Microbial enzymes play a fundamental role in ecosystem processes and nutrient mineralization. Therefore understanding enzyme responses to anthropogenic environmental change is important for predicting ecosystem function in the future. In a previous study, we used a reciprocal transplant design to examine the direct and indirect effects of drought and nitrogen (N) fertilization on litter decomposition in a southern California grassland. This work showed direct and indirect negative effects of drought on decomposition, and faster decomposition by N-adapted microbial communities in N-fertilized plots than in non-fertilized plots. Here we measured microbial biomass and the activities of nine extracellular enzymes to examine the microbial and enzymatic mechanisms underlying litter decomposition responses to drought and N. We hypothesized that changes in fungal biomass and potential extracellular enzyme activity (EEA) would relate directly to litter decomposition responses. We also predicted that fungal biomass would dominate the microbial community in our semi-arid study site. However, we found that the microbial community was dominated by bacterial biomass, and that bacteria responded negatively to drought treatment. In contrast to patterns in decomposition, fungal biomass and most potential EEA increased in direct response to drought treatment. Potential EEA was also decoupled from the decomposition response to N treatment. These results suggest that drought and N alter the efficiencies of EEA, defined as the mass of target substrate lost per unit potential EEA. Enzyme efficiencies declined with drought treatment, possibly because reduced water availability increased enzyme immobilization and reduced diffusion rates. In the N experiment, the efficiencies of β-glucosidase, β-xylosidase, and polyphenol oxidase were greater when microbes were transplanted into environments from which they originated. This increase in enzymatic efficiency suggests that microbial enzymes may adapt to their local environment. Overall, our results indicate that drought and N addition may have predictable impacts on the efficiencies of extracellular enzymes, providing a means of linking enzyme potentials with in-situ activities.

Solid-state chemical transformations at the nanoscale can be a powerful tool for achieving compositional complexity in nanomaterials. It is desirable to understand the mechanisms of such reactions and characterize the local-level composition of the resulting materials. Here, we examine how reaction temperature controls the elemental distribution in (Ga_1-xZn_x)(N_1-xO_x) nanocrystals (NCs) synthesized via the solid-state nitridation of a mixture of nanoscale ZnO and ZnGa₂O₄ NCs. (Ga_1-xZn_x)(N_1-xO_x) is a visible-light absorbing semiconductor that is of interest for applications in solar photochemistry. We couple elemental mapping using energy-dispersive X-ray spectroscopy in a scanning transmission electron microscope (STEM-EDS) with colocation analysis to study the elemental distribution and the degree of homogeneity in the (Ga_1-xZn_x)(N_1-xO_x) samples synthesized at temperatures ranging from 650 to 900 °C with varying ensemble compositions (i.e., x values). Over this range of temperatures, the elemental distribution ranges from highly heterogeneous at 650 °C, consisting of a mixture of larger particles with Ga and N enrichment near the surface and very small NCs, to uniform particles with evenly distributed constituent elements for most compositions at 800 °C and above. We propose a mechanism for the formation of the (Ga_1-xZn_x)(N_1-xO_x) NCs in the solid state that involves phase transformation of cubic spinel ZnGa₂O₄ to wurtzite (Ga_1-xZn_x)(N_1-xO_x) and diffusion of the elements along with nitrogen incorporation. The temperature-dependence of nitrogen incorporation, bulk diffusion, and vacancy-assisted diffusion processes determines the elemental distribution at each synthesis temperature. Finally, we discuss how the visible band gap of (Ga_1-xZn_x)(N_1-xO_x) NCs varies with composition and elemental distribution.

Background

Hematopoietic cell transplantation (HCT) is a potentially curative therapy for a wide range of pediatric malignant and nonmalignant diseases. However, complications, including blood stream infection (BSI) remain a major cause of morbidity and mortality. While certain bacteria that are abundant in the oral microbiome, such as S. mitis, can cause BSI, the role of the oral microbial community in the etiology of BSI is not well understood. The finding that the use of xylitol wipes, which specifically targets the cariogenic bacteria S. mutans is associated with reduced BSI in pediatric patients, lead us to investigate dental caries as a risk factor for BSI.

