Reclassification of seven honey bee symbiont strains as Bombella apis.

Honey bees are important pollinators of many major crops and add billions of dollars annually to the US economy through their services. Recent declines in the health of the honey bee have startled researchers and lay people alike as honey bees are agriculture's most important pollinator. One factor that may influence colony health is the microbial community. Although honey bee worker guts have a characteristic community of bee-specific microbes, the honey bee queen digestive tracts are colonized predominantly by a single acetic acid bacterium tentatively named 'Parasaccharibacter apium'. This bacterium is related to flower-associated microbes such as Saccharibacter floricola, and initial phylogenetic analyses placed it as sister to these environmental bacteria. We used a combination of phylogenetic and sequence identity methods to better resolve evolutionary relationships among 'P. apium', strains in the genus Saccharibacter, and strains in the closely related genus Bombella. Interestingly, measures of genome-wide average nucleotide identity and aligned fraction, coupled with phylogenetic placement, indicate that many strains labelled as 'P. apium' and Saccharibacter species are all the same species as Bombella apis. We propose reclassifying these strains as Bombella apis and outline the data supporting that classification below.

Insights into the Host Specificity of a New Oomycete Root Pathogen, Pythium brassicum P1: Whole Genome Sequencing and Comparative Analysis Reveals Contracted Regulation of Metabolism, Protein Families, and Distinct Pathogenicity Repertoire.

Pythium brassicum P1 Stanghellini, Mohammadi, Förster, and Adaskaveg is an oomycete root pathogen that has recently been characterized. It only attacks plant species belonging to Brassicaceae family, causing root necrosis, stunting, and yield loss. Since P. brassicum P1 is limited in its host range, this prompted us to sequence its whole genome and compare it to those of broad host range Pythium spp. such as P. aphanidermatum and P. ultimum var. ultimum. A genomic DNA library was constructed with a total of 374 million reads. The sequencing data were assembled using SOAPdenovo2, yielding a total genome size of 50.3 Mb contained in 5434 scaffolds, N50 of 30.2 Kb, 61.2% G+C content, and 13,232 putative protein-coding genes. Pythium brassicum P1 had 175 species-specific gene families, which is slightly below the normal average. Like P. ultimum, P. brassicum P1 genome did not encode any classical RxLR effectors or cutinases, suggesting a significant difference in virulence mechanisms compared to other oomycetes. Pythium brassicum P1 had a much smaller proportions of the YxSL sequence motif in both secreted and non-secreted proteins, relative to other Pythium species. Similarly, P. brassicum P1 had the fewest Crinkler (CRN) effectors of all the Pythium species. There were 633 proteins predicted to be secreted in the P. brassicum P1 genome, which is, again, slightly below average among Pythium genomes. Pythium brassicum P1 had only one cadherin gene with calcium ion-binding LDRE and DxND motifs, compared to Pythium ultimum having four copies. Pythium brassicum P1 had a reduced number of proteins falling under carbohydrate binding module and hydrolytic enzymes. Pythium brassicum P1 had a reduced complement of cellulase and pectinase genes in contrast to P. ultimum and was deficient in xylan degrading enzymes. The contraction in ABC transporter families in P. brassicum P1 is suggested to be the result of a lack of diversity in nutrient uptake and therefore host range.

The nuclear DEK interactome supports multi-functionality.

DEK is an oncoprotein that is overexpressed in many forms of cancer and participates in numerous cellular pathways. Of these different pathways, relevant interacting partners and functions of DEK are well described in regard to the regulation of chromatin structure, epigenetic marks, and transcription. Most of this understanding was derived by investigating DNA-binding and chromatin processing capabilities of the oncoprotein. To facilitate the generation of mechanism-driven hypotheses regarding DEK activities in underexplored areas, we have developed the first DEK interactome model using tandem-affinity purification and mass spectrometry. With this approach, we identify IMPDH2, DDX21, and RPL7a as novel DEK binding partners, hinting at new roles for the oncogene in de novo nucleotide biosynthesis and ribosome formation. Additionally, a hydroxyurea-specific interaction with replication protein A (RPA) was observed, suggesting that a DEK-RPA complex may form in response to DNA replication fork stalling. Taken together, these findings highlight diverse activities for DEK across cellular pathways and support a model wherein this molecule performs a plethora of functions.

Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders.

BACKGROUND: Primary immunodeficiency diseases (PIDDs) are clinically and genetically heterogeneous disorders thus far associated with mutations in more than 300 genes. The clinical phenotypes derived from distinct genotypes can overlap. Genetic etiology can be a prognostic indicator of disease severity and can influence treatment decisions. OBJECTIVE: We sought to investigate the ability of whole-exome screening methods to detect disease-causing variants in patients with PIDDs. METHODS: Patients with PIDDs from 278 families from 22 countries were investigated by using whole-exome sequencing. Computational copy number variant (CNV) prediction pipelines and an exome-tiling chromosomal microarray were also applied to identify intragenic CNVs. Analytic approaches initially focused on 475 known or candidate PIDD genes but were nonexclusive and further tailored based on clinical data, family history, and immunophenotyping. RESULTS: A likely molecular diagnosis was achieved in 110 (40%) unrelated probands. Clinical diagnosis was revised in about half (60/110) and management was directly altered in nearly a quarter (26/110) of families based on molecular findings. Twelve PIDD-causing CNVs were detected, including 7 smaller than 30 Kb that would not have been detected with conventional diagnostic CNV arrays. CONCLUSION: This high-throughput genomic approach enabled detection of disease-related variants in unexpected genes; permitted detection of low-grade constitutional, somatic, and revertant mosaicism; and provided evidence of a mutational burden in mixed PIDD immunophenotypes.

The reputational and social network benefits of prosociality in an Andean community.

Several theories have emerged to explain how group cooperation (collective action) can arise and be maintained in the face of incentives to engage in free riding. Explanations focusing on reputational benefits and partner choice have particular promise for cases in which punishment is absent or insufficient to deter free riding. In indigenous communities of highland Peru, collective action is pervasive and provides critical benefits. Participation in collective action is unequal across households, but all households share its benefits. Importantly, investment in collective action involves considerable time, energy, and risk. Differential participation in collective action can convey information about qualities of fellow community members that are not easily observable otherwise, such as cooperative intent, knowledge, work ethic, skill, and/or physical vitality. Conveying such information may enhance access to adaptive support networks. Interview and observational data collected in a Peruvian highland community indicate that persons who contributed more to collective action had greater reputations as reliable, hard workers with regard to collective action and also were considered the most respected, influential, and generous people in the community. Additionally, household heads with greater reputations had more social support partners (measured as network indegree centrality), and households with larger support networks experienced fewer illness symptoms.

The evolution of inequality.

Understanding how systems of political and economic inequality evolved from relatively egalitarian origins has long been a focus of anthropological inquiry. Many hypotheses have been suggested to link socio-ecological features with the rise and spread of inequality, and empirical tests of these hypotheses in prehistoric and extant societies are increasing. In this review, we synthesize several streams of theory relevant to understanding the evolutionary origins, spread, and adaptive significance of inequality. We argue that while inequality may be produced by a variety of localized processes, its evolution is fundamentally dependent on the economic defensibility and transmissibility of wealth. Furthermore, these properties of wealth could become persistent drivers of inequality only following a shift to a more stable climate in the Holocene. We conclude by noting several key areas for future empirical research, emphasizing the need for more analyses of contemporary shifts toward institutionalized inequality as well as prehistoric cases.

Successful hunting increases testosterone and cortisol in a subsistence population.

Controversy over the adaptive significance of male hunting in subsistence societies hinges on the relative importance of familial provisioning and mate-quality signalling. This paper examines the proximate and ultimate motivations of hunting behaviour from a neuroendocrine perspective, using salivary testosterone and cortisol data collected before, during and after hunting focal follows from 31 Tsimane hunters aged 18-82 years. Despite circadian declines in hormone levels, testosterone and cortisol of Tsimane hunters increased at the time of a kill, and remained high as successful hunters returned home. Previous studies of hormonal changes during competitions find that high-stakes and success in the presence of relevant audiences result in increased neuroendocrine arousal. If men hunt primarily to provision their families, then an additional audience would not be expected to impact testosterone or cortisol, nor would the size of the animal killed. However, if signalling male quality by 'showing off' was a larger relative driver of men's hunting behaviour, one would expect greater hormonal response in cases where men returned with large sharable kills, especially in the presence of community members. Consistent with provisioning models of male hunting motivation, neither kill size nor encountering an audience of villagers while returning from hunting was associated with hormonal changes for successful hunters.

