises concerns about the impact of this mosquito on malaria transmission in the region. Analysis of An. stephensi genetic diversity and population structure can provide insight into the history of the mosquito in the HOA to improve predictions of future spread. We investigated the genetic diversity of An. stephensi in eastern Ethiopia, where detection suggests a range expansion into this region, in order to understand the history of this invasive population.

METHODS

We sequenced the cytochrome oxidase subunit I (COI) and cytochrome B gene (CytB) in 187 An. stephensi collected from 10 sites in Ethiopia in 2018. Population genetic, phylogenetic, and minimum spanning network analyses were conducted for Ethiopian sequences. Molecular identification of blood meal sources was also performed using universal vertebrate CytB sequencing.

RESULTS

Six An. stephensi COI-CytB haplotypes were observed, with the highest number of haplotypes in the northeastern sites (Semera, Bati, and Gewana towns) relative to the southeastern sites (Kebridehar, Godey, and Degehabur) in eastern Ethiopia. We observed population differentiation, with the highest differentiation between the northeastern sites compared to central sites (Erer Gota, Dire Dawa, and Awash Sebat Kilo) and the southeastern sites. Phylogenetic and network analysis revealed that the HOA An. stephensi are more genetically similar to An. stephensi from southern Asia than from the Arabian Peninsula. Finally, molecular blood meal analysis revealed evidence of feeding on cows, goats, dogs, and humans, as well as evidence of multiple (mixed) blood meals.

CONCLUSION

We show that An. stephensi is genetically diverse in Ethiopia and with evidence of geographical structure. Variation in the level of diversity supports the hypothesis for a more recent introduction of An. stephensi into southeastern Ethiopia relative to the northeastern region. We also find evidence that supports the hypothesis that HOA An. stephensi populations originate from South Asia rather than the Arabian Peninsula. The evidence of both zoophagic and anthropophagic feeding support the need for additional investigation into the potential for livestock movement to play a role in vector spread in this region.

The Creative Neurons

Creativity generates novel solutions to tasks by processing information. Imagination and mental representations are part of the creative process; we can mull over ideas of our own making, and construct algorithms or scenarios from them. Social scenario-building can be viewed as a human cognitive "super-power" that involves abstraction, meta-representation, time-travel, and directed imaginative thought. We humans have a "theater in our minds" to play out a near-infinite array of social strategies and contingencies. Here we propose an integrative model for why and how humans evolved extraordinary creative abilities. We posit that a key aspect of hominin evolution involved relatively open and fluid social relationships among communities, enabled by a unique extended family structure similar to that of contemporary hunter-gatherer band societies. Intercommunity relationships facilitated the rapid flow of information-"Culture"-that underpinned arms-races in information processing, language, imagination, and creativity that distinguishes humans from other species.

Targeted chromosomal Escherichia coli:dnaB exterior surface residues regulate DNA helicase behavior to maintain genomic stability and organismal fitness

Helicase regulation involves modulation of unwinding speed to maintain coordination of DNA replication fork activities and is vital for replisome progression. Currently, mechanisms for helicase regulation that involve interactions with both DNA strands through a steric exclusion and wrapping (SEW) model and conformational shifts between dilated and constricted states have been examined in vitro. To better understand the mechanism and cellular impact of helicase regulation, we used CRISPR-Cas9 genome editing to study four previously identified SEW-deficient mutants of the bacterial replicative helicase DnaB. We discovered that these four SEW mutations stabilize constricted states, with more fully constricted mutants having a generally greater impact on genomic stress, suggesting a dynamic model for helicase regulation that involves both excluded strand interactions and conformational states. These dnaB mutations result in increased chromosome complexities, less stable genomes, and ultimately less viable and fit strains. Specifically, dnaB:mut strains present with increased mutational frequencies without significantly inducing SOS, consistent with leaving single-strand gaps in the genome during replication that are subsequently filled with lower fidelity. This work explores the genomic impacts of helicase dysregulation in vivo, supporting a combined dynamic regulatory mechanism involving a spectrum of DnaB conformational changes and relates current mechanistic understanding to functional helicase behavior at the replication fork.