Methods

A total of 41 pediatric patients admitted for allogenic or autologous HCT, age 8 months to 25 years, were enrolled. Subjects with high dental caries risk were identified as those who had dental restorations completed within 2 months of admission for transplant, or who had untreated decay. Fisher's exact test was used to determine if there was a significant association between caries risk and BSI. Dental plaque and saliva were collected on a cotton swab from a subset of four high caries risk (HCR) and four low caries risk (LCR) children following pretransplant conditioning. 16SrRNA sequencing was used to compare the microbiome of HCR and LCR subjects and to identify microbes that were significantly different between the two groups.

Results

There was a statistically significant association between caries risk and BSI (p < 0.035) (Fisher's exact test). Multivariate logistic regression analysis showed children in the high dental caries risk group were 21 times more likely to have BSI, with no significant effect of age or mucositis severity. HCR subjects showed significantly reduced microbial alpha diversity as compared to LCR subjects. LEfse metagenomic analyses, showed the oral microbiome in HCR children enriched in order Lactobacillales. This order includes Streptococcus and Lactobacillus, both which contain bacteria primarily associated with dental caries.

Discussion

These findings support the possibility that the cariogenic microbiome can enhance the risk of BSI in pediatric populations. Future metagenomic analyses to measure microbial differences at, before, and after conditioning related to caries risk, may further unravel the complex relationship between the oral microbiome, and whether it affects health outcomes such as BSI.

The magnitude and direction of carbon cycle feedbacks under climate warming remain uncertain due to insufficient knowledge about the temperature sensitivities of soil microbial processes. Enzymatic rates could increase at higher temperatures, but this response could change over time if soil microbes adapt to warming. We used the Arrhenius relationship, biochemical transition state theory, and thermal physiology theory to predict the responses of extracellular enzyme Vmax and Km to temperature. Based on these concepts, we hypothesized that Vmax and Km would correlate positively with each other and show positive temperature sensitivities. For enzymes from warmer environments, we expected to find lower Vmax , Km , and Km temperature sensitivity but higher Vmax temperature sensitivity. We tested these hypotheses with isolates of the filamentous fungus Neurospora discreta collected from around the globe and with decomposing leaf litter from a warming experiment in Alaskan boreal forest. For Neurospora extracellular enzymes, Vmax Q10 ranged from 1.48 to 2.25, and Km Q10 ranged from 0.71 to 2.80. In agreement with theory, Vmax and Km were positively correlated for some enzymes, and Vmax declined under experimental warming in Alaskan litter. However, the temperature sensitivities of Vmax and Km did not vary as expected with warming. We also found no relationship between temperature sensitivity of Vmax or Km and mean annual temperature of the isolation site for Neurospora strains. Declining Vmax in the Alaskan warming treatment implies a short-term negative feedback to climate change, but the Neurospora results suggest that climate-driven changes in plant inputs and soil properties are important controls on enzyme kinetics in the long term. Our empirical data on enzyme Vmax , Km , and temperature sensitivities should be useful for parameterizing existing biogeochemical models, but they reveal a need to develop new theory on thermal adaptation mechanisms.

We describe the synthesis and characterization of wurtzite (Ga1-xZnx)(N1-xOx) nanocrystals with a wide range of compositions and a focus on properties relevant for solar fuel generation. (Ga1-xZnx)(N1-xOx), a solid solution of GaN and ZnO, is an intriguing material because it exhibits composition-dependent visible absorption even though the parent semiconductors absorb in the UV. When functionalized with co-catalysts, (Ga1-xZnx)(N1-xOx) is also capable of water splitting under visible irradiation. Here, we examine the synthesis of (Ga1-xZnx)(N1-xOx) nanocrystals to understand how they form by nitridation of ZnO and ZnGa2O4 nanocrystalline precursors. We find that the ZnO precursor is critical for the formation of crystalline (Ga1-xZnx)(N1-xOx) at 650 °C, consistent with a mechanism in which wurtzite (Ga1-xZnx)(N1-xOx) nucleates topotactically on wurtzite ZnO at an interface with ZnGa2O4. Using this information, we expand the range of compositions from previously reported 0.30 ≤ x ≤ 0.87 to include the low-x and high-x ends of the range. The resulting compositions, 0.06 ≤ x ≤ 0.98, constitute the widest range of (Ga1-xZnx)(N1-xOx) compositions obtained by one synthetic method. We then examine how the band gap depends on sample composition and find a minimum of 2.25 eV at x = 0.87, corresponding to a maximum possible solar-to-H2 power conversion efficiency of 12%. Finally, we examine the photoelectrochemical (PEC) oxidation behavior of thick films of (Ga1-xZnx)(N1-xOx) nanocrystals with x = 0.40, 0.52, and 0.87 under visible illumination. (Ga1-xZnx)(N1-xOx) nanocrystals with x = 0.40 exhibit solar PEC oxidation activity that, while too low for practical applications, is higher than that of bulk (Ga1-xZnx)(N1-xOx) of the same composition. The highest photocurrents are observed at x = 0.52, even though x = 0.87 absorbs more visible light, illustrating that the observed photocurrents are a result of an interplay of multiple parameters which remain to be elucidated. This set of characterizations provides information useful for future studies of composition-dependent PEC properties of nanoscale (Ga1-xZnx)(N1-xOx).