The origins of musicality in the motion of primates.

Animals communicate acoustically to report location, identity, and emotive state to conspecifics. Acoustic signals can also function as displays to potential mates and as territorial advertisement. Music and song are terms often reserved only for humans and birds, but elements of both forms of acoustic display are also found in non-human primates. While culture, bonding, and side-effects all factor into the emergence of musicality, biophysical insights into what might be signaled by specific acoustic features are less well understood. OBJECTIVES: Here we probe the origins of musicality by evaluating the links between musical features (structural complexity, rhythm, interval, and tone) and a variety of potential ecological drivers of its evolution across primate species. Alongside other hypothesized causes (e.g. territoriality, sexual selection), we evaluated the hypothesis that perilous arboreal locomotion might favor musical calling in primates as a signal of capacities underlying spatio-temporal precision in motor tasks. MATERIALS AND METHODS: We used musical features found in spectrographs of vocalizations of 58 primate species and corresponding measures of locomotion, diet, ranging, and mating. Leveraging phylogenetic information helped us impute missing data and control for relatedness of species while selecting among candidate multivariate regression models. RESULTS: Results indicated that rapid inter-substrate arboreal locomotion is highly correlated with several metrics of music-like signaling. Diet, alongside mate-choice and range size, emerged as factors that also correlated with complex calling patterns. DISCUSSION: These results support the hypothesis that musical calling may function as a signal, to neighbors or potential mates, of accuracy in landing on relatively narrow targets.

Receptor tyrosine kinase inhibition leads to regression of acral melanoma by targeting the tumor microenvironment.

Acral melanoma (AM) is an aggressive melanoma variant that arises from palmar, plantar, and nail unit melanocytes. Compared to non-acral cutaneous melanoma (CM), AM is biologically distinct, has an equal incidence across genetic ancestries, typically presents in advanced stage disease, is less responsive to therapy, and has an overall worse prognosis. Independent analysis of published genomic and transcriptomic sequencing identified that receptor tyrosine kinase (RTK) ligands and adapter proteins are frequently amplified, translocated, and/or overexpressed in AM. To target these unique genetic changes, a zebrafish acral melanoma model was exposed to a panel of narrow and broad spectrum multi-RTK inhibitors, revealing that dual FGFR/VEGFR inhibitors decrease acral-analogous melanocyte proliferation and migration. The potent pan-FGFR/VEGFR inhibitor, Lenvatinib, uniformly induces tumor regression in AM patient-derived xenograft (PDX) tumors but only slows tumor growth in CM models. Unlike other multi-RTK inhibitors, Lenvatinib is not directly cytotoxic to dissociated AM PDX tumor cells and instead disrupts tumor architecture and vascular networks. Considering the great difficulty in establishing AM cell culture lines, these findings suggest that AM may be more sensitive to microenvironment perturbations than CM. In conclusion, dual FGFR/VEGFR inhibition may be a viable therapeutic strategy that targets the unique biology of AM.

Age-independent increases in male salivary testosterone during horticultural activity among Tsimane forager-farmers.

Testosterone plays an important role in mediating male reproductive trade-offs in many vertebrate species, augmenting muscle and influencing behavior necessary for male-male competition and mating-effort. Among humans, testosterone may also play a key role in facilitating male provisioning of offspring as muscular and neuromuscular performance are deeply influenced by acute changes in testosterone. This study examines acute changes in salivary testosterone among 63 Tsimane men ranging in age from 16-80 (mean 38.2) years during one-hour bouts of tree-chopping while clearing horticultural plots. The Tsimane forager-horticulturalists living in the Bolivian Amazon experience high energy expenditure associated with food production, have high levels of parasites and pathogens, and display significantly lower baseline salivary testosterone than age-matched US males. Mixed-effects models controlling for BMI and time of specimen collection reveal increased salivary testosterone (p<0.001) equivalent to a 48.6% rise, after one hour of tree chopping. Age had no effect on baseline (p=0.656) or change in testosterone (p=0.530); self-reported illness did not modify testosterone change (p=0.488). A comparison of these results to the relative change in testosterone during a competitive soccer tournament in the same population reveals larger relative changes in testosterone following resource production (tree chopping), compared to competition (soccer). These findings highlight the importance of moving beyond a unidimensional focus on changes in testosterone and male-male aggression to investigate the importance of testosterone-behavior interactions across additional male fitness-related activities. Acutely increased testosterone during muscularly intensive horticultural food production may facilitate male productivity and provisioning.