DNA replication is a vital biological process, and the proteins involved are structurally and functionally conserved across all domains of life. As our fundamental knowledge of genes and genetics grows, so does our awareness of links between acquired genetic mutations and disease. Understanding how genetic material is replicated accurately and efficiently and with high fidelity is the foundation to identifying and solving genome-based diseases. E. coli are model organisms, containing core replisome proteins, but lack the complexity of the human replication system, making them ideal for investigating conserved replisome behaviors. The helicase enzyme acts at the forefront of the replication fork to unwind the DNA helix and has also been shown to help coordinate other replisome functions. In this study, we examined specific mutations in the helicase that have been shown to regulate its conformation and speed of unwinding. We investigate how these mutations impact the growth, fitness, and cellular morphology of bacteria with the goal of understanding how helicase regulation mechanisms affect an organism’s ability to survive and maintain a stable genome.

Sulfur isotopes as a proxy for human diet and mobility from the preclassic through colonial periods in the Eastern Maya lowlands

Maya archaeologists have long been interested in understanding ancient diets because they provide information about broad-scale economic and societal transformations. Though paleodietary studies have primarily relied on stable carbon (δ13C) and nitrogen (δ15N) isotopic analyses of human bone collagen to document the types of food people consumed, stable sulfur (δ34S) isotope analysis can potentially provide valuable data to identify terrestrial, freshwater, or marine/coastal food sources, as well as determine human mobility and migration patterns. Here we assess applications of δ34S for investigating Maya diet and migration through stable isotope analyses of human bone collagen (δ13C, δ15N, and δ34S) from 114 individuals from 12 sites in the Eastern Maya lowlands, temporally spanning from the Late Preclassic (300 BCE-300 CE) through Colonial periods (1520-1800 CE). Results document a diet dominated by maize and other terrestrial resources, consistent with expectations for this inland region. Because δ34S values reflect local geology, our analyses also identified recent migrants to the Eastern lowlands who had non-local δ34S signatures. When combined with other indicators of mobility (e.g., strontium isotopes), sulfur isotopic data provide a powerful tool to investigate movement across a person's lifespan. This study represents the largest examination of archaeological human δ34S isotope values for the Maya lowlands and provides a foundation for novel insights into both subsistence practices and migration.

Comparative genomic analysis of sifakas (Propithecus) reveals selection for folivory and high heterozygosity despite endangered status

Sifakas (genus Propithecus) are critically endangered, large-bodied diurnal lemurs that eat leaf-based diets and show corresponding anatomical and microbial adaptations to folivory. We report on the genome assembly of Coquerel's sifaka (P. coquereli) and the resequenced genomes of Verreaux's (P. verreauxi), the golden-crowned (P. tattersalli), and the diademed (P. diadema) sifakas. We find high heterozygosity in all sifakas compared with other primates and endangered mammals. Demographic reconstructions nevertheless suggest declines in effective population size beginning before human arrival on Madagascar. Comparative genomic analyses indicate pervasive accelerated evolution in the ancestral sifaka lineage affecting genes in several complementary pathways relevant to folivory, including nutrient absorption and xenobiotic and fatty acid metabolism. Sifakas show convergent evolution at the level of the pathway, gene family, gene, and amino acid substitution with other folivores. Although sifakas have relatively generalized diets, the physiological challenges of habitual folivory likely led to strong selection.

Stakeholder Perceptions and Experiences of a College Live Mascot Program: a Study of Higher Education Ad Hoc Change

Organizational change is a complex and critical issue in higher education today. Changes experienced across institutional systems have both short-term and long-term impact, making this phenomenon ripe for educational leadership research. Many universities and colleges have applied Kotter's (1995) eight-step change model prescriptively to implement academic initiatives, curriculum revisions, and strategic vision. However, Kotter's (1995) model has not previously explored ad hoc changes over time and has not been used to study a college live mascot program. Although a decreasing campus tradition, college live mascots have a relationship and impact on a student's experience and college identification, as well as university engagement with alumni and the public. Therefore, understanding how change is identified and experienced by campus stakeholders of a college live mascot program describe the various complexities and issues that initiate a climate for institutional change. To explain the evolution of a college live mascot program, oral histories across twenty years of campus stakeholders, including student trainers, campus administrators, and external consultants were analyzed using Kotter's (1995) model. The findings of this study affirmed that the steps associated with Kotter's (1995) change model, with a specific focus on the first three steps, are relevant for ad hoc changes, and offer implications for higher education change.