Background

TGM1(transglutaminase 1) is an enzyme that crosslinks the cornified envelope of mature keratinocytes. Appropriate expression of the TGM1 gene is crucial for proper keratinocyte function as inactivating mutations lead to the debilitating skin disease, lamellar ichthyosis. TGM1 is also expressed in squamous metaplasia, a consequence in some epithelia of vitamin A deficiency or toxic insult that can lead to neoplasia. An understanding of the regulation of this gene in normal and abnormal differentiation states may contribute to better disease diagnosis and treatment.

Methods

In vivo requirements for expression of the TGM1 gene were studied by fusing various lengths of promoter DNA to a reporter and injecting the DNA into mouse embryos to generate transgenic animals. Expression of the reporter was ascertained by Western blotting and immunohistochemistry. Further delineation of a transcriptionally important distal region was determined by transfections of progressively shortened or mutated promoter DNA into cultured keratinocytes.

Results

In vivo analysis of a reporter transgene driven by the TGM1 promoter revealed that 1.6 kilobases, but not 1.1 kilobases, of DNA was sufficient to confer tissue-specific and cell layer-specific expression. This same region was responsible for reporter expression in tissues undergoing squamous metaplasia as a response to vitamin A deprivation. Mutation of a distal promoter AP1 site or proximal promoter CRE site, both identified as important transcriptional elements in transfection assays, did not prevent appropriate expression. Further searching for transcriptional elements using electrophoretic mobility shift (EMSA) and transfection assays in cultured keratinocytes identified two Sp1 elements in a transcriptionally active region between -1.6 and -1.4 kilobases. While mutation of either Sp1 site or the AP1 site singly had only a small effect, mutation of all three sites eliminated nearly all the transcriptional activity.

Conclusions

A distal region of the TGM1 gene promoter, containing AP1 and Sp1 binding sites, is evolutionarily conserved and responsible for high level expression in transgenic mice and in transfected keratinocyte cultures.

Astronauts experience bone loss after the long spaceflight missions. Identifying specific regions that undergo the greatest losses (e.g. the proximal femur) could reveal information about the processes of bone loss in disuse and disease. Methods for detecting such regions, however, remains an open problem. This paper focuses on statistical methods to detect such regions. We perform statistical parametric mapping to get t-maps of changes in images, and propose a new cross-validation method to select an optimum suprathreshold for forming clusters of pixels. Once these candidate clusters are formed, we use permutation testing of longitudinal labels to derive significant changes.

In many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. To test whether such environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid grassland ecosystem changed under reduced precipitation or increased N deposition. We monitored communities seasonally over a period of 2 years to place environmental change responses into the context of natural variation. Fungal and bacterial communities displayed strong seasonal patterns, Fungi being mostly detected during the dry season whereas Bacteria were common during wet periods. Most putative cellulose degraders were associated with 33 bacterial genera and predicted to constitute 18% of the microbial community. Precipitation reduction reduced bacterial abundance and cellulolytic potential whereas nitrogen addition did not affect the cellulolytic potential of the microbial community. Finally, we detected a strong correlation between the frequencies of genera of putative cellulose degraders and cellulase genes. Thus, microbial taxonomic composition was predictive of cellulolytic potential. This work provides a framework for how environmental changes affect microorganisms responsible for plant litter deconstruction.

Astronauts experience bone loss after the long spaceflight missions. Identifying specific regions that undergo the greatest losses (e.g. the proximal femur) could reveal information about the processes of bone loss in disuse and disease. Methods for detecting such regions, however, remains an open problem. This paper focuses on statistical methods to detect such regions. We perform statistical parametric mapping to get t-maps of changes in images, and propose a new cross-validation method to select an optimum suprathreshold for forming clusters of pixels. Once these candidate clusters are formed, we use permutation testing of longitudinal labels to derive significant changes.