Identification and characterization of small RNAs in Yersinia pestis.

Yersinia pestis, the etiologic agent of plague, is closely related to Yersinia pseudotuberculosis evolutionarily but has a very different mode of infection. The RNA-binding regulatory protein, Hfq, mediates regulation by small RNAs (sRNAs) and is required for virulence of both Y. pestis and Y. pseudotuberculosis. Moreover, Hfq is required for growth of Y. pestis, but not Y. pseudotuberculosis, at 37°C. Together, these observations suggest that sRNAs play important roles in the virulence and survival of Y. pestis, and that regulation by sRNAs may account for some of the differences between Y. pestis and Y. pseudotuberculosis. We have used a deep sequencing approach to identify 31 sRNAs in Y. pestis. The majority of these sRNAs are not conserved outside the Yersiniae. Expression of the sRNAs was confirmed by Northern analysis and we developed deep sequencing approaches to map 5' and 3' ends of many sRNAs simultaneously. Expression of the majority of the sRNAs we identified is dependent upon Hfq. We also observed temperature-dependent effects on the expression of many sRNAs, and differences in expression patterns between Y. pestis and Y. pseudotuberculosis. Thus, our data suggest that regulation by sRNAs plays an important role in the lifestyle switch from flea to mammalian host, and that regulation by sRNAs may contribute to the phenotypic differences between Y. pestis and Y. pseudotuberculosis.

Dysregulation of serine biosynthesis contributes to the growth defect of a Mycobacterium tuberculosis crp mutant.

Mycobacterium tuberculosis CRP(Mt), encoded by Rv3676 (crp), is a CRP-like transcription factor that binds with the serC-Rv0885 intergenic region. In the present study, we evaluated CRP(Mt) 's regulation of serC and Rv0885 in M. tuberculosis and M. bovis BCG, using site-specific mutagenesis, promoter fusions and reverse-transcriptase PCR (RT-PCR). The CRP(Mt) binding site was required for full expression of serC and Rv0885, and expression of both genes was reduced in M. tuberculosis and M. bovis BCG crp mutants. These data show that CRP(Mt) binding directly activates both serC and Rv0885 expression. M. tuberculosis serC restored the ability of an Escherichia coli serC mutant to grow in serine-dropout medium, demonstrating that M. tuberculosis serC encodes a phosphoserine aminotransferase. Serine supplementation, or overexpression of serC, accelerated the growth of M. tuberculosis and M. bovis BCG crp mutants in mycomedium, but not within macrophages. These results establish a role for CRP(Mt) in the regulation of amino acid biosynthesis, and show that reduced serine production contributes to the slow-growth phenotype of M. tuberculosis and M. bovis BCG crp mutants in vitro. Restoration of serine biosynthesis by serC expression will facilitate identification of additional CRP(Mt)-regulated factors required by M. tuberculosis during macrophage and host infection.

Physical competition increases testosterone among Amazonian forager-horticulturalists: a test of the 'challenge hypothesis'.