Social isolation induces hyperactivity and exploration in aged female mice

Prolonged social isolation is associated with poor physical and mental health outcomes, findings observed in both humans, and rodent models of isolation. Humans, like mice, may engage in enhanced exploratory and social behaviour following isolation, which may protect against subsequent cognitive decline and psychological distress. Understanding how these effects may impact behaviour in older adults is particularly relevant, as this population is likely to experience periods of late-life social isolation. We report that late-life social isolation in female mice did not lead to robust depressive-like symptomology, altered social interaction behaviour, sensitivity to context fear acquisition and memory, or alterations in inflammatory cytokines (IL-6, IL-1β, Tnf-α) or microglial activation (Itgam) within the hippocampus. Rather, isolation increased hyperactivity and exploration behaviours. These findings have translational value as the first female mouse model of late-life social isolation, and provide evidence to inform the development of interventions aimed at promoting functional recovery following isolation in late-life.

Gene flow between diploid and tetraploid junipers - two contrasting evolutionary pathways in two Juniperus populations

BACKGROUND

Gene flow and polyploidy have been found to be important in Juniperus evolution. However, little evidence has been published elucidating the association of both phenomena in juniper taxa in the wild. Two main areas were studied in Spain (Eastern Iberian Range and Sierra de Baza) with both diploid and tetraploid taxa present in sympatry. Gene flow and ploidy level were assessed for these taxa and the resulted offspring.

RESULTS

Twenty-two allo-triploid hybrids between J. sabina var. sabina and J. thurifera were found in the Eastern Iberian Range population. However, in the Sierra de Baza population no triploids were found. Instead, 18 allo-tetraploid hybrids between two tetraploid taxa: J. sabina var. balkanensis and J. thurifera were discovered. High genetic diversity was exhibited among the tetraploid hybrids at Sierra de Baza, in contrast to the genetically identical triploid hybrids at the Eastern Iberian Range; this suggests meiotic difficulties within the triploid hybrids. In addition, unidirectional gene flow was observed in both studied areas.

CONCLUSION

Polyploidy and hybridization can be complementary partners in the evolution of Juniperus taxa in sympatric occurrences. Juniperus was shown to be an ideal coniferous model to study these two phenomena, independently or in concert.

The influences of environmental change and development on leaf shape in Vitis

PREMISE

The size and shape (physiognomy) of woody, dicotyledonous angiosperm leaves are correlated with climate. These relationships are the basis for multiple paleoclimate proxies. Here we test whether Vitis exhibits phenotypic plasticity and whether physiognomy varies along the vine.

METHODS

We used Digital Leaf Physiognomy (DiLP) to measure leaf characters of four Vitis species from the USDA Germplasm Repository (Geneva, New York) from the 2012-2013 and 2014-2015 leaf-growing seasons, which had different environmental conditions.

RESULTS

Leaf shape changed allometrically through developmental stages; early stages were more linear than later stages. There were significant differences in physiognomy in the same developmental stage between the growing seasons, and species had significant differences in mean physiognomy between growing seasons. Phenotypic plasticity was defined as changes between growing seasons after controlling for developmental stage or after averaging all developmental stages. Vitis amurensis and V. riparia had the greatest phenotypic plasticity. North American species exhibited significant differences in tooth area:blade area. Intermediate developmental stages were most likely to exhibit phenotypic plasticity, and only V. amurensis exhibited phenotypic plasticity in later developmental stages.

CONCLUSIONS

Leaves have variable phenotypic plasticity along the vine. Environmental signal was strongest in intermediate developmental stages. This is significant for leaf physiognomic-paleoclimate proxies because these leaves are likely the most common in leaf litter and reflect leaves primarily included in paleoclimate reconstructions. Early season and early developmental stages have the potential to be confounding factors but are unlikely to exert significant influence because of differential preservation potential.

Status determinants, social incongruity and economic transition: Gender, relative material wealth and heterogeneity in the cultural lifestyle of forager-horticulturalists

For small-scale societies, transitions from self-sufficiency to cash-based labor in market economies have been associated with the exacerbation of existing, and the emergence of new, social incongruities. Social incongruity occurs when two or more of a person’s status determinants (e.g. age, gender, wealth) conflict, resulting in reduced social status. A central focus of theory and research on social incongruity is the relationship between the cultural prototype of what is needed to live a good life–or lifestyle–and status determinants. Assessment of status determinants is challenging because of their relative nature at multiple levels of analysis. This study uses theory and methods from cognitive anthropology to investigate whether and how individual knowledge of a cultural lifestyle prototype conflicts with status determinants at two levels of economic transition among 101 adults from a small-scale society of forager-horticulturalists in Bolivian Amazonia, the Tsimane’. Results support cultural consensus in a 38-item model labeled market lifestyle (explaining 72.7% of sample variance). While the model includes both overlapping traditional (e.g. weaving) and market-related (e.g. education) items and behaviors, most market alternatives were rated higher. When market lifestyle was tested for social incongruity against other status determinants, only gender predicted variation. Thematically, when lifestyle was stratified by gender, men rated several items of relational wealth higher than women did. Analysis of model residual agreement revealed heterogeneity in the form of a syncretic lifestyle model (explaining 18.2% of additional variance). Participants whose knowledge better matched syncretic lifestyle rated traditional items and market alternatives closer to parity. Agreement with the syncretic model correlated with lower material wealth and less market integration. In sum, the findings document a modern, market-oriented form of Tsimane’ lifestyle that varies ontologically from past modelling and ethnographic accounts in preferred forms of livelihood and wealth.

Exposure to Copper Oxide Nanoparticles and Arsenic Causes Intergenerational Effects on Rice (Oryza sativa japonica Koshihikari) Seed Germination and Seedling Growth

Offspring generation (F1) rice (Oryza sativa japonica Koshihikari) seed germination and seedling growth tests were conducted for 18 d to investigate intergenerational effects of arsenic (As) and copper oxide nanoparticles (nCuO), with seeds harvested from a life cycle study exposed to As (0 and 10 mg/kg) and nCuO (0, 0.1, 1.0, 10, 50, and 100 mg/L). Seed germination and seedling growth of F1 plants were influenced by treatments experienced by parent generation (F0) plants (p < 0.05). Seeds produced from plants in F0 treatment with nCuO 50 mg/L had the lowest germination percentage and shortest seedling shoot length and root length in F1 control (F1C) and As at 10 mg/kg (F1As) alone treatments (p < 0.05). The shoot length and root length were decreased, whereas the number of root branches was increased in F1As treatment compared with F1C (p < 0.001). Interaction of As and nCuO also caused differential seed germination and seedling growth at various nCuO concentrations in quasi-F0 treatment (seeds receiving the same exposure as F0 plants; p < 0.05). Copper and As uptake in F1C seedlings were not affected by seeds' F0 exposure; this indicated that the transgenerational effects on rice seedling growth were not dependent on total Cu or As uptake in seedlings. The enhanced effects on seedlings from quasi-F0 treatment were influenced by additional exposure to nCuO and As that also interacted to affect Cu and As uptake in seedlings. Environ Toxicol Chem 2019;38:1978-1987. © 2019 SETAC.

Sibship, physical activity, and sedentary behavior: a longitudinal, observational study among Mexican-heritage sibling dyads

BACKGROUND

Shared genetic and environmental factors suggest that family relationships are important predictors of obesity-related behaviors, yet little is known about how siblings influence physical activity and sedentary behaviors. This study examined physical activity and sedentary behavior between sibling dyads across summer and fall time points and determined if birth order and gender modify the relationship between sibling behaviors.

METHODS

Mexican-heritage families residing in colonias along the United States-Mexico border were recruited using promotoras de salud to participate in summer and school year surveys. Eighty-seven sibling dyads had complete data for the physical activity sub-study: 21 older brother-younger brother, 21 older brother-younger sister, 23 older sister-younger brother, and 22 older sister-younger sister dyads. Physical activity and sedentary behavior were measured using a validated 7-day recall instrument to create summary measures of weekly active, moderate-to-vigorous physical activity (MVPA) metabolic equivalents (MET), sitting, and screen time minutes. We used linear regression analyses to examine changes over time and the association between older and younger sibling behavior.

RESULTS

During summer, older siblings (mean age = 11.2 years) reported 1069 active minutes and 1244 sitting minutes per week; younger siblings (mean age = 8.3 years) reported 1201 active minutes and 1368 sitting minutes per week. Younger brothers reported fewer active minutes (mean = - 459.6; p = 0.01) and fewer MVPA MET-minutes (mean = - 2261.7; p = 0.02) of physical activity during the fall. Within all 87 dyads, older sibling physical activity was significantly associated with younger sibling active minutes (B = 0.45;p = 0.004) and MET-minutes (B = 0.45;p = 0.003) during summer but not fall; older sibling sedentary behavior was significantly associated with younger sibling sitting (B = 0.23;p = 0.01) and screen time minutes (B = 0.23;p = 0.004) during fall but not summer. After stratifying by gender dyad groups, younger brother behavior was strongly associated with older brother behavior at both time points.