The challenge hypothesis posits that acute increases in testosterone (T) during male-male competition enhance performance and survivability while limiting the physiological costs of consistently high T. Human challenge hypothesis research focuses on young men in industrial populations, who have higher baseline T levels than men in subsistence populations. We tested whether the Tsimane, pathogenically stressed forager-horticulturalists of the Bolivian Amazon, would express acute T increases in response to physical competition. Saliva was collected from 88 Tsimane men (aged 16-59 years) before and after a competitive soccer match. Tsimane men had significantly lower baseline levels of T (ß = -0.41, p < 0.001) when compared with age-matched United States (US) males. Linear mixed-effects models were used to establish that T increased significantly immediately following competition (ß = 0.23, p < 0.001), remaining high 1 h later (ß = 0.09, p = 0.007); equivalent to 30.1 and 15.5 per cent increases in T, respectively. We did not find larger increases in T among winners (p = 0.412), although T increases were positively associated with self-rated performance (ß = 9.07, p = 0.004). These results suggest that despite lower levels of T than US males, Tsimane males exhibit acute increases in T at the same relative magnitude reported by studies in industrialized settings, with larger increases in T for those who report better individual performance.

Have you caught that outlier yet? Evaluate the utility of repeat testing in nutritional and toxic element assessment.

Repeat testing is routinely required by regulatory bodies as a measure to rule out contamination in trace elements and heavy metal analysis, especially when the initial analysis result is outside the reference interval. However, its clinical utilities in detecting analytical measurement outliers have not been systematically evaluated in different clinical testing scenarios. In this study, we present an extensive evaluation of repeat testing and its comparison with the initial analysis in four serum and plasma trace element assays performed by inductively coupled plasma mass spectrometry. We demonstrate that the patient population distributions for these elements differ significantly from the reference interval established by healthy individuals. Accordingly, a significant proportion of the patient specimens would require repeat testing when using reference intervals as the threshold to perform repeat analysis. Crucially, comparison of the first analysis and repeat analysis reveals the limited utility of performing repeat measurements. The relative differences between the first and second measurements are consistent with the observed analytical imprecision of the assay and the likelihood of detecting actual analytical outliers is very low.

Orbital volume changes during growth and development in human children assessed using cone beam computed tomography.

OBJECTIVES: To measure growth-related changes in orbital volume from childhood to the late teenage years using cone-beam computed tomography (CBCT) scans. METHODS: This retrospective cohort study involved 65 (24 male, 41 female) healthy Caucasian children (ages 6-18 years) with existing serial craniofacial CBCT scans. CBCT scans were available for 292 orbits. Each orbit was transformed into a closed space with well-defined boundaries, and orbital volume was measured using manual segmentation. A novel statistical analysis was applied to extract the maximum amount of longitudinal information from the data. Intra- and inter-operator correlation coefficients were calculated from replications performed on a random subset of 10% of the sample. RESULTS: Orbital volume increased at a rate of 1-2% annually until the late teenage years. Intra- and inter-operator agreement between repeated measurements were >90%. CONCLUSIONS: Orbital volume increases by 1-2% per year throughout childhood continuing until the late teenage years. This annual increase is large enough to be clinically relevant as it may lead to less-than-optimal long term surgical outcomes when reconstructive surgery for the pediatric anophthalmic socket is required.

Multi-Year Mass-Trapping With Autocidal Gravid Ovitraps has Limited Influence on Insecticide Susceptibility in Aedes aegypti (Diptera: Culicidae) From Puerto Rico.

Mass-trapping has been used to control outbreaks of Aedes aegypti (Linnaeus) (Diptera: Culicidae) in Puerto Rico since 2011. We investigated the effect of multi-year, insecticide-free mass trapping had on the insecticide susceptibility profile of Ae. aegypti. Eggs collected in southern Puerto Rico were used to generate F1 populations that were tested for susceptibility to permethrin, sumethrin, bifenthrin, deltamethrin, and malathion according to CDC bottle bioassays protocols. All populations of Ae. aegypti were resistant to the synthetic pyrethroids and mosquitoes from two locations were partially resistant to malathion. Population genetic analysis, using a double digest restriction sites associated DNA sequencing (ddRADseq) approach, indicated a large amount of migration between study sites effectively homogenizing the mosquito populations. Mass-trapping using noninsecticidal autocidal gravid ovitraps did not restore susceptibility to five active ingredients that are found in commercial insecticides. Migration between communities was high and would have brought outside alleles, including resistant alleles to the treatment communities. Further investigation suggests that household use of commercially available insecticide products may continue to select for resistance in absence of public health space spraying of insecticides.

A Bacterial Symbiont Protects Honey Bees from Fungal Disease.

Fungal pathogens, among other stressors, negatively impact the productivity and population size of honey bees, one of our most important pollinators (1, 2), in particular their brood (larvae and pupae) (3, 4). Understanding the factors that influence disease incidence and prevalence in brood may help us improve colony health and productivity. Here, we examined the capacity of a honey bee-associated bacterium, Bombella apis, to suppress the growth of fungal pathogens and ultimately protect bee brood from infection. Our results showed that strains of B. apis inhibit the growth of two insect fungal pathogens, Beauveria bassiana and Aspergillus flavus, in vitro. This phenotype was recapitulated in vivo; bee broods supplemented with B. apis were significantly less likely to be infected by A. flavus. Additionally, the presence of B. apis reduced sporulation of A. flavus in the few bees that were infected. Analyses of biosynthetic gene clusters across B. apis strains suggest antifungal candidates, including a type 1 polyketide, terpene, and aryl polyene. Secreted metabolites from B. apis alone were sufficient to suppress fungal growth, supporting the hypothesis that fungal inhibition is mediated by an antifungal metabolite. Together, these data suggest that B. apis can suppress fungal infections in bee brood via secretion of an antifungal metabolite. IMPORTANCE Fungi can play critical roles in host microbiomes (5-7), yet bacterial-fungal interactions are understudied. For insects, fungi are the leading cause of disease (5, 8). In particular, populations of the European honey bee (Apis mellifera), an agriculturally and economically critical species, have declined in part due to fungal pathogens. The presence and prevalence of fungal pathogens in honey bees have far-reaching consequences, endangering other species and threatening food security (1, 2, 9). Our research highlights how a bacterial symbiont protects bee brood from fungal infection. Further mechanistic work could lead to the development of new antifungal treatments.

Molecular Biomarkers for Melanoma Screening, Diagnosis and Prognosis: Current State and Future Prospects.

Despite significant progress in the development of treatment options, melanoma remains a leading cause of death due to skin cancer. Advances in our understanding of the genetic, transcriptomic, and morphologic spectrum of benign and malignant melanocytic neoplasia have enabled the field to propose biomarkers with potential diagnostic, prognostic, and predictive value. While these proposed biomarkers have the potential to improve clinical decision making at multiple critical intervention points, most remain unvalidated. Clinical validation of even the most commonly assessed biomarkers will require substantial resources, including limited clinical specimens. It is therefore important to consider the properties that constitute a relevant and clinically-useful biomarker-based test prior to engaging in large validation studies. In this review article we adapt an established framework for determining minimally-useful biomarker test characteristics, and apply this framework to a discussion of currently used and proposed biomarkers designed to aid melanoma detection, staging, prognosis, and choice of treatment.

A ubiquitous disordered protein interaction module orchestrates transcription elongation.

During eukaryotic transcription elongation, RNA polymerase II (RNAP2) is regulated by a chorus of factors. Here, we identified a common binary interaction module consisting of TFIIS N-terminal domains (TNDs) and natively unstructured TND-interacting motifs (TIMs). This module was conserved among the elongation machinery and linked complexes including transcription factor TFIIS, Mediator, super elongation complex, elongin, IWS1, SPT6, PP1-PNUTS phosphatase, H3K36me3 readers, and other factors. Using nuclear magnetic resonance, live-cell microscopy, and mass spectrometry, we revealed the structural basis for these interactions and found that TND-TIM sequences were necessary and sufficient to induce strong and specific colocalization in the crowded nuclear environment. Disruption of a single TIM in IWS1 induced robust changes in gene expression and RNAP2 elongation dynamics, which underscores the functional importance of TND-TIM surfaces for transcription elongation.

The importance of the small RNA chaperone Hfq for growth of epidemic Yersinia pestis, but not Yersinia pseudotuberculosis, with implications for plague biology.

Yersinia pestis, the etiologic agent of plague, has only recently evolved from Yersinia pseudotuberculosis. hfq deletion caused severe growth restriction at 37 degrees C in Y. pestis but not in Y. pseudotuberculosis. Strains from all epidemic plague biovars were similarly affected, implicating Hfq, and likely small RNAs (sRNAs), in the unique biology of the plague bacillus.