CONCLUSION

Younger siblings appear to emulate the physical activity behaviors of their older siblings during non-school summer months and sedentary behaviors of older siblings during school-time fall months, especially older brother-younger brother dyads. Family-based interventions to increase physical activity and decrease sedentary behavior are growing in popularity, but more work is needed to understand the role of sibling influences.

Morphological characteristics of preparator air-scribe marks: Implications for taphonomic research

Taphonomic analyses of bone-surface modifications can provide key insights into past biotic involvement with animal remains, as well as elucidate the context(s) of other biostratinomic (pre-burial) processes, diagenesis, excavation, preparation and storage. Such analyses, however, first require researchers to rigorously disambiguate between continuums of damage morphologies prior to attributing individual marks to specific actors and effectors (e.g., carnivore tooth, stone tool cutting edge, etc.). To date, a number of bone-modifying agents have been identified, and criteria for identifying their traces have been published. Relatively little research, however, has focused on bone-surface modifications imparted during specimen preparation. Herein we report that air scribes, small pneumatic tools commonly used for preparation in museum contexts, can generate unintentional marks that may mimic surficial modification caused by carnivores. To aid investigators in assessing the hypothesis that a mark in question is derived from air-scribe preparation activities, we provide high-resolution, detailed morphological information imaged with scanning electron microscopy (SEM). The main diagnostic characteristic of air-scribe damage is the occurrence of sequential, variously spaced, sub-millimeter scallop-like stepped bone removals. This morphology can resemble damage imparted by carnivore teeth. In contrast to marks produced by trampling, stone tools and carnivores, however, no continuous internal features, such as linear microstriations, were observed within grooves produced by the air scribe. Thus, the presence of such features can be used to disprove an air-scribe origin. A culmination of the morphological criteria presented herein, cross-cutting relationships with other surficial features (e.g., diagenetic discoloration, weathering textures), the position of occurrence, and an overall contextual framework for the assemblage is suggested for accurate identification of such traces. The ability to recognize or disprove air-scribe damage will allow researchers to confidently proceed with interpreting past biological and sedimentological interactions with animal remains.

Phylogenomic evidence for ancient recombination between plastid genomes of the Cupressus-Juniperus-Xanthocyparis complex (Cupressaceae)

BACKGROUND

Phylogenetic relationships among Eastern Hemisphere cypresses, Western Hemisphere cypresses, junipers, and their closest relatives are controversial, and generic delimitations have been in flux for the past decade. To address relationships and attempt to produce a more robust classification, we sequenced 11 new plastid genomes (plastomes) from the five variously described genera in this complex (Callitropsis, Cupressus, Hesperocyparis, Juniperus, and Xanthocyparis) and compared them with additional plastomes from diverse members of Cupressaceae.

RESULTS

Phylogenetic analysis of protein-coding genes recovered a topology in which Juniperus is sister to Cupressus, whereas a tree based on whole plastomes indicated that the Callitropsis-Hesperocyparis-Xanthocyparis (CaHX) clade is sister to Cupressus. A sliding window analysis of site-specific phylogenetic support identified a ~ 15 kb region, spanning the genes ycf1 and ycf2, which harbored an anomalous signal relative to the rest of the genome. After excluding these genes, trees based on the remainder of the genes and genome consistently recovered a topology grouping the CaHX clade and Cupressus with strong bootstrap support. In contrast, trees based on the ycf1 and ycf2 region strongly supported a sister relationship between Cupressus and Juniperus.

CONCLUSIONS

These results demonstrate that standard phylogenomic analyses can result in strongly supported but conflicting trees. We suggest that the conflicting plastomic signals result from an ancient introgression event involving ycf1 and ycf2 that occurred in an ancestor of this species complex. The introgression event was facilitated by plastomic recombination in an ancestral heteroplasmic individual carrying distinct plastid haplotypes, offering further evidence that recombination occurs between plastomes. Finally, we provide strong support for previous proposals to recognize five genera in this species complex: Callitropsis, Cupressus, Hesperocyparis, Juniperus, and Xanthocyparis.